initialize repo

closes #1

.Rbuildignore

@@ -0,0 +1,53 @@
+# List files that should be included in the repo,
+#   but ignored by R when building the packages.
+#   Specify with a PCRE regular expression.
+#   See http://r-pkgs.had.co.nz/package.html#package
+
+# Directories used in many R-centric repos.
+^\.github$
+^docs$
+^revdep$
+^.*\.Rproj$
+^\.Rproj\.user$
+
+
+# Files used in many R-centric repos.
+^_pkgdown\.yml$
+^\.gitignore$
+^\.travis\.yml$
+^appveyor\.yml$
+^CONDUCT.md$
+^CODE_OF_CONDUCT.md$
+^CODE-OF-CONDUCT.md$
+^code-of-conduct.md$
+^config.yml$
+^cran-comments\.md$
+^flow.R$
+^README.html$
+^license\.md$
+^LICENSE\.md$
+^README.html$
+^shim_package\.sh$
+^wercker\.yml$
+
+
+# Directories occasionally used in R-centric repos written by the BBMC.
+^analysis$
+^data-private$
+^data-public$
+^data-unshared$
+^demonstration$
+^documentation$
+^documentation-for-developers$
+^figure$
+^libs$
+^manipulation$
+^sandbox$
+^scripts$
+^stitched-output$
+^playgrounds$
+^utility$
+
+
+# Files occasionally used in R-centric repos written by the BBMC.
+^documentation-peek.pdf$

.gitattributes

@@ -0,0 +1,11 @@
+#So HTML, MD, & CSS files aren't considered as code when determining language of repo.
+# https://github.com/github/linguist#using-gitattributes
+*.html linguist-documentation
+*.md linguist-documentation
+*.css linguist-documentation
+
+#For AppVeyor
+* text=auto
+data/* binary
+src/* text=lf
+R/* text=lf

.gitignore

@@ -1,39 +1,109 @@
-# History files
+# ---- R and RStudio files -----------------------------------------------
+.Rproj.user/
 .Rhistory
-.Rapp.history
-
-# Session Data files
 .RData
-
-# User-specific files
+.Rdata
 .Ruserdata
-
-# Example code in package build process
-*-Ex.R
+.Rapp.history
 
 # Output files from R CMD build
 /*.tar.gz
 
 # Output files from R CMD check
 /*.Rcheck/
 
-# RStudio files
-.Rproj.user/
-
-# produced vignettes
+# R package temporary files
+inst/doc
 vignettes/*.html
 vignettes/*.pdf
+vignettes/*.R
+
+# The devtools zip is downloaded when the package is updating itself.  If it's not deleted, there's no reason to commit it to the repository.
+devtools.zip
 
 # OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
 .httr-oauth
 
-# knitr and R markdown default cache directories
-*_cache/
-/cache/
-
 # Temporary files created by R markdown
 *.utf8.md
 *.knit.md
 
-# R Environment Variables
-.Renviron
+# Example code in package build process
+*-Ex.R
+
+# Shiny token, see https://shiny.rstudio.com/articles/shinyapps.html
+rsconnect/
+
+# ---- Protected Information -----------------------------------------------
+# see cubuspl42's answer in http://stackoverflow.com/questions/2415873/exceptions-in-gitignore
+/unshared-material/*
+/data-unshared/*
+/data/unshared/*
+
+# Dataset Exceptions
+!utility/package-dependency-list.csv
+
+# Keep the README files in the unshared directories.
+#   They provide documentation, and also force the directories to be created on other machines.
+#   Depending on how you do it, you might need to add w/ the command line
+#   eg, `git add -f ./data-unshared/raw/README.md`
+!README.md
+!data-unshared/contents.md
+!data-unshared/raw/README.md
+!data-unshared/derived/README.md
+!data/unshared/contents.md
+!data/unshared/raw/README.md
+!data/unshared/derived/README.md
+
+# ---- Caches -----------------------------------------------
+# Exclude caches in case they contain PHI
+cache/
+
+# knitr and RMarkdown default cache directories
+*_cache/
+
+# ---- Windows OS --------------------------------------------
+# Cached small image files
+Thumbs.db
+
+# Folder config file
+Desktop.ini
+
+# ---- OS X --------------------------------------------------
+.DS_Store
+
+# ---- Visual Studio Code (text editor) ----------------------
+.vscode/
+
+# ---- Locks ----------------------
+# Do not commit lock files.
+#   Programs like Microsoft Word create temporary files that don't contain info useful to the repo.
+
+~*.tmp
+~*.temp
+
+# Temporary files of Microsoft Office.
+~*.doc
+~*.docx
+~*.xlsx
+~*.pptx
+*.ldb
+*.laccdb
+
+# Temporary locks used by LibreOffice.
+*.odb.lck
+.~*.csv#
+.~*.odf#
+.~*.odp#
+.~*.ods#
+.~*.odt#
+.~*.docx#
+.~*.pptx#
+.~*.xlsx#
+
+# ---- Accidentally Added Code -------------------------------
+# The GitHub desktop client makes it easy to right-click a file and select 'ignore'.
+#   This will append the file name to the bottom of `.gitignore`.
+#   So the lines below should either be
+#     1. removed (because they were added unintentionally), or
+#     2. reorganized and moved above this chunk (so it won't be confused with files added unintentionally).

DESCRIPTION

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+Package: RAnalysisSkeleton
+Title: Displaying Health Data
+Description: Files and settings commonly used in analysis projects with R.
+Version: 0.0.1.9001
+Date: 2019-02-04
+Authors@R: c(person("Will", "Beasley", role = c("aut", "cre"), email =
+    "[email protected]", comment = c(ORCID = "0000-0002-5613-5006")),
+    person("Andrey", "Koval", role = "aut"))
+URL: https://github.com/wibeasley/RAnalysisSkeleton
+BugReports: https://github.com/wibeasley/RAnalysisSkeleton/issues
+Depends:
+    R(>= 3.0.0)
+Imports:
+    broom,
+    checkmate  (>= 1.8.4),
+    codified (>= 0.2.0),
+    config,
+    DBI (>= 0.7.0),
+    dplyr (>= 0.5.0),
+    DT,
+    flexdashboard,
+    ggplot2,
+    httr (>= 1.3.0),
+    kableExtra,
+    knitr (>= 1.18.0),
+    lme4,
+    magrittr,
+    mgcv,
+    methods,
+    odbc (>= 1.1.1),
+    OuhscMunge (>= 0.1.9.9009),
+    RColorBrewer,
+    readr (>= 1.2.1),
+    rmarkdown,
+    sessioninfo,
+    TabularManifest,
+    tibble (>= 1.4.0),
+    yaml
+Suggests:
+    devtools (>= 1.13.0),
+    ggalluvial,
+    ggrepel,
+    plotly,
+    purrr,
+    RcppRoll,
+    remotes,
+    rlang,
+    RSQLite,
+    scales,
+    testit,
+    testthat (>= 0.9),
+    tidyr (>= 0.7.0),
+    zoo
+Remotes:
+  github::OuhscBbmc/OuhscMunge,
+  github::Melinae/TabularManifest
+License: GPL-3 + file LICENSE
+LazyData: TRUE
+VignetteBuilder: knitr
+Encoding: UTF-8
+RoxygenNote: 6.1.0
+Roxygen: list(markdown = TRUE)

analysis/README.md

@@ -0,0 +1,4 @@
+`analysis/` Directory
+=========
+
+Files in this directory statistically analyze the data.  If multiple lines of analysis are needed, they should be contained in separate subfolders.