38 release dosefinding 14 1

DESCRIPTION

@@ -1,14 +1,17 @@
 Package: DoseFinding
 Type: Package
 Title: Planning and Analyzing Dose Finding Experiments
-Version: 1.3-1.9000
-Date: 2025-03-07
+Version: 1.4-1.9000
+Date: 2025-07-08
 Authors@R: c(
-   person("Bjoern", "Bornkamp", email = "bjoern.bornkamp@novartis.com", comment = c(ORCID = "0000-0002-6294-8185"), role = c("aut")),
+   person("Bjoern", "Bornkamp", email = "bjoern.bornkamp@novartis.com", 
+   comment = c(ORCID = "0000-0002-6294-8185"), role = c("aut")),
    person("Jose", "Pinheiro", role = "aut"),
    person("Frank", "Bretz", role = "aut"),
    person("Ludger", "Sandig", role = "aut"),
    person("Marius", "Thomas", role = c("aut", "cre"), email = "marius.thomas@novartis.com"),
+   person("Daniel", "Sabanes Bove", role = "aut", email = "daniel.sabanes_bove@rconis.com",
+           comment = c(ORCID = "0000-0002-0176-9239")),
    person(given = "Novartis Pharma AG", role = c("cph", "fnd")))
 Imports: ggplot2, lattice, mvtnorm
 Suggests: 

NEWS.md

@@ -1,3 +1,13 @@
+# DoseFinding (development version)
+
+# DoseFinding 1.4-1
+* Added powMCTInterim function to implement conditional/predictive power
+calculations for interim analyses (#10)
+* Added vignette illustrating analysis of longitudinal data (#29, thanks to Daniel Sabanes Bove for work on this and powMCTInterim)
+* replaced uses of ggplot2::qplot, which is deprecated (#22)
+* Minor updates to documentation and testing (#27 and #30) 
+* added hex sticker (#28) 
+
 # DoseFinding 1.3-1
 * Added maFitMod function to implement fitting of dose-response models via
 model averaging (#11, thanks to Björn Bornkamp)

R/powMCTInterim.R

@@ -5,7 +5,7 @@
 #' interim data, e.g. for a futility interim analysis. This function can also be applied
 #' to longitudinal endpoints, where at the time of interim analysis incomplete data is
 #' available. For more details see the vignette on longitudinal data analysis with
-#' MCP-Mod: \code{vignette("Longitudinal Data MCP-Mod", package = "DoseFinding")}.
+#' MCP-Mod: `vignette("Longitudinal Data MCP-Mod", package = "DoseFinding")`.
 #'
 #' @inheritParams powMCT
 #' @param S_0t The covariance matrix for the first stage estimates

cran-comments.md

@@ -1,3 +1,9 @@
+## Resubmission
+This is a resubmission. In this version I have made the following updates to reduce check time
+
+* added skips for long running tests
+* skipped evaluation for long-running vignette code
+
 ## R CMD check results
 
 0 errors | 0 warnings | 0 notes

tests/testthat/test-bMCTtest.R

@@ -207,6 +207,9 @@ test_that("unordered values in MCTtest work (unadjusted scale)", {
 })
 
 test_that("bMCTtest gives same results as RBesT two-sample analysis with non-informative prior", {
+  skip_on_cran()
+  skip_on_ci()
+
   require_rbest()
   set.seed(23)
   dd <- getDFdataSet_testsMCT()
@@ -222,6 +225,9 @@ test_that("bMCTtest gives same results as RBesT two-sample analysis with non-inf
 
 
 test_that("bMCTtest gives same results as RBesT two-sample analysis with informative prior for control", {
+  skip_on_cran()
+  skip_on_ci()
+
   require_rbest()
   set.seed(23)
   dd <- getDFdataSet_testsMCT()
@@ -238,6 +244,9 @@ test_that("bMCTtest gives same results as RBesT two-sample analysis with informa
 })
 
 test_that("bMCTtest gives same results as RBesT two-sample analysis with informative prior for both arms", {
+  skip_on_cran()
+  skip_on_ci()
+
   require_rbest()
   set.seed(24)
   dd <- getDFdataSet_testsMCT()

tests/testthat/test-sampSize.R

@@ -17,6 +17,7 @@ tFunc <- function(n) {
 #########################################################
 
 test_that("sampSize and sampSizeMCT work correctly", {
+  skip_on_cran()
   skip_on_ci()
 
   result1 <- sampSize(upperN = 80, targFunc = tFunc, target = 0.8, alRatio = rep(1, 6))
@@ -32,6 +33,7 @@ test_that("sampSize and sampSizeMCT work correctly", {
 })
 
 test_that("sampSize and sampSizeMCT work correctly with Ntype = total", {
+  skip_on_cran()
   skip_on_ci()
 
   result1 <- sampSize(upperN = 80, targFunc = tFunc, target = 0.8, alRatio = rep(1, 6), Ntype = "total")
@@ -47,6 +49,7 @@ test_that("sampSize and sampSizeMCT work correctly with Ntype = total", {
 })
 
 test_that("sampSize and sampSizeMCT work correctly with sumFct = min", {
+  skip_on_cran()
   skip_on_ci()
 
   result1 <- sampSize(upperN = 80, targFunc = tFunc, target = 0.8, alRatio = rep(1, 6), Ntype = "total")

vignettes/longitudinal_data.Rmd

@@ -528,7 +528,7 @@ run_scen <- function(n_sim, rho, maxEff,
 
 These functions can be used as follows:
 
-```{r}
+```{r, eval = FALSE}
 doses <- c(0, 0.5, 1, 2, 4, 8) # doses
 alRatio <- c(2, 1, 1, 1, 2, 2) # allocation ratio for doses
 alpha <- 0.025 # for MCTtest