Get Started
Thierry Gosselin
-2024-04-24
+2024-05-15
Source:vignettes/get_started.Rmd
get_started.RmdOverview
-Site built with pkgdown 2.0.7.
+Site built with pkgdown 2.0.9.
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 29137612..f9ba5fad 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -1,5 +1,5 @@
-Articles • radiator Articles • radiator
@@ -17,7 +17,7 @@
@@ -85,7 +85,7 @@ All vignettes
diff --git a/docs/articles/life_cycle.html b/docs/articles/life_cycle.html
index 78af7636..7f5b8100 100644
--- a/docs/articles/life_cycle.html
+++ b/docs/articles/life_cycle.html
@@ -6,7 +6,7 @@
Life Cycle • radiator
-
+
@@ -33,7 +33,7 @@
@@ -91,7 +91,7 @@ Life Cycle
Thierry
Gosselin
- 2024-04-24
+ 2024-05-15
Source: vignettes/life_cycle.Rmd
life_cycle.Rmd
@@ -148,7 +148,7 @@ 2024-04-24
diff --git a/docs/articles/rad_genomics_computer_setup.html b/docs/articles/rad_genomics_computer_setup.html
index 834f4399..7511b10a 100644
--- a/docs/articles/rad_genomics_computer_setup.html
+++ b/docs/articles/rad_genomics_computer_setup.html
@@ -6,7 +6,7 @@
RADseq Genomics in R • radiator
-
+
@@ -33,7 +33,7 @@
@@ -90,7 +90,7 @@
RADseq Genomics in R
computer setup
- 2024-04-24
+ 2024-05-15
Source: vignettes/rad_genomics_computer_setup.Rmd
rad_genomics_computer_setup.Rmd
@@ -680,9 +680,21 @@ Error related to install.packages("adegenet")
+Error: HTTP status was 404 Not Found
+
+This error is sometimes poping after a new R upgrade. Try installing
+the problematic package differently.
+Instead of:
+
+BiocManager::install("SeqArray")
+Try:
+
+remotes::install_local(path = "SeqArray_latest.tar.gz")
+
+
Error: C stacks usage
-
+
So far, I haven’t found the cure to this computer-specific
problem.
Potential solutions:
@@ -713,35 +725,35 @@
Better to install and compile them from source to enable OpenMP.
Install in the terminal zstd and lz4:
-cd ~/Downloads
-curl -L https://github.com/lz4/lz4/archive/refs/tags/v1.9.4.tar.gz | tar xf -
-cd lz4*
-make
-sudo make install
-cd ..
-sudo rm -R lz4*
-cd ~/Downloads
-curl -L https://github.com/facebook/zstd/archive/refs/tags/v1.5.5.tar.gz | tar xf -
-cd zstd*
-make
-sudo make install
-cd ..
-sudo rm -R zstd*
+cd ~/Downloads
+curl -L https://github.com/lz4/lz4/archive/refs/tags/v1.9.4.tar.gz | tar xf -
+cd lz4*
+make
+sudo make install
+cd ..
+sudo rm -R lz4*
+cd ~/Downloads
+curl -L https://github.com/facebook/zstd/archive/refs/tags/v1.5.5.tar.gz | tar xf -
+cd zstd*
+make
+sudo make install
+cd ..
+sudo rm -R zstd*
fstcore, fst and data.table
requires these R Makevars specifications. If you have other
lines, comment (#) before saving and installing from
source:
-
-usethis::edit_r_makevars()
-#fstcore fst data.table
-CC=/usr/local/bin/gcc -fopenmp
-CXX=/usr/local/bin/g++ -fopenmp
-CXX11=/usr/local/bin/g++ -fopenmp
-CXX14=/usr/local/bin/g++ -fopenmp
-CXX17=/usr/local/bin/g++ -fopenmp
-CXX1X=/usr/local/bin/g++ -fopenmp
-CXX98=/usr/local/bin/g++ -fopenmp
+usethis::edit_r_makevars()
+#fstcore fst data.table
+CC=/usr/local/bin/gcc -fopenmp
+CXX=/usr/local/bin/g++ -fopenmp
+CXX11=/usr/local/bin/g++ -fopenmp
+CXX14=/usr/local/bin/g++ -fopenmp
+CXX17=/usr/local/bin/g++ -fopenmp
+CXX1X=/usr/local/bin/g++ -fopenmp
+CXX98=/usr/local/bin/g++ -fopenmp
+
install.packages("fstcore", type = "source")
install.packages("fst", type = "source")
install.packages("data.table", type = "source")
@@ -754,9 +766,9 @@
Download
Download the latest github release of Allan Strand’s rmetasim
-
+
Modify the number of loci: MAXLOCI
@@ -767,7 +779,7 @@ Modify the number of loci: MAXLOCIrmetasim-master/src/const.h. Navigate to
lane 33 and change the integer to the desired maximum
number of loci. Or do this in the Terminal:
-
+
Makevars configuration
@@ -775,29 +787,29 @@ Makevars configuration
+
usethis::edit_r_makevars()
macOS
This latest os requires extra lines:
-CC=/usr/local/bin/clang
-CXX=/usr/local/bin/clang++
-CXX1X=/usr/local/bin/clang++
-FLIBS=-L/usr/local/lib
-LDFLAGS=-L/usr/local/lib
-SHLIB_OPENMP_CFLAGS= -fopenmp
-SHLIB_OPENMP_FCFLAGS= -fopenmp
-SHLIB_OPENMP_FFLAGS= -fopenmp
-SHLIB_OPENMP_CXXFLAGS= -fopenmp
-CFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
-CCFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
-CXXFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
-CPPFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
+CC=/usr/local/bin/clang
+CXX=/usr/local/bin/clang++
+CXX1X=/usr/local/bin/clang++
+FLIBS=-L/usr/local/lib
+LDFLAGS=-L/usr/local/lib
+SHLIB_OPENMP_CFLAGS= -fopenmp
+SHLIB_OPENMP_FCFLAGS= -fopenmp
+SHLIB_OPENMP_FFLAGS= -fopenmp
+SHLIB_OPENMP_CXXFLAGS= -fopenmp
+CFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
+CCFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
+CXXFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
+CPPFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
Compile
-
+
@@ -807,10 +819,10 @@
Error?
@@ -827,44 +839,44 @@ Modification# Go to line 1676
-# change
-ac_pkg_openmp=no
-# to
-ac_pkg_openmp=yes
-#save the file under the same name
+
Makevars configuration
XGBoost requires these Makevars specifications. If you
have other lines, comment (#) before compiling:
-
+
usethis::edit_r_makevars()
-CC=/usr/local/bin/gcc
-CXX=/usr/local/bin/g++
-CXX11=/usr/local/bin/g++
-CXX14=/usr/local/bin/g++
-CXX17=/usr/local/bin/g++
-SHLIB_OPENMP_CFLAGS= -fopenmp
-SHLIB_OPENMP_FCFLAGS= -fopenmp
-SHLIB_OPENMP_FFLAGS= -fopenmp
-SHLIB_OPENMP_CXXFLAGS= -fopenmp
-CFLAGS=-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe
-CXXFLAGS=-g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe
-LDFLAGS=-L/usr/local/lib -Wl,-rpath,/usr/local/lib
-CPPFLAGS=-I/usr/local/include -I/usr/local/include
+CC=/usr/local/bin/gcc
+CXX=/usr/local/bin/g++
+CXX11=/usr/local/bin/g++
+CXX14=/usr/local/bin/g++
+CXX17=/usr/local/bin/g++
+SHLIB_OPENMP_CFLAGS= -fopenmp
+SHLIB_OPENMP_FCFLAGS= -fopenmp
+SHLIB_OPENMP_FFLAGS= -fopenmp
+SHLIB_OPENMP_CXXFLAGS= -fopenmp
+CFLAGS=-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe
+CXXFLAGS=-g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe
+LDFLAGS=-L/usr/local/lib -Wl,-rpath,/usr/local/lib
+CPPFLAGS=-I/usr/local/include -I/usr/local/include
Test R-package
You should see a time difference between both runs
-
+
require(xgboost)
x <- matrix(rnorm(100*10000), 10000, 100)
y <- x %*% rnorm(100) + rnorm(1000)
@@ -884,28 +896,28 @@
Download and install CMake
-#In browser or using curl in Terminal
-https://cmake.org/files/v3.12/cmake-3.12.2-Darwin-x86_64.dmg
-# double-click on the disk image and follow instructions
+#In browser or using curl in Terminal
+https://cmake.org/files/v3.12/cmake-3.12.2-Darwin-x86_64.dmg
+# double-click on the disk image and follow instructions
To add CMake to the PATH:
-PATH="/Applications/CMake.app/Contents/bin":"$PATH"
-# Or, to install symlinks to '/usr/local/bin', run:
-sudo "/Applications/CMake.app/Contents/bin/cmake-gui" --install
-# Or, to install symlinks to another directory, run:
-sudo "/Applications/CMake.app/Contents/bin/cmake-gui" --install=/path/to/bin
-#Then, run the following commands to install LightGBM:
+PATH="/Applications/CMake.app/Contents/bin":"$PATH"
+# Or, to install symlinks to '/usr/local/bin', run:
+sudo "/Applications/CMake.app/Contents/bin/cmake-gui" --install
+# Or, to install symlinks to another directory, run:
+sudo "/Applications/CMake.app/Contents/bin/cmake-gui" --install=/path/to/bin
+#Then, run the following commands to install LightGBM:
Download and Install LightGBM
-
+
@@ -920,38 +932,38 @@ Makevars configuration
Check that the lines below are not commented in your
~/.R/Makevars file:
-
+
usethis::edit_r_makevars()
-CC=/usr/local/bin/gcc
-CXX=/usr/local/bin/g++
-CFLAGS=-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe
-CXXFLAGS=-g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe
-PKG_CFLAGS= -O3 -Wall -pipe -pedantic -std=gnu99 -fopenmp
-PKG_CXXFLAGS=-fopenmp -std=c++11
-FC=/usr/local/bin/gfortran
-F77=/usr/local/bin/gfortran
-LDFLAGS=-L/usr/local/lib
-PKG_LIBS = "-liconv"
+CC=/usr/local/bin/gcc
+CXX=/usr/local/bin/g++
+CFLAGS=-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe
+CXXFLAGS=-g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe
+PKG_CFLAGS= -O3 -Wall -pipe -pedantic -std=gnu99 -fopenmp
+PKG_CXXFLAGS=-fopenmp -std=c++11
+FC=/usr/local/bin/gfortran
+F77=/usr/local/bin/gfortran
+LDFLAGS=-L/usr/local/lib
+PKG_LIBS = "-liconv"
Download and install
From the Terminal run these steps to download and compile
randomForestSRC:
-cd ~/Downloads
-curl -L https://cran.r-project.org/src/contrib/randomForestSRC_2.9.3.tar.gz | tar xf -
-cd randomForestSRC
+cd ~/Downloads
+curl -L https://cran.r-project.org/src/contrib/randomForestSRC_2.9.3.tar.gz | tar xf -
+cd randomForestSRC
Make sure you have autoconf installed:
-
+
Should output: autoconf: error: no input file, if not,
install following the steps here.
-# in Terminal
-cd ~/Downloads/randomForestSRC
-autoconf
-cd ~/Downloads
-R CMD INSTALL --preclean --clean randomForestSRC
+# in Terminal
+cd ~/Downloads/randomForestSRC
+autoconf
+cd ~/Downloads
+R CMD INSTALL --preclean --clean randomForestSRC
You want to make sure that this line is printed during execution of
the previous command:
checking whether OpenMP will work in a package... yes or
@@ -964,7 +976,7 @@
ranger is easy to
install.
-
+
install.packages("ranger")
@@ -973,7 +985,7 @@
missRanger is
also very easy to install.
-
+
install.packages("missRanger")
@@ -982,7 +994,7 @@
miceRanger
easy to install.
-
+
install.packages("miceRanger")
@@ -991,7 +1003,7 @@
To install pcaMethods, from
bioconductor:
-
+
BiocManager::install("pcaMethods")
@@ -999,27 +1011,27 @@
fastsimcoal2
To install fastsimcoal2
-v.2.6.0.3, to use in grur::simulate_rad:
+v.2.6.0.3, to use in grur::simulate_rad:
LINUX
-
+
MacOS
-
+
@@ -1028,13 +1040,13 @@ PATH
To see the path of the installation, in the
Terminal:
-
+
If that doesn’t work, do:
-
+
Remove the files in the folder:
-
+
@@ -1047,14 +1059,14 @@
MacOS
The old openmpi version (openmpi-1.6.5) is required, saddly.
-cd ~/Downloads
-curl -L https://download.open-mpi.org/release/open-mpi/v1.6/openmpi-1.6.5.tar.gz | tar xf -
-cd openmpi-1.6.5
-export TMPDIR=/tmp
-./configure F77=gfortran #--prefix=/usr/local -openmp # no longer work for some reason
-make -j 12
-sudo make install
-sudo rm -R ~/Downloads/openmpi*
+cd ~/Downloads
+curl -L https://download.open-mpi.org/release/open-mpi/v1.6/openmpi-1.6.5.tar.gz | tar xf -
+cd openmpi-1.6.5
+export TMPDIR=/tmp
+./configure F77=gfortran #--prefix=/usr/local -openmp # no longer work for some reason
+make -j 12
+sudo make install
+sudo rm -R ~/Downloads/openmpi*
To download COLONY, follow instructions on Jinliang Wang ZSL website. The
file you need to uncompress is named:
colony2.mac_.20180730.zip.
@@ -1085,31 +1097,31 @@ Update
-cd ~/Downloads
-curl -L http://ftp.gnu.org/gnu/autoconf/autoconf-latest.tar.gz | tar xf -
-cd autoconf-2.69
-./configure
-make
-sudo make install
-cd ..
-sudo rm -R ~/Downloads/autoconf-*
+cd ~/Downloads
+curl -L http://ftp.gnu.org/gnu/autoconf/autoconf-latest.tar.gz | tar xf -
+cd autoconf-2.69
+./configure
+make
+sudo make install
+cd ..
+sudo rm -R ~/Downloads/autoconf-*
- Install Github
-git --version # show current git version installed
-which git # returns where is git on your computer
-cd ~/Downloads
-git clone https://github.com/git/git # install the latest Git
-cd git
-make configure
-./configure
-make -j12
-sudo make install
-cd ..
-sudo rm -R ~/Downloads/git/ # remove git folder
-source ~/.bash_profile # reload startup script
-git --version # confirmed the version you just installed
-which git # returns /usr/local/bin
+git --version # show current git version installed
+which git # returns where is git on your computer
+cd ~/Downloads
+git clone https://github.com/git/git # install the latest Git
+cd git
+make configure
+./configure
+make -j12
+sudo make install
+cd ..
+sudo rm -R ~/Downloads/git/ # remove git folder
+source ~/.bash_profile # reload startup script
+git --version # confirmed the version you just installed
+which git # returns /usr/local/bin
macOS Terminal from specific folder
@@ -1128,14 +1140,14 @@ Shortcut to folder path
With macOS, open the Automator
application.
-File -> New (cmd-N)
-Choose: Services
-Left panel, choose: Library -> Utilities
-Middle, choose: Copy to Clipboard and drag it to the right panel
-Now you want to have: Service receives selected FILES OR FOLDERS in FINDER>
-You should have something similar to the image below:
+File -> New (cmd-N)
+Choose: Services
+Left panel, choose: Library -> Utilities
+Middle, choose: Copy to Clipboard and drag it to the right panel
+Now you want to have: Service receives selected FILES OR FOLDERS in FINDER>
+You should have something similar to the image below:
-
+
Go in the Finder, select a folder and right click on it you should
see ‘copy path to clipboard’ at the bottom or in
Services.
@@ -1160,7 +1172,7 @@ Shortcut to folder path
-Site built with pkgdown 2.0.7.
+Site built with pkgdown 2.0.9.
diff --git a/docs/authors.html b/docs/authors.html
index 2e704015..72d0627b 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -1,5 +1,5 @@
-Authors and Citation • radiator Authors and Citation • radiator
@@ -17,7 +17,7 @@
@@ -63,7 +63,7 @@
diff --git a/docs/index.html b/docs/index.html
index 0b4f0649..510d9ab7 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -6,7 +6,7 @@
RADseq Data Exploration, Manipulation and Visualization using R • radiator
-
+
@@ -33,7 +33,7 @@
@@ -111,6 +111,7 @@ Installationdevtools::package_info(pkgs = "SeqArray") # to verify version
# If manually installing SeqArray is necessary
+install.packages("BiocManager")
BiocManager::install("SeqArray")
Web site with additional info: https://thierrygosselin.github.io/radiator/
@@ -176,8 +177,8 @@ Dev status
@@ -194,7 +195,7 @@ Dev status
diff --git a/docs/news/index.html b/docs/news/index.html
index db134455..3392e5c0 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -1,5 +1,5 @@
-Changelog • radiator Changelog • radiator
@@ -17,7 +17,7 @@
@@ -66,6 +66,16 @@ Changelog
Source: NEWS.md
+
+radiator 1.3.3 2024-05-15
+- Fix issue #188 related to coverage in DArT 1row and 2rows format
+
+
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 20f8fba7..2c5230e6 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,9 +1,9 @@
-pandoc: 3.1.1
-pkgdown: 2.0.7
+pandoc: 3.1.11
+pkgdown: 2.0.9
pkgdown_sha: ~
articles:
get_started: get_started.html
life_cycle: life_cycle.html
rad_genomics_computer_setup: rad_genomics_computer_setup.html
-last_built: 2024-04-24T14:02Z
+last_built: 2024-05-15T13:57Z
diff --git a/docs/reference/Exposition_pipe_operator.html b/docs/reference/Exposition_pipe_operator.html
index 7e585840..add8660c 100644
--- a/docs/reference/Exposition_pipe_operator.html
+++ b/docs/reference/Exposition_pipe_operator.html
@@ -1,5 +1,5 @@
-Exposition pipe-operator — %$% • radiator Exposition pipe-operator — %$% • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ Exposition pipe-operator
diff --git a/docs/reference/allele_count.html b/docs/reference/allele_count.html
index 6bcd42ca..565376ec 100644
--- a/docs/reference/allele_count.html
+++ b/docs/reference/allele_count.html
@@ -1,5 +1,5 @@
-allele_count — allele_count • radiator allele_count — allele_count • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ allele_count
diff --git a/docs/reference/allele_frequencies.html b/docs/reference/allele_frequencies.html
index 3b863a1b..d58b50db 100644
--- a/docs/reference/allele_frequencies.html
+++ b/docs/reference/allele_frequencies.html
@@ -1,5 +1,5 @@
-Compute allele frequencies per markers and populations — allele_frequencies • radiator Compute allele frequencies per markers and populations — allele_frequencies • radiator assign_defaults — assign_defaults • radiator assign_defaults — assign_defaults • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ assign_defaults
diff --git a/docs/reference/bayescan_one.html b/docs/reference/bayescan_one.html
index a8adae0b..8a6f12a7 100644
--- a/docs/reference/bayescan_one.html
+++ b/docs/reference/bayescan_one.html
@@ -1,5 +1,5 @@
-bayescan one iteration — bayescan_one • radiator bayescan one iteration — bayescan_one • radiator
@@ -17,7 +17,7 @@
@@ -103,7 +103,7 @@ bayescan one iteration
diff --git a/docs/reference/betas_estimator.html b/docs/reference/betas_estimator.html
index c1fdc4a1..b4db4eeb 100644
--- a/docs/reference/betas_estimator.html
+++ b/docs/reference/betas_estimator.html
@@ -1,5 +1,5 @@
-Estimate \(\beta\)s per population — betas_estimator • radiator Estimate \(\beta\)s per population — betas_estimator • radiator
@@ -17,7 +17,7 @@
@@ -172,7 +172,7 @@ Examples
diff --git a/docs/reference/blacklist_hw.html b/docs/reference/blacklist_hw.html
index 1c47c918..237ff851 100644
--- a/docs/reference/blacklist_hw.html
+++ b/docs/reference/blacklist_hw.html
@@ -1,5 +1,5 @@
-blacklist_hw — blacklist_hw • radiator blacklist_hw — blacklist_hw • radiator
@@ -17,7 +17,7 @@
@@ -99,7 +99,7 @@ Author
diff --git a/docs/reference/boxplot_stats.html b/docs/reference/boxplot_stats.html
index b5b179e9..c488e1c2 100644
--- a/docs/reference/boxplot_stats.html
+++ b/docs/reference/boxplot_stats.html
@@ -1,5 +1,5 @@
-boxplot_stats — boxplot_stats • radiator boxplot_stats — boxplot_stats • radiator
@@ -17,7 +17,7 @@
@@ -101,7 +101,7 @@ boxplot_stats
diff --git a/docs/reference/calibrate_alleles.html b/docs/reference/calibrate_alleles.html
index 0f867bc4..690ede22 100644
--- a/docs/reference/calibrate_alleles.html
+++ b/docs/reference/calibrate_alleles.html
@@ -1,5 +1,5 @@
-Calibrate REF and ALT alleles based on count — calibrate_alleles • radiator Calibrate REF and ALT alleles based on count — calibrate_alleles • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -165,7 +165,7 @@ Author
diff --git a/docs/reference/change_pop_names.html b/docs/reference/change_pop_names.html
index a09c11c8..47c61e5a 100644
--- a/docs/reference/change_pop_names.html
+++ b/docs/reference/change_pop_names.html
@@ -1,5 +1,5 @@
-Transform into a factor the STRATA column, change names and reorder the levels — change_pop_names • radiator Transform into a factor the STRATA column, change names and reorder the levels — change_pop_names • radiator check_args_class — check_args_class • radiator check_args_class — check_args_class • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ check_args_class
diff --git a/docs/reference/check_dart.html b/docs/reference/check_dart.html
index a93d4ee6..7a6b21a6 100644
--- a/docs/reference/check_dart.html
+++ b/docs/reference/check_dart.html
@@ -1,5 +1,5 @@
-check_dart — check_dart • radiator check_dart — check_dart • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ check_dart
diff --git a/docs/reference/check_header_source_vcf.html b/docs/reference/check_header_source_vcf.html
index 327b5485..bb585c73 100644
--- a/docs/reference/check_header_source_vcf.html
+++ b/docs/reference/check_header_source_vcf.html
@@ -1,5 +1,5 @@
-Check the vcf header and detect vcf source — check_header_source_vcf • radiator Check the vcf header and detect vcf source — check_header_source_vcf • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ Check the vcf header and detect vcf source
diff --git a/docs/reference/check_pop_levels.html b/docs/reference/check_pop_levels.html
index eb4f0879..f50fc651 100644
--- a/docs/reference/check_pop_levels.html
+++ b/docs/reference/check_pop_levels.html
@@ -1,5 +1,5 @@
-Check the use of pop.levels, pop.labels and pop.select arguments. — check_pop_levels • radiator Check the use of pop.levels, pop.labels and pop.select arguments. — check_pop_levels • radiator clean_dart_colnames — clean_dart_colnames • radiator clean_dart_colnames — clean_dart_colnames • radiator
@@ -17,7 +17,7 @@
@@ -93,7 +93,7 @@ clean_dart_colnames
diff --git a/docs/reference/clean_dart_locus.html b/docs/reference/clean_dart_locus.html
index d36c600d..bcf4cf4e 100644
--- a/docs/reference/clean_dart_locus.html
+++ b/docs/reference/clean_dart_locus.html
@@ -1,5 +1,5 @@
-clean_dart_locus — clean_dart_locus • radiator clean_dart_locus — clean_dart_locus • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ clean_dart_locus
diff --git a/docs/reference/clean_ind_names.html b/docs/reference/clean_ind_names.html
index f6566a96..71478aea 100644
--- a/docs/reference/clean_ind_names.html
+++ b/docs/reference/clean_ind_names.html
@@ -1,5 +1,5 @@
-Clean individual's names for radiator and other packages — clean_ind_names • radiator Clean individual's names for radiator and other packages — clean_ind_names • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -104,7 +104,7 @@ Arguments
diff --git a/docs/reference/clean_markers_names.html b/docs/reference/clean_markers_names.html
index 1a6e9aed..397d0bdc 100644
--- a/docs/reference/clean_markers_names.html
+++ b/docs/reference/clean_markers_names.html
@@ -1,5 +1,5 @@
-Clean marker's names for radiator and other packages — clean_markers_names • radiator Clean marker's names for radiator and other packages — clean_markers_names • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -106,7 +106,7 @@ Arguments
diff --git a/docs/reference/clean_pop_names.html b/docs/reference/clean_pop_names.html
index 296e6aba..94dd1e30 100644
--- a/docs/reference/clean_pop_names.html
+++ b/docs/reference/clean_pop_names.html
@@ -1,5 +1,5 @@
-Clean population's names for radiator and other packages — clean_pop_names • radiator Clean population's names for radiator and other packages — clean_pop_names • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -102,7 +102,7 @@ Arguments
diff --git a/docs/reference/compound_assignment_pipe_operator.html b/docs/reference/compound_assignment_pipe_operator.html
index 5a529ad4..f640917c 100644
--- a/docs/reference/compound_assignment_pipe_operator.html
+++ b/docs/reference/compound_assignment_pipe_operator.html
@@ -1,5 +1,5 @@
-compound assignment pipe operator — %<>% • radiator compound assignment pipe operator — %<>% • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ compound assignment pipe operator
diff --git a/docs/reference/compute_maf.html b/docs/reference/compute_maf.html
index 1c34155f..6b834ca0 100644
--- a/docs/reference/compute_maf.html
+++ b/docs/reference/compute_maf.html
@@ -1,5 +1,5 @@
-compute_maf — compute_maf • radiator compute_maf — compute_maf • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ compute_maf
diff --git a/docs/reference/count_monomorphic.html b/docs/reference/count_monomorphic.html
index e55d510e..0c38d811 100644
--- a/docs/reference/count_monomorphic.html
+++ b/docs/reference/count_monomorphic.html
@@ -1,5 +1,5 @@
-count_monomorphic — count_monomorphic • radiator count_monomorphic — count_monomorphic • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ count_monomorphic
diff --git a/docs/reference/dart2gds.html b/docs/reference/dart2gds.html
index 3dea5ec0..251edeea 100644
--- a/docs/reference/dart2gds.html
+++ b/docs/reference/dart2gds.html
@@ -1,5 +1,5 @@
-dart2gds — dart2gds • radiator dart2gds — dart2gds • radiator
@@ -17,7 +17,7 @@
@@ -99,7 +99,7 @@ dart2gds
diff --git a/docs/reference/data_info.html b/docs/reference/data_info.html
index a97edb43..936c40f2 100644
--- a/docs/reference/data_info.html
+++ b/docs/reference/data_info.html
@@ -1,5 +1,5 @@
-data_info — data_info • radiator data_info — data_info • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ data_info
diff --git a/docs/reference/detect_all_missing.html b/docs/reference/detect_all_missing.html
index 690c591f..84cf31f5 100644
--- a/docs/reference/detect_all_missing.html
+++ b/docs/reference/detect_all_missing.html
@@ -1,5 +1,5 @@
-Detect markers with all missing genotypes — detect_all_missing • radiator Detect markers with all missing genotypes — detect_all_missing • radiator Detect alternate allele problems — detect_allele_problems • radiator Detect alternate allele problems — detect_allele_problems • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -205,7 +205,7 @@ Examples
diff --git a/docs/reference/detect_biallelic_markers.html b/docs/reference/detect_biallelic_markers.html
index ac7683dc..5f2b50e3 100644
--- a/docs/reference/detect_biallelic_markers.html
+++ b/docs/reference/detect_biallelic_markers.html
@@ -1,5 +1,5 @@
-Detect biallelic data — detect_biallelic_markers • radiator Detect biallelic data — detect_biallelic_markers • radiator Detect biallelic problems — detect_biallelic_problems • radiator Detect biallelic problems — detect_biallelic_problems • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -133,7 +133,7 @@ Author
diff --git a/docs/reference/detect_dart_format.html b/docs/reference/detect_dart_format.html
index b6ba0b20..f52c93ab 100644
--- a/docs/reference/detect_dart_format.html
+++ b/docs/reference/detect_dart_format.html
@@ -1,5 +1,5 @@
-detect_dart_format — detect_dart_format • radiator detect_dart_format — detect_dart_format • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ detect_dart_format
diff --git a/docs/reference/detect_duplicate_genomes.html b/docs/reference/detect_duplicate_genomes.html
index 9e4f22d2..e6abab3e 100644
--- a/docs/reference/detect_duplicate_genomes.html
+++ b/docs/reference/detect_duplicate_genomes.html
@@ -1,7 +1,5 @@
-Compute pairwise genome similarity or distance between individuals
-to highligh potential duplicate individuals — detect_duplicate_genomes • radiator Compute pairwise genome similarity or distance between individuals to highligh potential duplicate individuals — detect_duplicate_genomes • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -69,8 +67,7 @@
- Compute pairwise genome similarity or distance between individuals
-to highligh potential duplicate individuals
+ Compute pairwise genome similarity or distance between individuals to highligh potential duplicate individuals
Source: R/detect_duplicate_genomes.R
detect_duplicate_genomes.Rd
@@ -297,7 +294,7 @@ Examples
diff --git a/docs/reference/detect_genomic_format.html b/docs/reference/detect_genomic_format.html
index 14d3d237..4b0d6ee4 100644
--- a/docs/reference/detect_genomic_format.html
+++ b/docs/reference/detect_genomic_format.html
@@ -1,5 +1,5 @@
-Used internally in radiator to detect the file format — detect_genomic_format • radiator Used internally in radiator to detect the file format — detect_genomic_format • radiator
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Examples
diff --git a/docs/reference/detect_het_outliers.html b/docs/reference/detect_het_outliers.html
index 702bf5f5..ca7342c0 100644
--- a/docs/reference/detect_het_outliers.html
+++ b/docs/reference/detect_het_outliers.html
@@ -1,5 +1,5 @@
