- addressing some Notes & Warning from devtools::check()

DESCRIPTION

@@ -24,7 +24,7 @@ LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
 Imports:
-    DoseFinding,
+    DoseFinding (>= 1.1-1),
     ggplot2,
     stats,
     RBesT,

R/BMCPMod.R

@@ -5,9 +5,13 @@
 #' @param n_patients Vector specifying the planned number of patients per dose group
 #' @param mods An object of class "Mods" as specified in the Dosefinding package.
 #' @param prior_list a prior_list object specifying the utilized prior for the different dose groups 
+#' @param sd tbd
 #' @param n_sim number of simulations to be performed
 #' @param alpha_crit_val critical value to be used for the testing (on the probability scale)
 #' @param simple boolean variable, defining whether simplified fit will be applied. Passed to the getModelFits function. Default FALSE.
+#' @param reestimate tbd Default FALSE
+#' @param contr tbd Default NULL
+#' @param dr_means tbd Default NULL
 #' 
 #' @export
 assessDesign <- function (
@@ -98,8 +102,10 @@ assessDesign <- function (
 #' 
 #' @param mods An object of class "Mods" as specified in the Dosefinding package.
 #' @param dose_levels vector containing the different doseage levels.
-#' @param dose_weights Vector specifying weights for the different doses
-#' @param prior_list a prior_list object
+#' @param dose_weights Vector specifying weights for the different doses. Default NULL
+#' @param prior_list a prior_list object. Default NULL
+#' @param sd_posterior tbd. Default NULL
+#' @param se_new_trial tbd. Default NULL
 #' 
 #' @return contr Object of class ‘⁠optContr⁠’. A list containing entries contMat and muMat, and CorrMat. Specified in the Dosefinding package.
 #' 
@@ -196,7 +202,7 @@ getCritProb <- function (
     doses  = dose_levels,
     w      = dose_weights)
 
-  crit_prob <- pnorm(DoseFinding:::critVal(
+  crit_prob <- stats::pnorm(DoseFinding::critVal(
     corMat      = contr$corMat,
     alpha       = alpha_crit_val,
     df          = 0,
@@ -212,7 +218,7 @@ getCritProb <- function (
 #' 
 #' @param posterior_list a getPosterior object
 #' @param contr a getContrMat object, contrast matrix to be used for the testing step.
-#' @param crit_prob a getCritProb object
+#' @param crit_prob_adj a getCritProb object
 #' @param simple boolean variable, defining whether simplified fit will be applied. Passed to the getModelFits function. Default FALSE.
 #' 
 #' @return bmcpmod test result as well as modelling result.
@@ -227,7 +233,7 @@ performBayesianMCPMod <- function (
 
 ) {
 
-  if (class(posterior_list) == "postList") {
+  if (inherits(posterior_list,  "postList")) {
 
     posterior_list <- list(posterior_list)
 
@@ -310,7 +316,7 @@ addSignificance <- function (
 #' 
 #' @param posterior_list a getPosterior object
 #' @param contr a getContrMat object, contrast matrix to be used for the testing step.
-#' @param crit_prob a getCritProb object, specifying the critical value to be used for the testing (on the probability scale)
+#' @param crit_prob_adj a getCritProb object, specifying the critical value to be used for the testing (on the probability scale)
 #' 
 #' @return b_mcp test result 
 #' 
@@ -323,7 +329,7 @@ performBayesianMCP <- function(
 
 ) {
 
-  if (class(posterior_list) == "postList") {
+  if (inherits(posterior_list,  "postList")) {
 
     posterior_list <- list(posterior_list)
 

R/bootstrapping.R

@@ -1,10 +1,10 @@
 #' @title getBootstrapQuantiles
 #'
 #' @param model_fits tbd
+#' @param quantiles tbd
 #' @param n_samples tbd
-#' @param alpha tbd
-#' @param avg_fit tbd
 #' @param doses tbd
+#' @param avg_fit tbd
 #'
 #' @return tbd
 #' @export

R/posterior.R

@@ -3,11 +3,12 @@
 #' 
 #' @description Either the patient level data or both the mu_hat as well as the sd_hat must to be provided.
 #' 
-#' @param data dataframe containing the information of dose and response.
-#' Also a simulateData object can be provided.
 #' @param prior_list prior_list object
+#' @param data dataframe containing the information of dose and response. Default NULL
+#' Also a simulateData object can be provided.
 #' @param mu_hat vector of estimated mean values
-#' @param sd_hat vector of estimated standard deviations.
+#' @param se_hat vector of estimated standard deviations.
+#' @param calc_ess tbd. Default NULL
 #'
 #' @export
 getPosterior <- function(

R/simulation.R

@@ -10,6 +10,7 @@
 #' @param true_model Default value is NULL.
 #' Assumed true underlying model. Provided via a String. e.g. "emax".
 #' In case of NULL, all dose-response models, included in the mods input parameter will be used.
+#' @param dr_means tbd. Default NULL.
 #' 
 #' @return sim_data one list object, containing patient level simulated data for all assumed true models.
 #' Also providing information about simulation iteration, patient number as well as dosage levels.