minor edits to examples

R/check_PSAstability.R

@@ -22,33 +22,32 @@
 #' @importFrom tidyr pivot_longer
 #'
 #' @examples
-#'
-#' \dontrun{
 #' # create example matrices
-#' m_eff <- as.matrix(gskVEOutils::Hyperphosphatemia_PSA$e)[,1:5]
-#' colnames(m_eff) <- LETTERS[1:length(colnames(m_eff))]
+#' n_psa <- 10000
 #'
-#' m_cost <- as.matrix(gskVEOutils::Hyperphosphatemia_PSA$c)[,1:5]
-#' colnames(m_cost) <- LETTERS[1:length(colnames(m_cost))]
+#' m_eff <- matrix(data = runif(n = n_psa * 4, min = 0, max = 1),
+#' nrow = n_psa,
+#' ncol = 4,
+#' dimnames = list(NULL, paste0("Strategy ", c("A", "B", "C", "D"))))
 #'
-#' v_strategy_labels <- setNames(object = paste0("Strategy ", colnames(m_eff)),
-#' nm = colnames(m_eff))
+#' m_cost <- matrix(data = runif(n = n_psa * 4, min = 5000, max = 20000),
+#' nrow = n_psa,
+#' ncol = 4,
+#' dimnames = list(NULL, paste0("Strategy ", c("A", "B", "C", "D"))))
 #'
 #' v_strategy_colors <- setNames(object = grDevices::palette.colors(n = ncol(m_eff)),
 #' nm = colnames(m_eff))
 #'
-#' plot_PSA_stability(m_eff = m_eff[, 1:5],
-#' m_cost = m_cost[, 1:5],
+#' plot_PSA_stability(m_eff = m_eff,
+#' m_cost = m_cost,
 #' lambda = 20000,
 #' currency_symbol = "\u0024",
-#' v_strategy_labels = v_strategy_labels,
+#' v_strategy_labels = colnames(m_eff),
 #' v_strategy_colors = v_strategy_colors,
 #' comparator = colnames(m_eff)[1],
-#' output = "icer",
-#' include_reference_line = T,
-#' log_x = F)
-#'
-#' } # end don't run.
+#' output = "inmb",
+#' include_reference_line = TRUE,
+#' log_x = FALSE)
 #'
 plot_PSA_stability <- function(m_eff,
  m_cost,
@@ -59,7 +58,7 @@ plot_PSA_stability <- function(m_eff,
  comparator = NULL,
  output = "inmb",
  include_reference_line = T,
- log_x = F) {
+ log_x = FALSE) {
  assertthat::assert_that(is.matrix(m_eff) &
  is.matrix(m_cost) & is.numeric(m_eff) & is.numeric(m_cost),
  msg = "m_eff and m_cost must be numeric matrices")

R/check_trans_probs.R

@@ -11,7 +11,6 @@
 #' @param dead_state character vector length 1 denoting dead state (e.g. "D")
 #'
 #' @examples
-#' \dontrun{
 #' v_hs_names <- c("H", "S", "D")
 #' n_hs <- length(v_hs_names)
 #' m_P <- matrix(data = 0, nrow = n_hs, ncol = n_hs,
@@ -22,9 +21,11 @@
 #' m_P["S", "H"] <- 0.5
 #' diag(m_P) <- (1 - rowSums(m_P))
 #' check_trans_prob_mat(m_P)
+#'
+#' \dontrun{
 #' # introduce error
 #' m_P["H", "S"] <- 0.2
-#' check_trans_prob_mat(m_P, confirm_ok = T, stop_if_not = T)
+#' check_trans_prob_mat(m_P, confirm_ok = TRUE, stop_if_not = TRUE)
 #' }
 #'
 #' @return A message indicating whether the matrix passed all the checks or a warning/error message if any check failed.

R/cheers_checker.R

@@ -6,12 +6,10 @@
 #' @return The next element of the vector after the value
 #' @export
 #' @examples
-#' \dontrun{
 #' find_next_vector_element(value = 5, vector = 1:10)
 #' find_next_vector_element(value = 5, vector = 1:4)
-#' find_next_vector_element(value = 5, vector = 1:5, LTE = F)
-#' find_next_vector_element(value = 5, vector = 1:5, LTE = T)
-#' }
+#' find_next_vector_element(value = 5, vector = 1:5, LTE = FALSE)
+#' find_next_vector_element(value = 5, vector = 1:5, LTE = TRUE)
 #'
 find_next_vector_element <- function(value, vector, LTE=FALSE) {
 

tests/testthat/test-check_PSAstability.R

@@ -49,7 +49,7 @@ test_that("plot_PSA_stability handles valid input", {
  comparator = colnames(m_eff)[1],
  output = "icer",
  include_reference_line = T,
- log_x = F
+ log_x = FALSE
  )
  })
 
@@ -121,7 +121,7 @@ test_that("plot_PSA_stability flags errors", {
  comparator = colnames(m_eff)[1],
  output = "icer",
  include_reference_line = T,
- log_x = F
+ log_x = FALSE
  )
  })