-Detect heterozygotes outliers and estimate miscall rate — detect_het_outliers • radiator Detect heterozygotes outliers and estimate miscall rate — detect_het_outliers • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -225,7 +225,7 @@ Examples
diff --git a/docs/reference/detect_microsatellites.html b/docs/reference/detect_microsatellites.html
index f7e5e99a..b60d6b7b 100644
--- a/docs/reference/detect_microsatellites.html
+++ b/docs/reference/detect_microsatellites.html
@@ -1,5 +1,5 @@
-Detect microsatellites — detect_microsatellites • radiator Detect microsatellites — detect_microsatellites • radiator Detect mixed genomes — detect_mixed_genomes • radiator Detect mixed genomes — detect_mixed_genomes • radiator Detect paralogs — detect_paralogs • radiator Detect paralogs — detect_paralogs • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -222,7 +222,7 @@ Examples
diff --git a/docs/reference/detect_ref_genome.html b/docs/reference/detect_ref_genome.html
index 05ee8f5e..4676fd68 100644
--- a/docs/reference/detect_ref_genome.html
+++ b/docs/reference/detect_ref_genome.html
@@ -1,5 +1,5 @@
-Detect reference genome — detect_ref_genome • radiator Detect reference genome — detect_ref_genome • radiator
@@ -17,7 +17,7 @@
@@ -127,7 +127,7 @@ Examples
diff --git a/docs/reference/diagnostic_maf.html b/docs/reference/diagnostic_maf.html
index dcecdbf8..b6b327e7 100644
--- a/docs/reference/diagnostic_maf.html
+++ b/docs/reference/diagnostic_maf.html
@@ -1,5 +1,5 @@
-MA diagnostic — diagnostic_ma • radiator MA diagnostic — diagnostic_ma • radiator
@@ -17,7 +17,7 @@
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/distance2tibble.html b/docs/reference/distance2tibble.html
index 36fdf555..157cfb52 100644
--- a/docs/reference/distance2tibble.html
+++ b/docs/reference/distance2tibble.html
@@ -1,5 +1,5 @@
-distance2tibble — distance2tibble • radiator distance2tibble — distance2tibble • radiator
@@ -17,7 +17,7 @@
@@ -96,7 +96,7 @@ distance2tibble
diff --git a/docs/reference/distance_individuals.html b/docs/reference/distance_individuals.html
index a423ff06..fe9f0c8d 100644
--- a/docs/reference/distance_individuals.html
+++ b/docs/reference/distance_individuals.html
@@ -1,5 +1,5 @@
-Distance individuals — distance_individuals • radiator Distance individuals — distance_individuals • radiator
@@ -17,7 +17,7 @@
@@ -93,7 +93,7 @@ Distance individuals
diff --git a/docs/reference/erase_genotypes.html b/docs/reference/erase_genotypes.html
index d0cc71f7..aeb4a710 100644
--- a/docs/reference/erase_genotypes.html
+++ b/docs/reference/erase_genotypes.html
@@ -1,5 +1,5 @@
-Erase genotypes — erase_genotypes • radiator Erase genotypes — erase_genotypes • radiator heterozygotes miscall rate — estimate_m • radiator heterozygotes miscall rate — estimate_m • radiator
@@ -17,7 +17,7 @@
@@ -126,7 +126,7 @@ Author
diff --git a/docs/reference/extract_coverage.html b/docs/reference/extract_coverage.html
index e2f7194e..2ab35ee5 100644
--- a/docs/reference/extract_coverage.html
+++ b/docs/reference/extract_coverage.html
@@ -1,5 +1,5 @@
-check_coverage — check_coverage • radiator check_coverage — check_coverage • radiator Extract DArT target id — extract_dart_target_id • radiator Extract DArT target id — extract_dart_target_id • radiator extract_data_source — extract_data_source • radiator extract_data_source — extract_data_source • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ extract_data_source
diff --git a/docs/reference/extract_dots.html b/docs/reference/extract_dots.html
index 26b971f3..4bc3de01 100644
--- a/docs/reference/extract_dots.html
+++ b/docs/reference/extract_dots.html
@@ -1,5 +1,5 @@
-extract_dots — extract_dots • radiator extract_dots — extract_dots • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ extract_dots
diff --git a/docs/reference/extract_genotypes_metadata.html b/docs/reference/extract_genotypes_metadata.html
index 2c89293f..c04158be 100644
--- a/docs/reference/extract_genotypes_metadata.html
+++ b/docs/reference/extract_genotypes_metadata.html
@@ -1,5 +1,5 @@
-extract_genotypes_metadata — extract_genotypes_metadata • radiator extract_genotypes_metadata — extract_genotypes_metadata • radiator
@@ -17,7 +17,7 @@
@@ -138,7 +138,7 @@ Arguments
diff --git a/docs/reference/extract_individuals_metadata.html b/docs/reference/extract_individuals_metadata.html
index bb8154cf..8d096840 100644
--- a/docs/reference/extract_individuals_metadata.html
+++ b/docs/reference/extract_individuals_metadata.html
@@ -1,5 +1,5 @@
-extract_individuals_metadata — extract_individuals_metadata • radiator extract_individuals_metadata — extract_individuals_metadata • radiator
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Arguments
diff --git a/docs/reference/extract_individuals_vcf.html b/docs/reference/extract_individuals_vcf.html
index 44dffcf8..af261215 100644
--- a/docs/reference/extract_individuals_vcf.html
+++ b/docs/reference/extract_individuals_vcf.html
@@ -1,5 +1,5 @@
-Extract individuals from vcf file — extract_individuals_vcf • radiator Extract individuals from vcf file — extract_individuals_vcf • radiator extract_info_vcf — extract_info_vcf • radiator extract_info_vcf — extract_info_vcf • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ extract_info_vcf
diff --git a/docs/reference/extract_markers_metadata.html b/docs/reference/extract_markers_metadata.html
index 8d87be81..a7dd8bab 100644
--- a/docs/reference/extract_markers_metadata.html
+++ b/docs/reference/extract_markers_metadata.html
@@ -1,5 +1,5 @@
-extract_markers_metadata — extract_markers_metadata • radiator extract_markers_metadata — extract_markers_metadata • radiator
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Arguments
diff --git a/docs/reference/filter_blacklist_genotypes.html b/docs/reference/filter_blacklist_genotypes.html
index 161e4acc..288991d3 100644
--- a/docs/reference/filter_blacklist_genotypes.html
+++ b/docs/reference/filter_blacklist_genotypes.html
@@ -1,5 +1,5 @@
-Filter dataset with blacklist of genotypes — filter_blacklist_genotypes • radiator Filter dataset with blacklist of genotypes — filter_blacklist_genotypes • radiator Filter common markers between strata — filter_common_markers • radiator Filter common markers between strata — filter_common_markers • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -167,7 +167,7 @@ Examples
diff --git a/docs/reference/filter_coverage.html b/docs/reference/filter_coverage.html
index 3c226460..8ea5b2cc 100644
--- a/docs/reference/filter_coverage.html
+++ b/docs/reference/filter_coverage.html
@@ -1,5 +1,5 @@
-Filter markers mean coverage — filter_coverage • radiator Filter markers mean coverage — filter_coverage • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -207,7 +207,7 @@ Examples
diff --git a/docs/reference/filter_dart_reproducibility.html b/docs/reference/filter_dart_reproducibility.html
index 4e2442e7..e5af3849 100644
--- a/docs/reference/filter_dart_reproducibility.html
+++ b/docs/reference/filter_dart_reproducibility.html
@@ -1,5 +1,5 @@
-Filter data based on DArT reproducibility statistics — filter_dart_reproducibility • radiator Filter data based on DArT reproducibility statistics — filter_dart_reproducibility • radiator Fis filter — filter_fis • radiator Fis filter — filter_fis • radiator
@@ -17,7 +17,7 @@
@@ -162,7 +162,7 @@ Author
diff --git a/docs/reference/filter_genotyping.html b/docs/reference/filter_genotyping.html
index 0da88aad..6e5d2357 100644
--- a/docs/reference/filter_genotyping.html
+++ b/docs/reference/filter_genotyping.html
@@ -1,5 +1,5 @@
-Filter markers based on genotyping/missing rate — filter_genotyping • radiator Filter markers based on genotyping/missing rate — filter_genotyping • radiator Heterozygosity filter — filter_het • radiator Heterozygosity filter — filter_het • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -345,7 +345,7 @@ See also
diff --git a/docs/reference/filter_hwe.html b/docs/reference/filter_hwe.html
index 4cc14942..c0e1080d 100644
--- a/docs/reference/filter_hwe.html
+++ b/docs/reference/filter_hwe.html
@@ -1,5 +1,5 @@
-Filter markers based on Hardy-Weinberg Equilibrium — filter_hwe • radiator Filter markers based on Hardy-Weinberg Equilibrium — filter_hwe • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -360,7 +360,7 @@ Examples
diff --git a/docs/reference/filter_individuals.html b/docs/reference/filter_individuals.html
index 8fefca43..e803b995 100644
--- a/docs/reference/filter_individuals.html
+++ b/docs/reference/filter_individuals.html
@@ -1,7 +1,5 @@
-Filter individuals based on genotyping/missingness rate,
-heterozygosity and total coverage — filter_individuals • radiator Filter individuals based on genotyping/missingness rate, heterozygosity and total coverage — filter_individuals • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -73,8 +71,7 @@
- Filter individuals based on genotyping/missingness rate,
-heterozygosity and total coverage
+ Filter individuals based on genotyping/missingness rate, heterozygosity and total coverage
Source: R/filter_individuals.R
filter_individuals.Rd
@@ -225,7 +222,7 @@ Examples
diff --git a/docs/reference/filter_ld.html b/docs/reference/filter_ld.html
index 20912083..952131bf 100644
--- a/docs/reference/filter_ld.html
+++ b/docs/reference/filter_ld.html
@@ -1,5 +1,5 @@
-GBS/RADseq short and long distance linkage disequilibrium pruning — filter_ld • radiator GBS/RADseq short and long distance linkage disequilibrium pruning — filter_ld • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -291,7 +291,7 @@ Examples
diff --git a/docs/reference/filter_monomorphic.html b/docs/reference/filter_monomorphic.html
index 93257372..83349936 100644
--- a/docs/reference/filter_monomorphic.html
+++ b/docs/reference/filter_monomorphic.html
@@ -1,5 +1,5 @@
-Filter monomorphic markers — filter_monomorphic • radiator Filter monomorphic markers — filter_monomorphic • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -173,7 +173,7 @@ Examples
diff --git a/docs/reference/filter_rad.html b/docs/reference/filter_rad.html
index e5362d09..9a213313 100644
--- a/docs/reference/filter_rad.html
+++ b/docs/reference/filter_rad.html
@@ -1,5 +1,5 @@
-ONE FUNCTION TO RULE THEM ALL — filter_rad • radiator ONE FUNCTION TO RULE THEM ALL — filter_rad • radiator Filter SNP number per locus/read — filter_snp_number • radiator
@@ -207,7 +207,7 @@ Examples
diff --git a/docs/reference/filter_snp_position_read.html b/docs/reference/filter_snp_position_read.html
index bca08dbe..bdee4aca 100644
--- a/docs/reference/filter_snp_position_read.html
+++ b/docs/reference/filter_snp_position_read.html
@@ -1,5 +1,5 @@
-Filter markers/SNP based on their position on the read — filter_snp_position_read • radiator Filter markers/SNP based on their position on the read — filter_snp_position_read • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -200,7 +200,7 @@ Examples
diff --git a/docs/reference/filter_whitelist.html b/docs/reference/filter_whitelist.html
index a7729b2f..41bcfaf2 100644
--- a/docs/reference/filter_whitelist.html
+++ b/docs/reference/filter_whitelist.html
@@ -1,5 +1,5 @@
-Filter dataset with whitelist of markers — filter_whitelist • radiator Filter dataset with whitelist of markers — filter_whitelist • radiator folder_prefix — folder_prefix • radiator folder_prefix — folder_prefix • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ folder_prefix
diff --git a/docs/reference/folder_short.html b/docs/reference/folder_short.html
index a8cff0a1..54236246 100644
--- a/docs/reference/folder_short.html
+++ b/docs/reference/folder_short.html
@@ -1,5 +1,5 @@
-folder_short — folder_short • radiator folder_short — folder_short • radiator
@@ -17,7 +17,7 @@
@@ -98,7 +98,7 @@ Author
diff --git a/docs/reference/gds2tidy.html b/docs/reference/gds2tidy.html
index 3b80f9c8..e0cfeea9 100644
--- a/docs/reference/gds2tidy.html
+++ b/docs/reference/gds2tidy.html
@@ -1,5 +1,5 @@
-gds2tidy — gds2tidy • radiator gds2tidy — gds2tidy • radiator
@@ -17,7 +17,7 @@
@@ -100,7 +100,7 @@ gds2tidy
diff --git a/docs/reference/generate_filename.html b/docs/reference/generate_filename.html
index 664cfa6c..c3c42a0a 100644
--- a/docs/reference/generate_filename.html
+++ b/docs/reference/generate_filename.html
@@ -1,5 +1,5 @@
-Filename radiator — generate_filename • radiator Filename radiator — generate_filename • radiator
@@ -17,7 +17,7 @@
@@ -95,7 +95,7 @@ Filename radiator
diff --git a/docs/reference/generate_folder.html b/docs/reference/generate_folder.html
index 201ae808..807918d8 100644
--- a/docs/reference/generate_folder.html
+++ b/docs/reference/generate_folder.html
@@ -1,5 +1,5 @@
-generate_folder — generate_folder • radiator generate_folder — generate_folder • radiator
@@ -17,7 +17,7 @@
@@ -135,7 +135,7 @@ Author
diff --git a/docs/reference/generate_geno_freq_boundaries.html b/docs/reference/generate_geno_freq_boundaries.html
index e30b3d3b..c67920ed 100644
--- a/docs/reference/generate_geno_freq_boundaries.html
+++ b/docs/reference/generate_geno_freq_boundaries.html
@@ -1,5 +1,5 @@
-generate_geno_freq_boundaries — generate_geno_freq_boundaries • radiator generate_geno_freq_boundaries — generate_geno_freq_boundaries • radiator generate_hzar — generate_hzar • radiator generate_hzar — generate_hzar • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ generate_hzar
diff --git a/docs/reference/generate_markers_metadata.html b/docs/reference/generate_markers_metadata.html
index eee683c3..17b90f9a 100644
--- a/docs/reference/generate_markers_metadata.html
+++ b/docs/reference/generate_markers_metadata.html
@@ -1,5 +1,5 @@
-Generate markers metadata — generate_markers_metadata • radiator Generate markers metadata — generate_markers_metadata • radiator generate_squeleton_folders — generate_squeleton_folders • radiator generate_squeleton_folders — generate_squeleton_folders • radiator
@@ -17,7 +17,7 @@
@@ -93,7 +93,7 @@ generate_squeleton_folders
diff --git a/docs/reference/generate_strata.html b/docs/reference/generate_strata.html
index b6274262..5d5aff18 100644
--- a/docs/reference/generate_strata.html
+++ b/docs/reference/generate_strata.html
@@ -1,5 +1,5 @@
-Generate strata object from the data — generate_strata • radiator Generate strata object from the data — generate_strata • radiator generate_whitelist — generate_whitelist • radiator generate_whitelist — generate_whitelist • radiator
@@ -17,7 +17,7 @@
@@ -92,7 +92,7 @@ Author
diff --git a/docs/reference/genome_similarity.html b/docs/reference/genome_similarity.html
index c6ef4036..5ac856a7 100644
--- a/docs/reference/genome_similarity.html
+++ b/docs/reference/genome_similarity.html
@@ -1,5 +1,5 @@
-genome_similarity — genome_similarity • radiator genome_similarity — genome_similarity • radiator
@@ -17,7 +17,7 @@
@@ -95,7 +95,7 @@ genome_similarity
diff --git a/docs/reference/genomic_converter.html b/docs/reference/genomic_converter.html
index fa82c724..dce77f29 100644
--- a/docs/reference/genomic_converter.html
+++ b/docs/reference/genomic_converter.html
@@ -1,5 +1,5 @@
-Conversion tool among several genomic formats — genomic_converter • radiator Conversion tool among several genomic formats — genomic_converter • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -356,7 +356,7 @@ Examples
radiator::detect_genomic_format(data = "populations.snps.vcf")
# The simplest form of the function:
-require(strataG) # for the gtypes format...
+require(strataG) # for the gtypes format...
snowcrab <- genomic_converter(
data = "populations.snps.vcf", strata = "snowcrab.strata.tsv",
output = c("genlight", "genepop", "gtypes"))
@@ -380,7 +380,7 @@ Examples
diff --git a/docs/reference/gt2array.html b/docs/reference/gt2array.html
index f68e906e..c79214dd 100644
--- a/docs/reference/gt2array.html
+++ b/docs/reference/gt2array.html
@@ -1,5 +1,5 @@
-gt2array — gt2array • radiator gt2array — gt2array • radiator haplotype_reconstruction — haplotype_reconstruction • radiator haplotype_reconstruction — haplotype_reconstruction • radiator
@@ -17,7 +17,7 @@
@@ -105,7 +105,7 @@ Arguments
diff --git a/docs/reference/hwe_analysis.html b/docs/reference/hwe_analysis.html
index e6a87236..6165b475 100644
--- a/docs/reference/hwe_analysis.html
+++ b/docs/reference/hwe_analysis.html
@@ -1,5 +1,5 @@
-hwe_analysis — hwe_analysis • radiator hwe_analysis — hwe_analysis • radiator
@@ -17,7 +17,7 @@
@@ -92,7 +92,7 @@ Author
diff --git a/docs/reference/ibdg_fh.html b/docs/reference/ibdg_fh.html
index 41f86bfe..84dead9c 100644
--- a/docs/reference/ibdg_fh.html
+++ b/docs/reference/ibdg_fh.html
@@ -1,5 +1,5 @@
-FH measure of IBDg — ibdg_fh • radiator FH measure of IBDg — ibdg_fh • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -245,7 +245,7 @@ Examples
diff --git a/docs/reference/import_dart.html b/docs/reference/import_dart.html
index 045b26b5..a4f02264 100644
--- a/docs/reference/import_dart.html
+++ b/docs/reference/import_dart.html
@@ -1,5 +1,5 @@
-import_dart — import_dart • radiator import_dart — import_dart • radiator
@@ -17,7 +17,7 @@
@@ -95,7 +95,7 @@ import_dart
diff --git a/docs/reference/ind_total_reads.html b/docs/reference/ind_total_reads.html
index 219b763a..605e8e8e 100644
--- a/docs/reference/ind_total_reads.html
+++ b/docs/reference/ind_total_reads.html
@@ -1,5 +1,5 @@
-ind_total_reads — ind_total_reads • radiator ind_total_reads — ind_total_reads • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ ind_total_reads
diff --git a/docs/reference/index.html b/docs/reference/index.html
index bd9be9f0..46de0e9f 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -1,5 +1,5 @@
-Function reference • radiator Function reference • radiator
@@ -17,7 +17,7 @@
@@ -236,8 +236,7 @@ Filter <
- Filter individuals based on genotyping/missingness rate,
-heterozygosity and total coverage
Filter individuals based on genotyping/missingness rate, heterozygosity and total coverage
@@ -301,8 +300,7 @@ Detect <
- Compute pairwise genome similarity or distance between individuals
-to highligh potential duplicate individuals
Compute pairwise genome similarity or distance between individuals to highligh potential duplicate individuals
@@ -390,8 +388,7 @@ Write
- Write a BayeScan
-file from a tidy data frame
Write a BayeScan file from a tidy data frame
@@ -439,8 +436,7 @@ Write
- Write a strataG object from
-radiator GDS and tidy data file or object.
Write a strataG object from radiator GDS and tidy data file or object.
@@ -464,8 +460,7 @@ Write
- Write a pcadapt
-file from a tidy data frame
Write a pcadapt file from a tidy data frame
@@ -575,7 +570,7 @@ Run software
diff --git a/docs/reference/individuals2strata.html b/docs/reference/individuals2strata.html
index f65e5c44..208a8235 100644
--- a/docs/reference/individuals2strata.html
+++ b/docs/reference/individuals2strata.html
@@ -1,5 +1,5 @@
-Create a strata file from a list of individuals — individuals2strata • radiator Create a strata file from a list of individuals — individuals2strata • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -168,7 +168,7 @@ Examples
diff --git a/docs/reference/join_strata.html b/docs/reference/join_strata.html
index 25aacfa1..f1dc86a2 100644
--- a/docs/reference/join_strata.html
+++ b/docs/reference/join_strata.html
@@ -1,5 +1,5 @@
-Join the strata with the data — join_strata • radiator Join the strata with the data — join_strata • radiator ld2df — ld2df • radiator ld2df — ld2df • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ ld2df
diff --git a/docs/reference/ld_boxplot.html b/docs/reference/ld_boxplot.html
index 4367f28a..30ce41f2 100644
--- a/docs/reference/ld_boxplot.html
+++ b/docs/reference/ld_boxplot.html
@@ -1,5 +1,5 @@
-ld_boxplot — ld_boxplot • radiator ld_boxplot — ld_boxplot • radiator Prune dataset based on LD and missingness. — ld_missing • radiator Prune dataset based on LD and missingness. — ld_missing • radiator Prune dataset based on LD. — ld_pruning • radiator Prune dataset based on LD. — ld_pruning • radiator List current active filters (individuals and markers) in radiator GDS object. — list_filters • radiator List current active filters (individuals and markers) in radiator GDS object. — list_filters • radiator
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/markers_genotyped_helper.html b/docs/reference/markers_genotyped_helper.html
index 3c9df84c..aede1ab0 100644
--- a/docs/reference/markers_genotyped_helper.html
+++ b/docs/reference/markers_genotyped_helper.html
@@ -1,5 +1,5 @@
-markers_genotyped_helper — markers_genotyped_helper • radiator markers_genotyped_helper — markers_genotyped_helper • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ markers_genotyped_helper
diff --git a/docs/reference/merge_dart.html b/docs/reference/merge_dart.html
index cb9c47dd..51313a01 100644
--- a/docs/reference/merge_dart.html
+++ b/docs/reference/merge_dart.html
@@ -1,5 +1,5 @@
-Merge DArT files — merge_dart • radiator Merge DArT files — merge_dart • radiator
@@ -17,7 +17,7 @@
@@ -192,7 +192,7 @@ Examples
diff --git a/docs/reference/message_func_call.html b/docs/reference/message_func_call.html
index 71e6fd17..b0a90bd4 100644
--- a/docs/reference/message_func_call.html
+++ b/docs/reference/message_func_call.html
@@ -1,5 +1,5 @@
-message_func_call — message_func_call • radiator message_func_call — message_func_call • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ message_func_call
diff --git a/docs/reference/missing_per_pop.html b/docs/reference/missing_per_pop.html
index 7f6547ff..f734e751 100644
--- a/docs/reference/missing_per_pop.html
+++ b/docs/reference/missing_per_pop.html
@@ -1,5 +1,5 @@
-missing_per_pop — missing_per_pop • radiator missing_per_pop — missing_per_pop • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ missing_per_pop
diff --git a/docs/reference/n.html b/docs/reference/n.html
index 241b72f8..650b55af 100644
--- a/docs/reference/n.html
+++ b/docs/reference/n.html
@@ -1,5 +1,5 @@
-The number of observations in the current group. — n • radiator The number of observations in the current group. — n • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ The number of observations in the current group.
diff --git a/docs/reference/not_common_markers.html b/docs/reference/not_common_markers.html
index 38474933..52702221 100644
--- a/docs/reference/not_common_markers.html
+++ b/docs/reference/not_common_markers.html
@@ -1,5 +1,5 @@
-not_common_markers — not_common_markers • radiator not_common_markers — not_common_markers • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ not_common_markers
diff --git a/docs/reference/parallel_core_opt.html b/docs/reference/parallel_core_opt.html
index c90d8951..5988fc0e 100644
--- a/docs/reference/parallel_core_opt.html
+++ b/docs/reference/parallel_core_opt.html
@@ -1,5 +1,5 @@
-parallel_core_opt — parallel_core_opt • radiator parallel_core_opt — parallel_core_opt • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ parallel_core_opt
diff --git a/docs/reference/parse_gds_metadata.html b/docs/reference/parse_gds_metadata.html
index 0d7ab646..ad2f807e 100644
--- a/docs/reference/parse_gds_metadata.html
+++ b/docs/reference/parse_gds_metadata.html
@@ -1,5 +1,5 @@
-parse_gds_metadata — parse_gds_metadata • radiator parse_gds_metadata — parse_gds_metadata • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ parse_gds_metadata
diff --git a/docs/reference/pi.html b/docs/reference/pi.html
index 85ae2ceb..ac69dca4 100644
--- a/docs/reference/pi.html
+++ b/docs/reference/pi.html
@@ -1,5 +1,5 @@
-Nucleotide diversity — pi • radiator Nucleotide diversity — pi • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -181,7 +181,7 @@ Examples
diff --git a/docs/reference/pi_pop.html b/docs/reference/pi_pop.html
index 94dd9b17..60944089 100644
--- a/docs/reference/pi_pop.html
+++ b/docs/reference/pi_pop.html
@@ -1,5 +1,5 @@
-pi_pop — pi_pop • radiator pi_pop — pi_pop • radiator
@@ -17,7 +17,7 @@
@@ -92,7 +92,7 @@ Author
diff --git a/docs/reference/pi_rad.html b/docs/reference/pi_rad.html
index 7f101caa..aacecefd 100644
--- a/docs/reference/pi_rad.html
+++ b/docs/reference/pi_rad.html
@@ -1,5 +1,5 @@
-pi_rad — pi_rad • radiator pi_rad — pi_rad • radiator
@@ -17,7 +17,7 @@
@@ -92,7 +92,7 @@ Author
diff --git a/docs/reference/pipe.html b/docs/reference/pipe.html
index 57a5bcc1..0585be18 100644
--- a/docs/reference/pipe.html
+++ b/docs/reference/pipe.html
@@ -1,5 +1,5 @@
-Forward-pipe operator — %>% • radiator Forward-pipe operator — %>% • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ Forward-pipe operator
diff --git a/docs/reference/plot_bayescan.html b/docs/reference/plot_bayescan.html
index 89023923..492e4e8e 100644
--- a/docs/reference/plot_bayescan.html
+++ b/docs/reference/plot_bayescan.html
@@ -1,5 +1,5 @@
-plot_bayescan — plot_bayescan • radiator plot_bayescan — plot_bayescan • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ plot_bayescan
diff --git a/docs/reference/plot_boxplot_coverage.html b/docs/reference/plot_boxplot_coverage.html
index 84b023bf..17fbd811 100644
--- a/docs/reference/plot_boxplot_coverage.html
+++ b/docs/reference/plot_boxplot_coverage.html
@@ -1,5 +1,5 @@
-Figure box plot of coverage summary statistics — plot_boxplot_coverage • radiator Figure box plot of coverage summary statistics — plot_boxplot_coverage • radiator Box plot of the diversity (Gene and Haplotypes) — plot_boxplot_diversity • radiator Box plot of the diversity (Gene and Haplotypes) — plot_boxplot_diversity • radiator Visual diagnostic of coverage imbalance — plot_coverage_imbalance_diagnostic • radiator Visual diagnostic of coverage imbalance — plot_coverage_imbalance_diagnostic • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -149,7 +149,7 @@ Details
diff --git a/docs/reference/plot_density_distribution_coverage.html b/docs/reference/plot_density_distribution_coverage.html
index 1146cb10..0937fe36 100644
--- a/docs/reference/plot_density_distribution_coverage.html
+++ b/docs/reference/plot_density_distribution_coverage.html
@@ -1,5 +1,5 @@
-Figure of distribution (histogram) — plot_histogram • radiator Figure of distribution (histogram) — plot_histogram • radiator Figure density distribution of the observed heterozygosity
-summary statistics. — plot_density_distribution_het • radiator Figure density distribution of the observed heterozygosity summary statistics. — plot_density_distribution_het • radiator Figure density distribution of minor allele frequency (MAF)
-summary statistics. — plot_density_distribution_maf • radiator Figure density distribution of minor allele frequency (MAF) summary statistics. — plot_density_distribution_maf • radiator
@@ -19,7 +17,7 @@
@@ -64,8 +62,7 @@
- Figure density distribution of minor allele frequency (MAF)
-summary statistics.
