Add value tags and update website

DESCRIPTION

@@ -25,7 +25,7 @@ LazyData: true
 biocViews:
 Depends: R (>= 3.5)
 VignetteBuilder: knitr
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 Roxygen: list(markdown = TRUE)
 NeedsCompilation: no
 Packaged: 2020-02-16 18:03:28 UTC; kgoldmann

R/polar_coords.R

@@ -173,6 +173,11 @@ polar_xy <- function(df, angle_offset = 0) {
 #'   statistical test.
 #' @importFrom Rfast ftests ttests kruskaltests
 #' @importFrom matrixTests row_wilcoxon_twosample
+#' @return Returns a list with first element representing a data frame of 
+#' unadjusted p-values and the second element adjusted p-values. Each dataframe 
+#' contains 4 columns: the first column is the 3-way comparison (LRT or ANOVA). 
+#' Columns 2-4 are pairwise comparisons between groups A vs B, A vs C and 
+#' B vs C, where A, B, C are the 3 levels in the outcome factor.
 #' @export
 #'
 calc_pvals <- function(outcome, 

R/polar_coords_2x3.R

@@ -183,6 +183,8 @@ polar_coords_2x3 <- function(data,
 #'   level response outcome. Current options are "t.test" or "wilcoxon".
 #' @param exact Logical for whether to use an exact test (Wilcoxon test only)
 #' @importFrom matrixTests col_t_welch col_wilcoxon_twosample
+#' @return A list containing a data frame with summary statistics for the 
+#' comparisons between the outcome, for each group level. 
 #' @export
 #' 
 calc_stats_2x3 <- function(data, outcome, group, padj.method,

R/significance_subset.R

@@ -15,6 +15,8 @@
 #' treatment response phenotypes.}
 #' \emph{Cell reports}, \strong{28}:9
 #' @importFrom methods slot
+#' @return Returns an object (type defined by `output`) with rows susbet to 
+#' those which satisfy the significance condition.  
 #' @export
 #' @examples
 #' data(example_data)

cran-comments.md

@@ -13,4 +13,7 @@ Package was archived on CRAN
 
 
 * This is a resubmission following package being archived.
-* author and maintainer's email has also been updated. 
+* Author and maintainer's email has also been updated. 
+* Since previous submission \value RD-tags have been added for: calc_pvals.Rd, calc_stats_2x3.Rd, and significance_subset.Rd
+* There is no reference describing the methods in the package
+* All instances of `install.packages()` in README and vignettes wrapped in eval=FALSE chunks