- added citation file

- added word list file
- further CRAN fixes: shortened example runtime

.Rbuildignore

@@ -9,3 +9,4 @@ docs
 ^doc$
 ^Meta$
 ^cran-comments\.md$
+^cran_submission_script\.R$

BayesianMCPMod.Rproj

@@ -15,3 +15,4 @@ LaTeX: pdfLaTeX
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: BayesianMCPMod
 Title: Simulate, Evaluate, and Analyze Dose Finding Trials with Bayesian
     MCPMod
-Version: 0.1.5
+Version: 1.0.0
 Authors@R: c(
     person("Boehringer Ingelheim Pharma GmbH & Co. KG", role = c("cph", "fnd")),
     person("Stephan", "Wojciekowski", , "[email protected]", role = c("aut", "cre")),

R/bootstrapping.R

@@ -20,23 +20,17 @@
 #'                        DG_2 = RBesT::mixnorm(comp1 = c(w = 1, m = 4, s = 1.5), sigma = 2) ,  
 #'                        DG_3 = RBesT::mixnorm(comp1 = c(w = 1, m = 6, s = 1.2), sigma = 2) ,
 #'                        DG_4 = RBesT::mixnorm(comp1 = c(w = 1, m = 6.5, s = 1.1), sigma = 2))
-#' models <- c("emax", "exponential", "sigEmax", "linear")
+#' models <- c("exponential", "linear")
 #' dose_levels <- c(0, 1, 2, 4, 8)
 #' fit <- getModelFits(models      = models,
 #'                     posterior   = posterior_list,
-#'                     dose_levels = dose_levels)
-#' fit_simple <- getModelFits(models      = models,
-#'                            posterior   = posterior_list,
-#'                            dose_levels = dose_levels,
-#'                            simple      = TRUE)
+#'                     dose_levels = dose_levels,
+#'                     simple      = TRUE)
+#'                            
 #' getBootstrapQuantiles(model_fits = fit,
 #'                       quantiles  = c(0.025, 0.5, 0.975),
-#'                       n_samples  = 100, # not recommended, speeding up example
-#'                       doses      = c(0, 1, 2, 3, 4, 6, 8))
-#' # getBootstrapQuantiles(model_fits = fit_simple,
-#' #                       quantiles  = c(0.025, 0.5, 0.975),
-#' #                       n_samples  = 2000,
-#' #                       doses      = c(0, 1, 2, 3, 4, 6, 8))
+#'                       n_samples  = 100, # speeding up example run time
+#'                       doses      = c(0, 6, 8))
 #' @return  A data frame with entries doses, models, and quantiles 
 #' @export
 getBootstrapQuantiles <- function (

R/plot.R

@@ -21,18 +21,14 @@
 #'                        DG_2 = RBesT::mixnorm(comp1 = c(w = 1, m = 4, s = 1.5), sigma = 2) ,  
 #'                        DG_3 = RBesT::mixnorm(comp1 = c(w = 1, m = 6, s = 1.2), sigma = 2) ,
 #'                        DG_4 = RBesT::mixnorm(comp1 = c(w = 1, m = 6.5, s = 1.1), sigma = 2))
-#' models <- c("emax", "exponential", "sigEmax", "linear")
+#' models <- c("exponential", "linear")
 #' dose_levels <- c(0, 1, 2, 4, 8)
 #' fit <- getModelFits(models      = models,
 #'                     posterior   = posterior_list,
-#'                     dose_levels = dose_levels)
-#' fit_simple <- getModelFits(models      = models,
-#'                            posterior   = posterior_list,
-#'                            dose_levels = dose_levels,
-#'                            simple      = TRUE)
+#'                     dose_levels = dose_levels,
+#'                     simple      = TRUE)
 #'                            
-#' plot(fit, cr_bands = TRUE)
-#' # plot(fit_simple, cr_bands = TRUE, alpha_CrB = c(0.05, 0.1, 0.5))
+#' plot(fit) 
 #' @return A ggplot2 object
 #' @export
 plot.modelFits <- function (

cran_submission_script.R

@@ -0,0 +1,70 @@
+usethis::use_build_ignore(c(".github", "_pkgdown.yml", "dev", "cran_submission_script.R"))
+
+
+# Update dependencies in DESCRIPTION
+# install.packages('attachment', repos = 'https://thinkr-open.r-universe.dev')
+attachment::att_amend_desc()
+
+# Run tests and examples
+devtools::test()
+devtools::run_examples()
+# autotest::autotest_package(test = TRUE)
+
+# Check package as CRAN
+rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"))
+
+# Check content
+# install.packages('checkhelper', repos = 'https://thinkr-open.r-universe.dev')
+checkhelper::find_missing_tags()
+# _Check that you let the house clean after the check, examples and tests
+all_files_remaining <- checkhelper::check_clean_userspace()
+all_files_remaining
+
+# Check spelling
+# usethis::use_spell_check()
+spelling::spell_check_package()
+
+# Check URL are correct
+# install.packages('urlchecker', repos = 'https://r-lib.r-universe.dev')
+urlchecker::url_check()
+urlchecker::url_update()
+
+# check on other distributions
+# _rhub
+devtools::check_rhub()
+rhub::check_on_windows(check_args = "--force-multiarch")
+rhub::check_on_solaris()
+# _win devel CRAN
+devtools::check_win_devel()
+# _macos CRAN
+devtools::check_mac_release()
+
+# Check reverse dependencies
+# remotes::install_github("r-lib/revdepcheck")
+install.packages('revdepcheck', repos = 'https://r-lib.r-universe.dev')
+usethis::use_git_ignore("revdep/")
+usethis::use_build_ignore("revdep/")
+
+devtools::revdep()
+library(revdepcheck)
+# In another session
+id <- rstudioapi::terminalExecute("Rscript -e 'revdepcheck::revdep_check(num_workers = 4)'")
+rstudioapi::terminalKill(id)
+# See outputs
+revdep_details(revdep = "pkg")
+revdep_summary()                 # table of results by package
+revdep_report() # in revdep/
+# Clean up when on CRAN
+revdep_reset()
+
+# Update NEWS
+# Bump version manually and add list of changes
+
+# Add comments for CRAN
+usethis::use_cran_comments(open = rlang::is_interactive())
+
+# Upgrade version number
+usethis::use_version(which = c("patch", "minor", "major", "dev")[1])
+
+# Verify you're ready for release, and release
+devtools::release()

inst/CITATION

@@ -0,0 +1,20 @@
+citHeader("To cite BayesianMCPMod in publications, please use:")
+
+year <- sub("-.*", "", meta$Date)
+note <- sprintf("R package version %s", meta$Version)
+
+bibentry(
+  bibtype     = "Manual",
+  title       = "BayesianMCPMod: Simulate, Evaluate, and Analyze Dose Finding Trials with Bayesian MCPMod",
+  author      = c(
+    person("Stephan", "Wojciekowski"),
+    person("Lars", "Andersen"),
+    person("Sebastian", "Bossert")
+  ),
+  year        = year,
+  note        = note,
+  url         = "https://CRAN.R-project.org/package=bhmbasket",
+  textVersion = paste0(
+    "Wojciekowski, S, Andersen, L, Bossert, S (", year, "). BayesianMCPMod: Simulate, Evaluate, and Analyze Dose Finding Trials with Bayesian MCPMod. ", note, "."
+  )
+)

inst/WORDLIST

@@ -0,0 +1,5 @@
+MCPMod
+Pinheiro
+Schmidli
+al
+et