+ Figure density distribution of minor allele frequency (MAF) summary statistics.
Source: R/visualization.R
plot_density_distribution_maf.Rd
@@ -134,7 +131,7 @@ Author
diff --git a/docs/reference/plot_distribution_diversity.html b/docs/reference/plot_distribution_diversity.html
index 2d82b11a..410c85b0 100644
--- a/docs/reference/plot_distribution_diversity.html
+++ b/docs/reference/plot_distribution_diversity.html
@@ -1,5 +1,5 @@
-Density distribution of diversity (Gene and Haplotypes) — plot_distribution_diversity • radiator Density distribution of diversity (Gene and Haplotypes) — plot_distribution_diversity • radiator
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_het_outliers.html b/docs/reference/plot_het_outliers.html
index e233c5f8..ae00754d 100644
--- a/docs/reference/plot_het_outliers.html
+++ b/docs/reference/plot_het_outliers.html
@@ -1,5 +1,5 @@
-plot_het_outliers — plot_het_outliers • radiator plot_het_outliers — plot_het_outliers • radiator Figure of the distribution of SNP per locus before and after filters — plot_snp_number_loci • radiator Figure of the distribution of SNP per locus before and after filters — plot_snp_number_loci • radiator
@@ -17,7 +17,7 @@
@@ -98,7 +98,7 @@ Arguments
diff --git a/docs/reference/plot_snp_position_read.html b/docs/reference/plot_snp_position_read.html
index 60991367..3d03575c 100644
--- a/docs/reference/plot_snp_position_read.html
+++ b/docs/reference/plot_snp_position_read.html
@@ -1,5 +1,5 @@
-Figure of the distribution of SNP nucleotide position alond the read — plot_snp_position_read • radiator Figure of the distribution of SNP nucleotide position alond the read — plot_snp_position_read • radiator
@@ -17,7 +17,7 @@
@@ -102,7 +102,7 @@ Arguments
diff --git a/docs/reference/plot_upset.html b/docs/reference/plot_upset.html
index 87e84ff1..aa1218d7 100644
--- a/docs/reference/plot_upset.html
+++ b/docs/reference/plot_upset.html
@@ -1,5 +1,5 @@
-plot_upset — plot_upset • radiator plot_upset — plot_upset • radiator
@@ -17,7 +17,7 @@
@@ -94,7 +94,7 @@ plot_upset
diff --git a/docs/reference/private_alleles.html b/docs/reference/private_alleles.html
index 1ac8a329..7ac1d578 100644
--- a/docs/reference/private_alleles.html
+++ b/docs/reference/private_alleles.html
@@ -1,5 +1,5 @@
-Find private alleles — private_alleles • radiator Find private alleles — private_alleles • radiator
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Examples
diff --git a/docs/reference/private_haplotypes.html b/docs/reference/private_haplotypes.html
index 70872333..1af437f0 100644
--- a/docs/reference/private_haplotypes.html
+++ b/docs/reference/private_haplotypes.html
@@ -1,5 +1,5 @@
-private haplotypes — private_haplotypes • radiator private haplotypes — private_haplotypes • radiator
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Author
diff --git a/docs/reference/radiator_common_arguments.html b/docs/reference/radiator_common_arguments.html
index d9f1b8fc..3e9357f3 100644
--- a/docs/reference/radiator_common_arguments.html
+++ b/docs/reference/radiator_common_arguments.html
@@ -1,5 +1,5 @@
-radiator common arguments — radiator_common_arguments • radiator radiator common arguments — radiator_common_arguments • radiator
@@ -17,7 +17,7 @@
@@ -73,6 +73,7 @@ radiator common arguments
radiator_common_arguments(
+ interactive.filter = TRUE,
gds,
data,
parallel.core = parallel::detectCores() - 1,
@@ -84,7 +85,14 @@ radiator common arguments
Arguments
- - gds
+ - interactive.filter
+(optional, logical) Do you want the filtering session to
+be interactive. Figures of distribution are shown before asking for filtering
+thresholds.
+Default: interactive.filter = TRUE.
- gds
(2 options) A Genomic Data Structure (GDS) file or object
How to get GDS ?
Look into tidy_genomic_data,
@@ -125,13 +133,6 @@
Arguments
for fine-tuning the function. Also used for legacy arguments (see details or
special section)- interactive.filter
-(optional, logical) Do you want the filtering session to
-be interactive. Figures of distribution are shown before asking for filtering
-thresholds.
-Default: interactive.filter = TRUE.
@@ -146,7 +147,7 @@ Arguments
diff --git a/docs/reference/radiator_dots.html b/docs/reference/radiator_dots.html
index 9c01f70b..4a63653c 100644
--- a/docs/reference/radiator_dots.html
+++ b/docs/reference/radiator_dots.html
@@ -1,5 +1,5 @@
-radiator_dots — radiator_dots • radiator radiator_dots — radiator_dots • radiator
@@ -17,7 +17,7 @@
@@ -93,7 +93,11 @@ radiator_dots
"keep.allele.names", "keep.gds", "calibrate.alleles", "vcf.metadata", "vcf.stats",
"wide", "whitelist.markers", "write.tidy", "missing.memory", "dart.sequence",
- "internal", "heatmap.fst", "tidy.check", "tidy.vcf", "tidy.dart"),
+ "internal", "heatmap.fst", "tidy.check", "tidy.vcf", "tidy.dart", "species",
+ "population", "tau", "threshold.y.markers", "threshold.y.silico.markers",
+ "sex.id.input", "threshold.x.markers.qr", "threshold.x.markers.RD",
+ "threshold.x.markers.RD.silico", "mis.threshold.data", "mis.threshold.silicodata",
+ "zoom.data", "zoom.silicodata", "sex.id.input", "het.qr.input"),
deprecated = c("maf.thresholds", "common.markers", "max.marker", "monomorphic.out",
"snp.ld", "filter.call.rate", "filter.markers.coverage", "filter.markers.missing",
"number.snp.reads", "mixed.genomes.analysis", "duplicate.genomes.analysis",
@@ -144,7 +148,11 @@ Arguments
"write.tidy",
"dart.sequence",
"missing.memory",
-"internal", "heatmap.fst", "tidy.check", "tidy.vcf", "tidy.dart").
+"internal", "heatmap.fst", "tidy.check", "tidy.vcf", "tidy.dart",
+"species", "population", "tau", "threshold.y.markers", "threshold.y.silico.markers",
+"sex.id.input", "threshold.x.markers.qr", "threshold.x.markers.RD", "threshold.x.markers.RD.silico",
+"mis.threshold.data", "mis.threshold.silicodata", "zoom.data", "zoom.silicodata",
+"sex.id.input", "het.qr.input").
deprecated
@@ -174,7 +182,7 @@ Arguments
diff --git a/docs/reference/radiator_folder.html b/docs/reference/radiator_folder.html
index fd38cd2d..f956f508 100644
--- a/docs/reference/radiator_folder.html
+++ b/docs/reference/radiator_folder.html
@@ -1,5 +1,5 @@
-radiator_folder — radiator_folder • radiator radiator_folder — radiator_folder • radiator
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Author
diff --git a/docs/reference/radiator_function_header.html b/docs/reference/radiator_function_header.html
index 35429f6d..c34ad494 100644
--- a/docs/reference/radiator_function_header.html
+++ b/docs/reference/radiator_function_header.html
@@ -1,5 +1,5 @@
-radiator_function_header — radiator_function_header • radiator radiator_function_header — radiator_function_header • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ radiator_function_header
diff --git a/docs/reference/radiator_gds.html b/docs/reference/radiator_gds.html
index 578aa681..28716746 100644
--- a/docs/reference/radiator_gds.html
+++ b/docs/reference/radiator_gds.html
@@ -1,5 +1,5 @@
-radiator gds constructor — radiator_gds • radiator radiator gds constructor — radiator_gds • radiator
@@ -17,7 +17,7 @@
@@ -102,7 +102,7 @@ radiator gds constructor
diff --git a/docs/reference/radiator_gds_skeleton.html b/docs/reference/radiator_gds_skeleton.html
index a78cfc55..793c3f81 100644
--- a/docs/reference/radiator_gds_skeleton.html
+++ b/docs/reference/radiator_gds_skeleton.html
@@ -1,5 +1,5 @@
-radiator_gds_skeleton — radiator_gds_skeleton • radiator radiator_gds_skeleton — radiator_gds_skeleton • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ radiator_gds_skeleton
diff --git a/docs/reference/radiator_packages_dep.html b/docs/reference/radiator_packages_dep.html
index 46f362aa..8204a250 100644
--- a/docs/reference/radiator_packages_dep.html
+++ b/docs/reference/radiator_packages_dep.html
@@ -1,5 +1,5 @@
-radiator_packages_dep — radiator_packages_dep • radiator radiator_packages_dep — radiator_packages_dep • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ radiator_packages_dep
diff --git a/docs/reference/radiator_parameters.html b/docs/reference/radiator_parameters.html
index b06bdaac..c22bcb3b 100644
--- a/docs/reference/radiator_parameters.html
+++ b/docs/reference/radiator_parameters.html
@@ -1,5 +1,5 @@
-radiator_parameters — radiator_parameters • radiator radiator_parameters — radiator_parameters • radiator radiator packages install helper — radiator_pkg_install • radiator radiator packages install helper — radiator_pkg_install • radiator radiator_question — radiator_question • radiator radiator_question — radiator_question • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ radiator_question
diff --git a/docs/reference/radiator_results_message.html b/docs/reference/radiator_results_message.html
index 641a55df..3d806023 100644
--- a/docs/reference/radiator_results_message.html
+++ b/docs/reference/radiator_results_message.html
@@ -1,5 +1,5 @@
-radiator_results_message — radiator_results_message • radiator radiator_results_message — radiator_results_message • radiator
@@ -17,7 +17,7 @@
@@ -93,7 +93,7 @@ radiator_results_message
diff --git a/docs/reference/radiator_snakecase.html b/docs/reference/radiator_snakecase.html
index 4fc158a6..bf64d00a 100644
--- a/docs/reference/radiator_snakecase.html
+++ b/docs/reference/radiator_snakecase.html
@@ -1,5 +1,5 @@
-radiator_snakecase — radiator_snakecase • radiator radiator_snakecase — radiator_snakecase • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ radiator_snakecase
diff --git a/docs/reference/radiator_split_tibble.html b/docs/reference/radiator_split_tibble.html
index 962743d9..3b099191 100644
--- a/docs/reference/radiator_split_tibble.html
+++ b/docs/reference/radiator_split_tibble.html
@@ -1,5 +1,5 @@
-radiator_split_tibble — radiator_split_tibble • radiator radiator_split_tibble — radiator_split_tibble • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ radiator_split_tibble
diff --git a/docs/reference/radiator_tic.html b/docs/reference/radiator_tic.html
index 99347514..c249da60 100644
--- a/docs/reference/radiator_tic.html
+++ b/docs/reference/radiator_tic.html
@@ -1,5 +1,5 @@
-radiator_tic — radiator_tic • radiator radiator_tic — radiator_tic • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ radiator_tic
diff --git a/docs/reference/radiator_toc.html b/docs/reference/radiator_toc.html
index bc6b2b2f..76510cd7 100644
--- a/docs/reference/radiator_toc.html
+++ b/docs/reference/radiator_toc.html
@@ -1,5 +1,5 @@
-radiator_toc — radiator_toc • radiator radiator_toc — radiator_toc • radiator
@@ -17,7 +17,7 @@
@@ -92,7 +92,7 @@ radiator_toc
diff --git a/docs/reference/read_blacklist_genotypes.html b/docs/reference/read_blacklist_genotypes.html
index 4901fe12..cd49840b 100644
--- a/docs/reference/read_blacklist_genotypes.html
+++ b/docs/reference/read_blacklist_genotypes.html
@@ -1,5 +1,5 @@
-read blacklist of genotypes — read_blacklist_genotypes • radiator read blacklist of genotypes — read_blacklist_genotypes • radiator read_blacklist_id — read_blacklist_id • radiator read_blacklist_id — read_blacklist_id • radiator Read and tidy DArT output files. — read_dart • radiator Read and tidy DArT output files. — read_dart • radiator Reads PLINK tped and bed files — read_plink • radiator Reads PLINK tped and bed files — read_plink • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -185,7 +185,7 @@ Examples
diff --git a/docs/reference/read_rad.html b/docs/reference/read_rad.html
index 40dab71c..5f85d666 100644
--- a/docs/reference/read_rad.html
+++ b/docs/reference/read_rad.html
@@ -1,5 +1,5 @@
-Read radiator file ending .gds, .rad, .gds.rad. — read_rad • radiator Read radiator file ending .gds, .rad, .gds.rad. — read_rad • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -198,7 +198,7 @@ Examples
diff --git a/docs/reference/read_strata.html b/docs/reference/read_strata.html
index 147738eb..59858576 100644
--- a/docs/reference/read_strata.html
+++ b/docs/reference/read_strata.html
@@ -1,5 +1,5 @@
-read strata — read_strata • radiator read strata — read_strata • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -269,7 +269,7 @@ Examples
diff --git a/docs/reference/read_vcf.html b/docs/reference/read_vcf.html
index fa3b6d0d..75b355f0 100644
--- a/docs/reference/read_vcf.html
+++ b/docs/reference/read_vcf.html
@@ -1,5 +1,5 @@
-Read VCF files and write a GDS file — read_vcf • radiator Read VCF files and write a GDS file — read_vcf • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -376,7 +376,7 @@ Examples
diff --git a/docs/reference/read_whitelist.html b/docs/reference/read_whitelist.html
index a4d664c2..b9942883 100644
--- a/docs/reference/read_whitelist.html
+++ b/docs/reference/read_whitelist.html
@@ -1,5 +1,5 @@
-read whitelist of markers — read_whitelist • radiator read whitelist of markers — read_whitelist • radiator Read tidy genomic data file ending .rad — remove_duplicates • radiator Read tidy genomic data file ending .rad — remove_duplicates • radiator replace_by_na — replace_by_na • radiator replace_by_na — replace_by_na • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ replace_by_na
diff --git a/docs/reference/reset_filters.html b/docs/reference/reset_filters.html
index dbb492d7..458020b2 100644
--- a/docs/reference/reset_filters.html
+++ b/docs/reference/reset_filters.html
@@ -1,5 +1,5 @@
-Reset filters (individuals and markers) in radiator GDS object. — reset_filters • radiator Reset filters (individuals and markers) in radiator GDS object. — reset_filters • radiator Run BayeScan — run_bayescan • radiator Run BayeScan — run_bayescan • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -326,7 +326,7 @@ Examples
diff --git a/docs/reference/separate_gt.html b/docs/reference/separate_gt.html
index df80123a..9eaebe4f 100644
--- a/docs/reference/separate_gt.html
+++ b/docs/reference/separate_gt.html
@@ -1,5 +1,5 @@
-separate_gt — separate_gt • radiator separate_gt — separate_gt • radiator
@@ -17,7 +17,7 @@
@@ -99,7 +99,7 @@ separate_gt
diff --git a/docs/reference/separate_markers.html b/docs/reference/separate_markers.html
index b209bfd0..cbd8734d 100644
--- a/docs/reference/separate_markers.html
+++ b/docs/reference/separate_markers.html
@@ -1,5 +1,5 @@
-Separate markers column into chrom, locus and pos — separate_markers • radiator Separate markers column into chrom, locus and pos — separate_markers • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -207,7 +207,7 @@ Examples
diff --git a/docs/reference/sex_markers_plot.html b/docs/reference/sex_markers_plot.html
index 4f8e71c0..a50121b0 100644
--- a/docs/reference/sex_markers_plot.html
+++ b/docs/reference/sex_markers_plot.html
@@ -1,5 +1,5 @@
-sex_markers_plot — sex_markers_plot • radiator sex_markers_plot — sex_markers_plot • radiator
@@ -17,7 +17,7 @@
@@ -87,7 +87,8 @@ sex_markers_plot
qreg = FALSE,
hist = FALSE,
RD = FALSE,
- plot.filename = NULL
+ plot.filename = NULL,
+ path = NULL
)
@@ -104,7 +105,7 @@ sex_markers_plot
diff --git a/docs/reference/sexy_markers.html b/docs/reference/sexy_markers.html
index 80804e96..666545ed 100644
--- a/docs/reference/sexy_markers.html
+++ b/docs/reference/sexy_markers.html
@@ -1,5 +1,5 @@
-sexy_markers finds sex-linked markers and re-assigns sex — sexy_markers • radiator sexy_markers finds sex-linked markers and re-assigns sex — sexy_markers • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -85,8 +85,8 @@ sexy_markers finds sex-linked markers and re-assigns sex
sexy_markers(
data,
silicodata = NULL,
- boost.analysis = FALSE,
strata = NULL,
+ boost.analysis = FALSE,
coverage.thresholds = 1,
filters = TRUE,
interactive.filter = TRUE,
@@ -111,13 +111,6 @@ Arguments
Default: silicodata = NULL.
-boost.analysis
-(optional, logical) This method uses machine learning
-approaches to find sex markers and re-assign samples in sex group.
-The approach is currently been tested and will be available for uses soon.
-Default: boost.analysis = FALSE.
strata
(file) A tab delimited file with a minimum of
2 columns (INDIVIDUALS, STRATA) for VCF files and 3 columns for DArT files
@@ -132,6 +125,13 @@
Arguments
functions: extract_dart_target_id and extract_individuals_vcfboost.analysis
+(optional, logical) This method uses machine learning
+approaches to find sex markers and re-assign samples in sex group.
+The approach is currently under construction.
+Default: boost.analysis = FALSE.
coverage.thresholds
(optional, integer) The minimum coverage required
to call a marker absent. For silico genotype data this must be < 1.
@@ -155,7 +155,7 @@
Arguments
folder.name
(optional,character) Name of the folder to store the results.
-Default: folder.name = "sexy_marker_date/time".
folder.name = NULL. The name sexy_markers_datetime will be generated.
parallel.core
@@ -250,7 +250,11 @@ Advance mode
-dots-dots-dots ... allows to pass several arguments for fine-tuning the function:
tau: The quantile used in regression to distinguish homogametic markers
+
dots-dots-dots ... allows to pass several arguments for fine-tuning the function:
species: To give your figures some meanings.
+Default species = NULL.
population: To give your figures some meanings.
+Default species = NULL.
tau: The quantile used in regression to distinguish homogametic markers
with the heterozygosity method. See rq.
Default tau = 0.03.
mis.threshold.data: Threshold to filter the SNP data on missingness.
