fix par names

openpharma · Aug 10, 2024 · 92421f2 · 92421f2
1 parent 8969205
commit 92421f2
Show file tree

Hide file tree

Showing 8 changed files with 20 additions and 20 deletions.
diff --git a/R/Simulations-class.R b/R/Simulations-class.R
@@ -713,30 +713,30 @@ PseudoDualSimulations <- function(fit_eff,
 #' efficacy responses using [`EffFlexi`] efficacy model.
 #' It extends [`PseudoDualSimulations`] by adding the capability to capture the sigma2betaW estimates.
 #'
-#' @slot sigma2_beta_west (`numeric`)\cr the vector of the final posterior mean sigma2betaW estimates
+#' @slot sigma2_beta_w_est (`numeric`)\cr the vector of the final posterior mean sigma2betaW estimates
 #' @aliases PseudoDualFlexiSimulations
 #' @export
 .PseudoDualFlexiSimulations <-
   setClass(
     Class = "PseudoDualFlexiSimulations",
-    slots = c(sigma2_beta_west = "numeric"),
-    prototype = prototype(sigma2_beta_west = c(0.001, 0.002)),
+    slots = c(sigma2_beta_w_est = "numeric"),
+    prototype = prototype(sigma2_beta_w_est = c(0.001, 0.002)),
     contains = "PseudoDualSimulations"
   )
 
 ## constructor ----
 
 #' @rdname PseudoDualFlexiSimulations-class
 #'
-#' @param sigma2_beta_west (`numeric`)\cr the vector of the final posterior mean sigma2betaW estimates
+#' @param sigma2_beta_w_est (`numeric`)\cr the vector of the final posterior mean sigma2betaW estimates
 #' @param \dots additional parameters from [`PseudoDualSimulations`]
 #'
 #' @export
-PseudoDualFlexiSimulations <- function(sigma2_beta_west,
+PseudoDualFlexiSimulations <- function(sigma2_beta_w_est,
                                        ...) {
   start <- PseudoDualSimulations(...)
   .PseudoDualFlexiSimulations(start,
-    sigma2_beta_west = sigma2_beta_west
+    sigma2_beta_w_est = sigma2_beta_w_est
   )
 }
 

diff --git a/R/Simulations-methods.R b/R/Simulations-methods.R
@@ -2408,7 +2408,7 @@ setMethod("plot",
         ## save the plot
         plotList[[plotIndex <- plotIndex + 1L]] <-
           qplot(factor(0),
-            y = y, data = data.frame(y = x@sigma2_beta_west), geom = "boxplot",
+            y = y, data = data.frame(y = x@sigma2_beta_w_est), geom = "boxplot",
             xlab = "", ylab = "Random walk model variance estimates"
           ) +
           coord_flip() + scale_x_discrete(breaks = NULL)

diff --git a/R/Simulations-validity.R b/R/Simulations-validity.R
@@ -138,15 +138,15 @@ v_pseudo_dual_simulations <- function(object) {
 }
 
 #' @describeIn v_pseudo_simulations validates that the [`PseudoDualFlexiSimulations`]
-#' object contains valid `sigma2_beta_west` vector of the final posterior mean
+#' object contains valid `sigma2_beta_w_est` vector of the final posterior mean
 #' sigma2betaW estimates.`FinalGstarEstimates` , `FinalGstarAtDoseGrid`,
 #'
 v_pseudo_dual_flex_simulations <- function(object) {
   v <- Validate()
   nSims <- length(object@data)
   v$check(
-    identical(length(object@sigma2_beta_west), nSims),
-    "sigma2_beta_west has to have same length as data"
+    identical(length(object@sigma2_beta_w_est), nSims),
+    "sigma2_beta_w_est has to have same length as data"
   )
   v$result()
 }

diff --git a/man/PseudoDualFlexiSimulations-class.Rd b/man/PseudoDualFlexiSimulations-class.Rd
diff --git a/man/crmPackExample.Rd b/man/crmPackExample.Rd
diff --git a/man/crmPackHelp.Rd b/man/crmPackHelp.Rd
diff --git a/man/v_pseudo_simulations.Rd b/man/v_pseudo_simulations.Rd
diff --git a/tests/testthat/test-Simulations-class.R b/tests/testthat/test-Simulations-class.R
@@ -495,7 +495,7 @@ test_that("PseudoDualFlexiSimulations can be instantiated using the constructor"
   final_optimal_dose <- c(0.5, 0.6)
   final_optimal_dose_at_dose_grid <- c(0.7, 0.8)
   sigma2_est <- c(0.01, 0.02)
-  sigma2_beta_west <- c(0.03, 0.04)
+  sigma2_beta_w_est <- c(0.03, 0.04)
 
   fit <- list(c(0.1, 0.2), c(0.3, 0.4))
   final_td_target_during_trial_estimates <- c(0.5, 0.6)
@@ -538,7 +538,7 @@ test_that("PseudoDualFlexiSimulations can be instantiated using the constructor"
     final_optimal_dose = final_optimal_dose,
     final_optimal_dose_at_dose_grid = final_optimal_dose_at_dose_grid,
     sigma2_est = sigma2_est,
-    sigma2_beta_west = sigma2_beta_west,
+    sigma2_beta_w_est = sigma2_beta_w_est,
     fit = fit,
     data = data,
     doses = doses,
@@ -556,14 +556,14 @@ test_that("PseudoDualFlexiSimulations can be instantiated using the constructor"
   )
 
   expect_valid(sim_obj, "PseudoDualFlexiSimulations")
-  expect_identical(sim_obj@sigma2_beta_west, sigma2_beta_west)
+  expect_identical(sim_obj@sigma2_beta_w_est, sigma2_beta_w_est)
 })
 
 test_that("PseudoDualFlexiSimulations user constructor argument names", {
   expect_function(
     PseudoDualFlexiSimulations,
     args = c(
-      "sigma2_beta_west", "..."
+      "sigma2_beta_w_est", "..."
     ),
     ordered = TRUE
   )