diff --git a/R/cluster.R b/R/cluster.R index 00ad1b8..ad7d54a 100644 --- a/R/cluster.R +++ b/R/cluster.R @@ -1,7 +1,7 @@ #' Read distance matrices #' #' Read in distances from a file that is formatted with three columns for the -#' row, column, and distance of a sparse, square matrix or in a Phylip-formatted +#' row, column, and distance of a sparse, square matrix or in a phylip-formatted #' distance matrix. #' #' @export @@ -54,7 +54,7 @@ read_dist <- function(distance_file, count_table, } -#' Cluster entitites together +#' Cluster entities together #' #' Clusters entities represented in a distance matrix and count table using #' one of several algorithms and outputs information about the composition and @@ -201,7 +201,7 @@ read_count <- function(count_table_path) { #' Create Sparse Matrix #' -#' Given a list of i indexs, j indexes, and distances values, +#' Given a list of i indexes, j indexes, and distances values, #' we can create a sparse distance matrix for you. Each vector #' must have the same size. #' @param i_index A list of i indexes, must be numeric diff --git a/R/cluster_object-getters.R b/R/cluster_object-getters.R index f01d285..fb91b0b 100644 --- a/R/cluster_object-getters.R +++ b/R/cluster_object-getters.R @@ -54,7 +54,7 @@ get_bins <- function(cluster_data) { #' #' @export #' @description -#' GetShared retuns the generated abundance `data.frame` +#' GetShared returns the generated abundance `data.frame` #' from the `cluster()` function #' @param cluster_data The output from the `cluster()` function. #' @examples diff --git a/README.Rmd b/README.Rmd index 3b6292f..8a4cd52 100644 --- a/README.Rmd +++ b/README.Rmd @@ -61,6 +61,6 @@ To get started, look at the ["Getting started"](https://www.schlosslab.org/clust ## Contributions -For feature request please visit the issue page in github and use the feature +For feature request please visit the issue page in GitHub and use the feature tag. If you would like to contribute pull request are welcomed! diff --git a/README.md b/README.md index 7a77d92..9577de8 100644 --- a/README.md +++ b/README.md @@ -48,5 +48,5 @@ started”](https://www.schlosslab.org/clustur/) page. ## Contributions -For feature request please visit the issue page in github and use the +For feature request please visit the issue page in GitHub and use the feature tag. If you would like to contribute pull request are welcomed! diff --git a/cran-comments.md b/cran-comments.md index 858617d..b28a985 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -3,3 +3,5 @@ 0 errors | 0 warnings | 1 note * This is a new release. +* All of our projects use C++ 11 so we can continue to support older architectures. +* Build checks for macos-latest (devel), ubuntu-lastest (devel), windows-latest (devel), windows latest (4.1), ubuntu-latest (release), ubuntu-latest (oldrel-1), ubuntu-latest (oldrel-2), and ubuntu-latest (oldrel-3) are currently passing via GitHub Actions. diff --git a/man/cluster.Rd b/man/cluster.Rd index 01297c3..9a0f0a0 100644 --- a/man/cluster.Rd +++ b/man/cluster.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/cluster.R \name{cluster} \alias{cluster} -\title{Cluster entitites together} +\title{Cluster entities together} \usage{ cluster( distance_object, diff --git a/man/clustur-package.Rd b/man/clustur-package.Rd index a3074d1..d4c0e10 100644 --- a/man/clustur-package.Rd +++ b/man/clustur-package.Rd @@ -23,6 +23,7 @@ Useful links: Authors: \itemize{ \item Gregory Johnson \email{grejoh@umich.edu} (\href{https://orcid.org/0009-0008-3890-0297}{ORCID}) + \item Sarah Westcott \email{swestcot@umich.edu} } } diff --git a/man/create_sparse_matrix.Rd b/man/create_sparse_matrix.Rd index abe7b4a..950cf77 100644 --- a/man/create_sparse_matrix.Rd +++ b/man/create_sparse_matrix.Rd @@ -17,7 +17,7 @@ create_sparse_matrix(i_index, j_index, distances) a `dgTMatrix` from the `Matrix` library. } \description{ -Given a list of i indexs, j indexes, and distances values, +Given a list of i indexes, j indexes, and distances values, we can create a sparse distance matrix for you. Each vector must have the same size. } diff --git a/man/get_abundance.Rd b/man/get_abundance.Rd index 0c45649..6be7f65 100644 --- a/man/get_abundance.Rd +++ b/man/get_abundance.Rd @@ -13,7 +13,7 @@ get_abundance(cluster_data) a shared data.frame } \description{ -GetShared retuns the generated abundance `data.frame` +GetShared returns the generated abundance `data.frame` from the `cluster()` function } \examples{ diff --git a/man/read_dist.Rd b/man/read_dist.Rd index 5de48ce..5701f95 100644 --- a/man/read_dist.Rd +++ b/man/read_dist.Rd @@ -25,7 +25,7 @@ distance information. Can be accessed using `get_distance_df()` } \description{ Read in distances from a file that is formatted with three columns for the -row, column, and distance of a sparse, square matrix or in a Phylip-formatted +row, column, and distance of a sparse, square matrix or in a phylip-formatted distance matrix. } \examples{ diff --git a/vignettes/clustur.Rmd b/vignettes/clustur.Rmd index e2818d8..7ebd647 100644 --- a/vignettes/clustur.Rmd +++ b/vignettes/clustur.Rmd @@ -18,7 +18,7 @@ knitr::opts_chunk$set( ## Background clustur was developed to be similar to [mothur's cluster function](https://mothur.org/wiki/cluster/) that was written in C++. In order to -cluster your data, users need to provide their own sparse or Phylip-formatted +cluster your data, users need to provide their own sparse or phylip-formatted distance matrix. They also need to provide a count table that either comes from mothur or that they create in R. Once these objects are built users can call the `cluster()` function. We currently support 5 methods: opticlust (default) and