@@ -325,7 +329,7 @@
Examples
diff --git a/docs/reference/simulate_genos_from_posterior.html b/docs/reference/simulate_genos_from_posterior.html
index 499054d1..8b9ec6f9 100644
--- a/docs/reference/simulate_genos_from_posterior.html
+++ b/docs/reference/simulate_genos_from_posterior.html
@@ -1,5 +1,5 @@
-simulate_genos_from_posterior — simulate_genos_from_posterior • radiator simulate_genos_from_posterior — simulate_genos_from_posterior • radiator split_tibble_rows — split_tibble_rows • radiator split_tibble_rows — split_tibble_rows • radiator
@@ -17,7 +17,7 @@
@@ -93,7 +93,7 @@ split_tibble_rows
diff --git a/docs/reference/split_vcf.html b/docs/reference/split_vcf.html
index a43e07de..66b27d42 100644
--- a/docs/reference/split_vcf.html
+++ b/docs/reference/split_vcf.html
@@ -1,5 +1,5 @@
-Split a VCF file — split_vcf • radiator Split a VCF file — split_vcf • radiator strata_haplo — strata_haplo • radiator strata_haplo — strata_haplo • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ strata_haplo
diff --git a/docs/reference/subsampling_data.html b/docs/reference/subsampling_data.html
index 60a1a87c..ae009819 100644
--- a/docs/reference/subsampling_data.html
+++ b/docs/reference/subsampling_data.html
@@ -1,5 +1,5 @@
-subsampling data — subsampling_data • radiator subsampling data — subsampling_data • radiator
@@ -17,7 +17,7 @@
@@ -93,7 +93,7 @@ subsampling data
diff --git a/docs/reference/summarise_genotypes.html b/docs/reference/summarise_genotypes.html
index b9959c59..109c2e28 100644
--- a/docs/reference/summarise_genotypes.html
+++ b/docs/reference/summarise_genotypes.html
@@ -1,5 +1,5 @@
-summarise genotypes — summarise_genotypes • radiator summarise genotypes — summarise_genotypes • radiator
@@ -17,7 +17,7 @@
@@ -92,7 +92,7 @@ Author
diff --git a/docs/reference/summarize_sex.html b/docs/reference/summarize_sex.html
index 14b66900..ff53f89d 100644
--- a/docs/reference/summarize_sex.html
+++ b/docs/reference/summarize_sex.html
@@ -1,5 +1,5 @@
-summarize_sex — summarize_sex • radiator summarize_sex — summarize_sex • radiator
@@ -17,7 +17,7 @@
@@ -94,7 +94,7 @@ summarize_sex
diff --git a/docs/reference/summary_gds.html b/docs/reference/summary_gds.html
index 3abfb279..13a224e6 100644
--- a/docs/reference/summary_gds.html
+++ b/docs/reference/summary_gds.html
@@ -1,5 +1,5 @@
-summary_gds — summary_gds • radiator summary_gds — summary_gds • radiator
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/summary_rad.html b/docs/reference/summary_rad.html
index 5cc5e1b1..7972e1e3 100644
--- a/docs/reference/summary_rad.html
+++ b/docs/reference/summary_rad.html
@@ -1,5 +1,5 @@
-Summary statistics for RADseq data — summary_rad • radiator Summary statistics for RADseq data — summary_rad • radiator Summary of strata — summary_strata • radiator Summary of strata — summary_strata • radiator switch_allele_count — switch_allele_count • radiator switch_allele_count — switch_allele_count • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ switch_allele_count
diff --git a/docs/reference/switch_genotypes.html b/docs/reference/switch_genotypes.html
index c13b7296..8d2d3cc4 100644
--- a/docs/reference/switch_genotypes.html
+++ b/docs/reference/switch_genotypes.html
@@ -1,5 +1,5 @@
-switch_genotypes — switch_genotypes • radiator switch_genotypes — switch_genotypes • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ switch_genotypes
diff --git a/docs/reference/sync_gds.html b/docs/reference/sync_gds.html
index c604aa3f..7e349b48 100644
--- a/docs/reference/sync_gds.html
+++ b/docs/reference/sync_gds.html
@@ -1,5 +1,5 @@
-sync_gds — sync_gds • radiator sync_gds — sync_gds • radiator tibble_stats — tibble_stats • radiator tibble_stats — tibble_stats • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ tibble_stats
diff --git a/docs/reference/tidy2gds.html b/docs/reference/tidy2gds.html
index 4cac68bc..a9d5a8e3 100644
--- a/docs/reference/tidy2gds.html
+++ b/docs/reference/tidy2gds.html
@@ -1,5 +1,5 @@
-tidy2gds — tidy2gds • radiator tidy2gds — tidy2gds • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ tidy2gds
diff --git a/docs/reference/tidy2wide.html b/docs/reference/tidy2wide.html
index 57a23746..3a97c801 100644
--- a/docs/reference/tidy2wide.html
+++ b/docs/reference/tidy2wide.html
@@ -1,5 +1,5 @@
-tidy2wide — tidy2wide • radiator tidy2wide — tidy2wide • radiator
@@ -17,7 +17,7 @@
@@ -96,7 +96,7 @@ tidy2wide
diff --git a/docs/reference/tidy_dart_metadata.html b/docs/reference/tidy_dart_metadata.html
index aa4a9d7d..1d0dbbc1 100644
--- a/docs/reference/tidy_dart_metadata.html
+++ b/docs/reference/tidy_dart_metadata.html
@@ -1,5 +1,5 @@
-Import and tidy DArT metadata. — tidy_dart_metadata • radiator Import and tidy DArT metadata. — tidy_dart_metadata • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -160,7 +160,7 @@ Examples
diff --git a/docs/reference/tidy_fstat.html b/docs/reference/tidy_fstat.html
index 108e395e..7ed7c4b4 100644
--- a/docs/reference/tidy_fstat.html
+++ b/docs/reference/tidy_fstat.html
@@ -1,5 +1,5 @@
-fstat file to tidy dataframe — tidy_fstat • radiator fstat file to tidy dataframe — tidy_fstat • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -180,7 +180,7 @@ Examples
diff --git a/docs/reference/tidy_genepop.html b/docs/reference/tidy_genepop.html
index 93bf51fd..03b6fcb7 100644
--- a/docs/reference/tidy_genepop.html
+++ b/docs/reference/tidy_genepop.html
@@ -1,5 +1,5 @@
-Import genepop file and convert to a tidy dataframe — tidy_genepop • radiator Import genepop file and convert to a tidy dataframe — tidy_genepop • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -253,7 +253,7 @@ Examples
diff --git a/docs/reference/tidy_genind.html b/docs/reference/tidy_genind.html
index 1acf7666..82e77677 100644
--- a/docs/reference/tidy_genind.html
+++ b/docs/reference/tidy_genind.html
@@ -1,5 +1,5 @@
-Tidy a genind object to a tidy dataframe — tidy_genind • radiator Tidy a genind object to a tidy dataframe — tidy_genind • radiator Tidy a genlight object to a tidy dataframe and/or GDS object/file — tidy_genlight • radiator Tidy a genlight object to a tidy dataframe and/or GDS object/file — tidy_genlight • radiator Transform common genomic dataset format in a tidy data frame — tidy_genomic_data • radiator Transform common genomic dataset format in a tidy data frame — tidy_genomic_data • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -247,7 +247,7 @@ Examples
diff --git a/docs/reference/tidy_gtypes.html b/docs/reference/tidy_gtypes.html
index cf8901d8..80a269d0 100644
--- a/docs/reference/tidy_gtypes.html
+++ b/docs/reference/tidy_gtypes.html
@@ -1,5 +1,5 @@
-Tidy a gtypes object to a tidy dataframe — tidy_gtypes • radiator Tidy a gtypes object to a tidy dataframe — tidy_gtypes • radiator Tidy PLINK tped and bed files — tidy_plink • radiator Tidy PLINK tped and bed files — tidy_plink • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -176,7 +176,7 @@ Examples
diff --git a/docs/reference/tidy_vcf.html b/docs/reference/tidy_vcf.html
index 2a5543b1..c62f87b1 100644
--- a/docs/reference/tidy_vcf.html
+++ b/docs/reference/tidy_vcf.html
@@ -1,5 +1,5 @@
-Tidy vcf file — tidy_vcf • radiator Tidy vcf file — tidy_vcf • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -326,7 +326,7 @@ Examples
diff --git a/docs/reference/tidy_wide.html b/docs/reference/tidy_wide.html
index 66a44b5b..b06ad6c8 100644
--- a/docs/reference/tidy_wide.html
+++ b/docs/reference/tidy_wide.html
@@ -1,5 +1,5 @@
-Read/Import a tidy genomic data frames. — tidy_wide • radiator Read/Import a tidy genomic data frames. — tidy_wide • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -160,7 +160,7 @@ Author
diff --git a/docs/reference/update_bl_individuals.html b/docs/reference/update_bl_individuals.html
index a1d79150..25b42f8f 100644
--- a/docs/reference/update_bl_individuals.html
+++ b/docs/reference/update_bl_individuals.html
@@ -1,5 +1,5 @@
-update_bl_individuals — update_bl_individuals • radiator update_bl_individuals — update_bl_individuals • radiator
@@ -17,7 +17,7 @@
@@ -94,7 +94,7 @@ update_bl_individuals
diff --git a/docs/reference/update_bl_markers.html b/docs/reference/update_bl_markers.html
index cf55b6ba..73bf184c 100644
--- a/docs/reference/update_bl_markers.html
+++ b/docs/reference/update_bl_markers.html
@@ -1,5 +1,5 @@
-update_bl_markers — update_bl_markers • radiator update_bl_markers — update_bl_markers • radiator
@@ -17,7 +17,7 @@
@@ -94,7 +94,7 @@ update_bl_markers
diff --git a/docs/reference/update_filter_parameter.html b/docs/reference/update_filter_parameter.html
index 5f2e7de4..46256cac 100644
--- a/docs/reference/update_filter_parameter.html
+++ b/docs/reference/update_filter_parameter.html
@@ -1,5 +1,5 @@
-update filter parameter file — update_filter_parameter • radiator update filter parameter file — update_filter_parameter • radiator
@@ -17,7 +17,7 @@
@@ -99,7 +99,7 @@ Author
diff --git a/docs/reference/update_radiator_gds.html b/docs/reference/update_radiator_gds.html
index a372c4dd..e8afd052 100644
--- a/docs/reference/update_radiator_gds.html
+++ b/docs/reference/update_radiator_gds.html
@@ -1,5 +1,5 @@
-update_radiator_gds — update_radiator_gds • radiator update_radiator_gds — update_radiator_gds • radiator
@@ -17,7 +17,7 @@
@@ -97,7 +97,7 @@ update_radiator_gds
diff --git a/docs/reference/vcf_strata.html b/docs/reference/vcf_strata.html
index a9630309..94c0861f 100644
--- a/docs/reference/vcf_strata.html
+++ b/docs/reference/vcf_strata.html
@@ -1,5 +1,5 @@
-Join stratification metadata to a VCF (population-aware VCF) — vcf_strata • radiator Join stratification metadata to a VCF (population-aware VCF) — vcf_strata • radiator Write an arlequin file from a tidy data frame — write_arlequin • radiator Write an arlequin file from a tidy data frame — write_arlequin • radiator Write a BayeScan
-file from a tidy data frame — write_bayescan • radiator Write a BayeScan file from a tidy data frame — write_bayescan • radiator Write a betadiv file from a tidy data frame — write_betadiv • radiator Write a betadiv file from a tidy data frame — write_betadiv • radiator Write a COLONY input file — write_colony • radiator Write a COLONY input file — write_colony • radiator
@@ -17,7 +17,7 @@
@@ -272,7 +272,7 @@ Examples
diff --git a/docs/reference/write_dadi.html b/docs/reference/write_dadi.html
index 0436c0be..373976e1 100644
--- a/docs/reference/write_dadi.html
+++ b/docs/reference/write_dadi.html
@@ -1,5 +1,5 @@
-Write a dadi SNP input file from a tidy data frame. — write_dadi • radiator Write a dadi SNP input file from a tidy data frame. — write_dadi • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -192,7 +192,7 @@ Examples
diff --git a/docs/reference/write_fasta.html b/docs/reference/write_fasta.html
index 9f17ee5f..eb180aff 100644
--- a/docs/reference/write_fasta.html
+++ b/docs/reference/write_fasta.html
@@ -1,5 +1,5 @@
-Export FASTA — write_fasta • radiator Export FASTA — write_fasta • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ Export FASTA
diff --git a/docs/reference/write_faststructure.html b/docs/reference/write_faststructure.html
index 02db9643..9bce50dc 100644
--- a/docs/reference/write_faststructure.html
+++ b/docs/reference/write_faststructure.html
@@ -1,5 +1,5 @@
-Write a faststructure file from a tidy data frame — write_faststructure • radiator Write a faststructure file from a tidy data frame — write_faststructure • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -156,7 +156,7 @@ Author
diff --git a/docs/reference/write_fineradstructure.html b/docs/reference/write_fineradstructure.html
index c7e40ff5..a5103558 100644
--- a/docs/reference/write_fineradstructure.html
+++ b/docs/reference/write_fineradstructure.html
@@ -1,5 +1,5 @@
-Write a fineRADstructure file from a tidy data frame — write_fineradstructure • radiator Write a fineRADstructure file from a tidy data frame — write_fineradstructure • radiator Write a GDS object from a tidy data frame — write_gds • radiator Write a GDS object from a tidy data frame — write_gds • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -165,7 +165,7 @@ Examples
diff --git a/docs/reference/write_genepop.html b/docs/reference/write_genepop.html
index 78f37767..0395c0bf 100644
--- a/docs/reference/write_genepop.html
+++ b/docs/reference/write_genepop.html
@@ -1,5 +1,5 @@
-Write a genepop file — write_genepop • radiator Write a genepop file — write_genepop • radiator Write a genepopedit flatten object — write_genepopedit • radiator Write a genepopedit flatten object — write_genepopedit • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -145,7 +145,7 @@ Author
diff --git a/docs/reference/write_genind.html b/docs/reference/write_genind.html
index a064abd3..6810055d 100644
--- a/docs/reference/write_genind.html
+++ b/docs/reference/write_genind.html
@@ -1,5 +1,5 @@
-Write a genind object from a tidy data frame or GDS file or object. — write_genind • radiator Write a genind object from a tidy data frame or GDS file or object. — write_genind • radiator Write a genlight object from a tidy data frame or GDS file or object. — write_genlight • radiator Write a genlight object from a tidy data frame or GDS file or object. — write_genlight • radiator Write a gsi_sim file from a data frame (wide or long/tidy). — write_gsi_sim • radiator Write a gsi_sim file from a data frame (wide or long/tidy). — write_gsi_sim • radiator Write a strataG object from
-radiator GDS and tidy data file or object. — write_gtypes • radiator Write a strataG object from radiator GDS and tidy data file or object. — write_gtypes • radiator Write a HapMap file from a tidy data frame — write_hapmap • radiator Write a HapMap file from a tidy data frame — write_hapmap • radiator Write a hierfstat file from a tidy data frame — write_hierfstat • radiator Write a hierfstat file from a tidy data frame — write_hierfstat • radiator Write a HZAR file from a tidy data frame. — write_hzar • radiator Write a HZAR file from a tidy data frame. — write_hzar • radiator Write a LDna object from a tidy data frame — write_ldna • radiator Write a LDna object from a tidy data frame — write_ldna • radiator Write a maverick file from a tidy data frame — write_maverick • radiator Write a maverick file from a tidy data frame — write_maverick • radiator Write a pcadapt
-file from a tidy data frame — write_pcadapt • radiator Write a pcadapt file from a tidy data frame — write_pcadapt • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -69,8 +67,7 @@
- Write a pcadapt
-file from a tidy data frame
+ Write a pcadapt file from a tidy data frame
Source: R/write_pcadapt.R
write_pcadapt.Rd
@@ -187,7 +184,7 @@ Author
diff --git a/docs/reference/write_plink.html b/docs/reference/write_plink.html
index 38314609..d5c324f3 100644
--- a/docs/reference/write_plink.html
+++ b/docs/reference/write_plink.html
@@ -1,5 +1,5 @@
-Write a plink tped/tfam file from a tidy data frame — write_plink • radiator Write a plink tped/tfam file from a tidy data frame — write_plink • radiator Write tidy genomic data file or close GDS file — write_rad • radiator Write tidy genomic data file or close GDS file — write_rad • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -199,7 +199,7 @@ Examples
diff --git a/docs/reference/write_related.html b/docs/reference/write_related.html
index f8b61592..2a39deb6 100644
--- a/docs/reference/write_related.html
+++ b/docs/reference/write_related.html
@@ -1,5 +1,5 @@
-Write a related file from a tidy data frame — write_related • radiator Write a related file from a tidy data frame — write_related • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -153,7 +153,7 @@ Author
diff --git a/docs/reference/write_rubias.html b/docs/reference/write_rubias.html
index 388f7faa..7865aeb9 100644
--- a/docs/reference/write_rubias.html
+++ b/docs/reference/write_rubias.html
@@ -1,5 +1,5 @@
-Write a rubias object — write_rubias • radiator Write a rubias object — write_rubias • radiator
@@ -17,7 +17,7 @@
@@ -155,7 +155,7 @@ Author
diff --git a/docs/reference/write_snprelate.html b/docs/reference/write_snprelate.html
index 7a243f3e..3e474925 100644
--- a/docs/reference/write_snprelate.html
+++ b/docs/reference/write_snprelate.html
@@ -1,5 +1,5 @@
-Write a SNPRelate object from a tidy data frame — write_snprelate • radiator Write a SNPRelate object from a tidy data frame — write_snprelate • radiator Write a stockR dataset from a tidy data frame or GDS file or object. — write_stockr • radiator Write a stockR dataset from a tidy data frame or GDS file or object. — write_stockr • radiator Write a structure file from a tidy data frame — write_structure • radiator Write a structure file from a tidy data frame — write_structure • radiator Write a vcf file from a tidy data frame — write_vcf • radiator Write a vcf file from a tidy data frame — write_vcf • radiator
life_cycle.Rmdrad_genomics_computer_setup.Rmd
+Error:
+
+
+
+Error: HTTP status was 404 Not Found
+
+This error is sometimes poping after a new R upgrade. Try installing +the problematic package differently.
+Instead of:
+
+BiocManager::install("SeqArray")Try:
+
+remotes::install_local(path = "SeqArray_latest.tar.gz")Error: C stacks usage
-
+
So far, I haven’t found the cure to this computer-specific problem.
Potential solutions:
@@ -713,35 +725,35 @@Better to install and compile them from source to enable OpenMP. Install in the terminal zstd and lz4:
-cd ~/Downloads
-curl -L https://github.com/lz4/lz4/archive/refs/tags/v1.9.4.tar.gz | tar xf -
-cd lz4*
-make
-sudo make install
-cd ..
-sudo rm -R lz4*cd ~/Downloads
-curl -L https://github.com/facebook/zstd/archive/refs/tags/v1.5.5.tar.gz | tar xf -
-cd zstd*
-make
-sudo make install
-cd ..
-sudo rm -R zstd*cd ~/Downloads
+curl -L https://github.com/lz4/lz4/archive/refs/tags/v1.9.4.tar.gz | tar xf -
+cd lz4*
+make
+sudo make install
+cd ..
+sudo rm -R lz4*cd ~/Downloads
+curl -L https://github.com/facebook/zstd/archive/refs/tags/v1.5.5.tar.gz | tar xf -
+cd zstd*
+make
+sudo make install
+cd ..
+sudo rm -R zstd*fstcore, fst and data.table
requires these R Makevars specifications. If you have other
lines, comment (#) before saving and installing from
source:
-usethis::edit_r_makevars()#fstcore fst data.table
-CC=/usr/local/bin/gcc -fopenmp
-CXX=/usr/local/bin/g++ -fopenmp
-CXX11=/usr/local/bin/g++ -fopenmp
-CXX14=/usr/local/bin/g++ -fopenmp
-CXX17=/usr/local/bin/g++ -fopenmp
-CXX1X=/usr/local/bin/g++ -fopenmp
-CXX98=/usr/local/bin/g++ -fopenmp
+usethis::edit_r_makevars()#fstcore fst data.table
+CC=/usr/local/bin/gcc -fopenmp
+CXX=/usr/local/bin/g++ -fopenmp
+CXX11=/usr/local/bin/g++ -fopenmp
+CXX14=/usr/local/bin/g++ -fopenmp
+CXX17=/usr/local/bin/g++ -fopenmp
+CXX1X=/usr/local/bin/g++ -fopenmp
+CXX98=/usr/local/bin/g++ -fopenmp
install.packages("fstcore", type = "source")
install.packages("fst", type = "source")
install.packages("data.table", type = "source")
Download
Download the latest github release of Allan Strand’s rmetasim
- +Modify the number of loci: MAXLOCI
@@ -767,7 +779,7 @@ Modify the number of loci: MAXLOCIrmetasim-master/src/const.h. Navigate to
lane 33 and change the integer to the desired maximum
number of loci. Or do this in the Terminal:
-
+
Makevars configuration
@@ -775,29 +787,29 @@ Makevars configuration
+
usethis::edit_r_makevars()
macOS
This latest os requires extra lines:
-CC=/usr/local/bin/clang
-CXX=/usr/local/bin/clang++
-CXX1X=/usr/local/bin/clang++
-FLIBS=-L/usr/local/lib
-LDFLAGS=-L/usr/local/lib
-SHLIB_OPENMP_CFLAGS= -fopenmp
-SHLIB_OPENMP_FCFLAGS= -fopenmp
-SHLIB_OPENMP_FFLAGS= -fopenmp
-SHLIB_OPENMP_CXXFLAGS= -fopenmp
-CFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
-CCFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
-CXXFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
-CPPFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
+CC=/usr/local/bin/clang
+CXX=/usr/local/bin/clang++
+CXX1X=/usr/local/bin/clang++
+FLIBS=-L/usr/local/lib
+LDFLAGS=-L/usr/local/lib
+SHLIB_OPENMP_CFLAGS= -fopenmp
+SHLIB_OPENMP_FCFLAGS= -fopenmp
+SHLIB_OPENMP_FFLAGS= -fopenmp
+SHLIB_OPENMP_CXXFLAGS= -fopenmp
+CFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
+CCFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
+CXXFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
+CPPFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
+usethis::edit_r_makevars()macOS
This latest os requires extra lines:
-+CC=/usr/local/bin/clang -CXX=/usr/local/bin/clang++ -CXX1X=/usr/local/bin/clang++ -FLIBS=-L/usr/local/lib -LDFLAGS=-L/usr/local/lib -SHLIB_OPENMP_CFLAGS= -fopenmp -SHLIB_OPENMP_FCFLAGS= -fopenmp -SHLIB_OPENMP_FFLAGS= -fopenmp -SHLIB_OPENMP_CXXFLAGS= -fopenmp -CFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -CCFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -CXXFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -CPPFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdkCC=/usr/local/bin/clang +CXX=/usr/local/bin/clang++ +CXX1X=/usr/local/bin/clang++ +FLIBS=-L/usr/local/lib +LDFLAGS=-L/usr/local/lib +SHLIB_OPENMP_CFLAGS= -fopenmp +SHLIB_OPENMP_FCFLAGS= -fopenmp +SHLIB_OPENMP_FFLAGS= -fopenmp +SHLIB_OPENMP_CXXFLAGS= -fopenmp +CFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk +CCFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk +CXXFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk +CPPFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
Compile
- +
@@ -807,10 +819,10 @@
Error?
@@ -827,44 +839,44 @@ Modification# Go to line 1676
-# change
-ac_pkg_openmp=no
-# to
-ac_pkg_openmp=yes
-#save the file under the same name
+
Error?
@@ -827,44 +839,44 @@ Modification# Go to line 1676
-# change
-ac_pkg_openmp=no
-# to
-ac_pkg_openmp=yes
-#save the file under the same name
# Go to line 1676
-# change
-ac_pkg_openmp=no
-# to
-ac_pkg_openmp=yes
-#save the file under the same nameMakevars configuration
XGBoost requires these Makevars specifications. If you
have other lines, comment (#) before compiling:
+-usethis::edit_r_makevars()+CC=/usr/local/bin/gcc -CXX=/usr/local/bin/g++ -CXX11=/usr/local/bin/g++ -CXX14=/usr/local/bin/g++ -CXX17=/usr/local/bin/g++ -SHLIB_OPENMP_CFLAGS= -fopenmp -SHLIB_OPENMP_FCFLAGS= -fopenmp -SHLIB_OPENMP_FFLAGS= -fopenmp -SHLIB_OPENMP_CXXFLAGS= -fopenmp -CFLAGS=-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -CXXFLAGS=-g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe -LDFLAGS=-L/usr/local/lib -Wl,-rpath,/usr/local/lib -CPPFLAGS=-I/usr/local/include -I/usr/local/includeCC=/usr/local/bin/gcc +CXX=/usr/local/bin/g++ +CXX11=/usr/local/bin/g++ +CXX14=/usr/local/bin/g++ +CXX17=/usr/local/bin/g++ +SHLIB_OPENMP_CFLAGS= -fopenmp +SHLIB_OPENMP_FCFLAGS= -fopenmp +SHLIB_OPENMP_FFLAGS= -fopenmp +SHLIB_OPENMP_CXXFLAGS= -fopenmp +CFLAGS=-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe +CXXFLAGS=-g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe +LDFLAGS=-L/usr/local/lib -Wl,-rpath,/usr/local/lib +CPPFLAGS=-I/usr/local/include -I/usr/local/include
Test R-package
You should see a time difference between both runs
-+require(xgboost) x <- matrix(rnorm(100*10000), 10000, 100) y <- x %*% rnorm(100) + rnorm(1000) @@ -884,28 +896,28 @@
Download and install CMake
-+#In browser or using curl in Terminal -https://cmake.org/files/v3.12/cmake-3.12.2-Darwin-x86_64.dmg -# double-click on the disk image and follow instructions#In browser or using curl in Terminal +https://cmake.org/files/v3.12/cmake-3.12.2-Darwin-x86_64.dmg +# double-click on the disk image and follow instructionsTo add CMake to the PATH:
-+PATH="/Applications/CMake.app/Contents/bin":"$PATH" -# Or, to install symlinks to '/usr/local/bin', run: -sudo "/Applications/CMake.app/Contents/bin/cmake-gui" --install -# Or, to install symlinks to another directory, run: -sudo "/Applications/CMake.app/Contents/bin/cmake-gui" --install=/path/to/bin -#Then, run the following commands to install LightGBM:PATH="/Applications/CMake.app/Contents/bin":"$PATH" +# Or, to install symlinks to '/usr/local/bin', run: +sudo "/Applications/CMake.app/Contents/bin/cmake-gui" --install +# Or, to install symlinks to another directory, run: +sudo "/Applications/CMake.app/Contents/bin/cmake-gui" --install=/path/to/bin +#Then, run the following commands to install LightGBM:Download and Install LightGBM
- +@@ -920,38 +932,38 @@@@ -66,6 +66,16 @@Makevars configuration
Check that the lines below are not commented in your
-~/.R/Makevarsfile:+-usethis::edit_r_makevars()+CC=/usr/local/bin/gcc -CXX=/usr/local/bin/g++ -CFLAGS=-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -CXXFLAGS=-g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe -PKG_CFLAGS= -O3 -Wall -pipe -pedantic -std=gnu99 -fopenmp -PKG_CXXFLAGS=-fopenmp -std=c++11 -FC=/usr/local/bin/gfortran -F77=/usr/local/bin/gfortran -LDFLAGS=-L/usr/local/lib -PKG_LIBS = "-liconv"CC=/usr/local/bin/gcc +CXX=/usr/local/bin/g++ +CFLAGS=-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe +CXXFLAGS=-g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe +PKG_CFLAGS= -O3 -Wall -pipe -pedantic -std=gnu99 -fopenmp +PKG_CXXFLAGS=-fopenmp -std=c++11 +FC=/usr/local/bin/gfortran +F77=/usr/local/bin/gfortran +LDFLAGS=-L/usr/local/lib +PKG_LIBS = "-liconv"Download and install
From the Terminal run these steps to download and compile randomForestSRC:
-+cd ~/Downloads -curl -L https://cran.r-project.org/src/contrib/randomForestSRC_2.9.3.tar.gz | tar xf - -cd randomForestSRCcd ~/Downloads +curl -L https://cran.r-project.org/src/contrib/randomForestSRC_2.9.3.tar.gz | tar xf - +cd randomForestSRCMake sure you have autoconf installed:
- +Should output:
-autoconf: error: no input file, if not, install following the steps here.+# in Terminal -cd ~/Downloads/randomForestSRC -autoconf -cd ~/Downloads -R CMD INSTALL --preclean --clean randomForestSRC# in Terminal +cd ~/Downloads/randomForestSRC +autoconf +cd ~/Downloads +R CMD INSTALL --preclean --clean randomForestSRCYou want to make sure that this line is printed during execution of the previous command:
checking whether OpenMP will work in a package... yesor @@ -964,7 +976,7 @@
ranger is easy to install.
-+install.packages("ranger")@@ -973,7 +985,7 @@@@ -111,6 +111,7 @@
missRanger is also very easy to install.
-+install.packages("missRanger")@@ -982,7 +994,7 @@@@ -63,7 +63,7 @@ diff --git a/docs/index.html b/docs/index.html index 0b4f0649..510d9ab7 100644 --- a/docs/index.html +++ b/docs/index.html @@ -6,7 +6,7 @@
miceRanger easy to install.
-+install.packages("miceRanger")@@ -991,7 +1003,7 @@
To install pcaMethods, from bioconductor:
-+BiocManager::install("pcaMethods")@@ -999,27 +1011,27 @@
fastsimcoal2To install fastsimcoal2 -v.2.6.0.3, to use in
+v.2.6.0.3, to use ingrur::simulate_rad:grur::simulate_rad:LINUX
- +@@ -1028,13 +1040,13 @@MacOS
- +PATH
To see the path of the installation, in the
- +Terminal:If that doesn’t work, do:
- +Remove the files in the folder:
- +@@ -1047,14 +1059,14 @@
MacOS
The old openmpi version (openmpi-1.6.5) is required, saddly.
-+cd ~/Downloads -curl -L https://download.open-mpi.org/release/open-mpi/v1.6/openmpi-1.6.5.tar.gz | tar xf - -cd openmpi-1.6.5 -export TMPDIR=/tmp -./configure F77=gfortran #--prefix=/usr/local -openmp # no longer work for some reason -make -j 12 -sudo make install -sudo rm -R ~/Downloads/openmpi*cd ~/Downloads +curl -L https://download.open-mpi.org/release/open-mpi/v1.6/openmpi-1.6.5.tar.gz | tar xf - +cd openmpi-1.6.5 +export TMPDIR=/tmp +./configure F77=gfortran #--prefix=/usr/local -openmp # no longer work for some reason +make -j 12 +sudo make install +sudo rm -R ~/Downloads/openmpi*To download COLONY, follow instructions on Jinliang Wang ZSL website. The file you need to uncompress is named:
@@ -1085,31 +1097,31 @@colony2.mac_.20180730.zip.Update -
+cd ~/Downloads -curl -L http://ftp.gnu.org/gnu/autoconf/autoconf-latest.tar.gz | tar xf - -cd autoconf-2.69 -./configure -make -sudo make install -cd .. -sudo rm -R ~/Downloads/autoconf-*cd ~/Downloads +curl -L http://ftp.gnu.org/gnu/autoconf/autoconf-latest.tar.gz | tar xf - +cd autoconf-2.69 +./configure +make +sudo make install +cd .. +sudo rm -R ~/Downloads/autoconf-*-
- Install Github
+git --version # show current git version installed -which git # returns where is git on your computer -cd ~/Downloads -git clone https://github.com/git/git # install the latest Git -cd git -make configure -./configure -make -j12 -sudo make install -cd .. -sudo rm -R ~/Downloads/git/ # remove git folder -source ~/.bash_profile # reload startup script -git --version # confirmed the version you just installed -which git # returns /usr/local/bingit --version # show current git version installed +which git # returns where is git on your computer +cd ~/Downloads +git clone https://github.com/git/git # install the latest Git +cd git +make configure +./configure +make -j12 +sudo make install +cd .. +sudo rm -R ~/Downloads/git/ # remove git folder +source ~/.bash_profile # reload startup script +git --version # confirmed the version you just installed +which git # returns /usr/local/bindiff --git a/docs/authors.html b/docs/authors.html index 2e704015..72d0627b 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -1,5 +1,5 @@ -macOS Terminal from specific folder @@ -1128,14 +1140,14 @@
Shortcut to folder path
With macOS, open the Automator application.
-+File -> New (cmd-N) -Choose: Services -Left panel, choose: Library -> Utilities -Middle, choose: Copy to Clipboard and drag it to the right panel -Now you want to have: Service receives selected FILES OR FOLDERS in FINDER> -You should have something similar to the image below:File -> New (cmd-N) +Choose: Services +Left panel, choose: Library -> Utilities +Middle, choose: Copy to Clipboard and drag it to the right panel +Now you want to have: Service receives selected FILES OR FOLDERS in FINDER> +You should have something similar to the image below:- +
Go in the Finder, select a folder and right click on it you should see ‘copy path to clipboard’ at the bottom or in Services.
@@ -1160,7 +1172,7 @@Shortcut to folder path -
Site built with pkgdown 2.0.7.
+Site built with pkgdown 2.0.9.
