add value to all .rd

apparently non-exported functions needed it too?

Author: gknowlt

CRAN-RELEASE

@@ -1,2 +1,2 @@
-This package was submitted to CRAN on 2021-01-19.
-Once it is accepted, delete this file and tag the release (commit 69a85e5).
+This package was submitted to CRAN on 2021-03-14.
+Once it is accepted, delete this file and tag the release (commit 6979905).

R/add_common_aes.R

@@ -20,6 +20,7 @@
 #' for how to modify this.
 #' @param ... further arguments to plot.
 #' This is not used by \code{dampack} but required for generic consistency.
+#' @return a \code{ggplot2} plot updated with a common aesthetic
 #'
 #' @import ggplot2
 #' @keywords internal
@@ -104,6 +105,7 @@ add_common_aes <- function(gplot, txtsize, scale_name = waiver(),
 #' used to automatically label continuous scales
 #' @keywords internal
 #' @param x axis breaks
+#' @return  a character vector giving a label for each input value
 labfun <- function(x) {
   if (any(x > 999, na.rm = TRUE)) {
     comma(x)
@@ -120,6 +122,7 @@ labfun <- function(x) {
 #' \code{ggplot2} plots. Non-integer values are rounded down.
 #' @section Details:
 #' Based on function \code{pretty}.
+#' @return a vector of axis-label breaks
 #' @keywords internal
 number_ticks <- function(n) {
   function(limits) {

R/calculate_outcome.R

@@ -4,7 +4,7 @@
 #' @param cost data frame with costs
 #' @param effect data frame with effects
 #' @param wtp willingness-to-pay threshold
-#'
+#' @return a data.frame of the desired outcome values for each strategy
 #' @keywords internal
 calculate_outcome <- function(outcome = c("nhb", "nmb", "eff", "cost", "nhb_loss",
                                           "nmb_loss", "nhb_loss_voi", "nmb_loss_voi"),

R/create_sa.R

@@ -20,6 +20,8 @@
 #' in the \code{\link{make.names}} help page, to avoid unexpected errors.
 #'
 #' @param currency symbol for the currency being used (ex. "$", "£")
+#' @return returns "sa" sensitivity analysis object.
+#' @keywords internal
 create_sa <- function(parameters, parnames, effectiveness, strategies,
                       cost, currency, other_outcome) {
   # checks that each is a dataframe

R/evsi.R

@@ -120,6 +120,8 @@ calc_evsi <- function(psa,
 #' @param object gam object
 #' @param n scalar or vector of new sample size to compute evsi on
 #' @param n0 scalar or vector of effective prior sample size
+#' @return the conditional loss associated with a gam, effective prior sample size,
+#' and new sample size
 #' @importFrom stats coef
 predict_ga <- function(object, n, n0) {
   # Name of parameters
@@ -191,7 +193,7 @@ predict_ga <- function(object, n, n0) {
 #' basis functions of a smooth for one parameter
 #'
 #' @keywords internal
-#'
+#' @return Pre-posterior for each basis function
 #' @importFrom mgcv PredictMat
 predict_smooth_ga <- function(object, param_vals, vrf = 1) {
   # Produce basis functions for one parameter
@@ -219,7 +221,7 @@ predict_smooth_ga <- function(object, param_vals, vrf = 1) {
 #' the tensor product if more than one parameter is selected
 #' (Heavily based on function Predict.matrix.tensor.smooth from
 #' mgcv package)
-#'
+#' @return tensor product based on list of pre-posterior distributions
 #' @keywords internal
 #' @importFrom mgcv tensor.prod.model.matrix Predict.matrix PredictMat
 predict_matrix_tensor_smooth_ga <- function(object,

R/metamodel.R

@@ -135,6 +135,7 @@ metamodel <- function(analysis = c("oneway", "twoway", "multiway"),
 #'
 #' @importFrom mgcv gam
 #' @keywords internal
+#' @return a statistical metamodel
 #' @inheritParams metamodel
 mm_run_reg <- function(analysis, dep, params, dat, type, poly.order, k) {
 
@@ -430,6 +431,7 @@ predict.metamodel <- function(object, ranges = NULL, nsamp = 100, ...) {
 #' @param nsamp number of points from the range
 #' @param psa_paramvals sampled values from the PSA. used to calculate the
 #' range if none is supplied
+#' @return a vector of parameter values spanning the range specified
 #' @keywords internal
 make_param_seq <- function(p, ranges, nsamp, psa_paramvals) {
   p_range <- ranges[[p]]

R/owsa.R

@@ -213,6 +213,7 @@ owsa_tornado <- function(owsa, return = c("plot", "data"),
 
 #' transformation for owsa_tornado
 #' @param offset the offset for the transformation (kind of the new 0)
+#' @return offset value supplied to ytrans in \code{add_common_aes}
 #' @keywords internal
 #' @importFrom scales trans_new
 offset_trans <- function(offset = 0) {
@@ -322,7 +323,11 @@ owsa_opt_strat <- function(owsa, params = NULL, maximize = TRUE,
   }
 }
 
-# check that is owsa object
+
+#' check that object is owsa object
+#' @param obj the object to be checked for the owsa class
+#' @return returns TRUE if object is "owsa" object and FALSE if not.
+#' @keywords internal
 is_owsa <- function(obj) {
   if (inherits(obj, "owsa")) {
     return(TRUE)

R/run_dsa.R

@@ -341,6 +341,7 @@ run_twsa_det <- function(params_range, params_basecase, nsamp = 40, FUN, outcome
 #' @param tmp_replace values from predetermined DSA samples that will replace some values in \code{tmp_input}
 #'
 #' @importFrom  utils setTxtProgressBar
+#' @return output of function defined by \code{user_fun}
 #' @keywords internal
 wrapper_of_user_model <- function(x, user_fun, param_name,
                                   tmp_input, tmp_replace,

cran-comments.md

@@ -1,15 +1,7 @@
 ## Resubmission
 This is a resubmission. In this version I have:
 
-* removed the name of the package from the start of the description.
-
-* changed the quotes around package title to undirected quotation marks.
-
-* Added \value to .Rd files regarding exported methods and explained the functions results in the documentation.
-
-* Unwrapped examples previously wrapped with \dontrun{}
-
-* removed write.table() and ggsave() function uses from the basic_cea.rmd vignette to comply with CRAN's policies. These were the only offending functions I could find--if there are others that I am overlooking, please let me know and I will happily fix them!
+* Added \value to .Rd files regarding exported methods.
 
 ## Test environments
 * local Win install, R 4.0.3