Authors and Citation • radiator Authors and Citation • radiator @@ -17,7 +17,7 @@RADseq Data Exploration, Manipulation and Visualization using R • radiator - + @@ -33,7 +33,7 @@Installationdevtools::package_info(pkgs = "SeqArray") # to verify version # If manually installing SeqArray is necessary +install.packages("BiocManager") BiocManager::install("SeqArray")
Web site with additional info: https://thierrygosselin.github.io/radiator/
@@ -176,8 +177,8 @@
Dev status
@@ -194,7 +195,7 @@
- -
- -
- +
- +
Dev status
diff --git a/docs/news/index.html b/docs/news/index.html index db134455..3392e5c0 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -1,5 +1,5 @@ -Changelog • radiator Changelog • radiator @@ -17,7 +17,7 @@Changelog
Source:NEWS.md
+
+
radiator 1.3.3 2024-05-15
+- Fix issue #188 related to coverage in DArT 1row and 2rows format +
Exposition pipe-operator
diff --git a/docs/reference/allele_count.html b/docs/reference/allele_count.html index 6bcd42ca..565376ec 100644 --- a/docs/reference/allele_count.html +++ b/docs/reference/allele_count.html @@ -1,5 +1,5 @@ -allele_count
diff --git a/docs/reference/allele_frequencies.html b/docs/reference/allele_frequencies.html index 3b863a1b..d58b50db 100644 --- a/docs/reference/allele_frequencies.html +++ b/docs/reference/allele_frequencies.html @@ -1,5 +1,5 @@ -assign_defaults
diff --git a/docs/reference/bayescan_one.html b/docs/reference/bayescan_one.html index a8adae0b..8a6f12a7 100644 --- a/docs/reference/bayescan_one.html +++ b/docs/reference/bayescan_one.html @@ -1,5 +1,5 @@ -bayescan one iteration
diff --git a/docs/reference/betas_estimator.html b/docs/reference/betas_estimator.html index c1fdc4a1..b4db4eeb 100644 --- a/docs/reference/betas_estimator.html +++ b/docs/reference/betas_estimator.html @@ -1,5 +1,5 @@ -Examples
diff --git a/docs/reference/blacklist_hw.html b/docs/reference/blacklist_hw.html index 1c47c918..237ff851 100644 --- a/docs/reference/blacklist_hw.html +++ b/docs/reference/blacklist_hw.html @@ -1,5 +1,5 @@ -Author
diff --git a/docs/reference/boxplot_stats.html b/docs/reference/boxplot_stats.html index b5b179e9..c488e1c2 100644 --- a/docs/reference/boxplot_stats.html +++ b/docs/reference/boxplot_stats.html @@ -1,5 +1,5 @@ -boxplot_stats
diff --git a/docs/reference/calibrate_alleles.html b/docs/reference/calibrate_alleles.html index 0f867bc4..690ede22 100644 --- a/docs/reference/calibrate_alleles.html +++ b/docs/reference/calibrate_alleles.html @@ -1,5 +1,5 @@ -Author
diff --git a/docs/reference/change_pop_names.html b/docs/reference/change_pop_names.html index a09c11c8..47c61e5a 100644 --- a/docs/reference/change_pop_names.html +++ b/docs/reference/change_pop_names.html @@ -1,5 +1,5 @@ -check_args_class
diff --git a/docs/reference/check_dart.html b/docs/reference/check_dart.html index a93d4ee6..7a6b21a6 100644 --- a/docs/reference/check_dart.html +++ b/docs/reference/check_dart.html @@ -1,5 +1,5 @@ -check_dart
diff --git a/docs/reference/check_header_source_vcf.html b/docs/reference/check_header_source_vcf.html index 327b5485..bb585c73 100644 --- a/docs/reference/check_header_source_vcf.html +++ b/docs/reference/check_header_source_vcf.html @@ -1,5 +1,5 @@ -Check the vcf header and detect vcf source
diff --git a/docs/reference/check_pop_levels.html b/docs/reference/check_pop_levels.html index eb4f0879..f50fc651 100644 --- a/docs/reference/check_pop_levels.html +++ b/docs/reference/check_pop_levels.html @@ -1,5 +1,5 @@ -clean_dart_colnames
diff --git a/docs/reference/clean_dart_locus.html b/docs/reference/clean_dart_locus.html index d36c600d..bcf4cf4e 100644 --- a/docs/reference/clean_dart_locus.html +++ b/docs/reference/clean_dart_locus.html @@ -1,5 +1,5 @@ -clean_dart_locus
diff --git a/docs/reference/clean_ind_names.html b/docs/reference/clean_ind_names.html index f6566a96..71478aea 100644 --- a/docs/reference/clean_ind_names.html +++ b/docs/reference/clean_ind_names.html @@ -1,5 +1,5 @@ -Arguments
diff --git a/docs/reference/clean_markers_names.html b/docs/reference/clean_markers_names.html index 1a6e9aed..397d0bdc 100644 --- a/docs/reference/clean_markers_names.html +++ b/docs/reference/clean_markers_names.html @@ -1,5 +1,5 @@ -Arguments
diff --git a/docs/reference/clean_pop_names.html b/docs/reference/clean_pop_names.html index 296e6aba..94dd1e30 100644 --- a/docs/reference/clean_pop_names.html +++ b/docs/reference/clean_pop_names.html @@ -1,5 +1,5 @@ -Arguments
diff --git a/docs/reference/compound_assignment_pipe_operator.html b/docs/reference/compound_assignment_pipe_operator.html index 5a529ad4..f640917c 100644 --- a/docs/reference/compound_assignment_pipe_operator.html +++ b/docs/reference/compound_assignment_pipe_operator.html @@ -1,5 +1,5 @@ -compound assignment pipe operator
diff --git a/docs/reference/compute_maf.html b/docs/reference/compute_maf.html index 1c34155f..6b834ca0 100644 --- a/docs/reference/compute_maf.html +++ b/docs/reference/compute_maf.html @@ -1,5 +1,5 @@ -compute_maf
diff --git a/docs/reference/count_monomorphic.html b/docs/reference/count_monomorphic.html index e55d510e..0c38d811 100644 --- a/docs/reference/count_monomorphic.html +++ b/docs/reference/count_monomorphic.html @@ -1,5 +1,5 @@ -count_monomorphic
diff --git a/docs/reference/dart2gds.html b/docs/reference/dart2gds.html index 3dea5ec0..251edeea 100644 --- a/docs/reference/dart2gds.html +++ b/docs/reference/dart2gds.html @@ -1,5 +1,5 @@ -dart2gds
diff --git a/docs/reference/data_info.html b/docs/reference/data_info.html index a97edb43..936c40f2 100644 --- a/docs/reference/data_info.html +++ b/docs/reference/data_info.html @@ -1,5 +1,5 @@ -data_info
diff --git a/docs/reference/detect_all_missing.html b/docs/reference/detect_all_missing.html index 690c591f..84cf31f5 100644 --- a/docs/reference/detect_all_missing.html +++ b/docs/reference/detect_all_missing.html @@ -1,5 +1,5 @@ -Examples
diff --git a/docs/reference/detect_biallelic_markers.html b/docs/reference/detect_biallelic_markers.html index ac7683dc..5f2b50e3 100644 --- a/docs/reference/detect_biallelic_markers.html +++ b/docs/reference/detect_biallelic_markers.html @@ -1,5 +1,5 @@ -Author
diff --git a/docs/reference/detect_dart_format.html b/docs/reference/detect_dart_format.html index b6ba0b20..f52c93ab 100644 --- a/docs/reference/detect_dart_format.html +++ b/docs/reference/detect_dart_format.html @@ -1,5 +1,5 @@ -detect_dart_format
diff --git a/docs/reference/detect_duplicate_genomes.html b/docs/reference/detect_duplicate_genomes.html index 9e4f22d2..e6abab3e 100644 --- a/docs/reference/detect_duplicate_genomes.html +++ b/docs/reference/detect_duplicate_genomes.html @@ -1,7 +1,5 @@ -
-
@@ -297,7 +294,7 @@ Compute pairwise genome similarity or distance between individuals -to highligh potential duplicate individuals
+Compute pairwise genome similarity or distance between individuals to highligh potential duplicate individuals
Source:R/detect_duplicate_genomes.R
detect_duplicate_genomes.RdExamples
Examples
diff --git a/docs/reference/detect_het_outliers.html b/docs/reference/detect_het_outliers.html index 702bf5f5..ca7342c0 100644 --- a/docs/reference/detect_het_outliers.html +++ b/docs/reference/detect_het_outliers.html @@ -1,5 +1,5 @@ -Examples
diff --git a/docs/reference/detect_microsatellites.html b/docs/reference/detect_microsatellites.html index f7e5e99a..b60d6b7b 100644 --- a/docs/reference/detect_microsatellites.html +++ b/docs/reference/detect_microsatellites.html @@ -1,5 +1,5 @@ -Examples
diff --git a/docs/reference/detect_ref_genome.html b/docs/reference/detect_ref_genome.html index 05ee8f5e..4676fd68 100644 --- a/docs/reference/detect_ref_genome.html +++ b/docs/reference/detect_ref_genome.html @@ -1,5 +1,5 @@ -Examples
diff --git a/docs/reference/diagnostic_maf.html b/docs/reference/diagnostic_maf.html index dcecdbf8..b6b327e7 100644 --- a/docs/reference/diagnostic_maf.html +++ b/docs/reference/diagnostic_maf.html @@ -1,5 +1,5 @@ -Examples
diff --git a/docs/reference/distance2tibble.html b/docs/reference/distance2tibble.html index 36fdf555..157cfb52 100644 --- a/docs/reference/distance2tibble.html +++ b/docs/reference/distance2tibble.html @@ -1,5 +1,5 @@ -distance2tibble
diff --git a/docs/reference/distance_individuals.html b/docs/reference/distance_individuals.html index a423ff06..fe9f0c8d 100644 --- a/docs/reference/distance_individuals.html +++ b/docs/reference/distance_individuals.html @@ -1,5 +1,5 @@ -Distance individuals
diff --git a/docs/reference/erase_genotypes.html b/docs/reference/erase_genotypes.html index d0cc71f7..aeb4a710 100644 --- a/docs/reference/erase_genotypes.html +++ b/docs/reference/erase_genotypes.html @@ -1,5 +1,5 @@ -Author
diff --git a/docs/reference/extract_coverage.html b/docs/reference/extract_coverage.html index e2f7194e..2ab35ee5 100644 --- a/docs/reference/extract_coverage.html +++ b/docs/reference/extract_coverage.html @@ -1,5 +1,5 @@ -extract_data_source
diff --git a/docs/reference/extract_dots.html b/docs/reference/extract_dots.html index 26b971f3..4bc3de01 100644 --- a/docs/reference/extract_dots.html +++ b/docs/reference/extract_dots.html @@ -1,5 +1,5 @@ -extract_dots
diff --git a/docs/reference/extract_genotypes_metadata.html b/docs/reference/extract_genotypes_metadata.html index 2c89293f..c04158be 100644 --- a/docs/reference/extract_genotypes_metadata.html +++ b/docs/reference/extract_genotypes_metadata.html @@ -1,5 +1,5 @@ -Arguments
diff --git a/docs/reference/extract_individuals_metadata.html b/docs/reference/extract_individuals_metadata.html index bb8154cf..8d096840 100644 --- a/docs/reference/extract_individuals_metadata.html +++ b/docs/reference/extract_individuals_metadata.html @@ -1,5 +1,5 @@ -Arguments
diff --git a/docs/reference/extract_individuals_vcf.html b/docs/reference/extract_individuals_vcf.html index 44dffcf8..af261215 100644 --- a/docs/reference/extract_individuals_vcf.html +++ b/docs/reference/extract_individuals_vcf.html @@ -1,5 +1,5 @@ -extract_info_vcf
diff --git a/docs/reference/extract_markers_metadata.html b/docs/reference/extract_markers_metadata.html index 8d87be81..a7dd8bab 100644 --- a/docs/reference/extract_markers_metadata.html +++ b/docs/reference/extract_markers_metadata.html @@ -1,5 +1,5 @@ -Arguments
diff --git a/docs/reference/filter_blacklist_genotypes.html b/docs/reference/filter_blacklist_genotypes.html index 161e4acc..288991d3 100644 --- a/docs/reference/filter_blacklist_genotypes.html +++ b/docs/reference/filter_blacklist_genotypes.html @@ -1,5 +1,5 @@ -Examples
diff --git a/docs/reference/filter_coverage.html b/docs/reference/filter_coverage.html index 3c226460..8ea5b2cc 100644 --- a/docs/reference/filter_coverage.html +++ b/docs/reference/filter_coverage.html @@ -1,5 +1,5 @@ -Examples
diff --git a/docs/reference/filter_dart_reproducibility.html b/docs/reference/filter_dart_reproducibility.html index 4e2442e7..e5af3849 100644 --- a/docs/reference/filter_dart_reproducibility.html +++ b/docs/reference/filter_dart_reproducibility.html @@ -1,5 +1,5 @@ -Author
diff --git a/docs/reference/filter_genotyping.html b/docs/reference/filter_genotyping.html index 0da88aad..6e5d2357 100644 --- a/docs/reference/filter_genotyping.html +++ b/docs/reference/filter_genotyping.html @@ -1,5 +1,5 @@ -See also
diff --git a/docs/reference/filter_hwe.html b/docs/reference/filter_hwe.html index 4cc14942..c0e1080d 100644 --- a/docs/reference/filter_hwe.html +++ b/docs/reference/filter_hwe.html @@ -1,5 +1,5 @@ -Examples
diff --git a/docs/reference/filter_individuals.html b/docs/reference/filter_individuals.html index 8fefca43..e803b995 100644 --- a/docs/reference/filter_individuals.html +++ b/docs/reference/filter_individuals.html @@ -1,7 +1,5 @@ -
-
@@ -225,7 +222,7 @@ Filter individuals based on genotyping/missingness rate, -heterozygosity and total coverage
+Filter individuals based on genotyping/missingness rate, heterozygosity and total coverage
Source:R/filter_individuals.R
filter_individuals.RdExamples
Examples
diff --git a/docs/reference/filter_monomorphic.html b/docs/reference/filter_monomorphic.html index 93257372..83349936 100644 --- a/docs/reference/filter_monomorphic.html +++ b/docs/reference/filter_monomorphic.html @@ -1,5 +1,5 @@ -Examples
diff --git a/docs/reference/filter_rad.html b/docs/reference/filter_rad.html index e5362d09..9a213313 100644 --- a/docs/reference/filter_rad.html +++ b/docs/reference/filter_rad.html @@ -1,5 +1,5 @@ -Examples
diff --git a/docs/reference/filter_snp_position_read.html b/docs/reference/filter_snp_position_read.html index bca08dbe..bdee4aca 100644 --- a/docs/reference/filter_snp_position_read.html +++ b/docs/reference/filter_snp_position_read.html @@ -1,5 +1,5 @@ -Examples
diff --git a/docs/reference/filter_whitelist.html b/docs/reference/filter_whitelist.html index a7729b2f..41bcfaf2 100644 --- a/docs/reference/filter_whitelist.html +++ b/docs/reference/filter_whitelist.html @@ -1,5 +1,5 @@ -folder_prefix
diff --git a/docs/reference/folder_short.html b/docs/reference/folder_short.html index a8cff0a1..54236246 100644 --- a/docs/reference/folder_short.html +++ b/docs/reference/folder_short.html @@ -1,5 +1,5 @@ -Author
diff --git a/docs/reference/gds2tidy.html b/docs/reference/gds2tidy.html index 3b80f9c8..e0cfeea9 100644 --- a/docs/reference/gds2tidy.html +++ b/docs/reference/gds2tidy.html @@ -1,5 +1,5 @@ -gds2tidy
diff --git a/docs/reference/generate_filename.html b/docs/reference/generate_filename.html index 664cfa6c..c3c42a0a 100644 --- a/docs/reference/generate_filename.html +++ b/docs/reference/generate_filename.html @@ -1,5 +1,5 @@ -Filename radiator
diff --git a/docs/reference/generate_folder.html b/docs/reference/generate_folder.html index 201ae808..807918d8 100644 --- a/docs/reference/generate_folder.html +++ b/docs/reference/generate_folder.html @@ -1,5 +1,5 @@ -Author
diff --git a/docs/reference/generate_geno_freq_boundaries.html b/docs/reference/generate_geno_freq_boundaries.html index e30b3d3b..c67920ed 100644 --- a/docs/reference/generate_geno_freq_boundaries.html +++ b/docs/reference/generate_geno_freq_boundaries.html @@ -1,5 +1,5 @@ -generate_hzar
diff --git a/docs/reference/generate_markers_metadata.html b/docs/reference/generate_markers_metadata.html index eee683c3..17b90f9a 100644 --- a/docs/reference/generate_markers_metadata.html +++ b/docs/reference/generate_markers_metadata.html @@ -1,5 +1,5 @@ -generate_squeleton_folders
diff --git a/docs/reference/generate_strata.html b/docs/reference/generate_strata.html index b6274262..5d5aff18 100644 --- a/docs/reference/generate_strata.html +++ b/docs/reference/generate_strata.html @@ -1,5 +1,5 @@ -Author
diff --git a/docs/reference/genome_similarity.html b/docs/reference/genome_similarity.html index c6ef4036..5ac856a7 100644 --- a/docs/reference/genome_similarity.html +++ b/docs/reference/genome_similarity.html @@ -1,5 +1,5 @@ -genome_similarity
diff --git a/docs/reference/genomic_converter.html b/docs/reference/genomic_converter.html index fa82c724..dce77f29 100644 --- a/docs/reference/genomic_converter.html +++ b/docs/reference/genomic_converter.html @@ -1,5 +1,5 @@ -Examples
radiator::detect_genomic_format(data = "populations.snps.vcf") # The simplest form of the function: -require(strataG) # for the gtypes format... +require(strataG) # for the gtypes format... snowcrab <- genomic_converter( data = "populations.snps.vcf", strata = "snowcrab.strata.tsv", output = c("genlight", "genepop", "gtypes")) @@ -380,7 +380,7 @@Examples
diff --git a/docs/reference/gt2array.html b/docs/reference/gt2array.html index f68e906e..c79214dd 100644 --- a/docs/reference/gt2array.html +++ b/docs/reference/gt2array.html @@ -1,5 +1,5 @@ -Arguments
diff --git a/docs/reference/hwe_analysis.html b/docs/reference/hwe_analysis.html index e6a87236..6165b475 100644 --- a/docs/reference/hwe_analysis.html +++ b/docs/reference/hwe_analysis.html @@ -1,5 +1,5 @@ -Author
diff --git a/docs/reference/ibdg_fh.html b/docs/reference/ibdg_fh.html index 41f86bfe..84dead9c 100644 --- a/docs/reference/ibdg_fh.html +++ b/docs/reference/ibdg_fh.html @@ -1,5 +1,5 @@ -Examples
diff --git a/docs/reference/import_dart.html b/docs/reference/import_dart.html index 045b26b5..a4f02264 100644 --- a/docs/reference/import_dart.html +++ b/docs/reference/import_dart.html @@ -1,5 +1,5 @@ -import_dart
diff --git a/docs/reference/ind_total_reads.html b/docs/reference/ind_total_reads.html index 219b763a..605e8e8e 100644 --- a/docs/reference/ind_total_reads.html +++ b/docs/reference/ind_total_reads.html @@ -1,5 +1,5 @@ -ind_total_reads
diff --git a/docs/reference/index.html b/docs/reference/index.html index bd9be9f0..46de0e9f 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1,5 +1,5 @@ -Filter <
- Filter individuals based on genotyping/missingness rate,
-heterozygosity and total coverage
Filter individuals based on genotyping/missingness rate, heterozygosity and total coverage
@@ -301,8 +300,7 @@ Detect <
- Compute pairwise genome similarity or distance between individuals
-to highligh potential duplicate individuals
Compute pairwise genome similarity or distance between individuals to highligh potential duplicate individuals
@@ -390,8 +388,7 @@ Write
- Write a BayeScan
-file from a tidy data frame
Write a BayeScan file from a tidy data frame
@@ -439,8 +436,7 @@ Write
- Write a strataG object from
-radiator GDS and tidy data file or object.
Write a strataG object from radiator GDS and tidy data file or object.
@@ -464,8 +460,7 @@ Write
- Write a pcadapt
-file from a tidy data frame
Write a pcadapt file from a tidy data frame
@@ -575,7 +570,7 @@ Run software
diff --git a/docs/reference/individuals2strata.html b/docs/reference/individuals2strata.html
index f65e5c44..208a8235 100644
--- a/docs/reference/individuals2strata.html
+++ b/docs/reference/individuals2strata.html
@@ -1,5 +1,5 @@
-Create a strata file from a list of individuals — individuals2strata • radiator Create a strata file from a list of individuals — individuals2strata • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -168,7 +168,7 @@ Examples
diff --git a/docs/reference/join_strata.html b/docs/reference/join_strata.html
index 25aacfa1..f1dc86a2 100644
--- a/docs/reference/join_strata.html
+++ b/docs/reference/join_strata.html
@@ -1,5 +1,5 @@
-Join the strata with the data — join_strata • radiator Join the strata with the data — join_strata • radiator ld2df — ld2df • radiator ld2df — ld2df • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ ld2df
diff --git a/docs/reference/ld_boxplot.html b/docs/reference/ld_boxplot.html
index 4367f28a..30ce41f2 100644
--- a/docs/reference/ld_boxplot.html
+++ b/docs/reference/ld_boxplot.html
@@ -1,5 +1,5 @@
-ld_boxplot — ld_boxplot • radiator ld_boxplot — ld_boxplot • radiator Prune dataset based on LD and missingness. — ld_missing • radiator Prune dataset based on LD and missingness. — ld_missing • radiator Prune dataset based on LD. — ld_pruning • radiator Prune dataset based on LD. — ld_pruning • radiator List current active filters (individuals and markers) in radiator GDS object. — list_filters • radiator List current active filters (individuals and markers) in radiator GDS object. — list_filters • radiator
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/markers_genotyped_helper.html b/docs/reference/markers_genotyped_helper.html
index 3c9df84c..aede1ab0 100644
--- a/docs/reference/markers_genotyped_helper.html
+++ b/docs/reference/markers_genotyped_helper.html
@@ -1,5 +1,5 @@
-markers_genotyped_helper — markers_genotyped_helper • radiator markers_genotyped_helper — markers_genotyped_helper • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ markers_genotyped_helper
diff --git a/docs/reference/merge_dart.html b/docs/reference/merge_dart.html
index cb9c47dd..51313a01 100644
--- a/docs/reference/merge_dart.html
+++ b/docs/reference/merge_dart.html
@@ -1,5 +1,5 @@
-Merge DArT files — merge_dart • radiator Merge DArT files — merge_dart • radiator
@@ -17,7 +17,7 @@
@@ -192,7 +192,7 @@ Examples
diff --git a/docs/reference/message_func_call.html b/docs/reference/message_func_call.html
index 71e6fd17..b0a90bd4 100644
--- a/docs/reference/message_func_call.html
+++ b/docs/reference/message_func_call.html
@@ -1,5 +1,5 @@
-message_func_call — message_func_call • radiator message_func_call — message_func_call • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ message_func_call
diff --git a/docs/reference/missing_per_pop.html b/docs/reference/missing_per_pop.html
index 7f6547ff..f734e751 100644
--- a/docs/reference/missing_per_pop.html
+++ b/docs/reference/missing_per_pop.html
@@ -1,5 +1,5 @@
-missing_per_pop — missing_per_pop • radiator missing_per_pop — missing_per_pop • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ missing_per_pop
diff --git a/docs/reference/n.html b/docs/reference/n.html
index 241b72f8..650b55af 100644
--- a/docs/reference/n.html
+++ b/docs/reference/n.html
@@ -1,5 +1,5 @@
-The number of observations in the current group. — n • radiator The number of observations in the current group. — n • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ The number of observations in the current group.
diff --git a/docs/reference/not_common_markers.html b/docs/reference/not_common_markers.html
index 38474933..52702221 100644
--- a/docs/reference/not_common_markers.html
+++ b/docs/reference/not_common_markers.html
@@ -1,5 +1,5 @@
-not_common_markers — not_common_markers • radiator not_common_markers — not_common_markers • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ not_common_markers
diff --git a/docs/reference/parallel_core_opt.html b/docs/reference/parallel_core_opt.html
index c90d8951..5988fc0e 100644
--- a/docs/reference/parallel_core_opt.html
+++ b/docs/reference/parallel_core_opt.html
@@ -1,5 +1,5 @@
-parallel_core_opt — parallel_core_opt • radiator parallel_core_opt — parallel_core_opt • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ parallel_core_opt
diff --git a/docs/reference/parse_gds_metadata.html b/docs/reference/parse_gds_metadata.html
index 0d7ab646..ad2f807e 100644
--- a/docs/reference/parse_gds_metadata.html
+++ b/docs/reference/parse_gds_metadata.html
@@ -1,5 +1,5 @@
-parse_gds_metadata — parse_gds_metadata • radiator parse_gds_metadata — parse_gds_metadata • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ parse_gds_metadata
diff --git a/docs/reference/pi.html b/docs/reference/pi.html
index 85ae2ceb..ac69dca4 100644
--- a/docs/reference/pi.html
+++ b/docs/reference/pi.html
@@ -1,5 +1,5 @@
-Nucleotide diversity — pi • radiator Nucleotide diversity — pi • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -181,7 +181,7 @@ Examples
diff --git a/docs/reference/pi_pop.html b/docs/reference/pi_pop.html
index 94dd9b17..60944089 100644
--- a/docs/reference/pi_pop.html
+++ b/docs/reference/pi_pop.html
@@ -1,5 +1,5 @@
-pi_pop — pi_pop • radiator pi_pop — pi_pop • radiator
@@ -17,7 +17,7 @@
@@ -92,7 +92,7 @@ Author
diff --git a/docs/reference/pi_rad.html b/docs/reference/pi_rad.html
index 7f101caa..aacecefd 100644
--- a/docs/reference/pi_rad.html
+++ b/docs/reference/pi_rad.html
@@ -1,5 +1,5 @@
-pi_rad — pi_rad • radiator pi_rad — pi_rad • radiator
@@ -17,7 +17,7 @@
@@ -92,7 +92,7 @@ Author
diff --git a/docs/reference/pipe.html b/docs/reference/pipe.html
index 57a5bcc1..0585be18 100644
--- a/docs/reference/pipe.html
+++ b/docs/reference/pipe.html
@@ -1,5 +1,5 @@
-Forward-pipe operator — %>% • radiator Forward-pipe operator — %>% • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ Forward-pipe operator
diff --git a/docs/reference/plot_bayescan.html b/docs/reference/plot_bayescan.html
index 89023923..492e4e8e 100644
--- a/docs/reference/plot_bayescan.html
+++ b/docs/reference/plot_bayescan.html
@@ -1,5 +1,5 @@
-plot_bayescan — plot_bayescan • radiator plot_bayescan — plot_bayescan • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ plot_bayescan
diff --git a/docs/reference/plot_boxplot_coverage.html b/docs/reference/plot_boxplot_coverage.html
index 84b023bf..17fbd811 100644
--- a/docs/reference/plot_boxplot_coverage.html
+++ b/docs/reference/plot_boxplot_coverage.html
@@ -1,5 +1,5 @@
-Figure box plot of coverage summary statistics — plot_boxplot_coverage • radiator Figure box plot of coverage summary statistics — plot_boxplot_coverage • radiator Box plot of the diversity (Gene and Haplotypes) — plot_boxplot_diversity • radiator Box plot of the diversity (Gene and Haplotypes) — plot_boxplot_diversity • radiator Visual diagnostic of coverage imbalance — plot_coverage_imbalance_diagnostic • radiator Visual diagnostic of coverage imbalance — plot_coverage_imbalance_diagnostic • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -149,7 +149,7 @@ Details
diff --git a/docs/reference/plot_density_distribution_coverage.html b/docs/reference/plot_density_distribution_coverage.html
index 1146cb10..0937fe36 100644
--- a/docs/reference/plot_density_distribution_coverage.html
+++ b/docs/reference/plot_density_distribution_coverage.html
@@ -1,5 +1,5 @@
-Figure of distribution (histogram) — plot_histogram • radiator Figure of distribution (histogram) — plot_histogram • radiator Figure density distribution of the observed heterozygosity
-summary statistics. — plot_density_distribution_het • radiator Figure density distribution of the observed heterozygosity summary statistics. — plot_density_distribution_het • radiator Figure density distribution of minor allele frequency (MAF)
-summary statistics. — plot_density_distribution_maf • radiator Figure density distribution of minor allele frequency (MAF) summary statistics. — plot_density_distribution_maf • radiator
@@ -19,7 +17,7 @@
@@ -64,8 +62,7 @@
- Figure density distribution of minor allele frequency (MAF)
-summary statistics.
+ Figure density distribution of minor allele frequency (MAF) summary statistics.
Source: R/visualization.R
plot_density_distribution_maf.Rd
@@ -134,7 +131,7 @@ Author
diff --git a/docs/reference/plot_distribution_diversity.html b/docs/reference/plot_distribution_diversity.html
index 2d82b11a..410c85b0 100644
--- a/docs/reference/plot_distribution_diversity.html
+++ b/docs/reference/plot_distribution_diversity.html
@@ -1,5 +1,5 @@
-Density distribution of diversity (Gene and Haplotypes) — plot_distribution_diversity • radiator Density distribution of diversity (Gene and Haplotypes) — plot_distribution_diversity • radiator
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_het_outliers.html b/docs/reference/plot_het_outliers.html
index e233c5f8..ae00754d 100644
--- a/docs/reference/plot_het_outliers.html
+++ b/docs/reference/plot_het_outliers.html
@@ -1,5 +1,5 @@
-plot_het_outliers — plot_het_outliers • radiator plot_het_outliers — plot_het_outliers • radiator Figure of the distribution of SNP per locus before and after filters — plot_snp_number_loci • radiator Figure of the distribution of SNP per locus before and after filters — plot_snp_number_loci • radiator
@@ -17,7 +17,7 @@
@@ -98,7 +98,7 @@ Arguments
diff --git a/docs/reference/plot_snp_position_read.html b/docs/reference/plot_snp_position_read.html
index 60991367..3d03575c 100644
--- a/docs/reference/plot_snp_position_read.html
+++ b/docs/reference/plot_snp_position_read.html
@@ -1,5 +1,5 @@
-Figure of the distribution of SNP nucleotide position alond the read — plot_snp_position_read • radiator Figure of the distribution of SNP nucleotide position alond the read — plot_snp_position_read • radiator
@@ -17,7 +17,7 @@
@@ -102,7 +102,7 @@ Arguments
diff --git a/docs/reference/plot_upset.html b/docs/reference/plot_upset.html
index 87e84ff1..aa1218d7 100644
--- a/docs/reference/plot_upset.html
+++ b/docs/reference/plot_upset.html
@@ -1,5 +1,5 @@
-plot_upset — plot_upset • radiator plot_upset — plot_upset • radiator
@@ -17,7 +17,7 @@
@@ -94,7 +94,7 @@ plot_upset
diff --git a/docs/reference/private_alleles.html b/docs/reference/private_alleles.html
index 1ac8a329..7ac1d578 100644
--- a/docs/reference/private_alleles.html
+++ b/docs/reference/private_alleles.html
@@ -1,5 +1,5 @@
-Find private alleles — private_alleles • radiator Find private alleles — private_alleles • radiator
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Examples
diff --git a/docs/reference/private_haplotypes.html b/docs/reference/private_haplotypes.html
index 70872333..1af437f0 100644
--- a/docs/reference/private_haplotypes.html
+++ b/docs/reference/private_haplotypes.html
@@ -1,5 +1,5 @@
-private haplotypes — private_haplotypes • radiator private haplotypes — private_haplotypes • radiator
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Author
diff --git a/docs/reference/radiator_common_arguments.html b/docs/reference/radiator_common_arguments.html
index d9f1b8fc..3e9357f3 100644
--- a/docs/reference/radiator_common_arguments.html
+++ b/docs/reference/radiator_common_arguments.html
@@ -1,5 +1,5 @@
-radiator common arguments — radiator_common_arguments • radiator radiator common arguments — radiator_common_arguments • radiator
@@ -17,7 +17,7 @@
@@ -73,6 +73,7 @@ radiator common arguments
radiator_common_arguments(
+ interactive.filter = TRUE,
gds,
data,
parallel.core = parallel::detectCores() - 1,
@@ -84,7 +85,14 @@ radiator common arguments
Arguments
- - gds
+ - interactive.filter
+(optional, logical) Do you want the filtering session to
+be interactive. Figures of distribution are shown before asking for filtering
+thresholds.
+Default: interactive.filter = TRUE.
- gds
(2 options) A Genomic Data Structure (GDS) file or object
How to get GDS ?
Look into tidy_genomic_data,
@@ -125,13 +133,6 @@
Arguments
for fine-tuning the function. Also used for legacy arguments (see details or
special section)- interactive.filter
-(optional, logical) Do you want the filtering session to
-be interactive. Figures of distribution are shown before asking for filtering
-thresholds.
-Default: interactive.filter = TRUE.
@@ -146,7 +147,7 @@ Arguments
diff --git a/docs/reference/radiator_dots.html b/docs/reference/radiator_dots.html
index 9c01f70b..4a63653c 100644
--- a/docs/reference/radiator_dots.html
+++ b/docs/reference/radiator_dots.html
@@ -1,5 +1,5 @@
-radiator_dots — radiator_dots • radiator radiator_dots — radiator_dots • radiator
@@ -17,7 +17,7 @@
@@ -93,7 +93,11 @@ radiator_dots
"keep.allele.names", "keep.gds", "calibrate.alleles", "vcf.metadata", "vcf.stats",
"wide", "whitelist.markers", "write.tidy", "missing.memory", "dart.sequence",
- "internal", "heatmap.fst", "tidy.check", "tidy.vcf", "tidy.dart"),
+ "internal", "heatmap.fst", "tidy.check", "tidy.vcf", "tidy.dart", "species",
+ "population", "tau", "threshold.y.markers", "threshold.y.silico.markers",
+ "sex.id.input", "threshold.x.markers.qr", "threshold.x.markers.RD",
+ "threshold.x.markers.RD.silico", "mis.threshold.data", "mis.threshold.silicodata",
+ "zoom.data", "zoom.silicodata", "sex.id.input", "het.qr.input"),
deprecated = c("maf.thresholds", "common.markers", "max.marker", "monomorphic.out",
"snp.ld", "filter.call.rate", "filter.markers.coverage", "filter.markers.missing",
"number.snp.reads", "mixed.genomes.analysis", "duplicate.genomes.analysis",
@@ -144,7 +148,11 @@ Arguments
"write.tidy",
"dart.sequence",
"missing.memory",
-"internal", "heatmap.fst", "tidy.check", "tidy.vcf", "tidy.dart").
+"internal", "heatmap.fst", "tidy.check", "tidy.vcf", "tidy.dart",
+"species", "population", "tau", "threshold.y.markers", "threshold.y.silico.markers",
+"sex.id.input", "threshold.x.markers.qr", "threshold.x.markers.RD", "threshold.x.markers.RD.silico",
+"mis.threshold.data", "mis.threshold.silicodata", "zoom.data", "zoom.silicodata",
+"sex.id.input", "het.qr.input").
deprecated
@@ -174,7 +182,7 @@ Arguments
diff --git a/docs/reference/radiator_folder.html b/docs/reference/radiator_folder.html
index fd38cd2d..f956f508 100644
--- a/docs/reference/radiator_folder.html
+++ b/docs/reference/radiator_folder.html
@@ -1,5 +1,5 @@
-radiator_folder — radiator_folder • radiator radiator_folder — radiator_folder • radiator
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Author
diff --git a/docs/reference/radiator_function_header.html b/docs/reference/radiator_function_header.html
index 35429f6d..c34ad494 100644
--- a/docs/reference/radiator_function_header.html
+++ b/docs/reference/radiator_function_header.html
@@ -1,5 +1,5 @@
-radiator_function_header — radiator_function_header • radiator radiator_function_header — radiator_function_header • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ radiator_function_header
diff --git a/docs/reference/radiator_gds.html b/docs/reference/radiator_gds.html
index 578aa681..28716746 100644
--- a/docs/reference/radiator_gds.html
+++ b/docs/reference/radiator_gds.html
@@ -1,5 +1,5 @@
-radiator gds constructor — radiator_gds • radiator radiator gds constructor — radiator_gds • radiator
@@ -17,7 +17,7 @@
@@ -102,7 +102,7 @@ radiator gds constructor
diff --git a/docs/reference/radiator_gds_skeleton.html b/docs/reference/radiator_gds_skeleton.html
index a78cfc55..793c3f81 100644
--- a/docs/reference/radiator_gds_skeleton.html
+++ b/docs/reference/radiator_gds_skeleton.html
@@ -1,5 +1,5 @@
-radiator_gds_skeleton — radiator_gds_skeleton • radiator radiator_gds_skeleton — radiator_gds_skeleton • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ radiator_gds_skeleton
diff --git a/docs/reference/radiator_packages_dep.html b/docs/reference/radiator_packages_dep.html
index 46f362aa..8204a250 100644
--- a/docs/reference/radiator_packages_dep.html
+++ b/docs/reference/radiator_packages_dep.html
@@ -1,5 +1,5 @@
-radiator_packages_dep — radiator_packages_dep • radiator radiator_packages_dep — radiator_packages_dep • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ radiator_packages_dep
diff --git a/docs/reference/radiator_parameters.html b/docs/reference/radiator_parameters.html
index b06bdaac..c22bcb3b 100644
--- a/docs/reference/radiator_parameters.html
+++ b/docs/reference/radiator_parameters.html
@@ -1,5 +1,5 @@
-radiator_parameters — radiator_parameters • radiator radiator_parameters — radiator_parameters • radiator radiator packages install helper — radiator_pkg_install • radiator radiator packages install helper — radiator_pkg_install • radiator radiator_question — radiator_question • radiator radiator_question — radiator_question • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ radiator_question
diff --git a/docs/reference/radiator_results_message.html b/docs/reference/radiator_results_message.html
index 641a55df..3d806023 100644
--- a/docs/reference/radiator_results_message.html
+++ b/docs/reference/radiator_results_message.html
@@ -1,5 +1,5 @@
-radiator_results_message — radiator_results_message • radiator radiator_results_message — radiator_results_message • radiator
@@ -17,7 +17,7 @@
@@ -93,7 +93,7 @@ radiator_results_message
diff --git a/docs/reference/radiator_snakecase.html b/docs/reference/radiator_snakecase.html
index 4fc158a6..bf64d00a 100644
--- a/docs/reference/radiator_snakecase.html
+++ b/docs/reference/radiator_snakecase.html
@@ -1,5 +1,5 @@
-radiator_snakecase — radiator_snakecase • radiator radiator_snakecase — radiator_snakecase • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ radiator_snakecase
diff --git a/docs/reference/radiator_split_tibble.html b/docs/reference/radiator_split_tibble.html
index 962743d9..3b099191 100644
--- a/docs/reference/radiator_split_tibble.html
+++ b/docs/reference/radiator_split_tibble.html
@@ -1,5 +1,5 @@
-radiator_split_tibble — radiator_split_tibble • radiator radiator_split_tibble — radiator_split_tibble • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ radiator_split_tibble
diff --git a/docs/reference/radiator_tic.html b/docs/reference/radiator_tic.html
index 99347514..c249da60 100644
--- a/docs/reference/radiator_tic.html
+++ b/docs/reference/radiator_tic.html
@@ -1,5 +1,5 @@
-radiator_tic — radiator_tic • radiator radiator_tic — radiator_tic • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ radiator_tic
diff --git a/docs/reference/radiator_toc.html b/docs/reference/radiator_toc.html
index bc6b2b2f..76510cd7 100644
--- a/docs/reference/radiator_toc.html
+++ b/docs/reference/radiator_toc.html
@@ -1,5 +1,5 @@
-radiator_toc — radiator_toc • radiator radiator_toc — radiator_toc • radiator
@@ -17,7 +17,7 @@
@@ -92,7 +92,7 @@ radiator_toc
diff --git a/docs/reference/read_blacklist_genotypes.html b/docs/reference/read_blacklist_genotypes.html
index 4901fe12..cd49840b 100644
--- a/docs/reference/read_blacklist_genotypes.html
+++ b/docs/reference/read_blacklist_genotypes.html
@@ -1,5 +1,5 @@
-read blacklist of genotypes — read_blacklist_genotypes • radiator read blacklist of genotypes — read_blacklist_genotypes • radiator read_blacklist_id — read_blacklist_id • radiator read_blacklist_id — read_blacklist_id • radiator Read and tidy DArT output files. — read_dart • radiator Read and tidy DArT output files. — read_dart • radiator Reads PLINK tped and bed files — read_plink • radiator Reads PLINK tped and bed files — read_plink • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -185,7 +185,7 @@ Examples
diff --git a/docs/reference/read_rad.html b/docs/reference/read_rad.html
index 40dab71c..5f85d666 100644
--- a/docs/reference/read_rad.html
+++ b/docs/reference/read_rad.html
@@ -1,5 +1,5 @@
-Read radiator file ending .gds, .rad, .gds.rad. — read_rad • radiator Read radiator file ending .gds, .rad, .gds.rad. — read_rad • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -198,7 +198,7 @@ Examples
diff --git a/docs/reference/read_strata.html b/docs/reference/read_strata.html
index 147738eb..59858576 100644
--- a/docs/reference/read_strata.html
+++ b/docs/reference/read_strata.html
@@ -1,5 +1,5 @@
-read strata — read_strata • radiator read strata — read_strata • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -269,7 +269,7 @@ Examples
diff --git a/docs/reference/read_vcf.html b/docs/reference/read_vcf.html
index fa3b6d0d..75b355f0 100644
--- a/docs/reference/read_vcf.html
+++ b/docs/reference/read_vcf.html
@@ -1,5 +1,5 @@
-Read VCF files and write a GDS file — read_vcf • radiator Read VCF files and write a GDS file — read_vcf • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -376,7 +376,7 @@ Examples
diff --git a/docs/reference/read_whitelist.html b/docs/reference/read_whitelist.html
index a4d664c2..b9942883 100644
--- a/docs/reference/read_whitelist.html
+++ b/docs/reference/read_whitelist.html
@@ -1,5 +1,5 @@
-read whitelist of markers — read_whitelist • radiator read whitelist of markers — read_whitelist • radiator Read tidy genomic data file ending .rad — remove_duplicates • radiator Read tidy genomic data file ending .rad — remove_duplicates • radiator replace_by_na — replace_by_na • radiator replace_by_na — replace_by_na • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ replace_by_na
diff --git a/docs/reference/reset_filters.html b/docs/reference/reset_filters.html
index dbb492d7..458020b2 100644
--- a/docs/reference/reset_filters.html
+++ b/docs/reference/reset_filters.html
@@ -1,5 +1,5 @@
-Reset filters (individuals and markers) in radiator GDS object. — reset_filters • radiator Reset filters (individuals and markers) in radiator GDS object. — reset_filters • radiator Run BayeScan — run_bayescan • radiator Run BayeScan — run_bayescan • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -326,7 +326,7 @@ Examples
diff --git a/docs/reference/separate_gt.html b/docs/reference/separate_gt.html
index df80123a..9eaebe4f 100644
--- a/docs/reference/separate_gt.html
+++ b/docs/reference/separate_gt.html
@@ -1,5 +1,5 @@
-separate_gt — separate_gt • radiator separate_gt — separate_gt • radiator
@@ -17,7 +17,7 @@
@@ -99,7 +99,7 @@ separate_gt
diff --git a/docs/reference/separate_markers.html b/docs/reference/separate_markers.html
index b209bfd0..cbd8734d 100644
--- a/docs/reference/separate_markers.html
+++ b/docs/reference/separate_markers.html
@@ -1,5 +1,5 @@
-Separate markers column into chrom, locus and pos — separate_markers • radiator Separate markers column into chrom, locus and pos — separate_markers • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -207,7 +207,7 @@ Examples
diff --git a/docs/reference/sex_markers_plot.html b/docs/reference/sex_markers_plot.html
index 4f8e71c0..a50121b0 100644
--- a/docs/reference/sex_markers_plot.html
+++ b/docs/reference/sex_markers_plot.html
@@ -1,5 +1,5 @@
-sex_markers_plot — sex_markers_plot • radiator sex_markers_plot — sex_markers_plot • radiator
@@ -17,7 +17,7 @@
@@ -87,7 +87,8 @@ sex_markers_plot
qreg = FALSE,
hist = FALSE,
RD = FALSE,
- plot.filename = NULL
+ plot.filename = NULL,
+ path = NULL
)
@@ -104,7 +105,7 @@ sex_markers_plot
diff --git a/docs/reference/sexy_markers.html b/docs/reference/sexy_markers.html
index 80804e96..666545ed 100644
--- a/docs/reference/sexy_markers.html
+++ b/docs/reference/sexy_markers.html
@@ -1,5 +1,5 @@
-sexy_markers finds sex-linked markers and re-assigns sex — sexy_markers • radiator sexy_markers finds sex-linked markers and re-assigns sex — sexy_markers • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -85,8 +85,8 @@ sexy_markers finds sex-linked markers and re-assigns sex
sexy_markers(
data,
silicodata = NULL,
- boost.analysis = FALSE,
strata = NULL,
+ boost.analysis = FALSE,
coverage.thresholds = 1,
filters = TRUE,
interactive.filter = TRUE,
@@ -111,13 +111,6 @@ Arguments
Default: silicodata = NULL.
-boost.analysis
-(optional, logical) This method uses machine learning
-approaches to find sex markers and re-assign samples in sex group.
-The approach is currently been tested and will be available for uses soon.
-Default: boost.analysis = FALSE.
strata
(file) A tab delimited file with a minimum of
2 columns (INDIVIDUALS, STRATA) for VCF files and 3 columns for DArT files
@@ -132,6 +125,13 @@
Arguments
functions: extract_dart_target_id and extract_individuals_vcfboost.analysis
+(optional, logical) This method uses machine learning
+approaches to find sex markers and re-assign samples in sex group.
+The approach is currently under construction.
+Default: boost.analysis = FALSE.
coverage.thresholds
(optional, integer) The minimum coverage required
to call a marker absent. For silico genotype data this must be < 1.
@@ -155,7 +155,7 @@
Arguments
folder.name
(optional,character) Name of the folder to store the results.
-Default: folder.name = "sexy_marker_date/time".
folder.name = NULL. The name sexy_markers_datetime will be generated.
parallel.core
@@ -250,7 +250,11 @@ Advance mode
-dots-dots-dots ... allows to pass several arguments for fine-tuning the function:
tau: The quantile used in regression to distinguish homogametic markers
+
dots-dots-dots ... allows to pass several arguments for fine-tuning the function:
species: To give your figures some meanings.
+Default species = NULL.
population: To give your figures some meanings.
+Default species = NULL.
tau: The quantile used in regression to distinguish homogametic markers
with the heterozygosity method. See rq.
Default tau = 0.03.
mis.threshold.data: Threshold to filter the SNP data on missingness.
@@ -325,7 +329,7 @@
Examples
diff --git a/docs/reference/simulate_genos_from_posterior.html b/docs/reference/simulate_genos_from_posterior.html
index 499054d1..8b9ec6f9 100644
--- a/docs/reference/simulate_genos_from_posterior.html
+++ b/docs/reference/simulate_genos_from_posterior.html
@@ -1,5 +1,5 @@
-simulate_genos_from_posterior — simulate_genos_from_posterior • radiator simulate_genos_from_posterior — simulate_genos_from_posterior • radiator split_tibble_rows — split_tibble_rows • radiator split_tibble_rows — split_tibble_rows • radiator
@@ -17,7 +17,7 @@
@@ -93,7 +93,7 @@ split_tibble_rows
diff --git a/docs/reference/split_vcf.html b/docs/reference/split_vcf.html
index a43e07de..66b27d42 100644
--- a/docs/reference/split_vcf.html
+++ b/docs/reference/split_vcf.html
@@ -1,5 +1,5 @@
-Split a VCF file — split_vcf • radiator Split a VCF file — split_vcf • radiator strata_haplo — strata_haplo • radiator strata_haplo — strata_haplo • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ strata_haplo
diff --git a/docs/reference/subsampling_data.html b/docs/reference/subsampling_data.html
index 60a1a87c..ae009819 100644
--- a/docs/reference/subsampling_data.html
+++ b/docs/reference/subsampling_data.html
@@ -1,5 +1,5 @@
-subsampling data — subsampling_data • radiator subsampling data — subsampling_data • radiator
@@ -17,7 +17,7 @@
@@ -93,7 +93,7 @@ subsampling data
diff --git a/docs/reference/summarise_genotypes.html b/docs/reference/summarise_genotypes.html
index b9959c59..109c2e28 100644
--- a/docs/reference/summarise_genotypes.html
+++ b/docs/reference/summarise_genotypes.html
@@ -1,5 +1,5 @@
-summarise genotypes — summarise_genotypes • radiator summarise genotypes — summarise_genotypes • radiator
@@ -17,7 +17,7 @@
@@ -92,7 +92,7 @@ Author
diff --git a/docs/reference/summarize_sex.html b/docs/reference/summarize_sex.html
index 14b66900..ff53f89d 100644
--- a/docs/reference/summarize_sex.html
+++ b/docs/reference/summarize_sex.html
@@ -1,5 +1,5 @@
-summarize_sex — summarize_sex • radiator summarize_sex — summarize_sex • radiator
@@ -17,7 +17,7 @@
@@ -94,7 +94,7 @@ summarize_sex
diff --git a/docs/reference/summary_gds.html b/docs/reference/summary_gds.html
index 3abfb279..13a224e6 100644
--- a/docs/reference/summary_gds.html
+++ b/docs/reference/summary_gds.html
@@ -1,5 +1,5 @@
-summary_gds — summary_gds • radiator summary_gds — summary_gds • radiator
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/summary_rad.html b/docs/reference/summary_rad.html
index 5cc5e1b1..7972e1e3 100644
--- a/docs/reference/summary_rad.html
+++ b/docs/reference/summary_rad.html
@@ -1,5 +1,5 @@
-Summary statistics for RADseq data — summary_rad • radiator Summary statistics for RADseq data — summary_rad • radiator Summary of strata — summary_strata • radiator Summary of strata — summary_strata • radiator switch_allele_count — switch_allele_count • radiator switch_allele_count — switch_allele_count • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ switch_allele_count
diff --git a/docs/reference/switch_genotypes.html b/docs/reference/switch_genotypes.html
index c13b7296..8d2d3cc4 100644
--- a/docs/reference/switch_genotypes.html
+++ b/docs/reference/switch_genotypes.html
@@ -1,5 +1,5 @@
-switch_genotypes — switch_genotypes • radiator switch_genotypes — switch_genotypes • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ switch_genotypes
diff --git a/docs/reference/sync_gds.html b/docs/reference/sync_gds.html
index c604aa3f..7e349b48 100644
--- a/docs/reference/sync_gds.html
+++ b/docs/reference/sync_gds.html
@@ -1,5 +1,5 @@
-sync_gds — sync_gds • radiator sync_gds — sync_gds • radiator tibble_stats — tibble_stats • radiator tibble_stats — tibble_stats • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ tibble_stats
diff --git a/docs/reference/tidy2gds.html b/docs/reference/tidy2gds.html
index 4cac68bc..a9d5a8e3 100644
--- a/docs/reference/tidy2gds.html
+++ b/docs/reference/tidy2gds.html
@@ -1,5 +1,5 @@
-tidy2gds — tidy2gds • radiator tidy2gds — tidy2gds • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ tidy2gds
diff --git a/docs/reference/tidy2wide.html b/docs/reference/tidy2wide.html
index 57a23746..3a97c801 100644
--- a/docs/reference/tidy2wide.html
+++ b/docs/reference/tidy2wide.html
@@ -1,5 +1,5 @@
-tidy2wide — tidy2wide • radiator tidy2wide — tidy2wide • radiator
@@ -17,7 +17,7 @@
@@ -96,7 +96,7 @@ tidy2wide
diff --git a/docs/reference/tidy_dart_metadata.html b/docs/reference/tidy_dart_metadata.html
index aa4a9d7d..1d0dbbc1 100644
--- a/docs/reference/tidy_dart_metadata.html
+++ b/docs/reference/tidy_dart_metadata.html
@@ -1,5 +1,5 @@
-Import and tidy DArT metadata. — tidy_dart_metadata • radiator Import and tidy DArT metadata. — tidy_dart_metadata • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -160,7 +160,7 @@ Examples
diff --git a/docs/reference/tidy_fstat.html b/docs/reference/tidy_fstat.html
index 108e395e..7ed7c4b4 100644
--- a/docs/reference/tidy_fstat.html
+++ b/docs/reference/tidy_fstat.html
@@ -1,5 +1,5 @@
-fstat file to tidy dataframe — tidy_fstat • radiator fstat file to tidy dataframe — tidy_fstat • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -180,7 +180,7 @@ Examples
diff --git a/docs/reference/tidy_genepop.html b/docs/reference/tidy_genepop.html
index 93bf51fd..03b6fcb7 100644
--- a/docs/reference/tidy_genepop.html
+++ b/docs/reference/tidy_genepop.html
@@ -1,5 +1,5 @@
-Import genepop file and convert to a tidy dataframe — tidy_genepop • radiator Import genepop file and convert to a tidy dataframe — tidy_genepop • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -253,7 +253,7 @@ Examples
diff --git a/docs/reference/tidy_genind.html b/docs/reference/tidy_genind.html
index 1acf7666..82e77677 100644
--- a/docs/reference/tidy_genind.html
+++ b/docs/reference/tidy_genind.html
@@ -1,5 +1,5 @@
-Tidy a genind object to a tidy dataframe — tidy_genind • radiator Tidy a genind object to a tidy dataframe — tidy_genind • radiator Tidy a genlight object to a tidy dataframe and/or GDS object/file — tidy_genlight • radiator Tidy a genlight object to a tidy dataframe and/or GDS object/file — tidy_genlight • radiator Transform common genomic dataset format in a tidy data frame — tidy_genomic_data • radiator Transform common genomic dataset format in a tidy data frame — tidy_genomic_data • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -247,7 +247,7 @@ Examples
diff --git a/docs/reference/tidy_gtypes.html b/docs/reference/tidy_gtypes.html
index cf8901d8..80a269d0 100644
--- a/docs/reference/tidy_gtypes.html
+++ b/docs/reference/tidy_gtypes.html
@@ -1,5 +1,5 @@
-Tidy a gtypes object to a tidy dataframe — tidy_gtypes • radiator Tidy a gtypes object to a tidy dataframe — tidy_gtypes • radiator Tidy PLINK tped and bed files — tidy_plink • radiator Tidy PLINK tped and bed files — tidy_plink • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -176,7 +176,7 @@ Examples
diff --git a/docs/reference/tidy_vcf.html b/docs/reference/tidy_vcf.html
index 2a5543b1..c62f87b1 100644
--- a/docs/reference/tidy_vcf.html
+++ b/docs/reference/tidy_vcf.html
@@ -1,5 +1,5 @@
-Tidy vcf file — tidy_vcf • radiator Tidy vcf file — tidy_vcf • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -326,7 +326,7 @@ Examples
diff --git a/docs/reference/tidy_wide.html b/docs/reference/tidy_wide.html
index 66a44b5b..b06ad6c8 100644
--- a/docs/reference/tidy_wide.html
+++ b/docs/reference/tidy_wide.html
@@ -1,5 +1,5 @@
-Read/Import a tidy genomic data frames. — tidy_wide • radiator Read/Import a tidy genomic data frames. — tidy_wide • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -160,7 +160,7 @@ Author
diff --git a/docs/reference/update_bl_individuals.html b/docs/reference/update_bl_individuals.html
index a1d79150..25b42f8f 100644
--- a/docs/reference/update_bl_individuals.html
+++ b/docs/reference/update_bl_individuals.html
@@ -1,5 +1,5 @@
-update_bl_individuals — update_bl_individuals • radiator update_bl_individuals — update_bl_individuals • radiator
@@ -17,7 +17,7 @@
@@ -94,7 +94,7 @@ update_bl_individuals
diff --git a/docs/reference/update_bl_markers.html b/docs/reference/update_bl_markers.html
index cf55b6ba..73bf184c 100644
--- a/docs/reference/update_bl_markers.html
+++ b/docs/reference/update_bl_markers.html
@@ -1,5 +1,5 @@
-update_bl_markers — update_bl_markers • radiator update_bl_markers — update_bl_markers • radiator
@@ -17,7 +17,7 @@
@@ -94,7 +94,7 @@ update_bl_markers
diff --git a/docs/reference/update_filter_parameter.html b/docs/reference/update_filter_parameter.html
index 5f2e7de4..46256cac 100644
--- a/docs/reference/update_filter_parameter.html
+++ b/docs/reference/update_filter_parameter.html
@@ -1,5 +1,5 @@
-update filter parameter file — update_filter_parameter • radiator update filter parameter file — update_filter_parameter • radiator
@@ -17,7 +17,7 @@
@@ -99,7 +99,7 @@ Author
diff --git a/docs/reference/update_radiator_gds.html b/docs/reference/update_radiator_gds.html
index a372c4dd..e8afd052 100644
--- a/docs/reference/update_radiator_gds.html
+++ b/docs/reference/update_radiator_gds.html
@@ -1,5 +1,5 @@
-update_radiator_gds — update_radiator_gds • radiator update_radiator_gds — update_radiator_gds • radiator
@@ -17,7 +17,7 @@
@@ -97,7 +97,7 @@ update_radiator_gds
diff --git a/docs/reference/vcf_strata.html b/docs/reference/vcf_strata.html
index a9630309..94c0861f 100644
--- a/docs/reference/vcf_strata.html
+++ b/docs/reference/vcf_strata.html
@@ -1,5 +1,5 @@
-Join stratification metadata to a VCF (population-aware VCF) — vcf_strata • radiator Join stratification metadata to a VCF (population-aware VCF) — vcf_strata • radiator Write an arlequin file from a tidy data frame — write_arlequin • radiator Write an arlequin file from a tidy data frame — write_arlequin • radiator Write a BayeScan
-file from a tidy data frame — write_bayescan • radiator Write a BayeScan file from a tidy data frame — write_bayescan • radiator Write a betadiv file from a tidy data frame — write_betadiv • radiator Write a betadiv file from a tidy data frame — write_betadiv • radiator Write a COLONY input file — write_colony • radiator Write a COLONY input file — write_colony • radiator
@@ -17,7 +17,7 @@
@@ -272,7 +272,7 @@ Examples
diff --git a/docs/reference/write_dadi.html b/docs/reference/write_dadi.html
index 0436c0be..373976e1 100644
--- a/docs/reference/write_dadi.html
+++ b/docs/reference/write_dadi.html
@@ -1,5 +1,5 @@
-Write a dadi SNP input file from a tidy data frame. — write_dadi • radiator Write a dadi SNP input file from a tidy data frame. — write_dadi • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -192,7 +192,7 @@ Examples
diff --git a/docs/reference/write_fasta.html b/docs/reference/write_fasta.html
index 9f17ee5f..eb180aff 100644
--- a/docs/reference/write_fasta.html
+++ b/docs/reference/write_fasta.html
@@ -1,5 +1,5 @@
-Export FASTA — write_fasta • radiator Export FASTA — write_fasta • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ Export FASTA
diff --git a/docs/reference/write_faststructure.html b/docs/reference/write_faststructure.html
index 02db9643..9bce50dc 100644
--- a/docs/reference/write_faststructure.html
+++ b/docs/reference/write_faststructure.html
@@ -1,5 +1,5 @@
-Write a faststructure file from a tidy data frame — write_faststructure • radiator Write a faststructure file from a tidy data frame — write_faststructure • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -156,7 +156,7 @@ Author
diff --git a/docs/reference/write_fineradstructure.html b/docs/reference/write_fineradstructure.html
index c7e40ff5..a5103558 100644
--- a/docs/reference/write_fineradstructure.html
+++ b/docs/reference/write_fineradstructure.html
@@ -1,5 +1,5 @@
-Write a fineRADstructure file from a tidy data frame — write_fineradstructure • radiator Write a fineRADstructure file from a tidy data frame — write_fineradstructure • radiator Write a GDS object from a tidy data frame — write_gds • radiator Write a GDS object from a tidy data frame — write_gds • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -165,7 +165,7 @@ Examples
diff --git a/docs/reference/write_genepop.html b/docs/reference/write_genepop.html
index 78f37767..0395c0bf 100644
--- a/docs/reference/write_genepop.html
+++ b/docs/reference/write_genepop.html
@@ -1,5 +1,5 @@
-Write a genepop file — write_genepop • radiator Write a genepop file — write_genepop • radiator Write a genepopedit flatten object — write_genepopedit • radiator Write a genepopedit flatten object — write_genepopedit • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -145,7 +145,7 @@ Author
diff --git a/docs/reference/write_genind.html b/docs/reference/write_genind.html
index a064abd3..6810055d 100644
--- a/docs/reference/write_genind.html
+++ b/docs/reference/write_genind.html
@@ -1,5 +1,5 @@
-Write a genind object from a tidy data frame or GDS file or object. — write_genind • radiator Write a genind object from a tidy data frame or GDS file or object. — write_genind • radiator Write a genlight object from a tidy data frame or GDS file or object. — write_genlight • radiator Write a genlight object from a tidy data frame or GDS file or object. — write_genlight • radiator Write a gsi_sim file from a data frame (wide or long/tidy). — write_gsi_sim • radiator Write a gsi_sim file from a data frame (wide or long/tidy). — write_gsi_sim • radiator Write a strataG object from
-radiator GDS and tidy data file or object. — write_gtypes • radiator Write a strataG object from radiator GDS and tidy data file or object. — write_gtypes • radiator Write a HapMap file from a tidy data frame — write_hapmap • radiator Write a HapMap file from a tidy data frame — write_hapmap • radiator Write a hierfstat file from a tidy data frame — write_hierfstat • radiator Write a hierfstat file from a tidy data frame — write_hierfstat • radiator Write a HZAR file from a tidy data frame. — write_hzar • radiator Write a HZAR file from a tidy data frame. — write_hzar • radiator Write a LDna object from a tidy data frame — write_ldna • radiator Write a LDna object from a tidy data frame — write_ldna • radiator Write a maverick file from a tidy data frame — write_maverick • radiator Write a maverick file from a tidy data frame — write_maverick • radiator Write a pcadapt
-file from a tidy data frame — write_pcadapt • radiator Write a pcadapt file from a tidy data frame — write_pcadapt • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -69,8 +67,7 @@
- Write a pcadapt
-file from a tidy data frame
+ Write a pcadapt file from a tidy data frame
Source: R/write_pcadapt.R
write_pcadapt.Rd
@@ -187,7 +184,7 @@ Author
diff --git a/docs/reference/write_plink.html b/docs/reference/write_plink.html
index 38314609..d5c324f3 100644
--- a/docs/reference/write_plink.html
+++ b/docs/reference/write_plink.html
@@ -1,5 +1,5 @@
-Write a plink tped/tfam file from a tidy data frame — write_plink • radiator Write a plink tped/tfam file from a tidy data frame — write_plink • radiator Write tidy genomic data file or close GDS file — write_rad • radiator Write tidy genomic data file or close GDS file — write_rad • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -199,7 +199,7 @@ Examples
diff --git a/docs/reference/write_related.html b/docs/reference/write_related.html
index f8b61592..2a39deb6 100644
--- a/docs/reference/write_related.html
+++ b/docs/reference/write_related.html
@@ -1,5 +1,5 @@
-Write a related file from a tidy data frame — write_related • radiator Write a related file from a tidy data frame — write_related • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -153,7 +153,7 @@ Author
diff --git a/docs/reference/write_rubias.html b/docs/reference/write_rubias.html
index 388f7faa..7865aeb9 100644
--- a/docs/reference/write_rubias.html
+++ b/docs/reference/write_rubias.html
@@ -1,5 +1,5 @@
-Write a rubias object — write_rubias • radiator Write a rubias object — write_rubias • radiator
@@ -17,7 +17,7 @@
@@ -155,7 +155,7 @@ Author
diff --git a/docs/reference/write_snprelate.html b/docs/reference/write_snprelate.html
index 7a243f3e..3e474925 100644
--- a/docs/reference/write_snprelate.html
+++ b/docs/reference/write_snprelate.html
@@ -1,5 +1,5 @@
-Write a SNPRelate object from a tidy data frame — write_snprelate • radiator Write a SNPRelate object from a tidy data frame — write_snprelate • radiator Write a stockR dataset from a tidy data frame or GDS file or object. — write_stockr • radiator Write a stockR dataset from a tidy data frame or GDS file or object. — write_stockr • radiator Write a structure file from a tidy data frame — write_structure • radiator Write a structure file from a tidy data frame — write_structure • radiator Write a vcf file from a tidy data frame — write_vcf • radiator Write a vcf file from a tidy data frame — write_vcf • radiator
Filter individuals based on genotyping/missingness rate, -heterozygosity and total coverage
Filter individuals based on genotyping/missingness rate, heterozygosity and total coverage
Detect <
Compute pairwise genome similarity or distance between individuals -to highligh potential duplicate individuals
Compute pairwise genome similarity or distance between individuals to highligh potential duplicate individuals
Write
Write a BayeScan -file from a tidy data frame
Write a BayeScan file from a tidy data frame
Write
Write a strataG object from -radiator GDS and tidy data file or object.
Write a strataG object from radiator GDS and tidy data file or object.
Write
Write a pcadapt -file from a tidy data frame
Write a pcadapt file from a tidy data frame
Run software
diff --git a/docs/reference/individuals2strata.html b/docs/reference/individuals2strata.html
index f65e5c44..208a8235 100644
--- a/docs/reference/individuals2strata.html
+++ b/docs/reference/individuals2strata.html
@@ -1,5 +1,5 @@
-Create a strata file from a list of individuals — individuals2strata • radiator Create a strata file from a list of individuals — individuals2strata • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -168,7 +168,7 @@ Examples
diff --git a/docs/reference/join_strata.html b/docs/reference/join_strata.html
index 25aacfa1..f1dc86a2 100644
--- a/docs/reference/join_strata.html
+++ b/docs/reference/join_strata.html
@@ -1,5 +1,5 @@
-Join the strata with the data — join_strata • radiator Join the strata with the data — join_strata • radiator ld2df — ld2df • radiator ld2df — ld2df • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ ld2df
diff --git a/docs/reference/ld_boxplot.html b/docs/reference/ld_boxplot.html
index 4367f28a..30ce41f2 100644
--- a/docs/reference/ld_boxplot.html
+++ b/docs/reference/ld_boxplot.html
@@ -1,5 +1,5 @@
-ld_boxplot — ld_boxplot • radiator ld_boxplot — ld_boxplot • radiator Prune dataset based on LD and missingness. — ld_missing • radiator Prune dataset based on LD and missingness. — ld_missing • radiator Prune dataset based on LD. — ld_pruning • radiator Prune dataset based on LD. — ld_pruning • radiator List current active filters (individuals and markers) in radiator GDS object. — list_filters • radiator List current active filters (individuals and markers) in radiator GDS object. — list_filters • radiator
@@ -17,7 +17,7 @@
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/markers_genotyped_helper.html b/docs/reference/markers_genotyped_helper.html
index 3c9df84c..aede1ab0 100644
--- a/docs/reference/markers_genotyped_helper.html
+++ b/docs/reference/markers_genotyped_helper.html
@@ -1,5 +1,5 @@
-markers_genotyped_helper — markers_genotyped_helper • radiator markers_genotyped_helper — markers_genotyped_helper • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ markers_genotyped_helper
diff --git a/docs/reference/merge_dart.html b/docs/reference/merge_dart.html
index cb9c47dd..51313a01 100644
--- a/docs/reference/merge_dart.html
+++ b/docs/reference/merge_dart.html
@@ -1,5 +1,5 @@
-Merge DArT files — merge_dart • radiator Merge DArT files — merge_dart • radiator
@@ -17,7 +17,7 @@
@@ -192,7 +192,7 @@ Examples
diff --git a/docs/reference/message_func_call.html b/docs/reference/message_func_call.html
index 71e6fd17..b0a90bd4 100644
--- a/docs/reference/message_func_call.html
+++ b/docs/reference/message_func_call.html
@@ -1,5 +1,5 @@
-message_func_call — message_func_call • radiator message_func_call — message_func_call • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ message_func_call
diff --git a/docs/reference/missing_per_pop.html b/docs/reference/missing_per_pop.html
index 7f6547ff..f734e751 100644
--- a/docs/reference/missing_per_pop.html
+++ b/docs/reference/missing_per_pop.html
@@ -1,5 +1,5 @@
-missing_per_pop — missing_per_pop • radiator missing_per_pop — missing_per_pop • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ missing_per_pop
diff --git a/docs/reference/n.html b/docs/reference/n.html
index 241b72f8..650b55af 100644
--- a/docs/reference/n.html
+++ b/docs/reference/n.html
@@ -1,5 +1,5 @@
-The number of observations in the current group. — n • radiator The number of observations in the current group. — n • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ The number of observations in the current group.
diff --git a/docs/reference/not_common_markers.html b/docs/reference/not_common_markers.html
index 38474933..52702221 100644
--- a/docs/reference/not_common_markers.html
+++ b/docs/reference/not_common_markers.html
@@ -1,5 +1,5 @@
-not_common_markers — not_common_markers • radiator not_common_markers — not_common_markers • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ not_common_markers
diff --git a/docs/reference/parallel_core_opt.html b/docs/reference/parallel_core_opt.html
index c90d8951..5988fc0e 100644
--- a/docs/reference/parallel_core_opt.html
+++ b/docs/reference/parallel_core_opt.html
@@ -1,5 +1,5 @@
-parallel_core_opt — parallel_core_opt • radiator parallel_core_opt — parallel_core_opt • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ parallel_core_opt
diff --git a/docs/reference/parse_gds_metadata.html b/docs/reference/parse_gds_metadata.html
index 0d7ab646..ad2f807e 100644
--- a/docs/reference/parse_gds_metadata.html
+++ b/docs/reference/parse_gds_metadata.html
@@ -1,5 +1,5 @@
-parse_gds_metadata — parse_gds_metadata • radiator parse_gds_metadata — parse_gds_metadata • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ parse_gds_metadata
diff --git a/docs/reference/pi.html b/docs/reference/pi.html
index 85ae2ceb..ac69dca4 100644
--- a/docs/reference/pi.html
+++ b/docs/reference/pi.html
@@ -1,5 +1,5 @@
-Nucleotide diversity — pi • radiator Nucleotide diversity — pi • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -181,7 +181,7 @@ Examples
diff --git a/docs/reference/pi_pop.html b/docs/reference/pi_pop.html
index 94dd9b17..60944089 100644
--- a/docs/reference/pi_pop.html
+++ b/docs/reference/pi_pop.html
@@ -1,5 +1,5 @@
-pi_pop — pi_pop • radiator pi_pop — pi_pop • radiator
@@ -17,7 +17,7 @@
@@ -92,7 +92,7 @@ Author
diff --git a/docs/reference/pi_rad.html b/docs/reference/pi_rad.html
index 7f101caa..aacecefd 100644
--- a/docs/reference/pi_rad.html
+++ b/docs/reference/pi_rad.html
@@ -1,5 +1,5 @@
-pi_rad — pi_rad • radiator pi_rad — pi_rad • radiator
@@ -17,7 +17,7 @@
@@ -92,7 +92,7 @@ Author
diff --git a/docs/reference/pipe.html b/docs/reference/pipe.html
index 57a5bcc1..0585be18 100644
--- a/docs/reference/pipe.html
+++ b/docs/reference/pipe.html
@@ -1,5 +1,5 @@
-Forward-pipe operator — %>% • radiator Forward-pipe operator — %>% • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ Forward-pipe operator
diff --git a/docs/reference/plot_bayescan.html b/docs/reference/plot_bayescan.html
index 89023923..492e4e8e 100644
--- a/docs/reference/plot_bayescan.html
+++ b/docs/reference/plot_bayescan.html
@@ -1,5 +1,5 @@
-plot_bayescan — plot_bayescan • radiator plot_bayescan — plot_bayescan • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ plot_bayescan
diff --git a/docs/reference/plot_boxplot_coverage.html b/docs/reference/plot_boxplot_coverage.html
index 84b023bf..17fbd811 100644
--- a/docs/reference/plot_boxplot_coverage.html
+++ b/docs/reference/plot_boxplot_coverage.html
@@ -1,5 +1,5 @@
-Figure box plot of coverage summary statistics — plot_boxplot_coverage • radiator Figure box plot of coverage summary statistics — plot_boxplot_coverage • radiator Box plot of the diversity (Gene and Haplotypes) — plot_boxplot_diversity • radiator Box plot of the diversity (Gene and Haplotypes) — plot_boxplot_diversity • radiator Visual diagnostic of coverage imbalance — plot_coverage_imbalance_diagnostic • radiator Visual diagnostic of coverage imbalance — plot_coverage_imbalance_diagnostic • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -149,7 +149,7 @@ Details
diff --git a/docs/reference/plot_density_distribution_coverage.html b/docs/reference/plot_density_distribution_coverage.html
index 1146cb10..0937fe36 100644
--- a/docs/reference/plot_density_distribution_coverage.html
+++ b/docs/reference/plot_density_distribution_coverage.html
@@ -1,5 +1,5 @@
-Figure of distribution (histogram) — plot_histogram • radiator Figure of distribution (histogram) — plot_histogram • radiator Figure density distribution of the observed heterozygosity
-summary statistics. — plot_density_distribution_het • radiator Figure density distribution of the observed heterozygosity summary statistics. — plot_density_distribution_het • radiator Figure density distribution of minor allele frequency (MAF)
-summary statistics. — plot_density_distribution_maf • radiator Figure density distribution of minor allele frequency (MAF) summary statistics. — plot_density_distribution_maf • radiator
@@ -19,7 +17,7 @@
@@ -64,8 +62,7 @@
- Figure density distribution of minor allele frequency (MAF)
-summary statistics.
+ Figure density distribution of minor allele frequency (MAF) summary statistics.
Source: R/visualization.R
plot_density_distribution_maf.Rd
@@ -134,7 +131,7 @@ Author
diff --git a/docs/reference/plot_distribution_diversity.html b/docs/reference/plot_distribution_diversity.html
index 2d82b11a..410c85b0 100644
--- a/docs/reference/plot_distribution_diversity.html
+++ b/docs/reference/plot_distribution_diversity.html
@@ -1,5 +1,5 @@
-Density distribution of diversity (Gene and Haplotypes) — plot_distribution_diversity • radiator Density distribution of diversity (Gene and Haplotypes) — plot_distribution_diversity • radiator
@@ -17,7 +17,7 @@
@@ -112,7 +112,7 @@ Arguments
diff --git a/docs/reference/plot_het_outliers.html b/docs/reference/plot_het_outliers.html
index e233c5f8..ae00754d 100644
--- a/docs/reference/plot_het_outliers.html
+++ b/docs/reference/plot_het_outliers.html
@@ -1,5 +1,5 @@
-plot_het_outliers — plot_het_outliers • radiator plot_het_outliers — plot_het_outliers • radiator Figure of the distribution of SNP per locus before and after filters — plot_snp_number_loci • radiator Figure of the distribution of SNP per locus before and after filters — plot_snp_number_loci • radiator
@@ -17,7 +17,7 @@
@@ -98,7 +98,7 @@ Arguments
diff --git a/docs/reference/plot_snp_position_read.html b/docs/reference/plot_snp_position_read.html
index 60991367..3d03575c 100644
--- a/docs/reference/plot_snp_position_read.html
+++ b/docs/reference/plot_snp_position_read.html
@@ -1,5 +1,5 @@
-Figure of the distribution of SNP nucleotide position alond the read — plot_snp_position_read • radiator Figure of the distribution of SNP nucleotide position alond the read — plot_snp_position_read • radiator
@@ -17,7 +17,7 @@
@@ -102,7 +102,7 @@ Arguments
diff --git a/docs/reference/plot_upset.html b/docs/reference/plot_upset.html
index 87e84ff1..aa1218d7 100644
--- a/docs/reference/plot_upset.html
+++ b/docs/reference/plot_upset.html
@@ -1,5 +1,5 @@
-plot_upset — plot_upset • radiator plot_upset — plot_upset • radiator
@@ -17,7 +17,7 @@
@@ -94,7 +94,7 @@ plot_upset
diff --git a/docs/reference/private_alleles.html b/docs/reference/private_alleles.html
index 1ac8a329..7ac1d578 100644
--- a/docs/reference/private_alleles.html
+++ b/docs/reference/private_alleles.html
@@ -1,5 +1,5 @@
-Find private alleles — private_alleles • radiator Find private alleles — private_alleles • radiator
@@ -17,7 +17,7 @@
@@ -130,7 +130,7 @@ Examples
diff --git a/docs/reference/private_haplotypes.html b/docs/reference/private_haplotypes.html
index 70872333..1af437f0 100644
--- a/docs/reference/private_haplotypes.html
+++ b/docs/reference/private_haplotypes.html
@@ -1,5 +1,5 @@
-private haplotypes — private_haplotypes • radiator private haplotypes — private_haplotypes • radiator
@@ -17,7 +17,7 @@
@@ -123,7 +123,7 @@ Author
diff --git a/docs/reference/radiator_common_arguments.html b/docs/reference/radiator_common_arguments.html
index d9f1b8fc..3e9357f3 100644
--- a/docs/reference/radiator_common_arguments.html
+++ b/docs/reference/radiator_common_arguments.html
@@ -1,5 +1,5 @@
-radiator common arguments — radiator_common_arguments • radiator radiator common arguments — radiator_common_arguments • radiator
@@ -17,7 +17,7 @@
@@ -73,6 +73,7 @@ radiator common arguments
radiator_common_arguments(
+ interactive.filter = TRUE,
gds,
data,
parallel.core = parallel::detectCores() - 1,
@@ -84,7 +85,14 @@ radiator common arguments
Arguments
- - gds
+ - interactive.filter
+(optional, logical) Do you want the filtering session to
+be interactive. Figures of distribution are shown before asking for filtering
+thresholds.
+Default: interactive.filter = TRUE.
- gds
(2 options) A Genomic Data Structure (GDS) file or object
How to get GDS ?
Look into tidy_genomic_data,
@@ -125,13 +133,6 @@
Arguments
for fine-tuning the function. Also used for legacy arguments (see details or
special section)- interactive.filter
-(optional, logical) Do you want the filtering session to
-be interactive. Figures of distribution are shown before asking for filtering
-thresholds.
-Default: interactive.filter = TRUE.
@@ -146,7 +147,7 @@ Arguments
diff --git a/docs/reference/radiator_dots.html b/docs/reference/radiator_dots.html
index 9c01f70b..4a63653c 100644
--- a/docs/reference/radiator_dots.html
+++ b/docs/reference/radiator_dots.html
@@ -1,5 +1,5 @@
-radiator_dots — radiator_dots • radiator radiator_dots — radiator_dots • radiator
@@ -17,7 +17,7 @@
@@ -93,7 +93,11 @@ radiator_dots
"keep.allele.names", "keep.gds", "calibrate.alleles", "vcf.metadata", "vcf.stats",
"wide", "whitelist.markers", "write.tidy", "missing.memory", "dart.sequence",
- "internal", "heatmap.fst", "tidy.check", "tidy.vcf", "tidy.dart"),
+ "internal", "heatmap.fst", "tidy.check", "tidy.vcf", "tidy.dart", "species",
+ "population", "tau", "threshold.y.markers", "threshold.y.silico.markers",
+ "sex.id.input", "threshold.x.markers.qr", "threshold.x.markers.RD",
+ "threshold.x.markers.RD.silico", "mis.threshold.data", "mis.threshold.silicodata",
+ "zoom.data", "zoom.silicodata", "sex.id.input", "het.qr.input"),
deprecated = c("maf.thresholds", "common.markers", "max.marker", "monomorphic.out",
"snp.ld", "filter.call.rate", "filter.markers.coverage", "filter.markers.missing",
"number.snp.reads", "mixed.genomes.analysis", "duplicate.genomes.analysis",
@@ -144,7 +148,11 @@ Arguments
"write.tidy",
"dart.sequence",
"missing.memory",
-"internal", "heatmap.fst", "tidy.check", "tidy.vcf", "tidy.dart").
+"internal", "heatmap.fst", "tidy.check", "tidy.vcf", "tidy.dart",
+"species", "population", "tau", "threshold.y.markers", "threshold.y.silico.markers",
+"sex.id.input", "threshold.x.markers.qr", "threshold.x.markers.RD", "threshold.x.markers.RD.silico",
+"mis.threshold.data", "mis.threshold.silicodata", "zoom.data", "zoom.silicodata",
+"sex.id.input", "het.qr.input").
deprecated
@@ -174,7 +182,7 @@ Arguments
diff --git a/docs/reference/radiator_folder.html b/docs/reference/radiator_folder.html
index fd38cd2d..f956f508 100644
--- a/docs/reference/radiator_folder.html
+++ b/docs/reference/radiator_folder.html
@@ -1,5 +1,5 @@
-radiator_folder — radiator_folder • radiator radiator_folder — radiator_folder • radiator
@@ -17,7 +17,7 @@
@@ -107,7 +107,7 @@ Author
diff --git a/docs/reference/radiator_function_header.html b/docs/reference/radiator_function_header.html
index 35429f6d..c34ad494 100644
--- a/docs/reference/radiator_function_header.html
+++ b/docs/reference/radiator_function_header.html
@@ -1,5 +1,5 @@
-radiator_function_header — radiator_function_header • radiator radiator_function_header — radiator_function_header • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ radiator_function_header
diff --git a/docs/reference/radiator_gds.html b/docs/reference/radiator_gds.html
index 578aa681..28716746 100644
--- a/docs/reference/radiator_gds.html
+++ b/docs/reference/radiator_gds.html
@@ -1,5 +1,5 @@
-radiator gds constructor — radiator_gds • radiator radiator gds constructor — radiator_gds • radiator
@@ -17,7 +17,7 @@
@@ -102,7 +102,7 @@ radiator gds constructor
diff --git a/docs/reference/radiator_gds_skeleton.html b/docs/reference/radiator_gds_skeleton.html
index a78cfc55..793c3f81 100644
--- a/docs/reference/radiator_gds_skeleton.html
+++ b/docs/reference/radiator_gds_skeleton.html
@@ -1,5 +1,5 @@
-radiator_gds_skeleton — radiator_gds_skeleton • radiator radiator_gds_skeleton — radiator_gds_skeleton • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ radiator_gds_skeleton
diff --git a/docs/reference/radiator_packages_dep.html b/docs/reference/radiator_packages_dep.html
index 46f362aa..8204a250 100644
--- a/docs/reference/radiator_packages_dep.html
+++ b/docs/reference/radiator_packages_dep.html
@@ -1,5 +1,5 @@
-radiator_packages_dep — radiator_packages_dep • radiator radiator_packages_dep — radiator_packages_dep • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ radiator_packages_dep
diff --git a/docs/reference/radiator_parameters.html b/docs/reference/radiator_parameters.html
index b06bdaac..c22bcb3b 100644
--- a/docs/reference/radiator_parameters.html
+++ b/docs/reference/radiator_parameters.html
@@ -1,5 +1,5 @@
-radiator_parameters — radiator_parameters • radiator radiator_parameters — radiator_parameters • radiator radiator packages install helper — radiator_pkg_install • radiator radiator packages install helper — radiator_pkg_install • radiator radiator_question — radiator_question • radiator radiator_question — radiator_question • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ radiator_question
diff --git a/docs/reference/radiator_results_message.html b/docs/reference/radiator_results_message.html
index 641a55df..3d806023 100644
--- a/docs/reference/radiator_results_message.html
+++ b/docs/reference/radiator_results_message.html
@@ -1,5 +1,5 @@
-radiator_results_message — radiator_results_message • radiator radiator_results_message — radiator_results_message • radiator
@@ -17,7 +17,7 @@
@@ -93,7 +93,7 @@ radiator_results_message
diff --git a/docs/reference/radiator_snakecase.html b/docs/reference/radiator_snakecase.html
index 4fc158a6..bf64d00a 100644
--- a/docs/reference/radiator_snakecase.html
+++ b/docs/reference/radiator_snakecase.html
@@ -1,5 +1,5 @@
-radiator_snakecase — radiator_snakecase • radiator radiator_snakecase — radiator_snakecase • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ radiator_snakecase
diff --git a/docs/reference/radiator_split_tibble.html b/docs/reference/radiator_split_tibble.html
index 962743d9..3b099191 100644
--- a/docs/reference/radiator_split_tibble.html
+++ b/docs/reference/radiator_split_tibble.html
@@ -1,5 +1,5 @@
-radiator_split_tibble — radiator_split_tibble • radiator radiator_split_tibble — radiator_split_tibble • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ radiator_split_tibble
diff --git a/docs/reference/radiator_tic.html b/docs/reference/radiator_tic.html
index 99347514..c249da60 100644
--- a/docs/reference/radiator_tic.html
+++ b/docs/reference/radiator_tic.html
@@ -1,5 +1,5 @@
-radiator_tic — radiator_tic • radiator radiator_tic — radiator_tic • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ radiator_tic
diff --git a/docs/reference/radiator_toc.html b/docs/reference/radiator_toc.html
index bc6b2b2f..76510cd7 100644
--- a/docs/reference/radiator_toc.html
+++ b/docs/reference/radiator_toc.html
@@ -1,5 +1,5 @@
-radiator_toc — radiator_toc • radiator radiator_toc — radiator_toc • radiator
@@ -17,7 +17,7 @@
@@ -92,7 +92,7 @@ radiator_toc
diff --git a/docs/reference/read_blacklist_genotypes.html b/docs/reference/read_blacklist_genotypes.html
index 4901fe12..cd49840b 100644
--- a/docs/reference/read_blacklist_genotypes.html
+++ b/docs/reference/read_blacklist_genotypes.html
@@ -1,5 +1,5 @@
-read blacklist of genotypes — read_blacklist_genotypes • radiator read blacklist of genotypes — read_blacklist_genotypes • radiator read_blacklist_id — read_blacklist_id • radiator read_blacklist_id — read_blacklist_id • radiator Read and tidy DArT output files. — read_dart • radiator Read and tidy DArT output files. — read_dart • radiator Reads PLINK tped and bed files — read_plink • radiator Reads PLINK tped and bed files — read_plink • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -185,7 +185,7 @@ Examples
diff --git a/docs/reference/read_rad.html b/docs/reference/read_rad.html
index 40dab71c..5f85d666 100644
--- a/docs/reference/read_rad.html
+++ b/docs/reference/read_rad.html
@@ -1,5 +1,5 @@
-Read radiator file ending .gds, .rad, .gds.rad. — read_rad • radiator Read radiator file ending .gds, .rad, .gds.rad. — read_rad • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -198,7 +198,7 @@ Examples
diff --git a/docs/reference/read_strata.html b/docs/reference/read_strata.html
index 147738eb..59858576 100644
--- a/docs/reference/read_strata.html
+++ b/docs/reference/read_strata.html
@@ -1,5 +1,5 @@
-read strata — read_strata • radiator read strata — read_strata • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -269,7 +269,7 @@ Examples
diff --git a/docs/reference/read_vcf.html b/docs/reference/read_vcf.html
index fa3b6d0d..75b355f0 100644
--- a/docs/reference/read_vcf.html
+++ b/docs/reference/read_vcf.html
@@ -1,5 +1,5 @@
-Read VCF files and write a GDS file — read_vcf • radiator Read VCF files and write a GDS file — read_vcf • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -376,7 +376,7 @@ Examples
diff --git a/docs/reference/read_whitelist.html b/docs/reference/read_whitelist.html
index a4d664c2..b9942883 100644
--- a/docs/reference/read_whitelist.html
+++ b/docs/reference/read_whitelist.html
@@ -1,5 +1,5 @@
-read whitelist of markers — read_whitelist • radiator read whitelist of markers — read_whitelist • radiator Read tidy genomic data file ending .rad — remove_duplicates • radiator Read tidy genomic data file ending .rad — remove_duplicates • radiator replace_by_na — replace_by_na • radiator replace_by_na — replace_by_na • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ replace_by_na
diff --git a/docs/reference/reset_filters.html b/docs/reference/reset_filters.html
index dbb492d7..458020b2 100644
--- a/docs/reference/reset_filters.html
+++ b/docs/reference/reset_filters.html
@@ -1,5 +1,5 @@
-Reset filters (individuals and markers) in radiator GDS object. — reset_filters • radiator Reset filters (individuals and markers) in radiator GDS object. — reset_filters • radiator Run BayeScan — run_bayescan • radiator Run BayeScan — run_bayescan • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -326,7 +326,7 @@ Examples
diff --git a/docs/reference/separate_gt.html b/docs/reference/separate_gt.html
index df80123a..9eaebe4f 100644
--- a/docs/reference/separate_gt.html
+++ b/docs/reference/separate_gt.html
@@ -1,5 +1,5 @@
-separate_gt — separate_gt • radiator separate_gt — separate_gt • radiator
@@ -17,7 +17,7 @@
@@ -99,7 +99,7 @@ separate_gt
diff --git a/docs/reference/separate_markers.html b/docs/reference/separate_markers.html
index b209bfd0..cbd8734d 100644
--- a/docs/reference/separate_markers.html
+++ b/docs/reference/separate_markers.html
@@ -1,5 +1,5 @@
-Separate markers column into chrom, locus and pos — separate_markers • radiator Separate markers column into chrom, locus and pos — separate_markers • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -207,7 +207,7 @@ Examples
diff --git a/docs/reference/sex_markers_plot.html b/docs/reference/sex_markers_plot.html
index 4f8e71c0..a50121b0 100644
--- a/docs/reference/sex_markers_plot.html
+++ b/docs/reference/sex_markers_plot.html
@@ -1,5 +1,5 @@
-sex_markers_plot — sex_markers_plot • radiator sex_markers_plot — sex_markers_plot • radiator
@@ -17,7 +17,7 @@
@@ -87,7 +87,8 @@ sex_markers_plot
qreg = FALSE,
hist = FALSE,
RD = FALSE,
- plot.filename = NULL
+ plot.filename = NULL,
+ path = NULL
)
@@ -104,7 +105,7 @@ sex_markers_plot
diff --git a/docs/reference/sexy_markers.html b/docs/reference/sexy_markers.html
index 80804e96..666545ed 100644
--- a/docs/reference/sexy_markers.html
+++ b/docs/reference/sexy_markers.html
@@ -1,5 +1,5 @@
-sexy_markers finds sex-linked markers and re-assigns sex — sexy_markers • radiator sexy_markers finds sex-linked markers and re-assigns sex — sexy_markers • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -85,8 +85,8 @@ sexy_markers finds sex-linked markers and re-assigns sex
sexy_markers(
data,
silicodata = NULL,
- boost.analysis = FALSE,
strata = NULL,
+ boost.analysis = FALSE,
coverage.thresholds = 1,
filters = TRUE,
interactive.filter = TRUE,
@@ -111,13 +111,6 @@ Arguments
Default: silicodata = NULL.
-boost.analysis
-(optional, logical) This method uses machine learning
-approaches to find sex markers and re-assign samples in sex group.
-The approach is currently been tested and will be available for uses soon.
-Default: boost.analysis = FALSE.
strata
(file) A tab delimited file with a minimum of
2 columns (INDIVIDUALS, STRATA) for VCF files and 3 columns for DArT files
@@ -132,6 +125,13 @@
Arguments
functions: extract_dart_target_id and extract_individuals_vcfboost.analysis
+(optional, logical) This method uses machine learning
+approaches to find sex markers and re-assign samples in sex group.
+The approach is currently under construction.
+Default: boost.analysis = FALSE.
coverage.thresholds
(optional, integer) The minimum coverage required
to call a marker absent. For silico genotype data this must be < 1.
@@ -155,7 +155,7 @@
Arguments
folder.name
(optional,character) Name of the folder to store the results.
-Default: folder.name = "sexy_marker_date/time".
folder.name = NULL. The name sexy_markers_datetime will be generated.
parallel.core
@@ -250,7 +250,11 @@ Advance mode
-dots-dots-dots ... allows to pass several arguments for fine-tuning the function:
tau: The quantile used in regression to distinguish homogametic markers
+
dots-dots-dots ... allows to pass several arguments for fine-tuning the function:
species: To give your figures some meanings.
+Default species = NULL.
population: To give your figures some meanings.
+Default species = NULL.
tau: The quantile used in regression to distinguish homogametic markers
with the heterozygosity method. See rq.
Default tau = 0.03.
mis.threshold.data: Threshold to filter the SNP data on missingness.
@@ -325,7 +329,7 @@
Examples
diff --git a/docs/reference/simulate_genos_from_posterior.html b/docs/reference/simulate_genos_from_posterior.html
index 499054d1..8b9ec6f9 100644
--- a/docs/reference/simulate_genos_from_posterior.html
+++ b/docs/reference/simulate_genos_from_posterior.html
@@ -1,5 +1,5 @@
-simulate_genos_from_posterior — simulate_genos_from_posterior • radiator simulate_genos_from_posterior — simulate_genos_from_posterior • radiator split_tibble_rows — split_tibble_rows • radiator split_tibble_rows — split_tibble_rows • radiator
@@ -17,7 +17,7 @@
@@ -93,7 +93,7 @@ split_tibble_rows
diff --git a/docs/reference/split_vcf.html b/docs/reference/split_vcf.html
index a43e07de..66b27d42 100644
--- a/docs/reference/split_vcf.html
+++ b/docs/reference/split_vcf.html
@@ -1,5 +1,5 @@
-Split a VCF file — split_vcf • radiator Split a VCF file — split_vcf • radiator strata_haplo — strata_haplo • radiator strata_haplo — strata_haplo • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ strata_haplo
diff --git a/docs/reference/subsampling_data.html b/docs/reference/subsampling_data.html
index 60a1a87c..ae009819 100644
--- a/docs/reference/subsampling_data.html
+++ b/docs/reference/subsampling_data.html
@@ -1,5 +1,5 @@
-subsampling data — subsampling_data • radiator subsampling data — subsampling_data • radiator
@@ -17,7 +17,7 @@
@@ -93,7 +93,7 @@ subsampling data
diff --git a/docs/reference/summarise_genotypes.html b/docs/reference/summarise_genotypes.html
index b9959c59..109c2e28 100644
--- a/docs/reference/summarise_genotypes.html
+++ b/docs/reference/summarise_genotypes.html
@@ -1,5 +1,5 @@
-summarise genotypes — summarise_genotypes • radiator summarise genotypes — summarise_genotypes • radiator
@@ -17,7 +17,7 @@
@@ -92,7 +92,7 @@ Author
diff --git a/docs/reference/summarize_sex.html b/docs/reference/summarize_sex.html
index 14b66900..ff53f89d 100644
--- a/docs/reference/summarize_sex.html
+++ b/docs/reference/summarize_sex.html
@@ -1,5 +1,5 @@
-summarize_sex — summarize_sex • radiator summarize_sex — summarize_sex • radiator
@@ -17,7 +17,7 @@
@@ -94,7 +94,7 @@ summarize_sex
diff --git a/docs/reference/summary_gds.html b/docs/reference/summary_gds.html
index 3abfb279..13a224e6 100644
--- a/docs/reference/summary_gds.html
+++ b/docs/reference/summary_gds.html
@@ -1,5 +1,5 @@
-summary_gds — summary_gds • radiator summary_gds — summary_gds • radiator
@@ -17,7 +17,7 @@
@@ -109,7 +109,7 @@ Arguments
diff --git a/docs/reference/summary_rad.html b/docs/reference/summary_rad.html
index 5cc5e1b1..7972e1e3 100644
--- a/docs/reference/summary_rad.html
+++ b/docs/reference/summary_rad.html
@@ -1,5 +1,5 @@
-Summary statistics for RADseq data — summary_rad • radiator Summary statistics for RADseq data — summary_rad • radiator Summary of strata — summary_strata • radiator Summary of strata — summary_strata • radiator switch_allele_count — switch_allele_count • radiator switch_allele_count — switch_allele_count • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ switch_allele_count
diff --git a/docs/reference/switch_genotypes.html b/docs/reference/switch_genotypes.html
index c13b7296..8d2d3cc4 100644
--- a/docs/reference/switch_genotypes.html
+++ b/docs/reference/switch_genotypes.html
@@ -1,5 +1,5 @@
-switch_genotypes — switch_genotypes • radiator switch_genotypes — switch_genotypes • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ switch_genotypes
diff --git a/docs/reference/sync_gds.html b/docs/reference/sync_gds.html
index c604aa3f..7e349b48 100644
--- a/docs/reference/sync_gds.html
+++ b/docs/reference/sync_gds.html
@@ -1,5 +1,5 @@
-sync_gds — sync_gds • radiator sync_gds — sync_gds • radiator tibble_stats — tibble_stats • radiator tibble_stats — tibble_stats • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ tibble_stats
diff --git a/docs/reference/tidy2gds.html b/docs/reference/tidy2gds.html
index 4cac68bc..a9d5a8e3 100644
--- a/docs/reference/tidy2gds.html
+++ b/docs/reference/tidy2gds.html
@@ -1,5 +1,5 @@
-tidy2gds — tidy2gds • radiator tidy2gds — tidy2gds • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ tidy2gds
diff --git a/docs/reference/tidy2wide.html b/docs/reference/tidy2wide.html
index 57a23746..3a97c801 100644
--- a/docs/reference/tidy2wide.html
+++ b/docs/reference/tidy2wide.html
@@ -1,5 +1,5 @@
-tidy2wide — tidy2wide • radiator tidy2wide — tidy2wide • radiator
@@ -17,7 +17,7 @@
@@ -96,7 +96,7 @@ tidy2wide
diff --git a/docs/reference/tidy_dart_metadata.html b/docs/reference/tidy_dart_metadata.html
index aa4a9d7d..1d0dbbc1 100644
--- a/docs/reference/tidy_dart_metadata.html
+++ b/docs/reference/tidy_dart_metadata.html
@@ -1,5 +1,5 @@
-Import and tidy DArT metadata. — tidy_dart_metadata • radiator Import and tidy DArT metadata. — tidy_dart_metadata • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -160,7 +160,7 @@ Examples
diff --git a/docs/reference/tidy_fstat.html b/docs/reference/tidy_fstat.html
index 108e395e..7ed7c4b4 100644
--- a/docs/reference/tidy_fstat.html
+++ b/docs/reference/tidy_fstat.html
@@ -1,5 +1,5 @@
-fstat file to tidy dataframe — tidy_fstat • radiator fstat file to tidy dataframe — tidy_fstat • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -180,7 +180,7 @@ Examples
diff --git a/docs/reference/tidy_genepop.html b/docs/reference/tidy_genepop.html
index 93bf51fd..03b6fcb7 100644
--- a/docs/reference/tidy_genepop.html
+++ b/docs/reference/tidy_genepop.html
@@ -1,5 +1,5 @@
-Import genepop file and convert to a tidy dataframe — tidy_genepop • radiator Import genepop file and convert to a tidy dataframe — tidy_genepop • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -253,7 +253,7 @@ Examples
diff --git a/docs/reference/tidy_genind.html b/docs/reference/tidy_genind.html
index 1acf7666..82e77677 100644
--- a/docs/reference/tidy_genind.html
+++ b/docs/reference/tidy_genind.html
@@ -1,5 +1,5 @@
-Tidy a genind object to a tidy dataframe — tidy_genind • radiator Tidy a genind object to a tidy dataframe — tidy_genind • radiator Tidy a genlight object to a tidy dataframe and/or GDS object/file — tidy_genlight • radiator Tidy a genlight object to a tidy dataframe and/or GDS object/file — tidy_genlight • radiator Transform common genomic dataset format in a tidy data frame — tidy_genomic_data • radiator Transform common genomic dataset format in a tidy data frame — tidy_genomic_data • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -247,7 +247,7 @@ Examples
diff --git a/docs/reference/tidy_gtypes.html b/docs/reference/tidy_gtypes.html
index cf8901d8..80a269d0 100644
--- a/docs/reference/tidy_gtypes.html
+++ b/docs/reference/tidy_gtypes.html
@@ -1,5 +1,5 @@
-Tidy a gtypes object to a tidy dataframe — tidy_gtypes • radiator Tidy a gtypes object to a tidy dataframe — tidy_gtypes • radiator Tidy PLINK tped and bed files — tidy_plink • radiator Tidy PLINK tped and bed files — tidy_plink • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -176,7 +176,7 @@ Examples
diff --git a/docs/reference/tidy_vcf.html b/docs/reference/tidy_vcf.html
index 2a5543b1..c62f87b1 100644
--- a/docs/reference/tidy_vcf.html
+++ b/docs/reference/tidy_vcf.html
@@ -1,5 +1,5 @@
-Tidy vcf file — tidy_vcf • radiator Tidy vcf file — tidy_vcf • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -326,7 +326,7 @@ Examples
diff --git a/docs/reference/tidy_wide.html b/docs/reference/tidy_wide.html
index 66a44b5b..b06ad6c8 100644
--- a/docs/reference/tidy_wide.html
+++ b/docs/reference/tidy_wide.html
@@ -1,5 +1,5 @@
-Read/Import a tidy genomic data frames. — tidy_wide • radiator Read/Import a tidy genomic data frames. — tidy_wide • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -160,7 +160,7 @@ Author
diff --git a/docs/reference/update_bl_individuals.html b/docs/reference/update_bl_individuals.html
index a1d79150..25b42f8f 100644
--- a/docs/reference/update_bl_individuals.html
+++ b/docs/reference/update_bl_individuals.html
@@ -1,5 +1,5 @@
-update_bl_individuals — update_bl_individuals • radiator update_bl_individuals — update_bl_individuals • radiator
@@ -17,7 +17,7 @@
@@ -94,7 +94,7 @@ update_bl_individuals
diff --git a/docs/reference/update_bl_markers.html b/docs/reference/update_bl_markers.html
index cf55b6ba..73bf184c 100644
--- a/docs/reference/update_bl_markers.html
+++ b/docs/reference/update_bl_markers.html
@@ -1,5 +1,5 @@
-update_bl_markers — update_bl_markers • radiator update_bl_markers — update_bl_markers • radiator
@@ -17,7 +17,7 @@
@@ -94,7 +94,7 @@ update_bl_markers
diff --git a/docs/reference/update_filter_parameter.html b/docs/reference/update_filter_parameter.html
index 5f2e7de4..46256cac 100644
--- a/docs/reference/update_filter_parameter.html
+++ b/docs/reference/update_filter_parameter.html
@@ -1,5 +1,5 @@
-update filter parameter file — update_filter_parameter • radiator update filter parameter file — update_filter_parameter • radiator
@@ -17,7 +17,7 @@
@@ -99,7 +99,7 @@ Author
diff --git a/docs/reference/update_radiator_gds.html b/docs/reference/update_radiator_gds.html
index a372c4dd..e8afd052 100644
--- a/docs/reference/update_radiator_gds.html
+++ b/docs/reference/update_radiator_gds.html
@@ -1,5 +1,5 @@
-update_radiator_gds — update_radiator_gds • radiator update_radiator_gds — update_radiator_gds • radiator
@@ -17,7 +17,7 @@
@@ -97,7 +97,7 @@ update_radiator_gds
diff --git a/docs/reference/vcf_strata.html b/docs/reference/vcf_strata.html
index a9630309..94c0861f 100644
--- a/docs/reference/vcf_strata.html
+++ b/docs/reference/vcf_strata.html
@@ -1,5 +1,5 @@
-Join stratification metadata to a VCF (population-aware VCF) — vcf_strata • radiator Join stratification metadata to a VCF (population-aware VCF) — vcf_strata • radiator Write an arlequin file from a tidy data frame — write_arlequin • radiator Write an arlequin file from a tidy data frame — write_arlequin • radiator Write a BayeScan
-file from a tidy data frame — write_bayescan • radiator Write a BayeScan file from a tidy data frame — write_bayescan • radiator Write a betadiv file from a tidy data frame — write_betadiv • radiator Write a betadiv file from a tidy data frame — write_betadiv • radiator Write a COLONY input file — write_colony • radiator Write a COLONY input file — write_colony • radiator
@@ -17,7 +17,7 @@
@@ -272,7 +272,7 @@ Examples
diff --git a/docs/reference/write_dadi.html b/docs/reference/write_dadi.html
index 0436c0be..373976e1 100644
--- a/docs/reference/write_dadi.html
+++ b/docs/reference/write_dadi.html
@@ -1,5 +1,5 @@
-Write a dadi SNP input file from a tidy data frame. — write_dadi • radiator Write a dadi SNP input file from a tidy data frame. — write_dadi • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -192,7 +192,7 @@ Examples
diff --git a/docs/reference/write_fasta.html b/docs/reference/write_fasta.html
index 9f17ee5f..eb180aff 100644
--- a/docs/reference/write_fasta.html
+++ b/docs/reference/write_fasta.html
@@ -1,5 +1,5 @@
-Export FASTA — write_fasta • radiator Export FASTA — write_fasta • radiator
@@ -17,7 +17,7 @@
@@ -88,7 +88,7 @@ Export FASTA
diff --git a/docs/reference/write_faststructure.html b/docs/reference/write_faststructure.html
index 02db9643..9bce50dc 100644
--- a/docs/reference/write_faststructure.html
+++ b/docs/reference/write_faststructure.html
@@ -1,5 +1,5 @@
-Write a faststructure file from a tidy data frame — write_faststructure • radiator Write a faststructure file from a tidy data frame — write_faststructure • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -156,7 +156,7 @@ Author
diff --git a/docs/reference/write_fineradstructure.html b/docs/reference/write_fineradstructure.html
index c7e40ff5..a5103558 100644
--- a/docs/reference/write_fineradstructure.html
+++ b/docs/reference/write_fineradstructure.html
@@ -1,5 +1,5 @@
-Write a fineRADstructure file from a tidy data frame — write_fineradstructure • radiator Write a fineRADstructure file from a tidy data frame — write_fineradstructure • radiator Write a GDS object from a tidy data frame — write_gds • radiator Write a GDS object from a tidy data frame — write_gds • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -165,7 +165,7 @@ Examples
diff --git a/docs/reference/write_genepop.html b/docs/reference/write_genepop.html
index 78f37767..0395c0bf 100644
--- a/docs/reference/write_genepop.html
+++ b/docs/reference/write_genepop.html
@@ -1,5 +1,5 @@
-Write a genepop file — write_genepop • radiator Write a genepop file — write_genepop • radiator Write a genepopedit flatten object — write_genepopedit • radiator Write a genepopedit flatten object — write_genepopedit • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -145,7 +145,7 @@ Author
diff --git a/docs/reference/write_genind.html b/docs/reference/write_genind.html
index a064abd3..6810055d 100644
--- a/docs/reference/write_genind.html
+++ b/docs/reference/write_genind.html
@@ -1,5 +1,5 @@
-Write a genind object from a tidy data frame or GDS file or object. — write_genind • radiator Write a genind object from a tidy data frame or GDS file or object. — write_genind • radiator Write a genlight object from a tidy data frame or GDS file or object. — write_genlight • radiator Write a genlight object from a tidy data frame or GDS file or object. — write_genlight • radiator Write a gsi_sim file from a data frame (wide or long/tidy). — write_gsi_sim • radiator Write a gsi_sim file from a data frame (wide or long/tidy). — write_gsi_sim • radiator Write a strataG object from
-radiator GDS and tidy data file or object. — write_gtypes • radiator Write a strataG object from radiator GDS and tidy data file or object. — write_gtypes • radiator Write a HapMap file from a tidy data frame — write_hapmap • radiator Write a HapMap file from a tidy data frame — write_hapmap • radiator Write a hierfstat file from a tidy data frame — write_hierfstat • radiator Write a hierfstat file from a tidy data frame — write_hierfstat • radiator Write a HZAR file from a tidy data frame. — write_hzar • radiator Write a HZAR file from a tidy data frame. — write_hzar • radiator Write a LDna object from a tidy data frame — write_ldna • radiator Write a LDna object from a tidy data frame — write_ldna • radiator Write a maverick file from a tidy data frame — write_maverick • radiator Write a maverick file from a tidy data frame — write_maverick • radiator Write a pcadapt
-file from a tidy data frame — write_pcadapt • radiator Write a pcadapt file from a tidy data frame — write_pcadapt • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -69,8 +67,7 @@
- Write a pcadapt
-file from a tidy data frame
+ Write a pcadapt file from a tidy data frame
Source: R/write_pcadapt.R
write_pcadapt.Rd
@@ -187,7 +184,7 @@ Author
diff --git a/docs/reference/write_plink.html b/docs/reference/write_plink.html
index 38314609..d5c324f3 100644
--- a/docs/reference/write_plink.html
+++ b/docs/reference/write_plink.html
@@ -1,5 +1,5 @@
-Write a plink tped/tfam file from a tidy data frame — write_plink • radiator Write a plink tped/tfam file from a tidy data frame — write_plink • radiator Write tidy genomic data file or close GDS file — write_rad • radiator Write tidy genomic data file or close GDS file — write_rad • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -199,7 +199,7 @@ Examples
diff --git a/docs/reference/write_related.html b/docs/reference/write_related.html
index f8b61592..2a39deb6 100644
--- a/docs/reference/write_related.html
+++ b/docs/reference/write_related.html
@@ -1,5 +1,5 @@
-Write a related file from a tidy data frame — write_related • radiator Write a related file from a tidy data frame — write_related • radiator
radiator
- 1.3.1
+ 1.3.3
@@ -153,7 +153,7 @@ Author
diff --git a/docs/reference/write_rubias.html b/docs/reference/write_rubias.html
index 388f7faa..7865aeb9 100644
--- a/docs/reference/write_rubias.html
+++ b/docs/reference/write_rubias.html
@@ -1,5 +1,5 @@
-Write a rubias object — write_rubias • radiator Write a rubias object — write_rubias • radiator
@@ -17,7 +17,7 @@
@@ -155,7 +155,7 @@ Author
diff --git a/docs/reference/write_snprelate.html b/docs/reference/write_snprelate.html
index 7a243f3e..3e474925 100644
--- a/docs/reference/write_snprelate.html
+++ b/docs/reference/write_snprelate.html
@@ -1,5 +1,5 @@
-Write a SNPRelate object from a tidy data frame — write_snprelate • radiator Write a SNPRelate object from a tidy data frame — write_snprelate • radiator Write a stockR dataset from a tidy data frame or GDS file or object. — write_stockr • radiator Write a stockR dataset from a tidy data frame or GDS file or object. — write_stockr • radiator Write a structure file from a tidy data frame — write_structure • radiator Write a structure file from a tidy data frame — write_structure • radiator Write a vcf file from a tidy data frame — write_vcf • radiator Write a vcf file from a tidy data frame — write_vcf • radiator
-
@@ -134,7 +131,7 @@ Figure density distribution of minor allele frequency (MAF) -summary statistics.
+Figure density distribution of minor allele frequency (MAF) summary statistics.
Source:R/visualization.R
plot_density_distribution_maf.RdAuthor
radiator_common_arguments(
+ interactive.filter = TRUE,
gds,
data,
parallel.core = parallel::detectCores() - 1,
@@ -84,7 +85,14 @@ radiator common arguments
Arguments
- - gds
+ - interactive.filter
+(optional, logical) Do you want the filtering session to
+be interactive. Figures of distribution are shown before asking for filtering
+thresholds.
+Default: interactive.filter = TRUE.
- gds
(2 options) A Genomic Data Structure (GDS) file or object
How to get GDS ?
Look into tidy_genomic_data,
@@ -125,13 +133,6 @@
Arguments
for fine-tuning the function. Also used for legacy arguments (see details or
special section)- interactive.filter
-(optional, logical) Do you want the filtering session to
-be interactive. Figures of distribution are shown before asking for filtering
-thresholds.
-Default: interactive.filter = TRUE.
Arguments
sexy_markers(
data,
silicodata = NULL,
- boost.analysis = FALSE,
strata = NULL,
+ boost.analysis = FALSE,
coverage.thresholds = 1,
filters = TRUE,
interactive.filter = TRUE,
@@ -111,13 +111,6 @@ Arguments
Default: silicodata = NULL.
-boost.analysis
-(optional, logical) This method uses machine learning
-approaches to find sex markers and re-assign samples in sex group.
-The approach is currently been tested and will be available for uses soon.
-Default: boost.analysis = FALSE.
strata
(file) A tab delimited file with a minimum of
2 columns (INDIVIDUALS, STRATA) for VCF files and 3 columns for DArT files
@@ -132,6 +125,13 @@
Arguments
functions: extract_dart_target_id and extract_individuals_vcfboost.analysis
+(optional, logical) This method uses machine learning
+approaches to find sex markers and re-assign samples in sex group.
+The approach is currently under construction.
+Default: boost.analysis = FALSE.
coverage.thresholds
(optional, integer) The minimum coverage required
to call a marker absent. For silico genotype data this must be < 1.
@@ -155,7 +155,7 @@
Arguments
folder.name
(optional,character) Name of the folder to store the results.
-Default: folder.name = "sexy_marker_date/time".
folder.name = NULL. The name sexy_markers_datetime will be generated.
parallel.core
@@ -250,7 +250,11 @@ Advance mode
-dots-dots-dots ... allows to pass several arguments for fine-tuning the function:
tau: The quantile used in regression to distinguish homogametic markers
+
dots-dots-dots ... allows to pass several arguments for fine-tuning the function:
species: To give your figures some meanings.
+Default species = NULL.
population: To give your figures some meanings.
+Default species = NULL.
tau: The quantile used in regression to distinguish homogametic markers
with the heterozygosity method. See rq.
Default tau = 0.03.
mis.threshold.data: Threshold to filter the SNP data on missingness.
@@ -325,7 +329,7 @@
Examples
-
@@ -187,7 +184,7 @@ Write a pcadapt -file from a tidy data frame
+Write a pcadapt file from a tidy data frame
Source:R/write_pcadapt.R
write_pcadapt.Rd