Merge branch 'main' of https://github.com/INCEPTdk/adaptr

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: adaptr
 Title: Adaptive Trial Simulator
-Version: 1.1.0
-Date: 2022-06-16
+Version: 1.1.1
+Date: 2022-08-16
 Authors@R: 
     c(person("Anders", "Granholm",
              email = "[email protected]",

NEWS.md

@@ -1,3 +1,15 @@
+# adaptr 1.1.1
+
+This is a patch release triggered by a CRAN request for updates.
+
+* Minor formatting changes to the `adaptr-package` help page to comply with CRAN
+request to only use HTML5 (as used by R >=4.2.0).
+
+* Minor bugfixes in print methods for trial specifications and summaries of
+multiple trial results.
+
+* Minor updates in messages in setup_trial.
+
 # adaptr 1.1.0
 
 Minor release:

R/adaptr-package.R

@@ -5,7 +5,10 @@
 #' @aliases adaptr
 #'
 #' @description
-#' \if{html}{\figure{adaptr.png}{options: align="right" width="120" alt="logo"}}
+#' \if{html}{
+#'   \figure{adaptr.png}{options: width="120" alt="logo"}
+#'   \emph{Adaptive Trial Simulator}
+#' }
 #'
 #' The `adaptr` package simulates adaptive (multi-arm) trials using adaptive
 #' stopping, adaptive arm dropping and/or response-adaptive randomisation.

R/print.R

@@ -48,7 +48,7 @@ print.trial_spec <- function(x, prob_digits = 3, ...) {
           cat("* Control arm probability matched to best non-control arm")
         } else {
           cat0("* Control arm probability fixed at ",
-               round(x$control_prob_fixed), prob_digits) # Fixed at same value all the time
+               round(x$control_prob_fixed, prob_digits)) # Fixed at same value all the time
         }
       } else {
         cat0("* Control arm probability fixed at ")
@@ -308,7 +308,7 @@ print.trial_results_summary <- function(x, digits = 1, ...) {
                                                    character(1)), collapse = " | "), "\n",
       "* RMSE: ", fmt_dig(x$rmse, 5), "\n",
       "* RMSE treatment effect: ", ifelse(is.na(x$rmse_te), "not estimated", fmt_dig(x$rmse_te, 5)), "\n",
-      "* Ideal design percentage: ", fmt_dig(x$idp, digits), "%",
+      "* Ideal design percentage: ", ifelse(is.nan(x$idp), "not estimable", paste0(fmt_dig(x$idp, digits), "%")),
 
       # Technical simulation details
       "\n\nSimulation details:",

R/setup_trial.R

@@ -283,7 +283,7 @@ validate_trial <- function(arms, true_ys, start_probs = NULL,
   best_arm <- arms[true_ys == ifelse(highest_is_best, max(true_ys), min(true_ys))]
   if (length(best_arm) > 1) {
     message(paste0("Notice: trial specification does not contain a single superior arm -", "
-                   multiple arms have the best value in true_ys: ", paste0(best_arm, collapse = " and ")))
+                   multiple arms have the best value in true_ys: ", paste0(best_arm, collapse = ", ")))
   }
 
   # Validate Bayesian settings

README.Rmd

@@ -39,9 +39,9 @@ The full package documentation is available as a stand-alone website at [inceptd
 # The easiest way is to install from CRAN directly
 install.packages("adaptr")
 
-# But you can also get the newest version from GitHub (requires the remotes package)
+# But you can also install the development version from GitHub (requires the remotes package)
 # install.packages("remotes") 
-remotes::install_github("INCEPTdk/adaptr")
+remotes::install_github("INCEPTdk/adaptr@dev")
 ```
 
 ## Example

README.md

@@ -31,9 +31,9 @@ The full package documentation is available as a stand-alone website at
 # The easiest way is to install from CRAN directly
 install.packages("adaptr")
 
-# But you can also get the newest version from GitHub (requires the remotes package)
+# But you can also install the development version from GitHub (requires the remotes package)
 # install.packages("remotes") 
-remotes::install_github("INCEPTdk/adaptr")
+remotes::install_github("INCEPTdk/adaptr@dev")
 ```
 
 ## Example
@@ -46,7 +46,7 @@ general `setup_trial()` function, or one of the special case functions,
 
 ``` r
 library(adaptr)
-#> Loading adaptr package (version 1.1.0).
+#> Loading adaptr package (version 1.1.1).
 #> See 'help("adaptr")' or 'vignette("Overview", "adaptr")' for help.
 #> Further information available on https://inceptdk.github.io/adaptr/.
 
@@ -171,7 +171,7 @@ print(res_sum, digits = 1)
 #> * Ideal design percentage: 100.0%
 #> 
 #> Simulation details:
-#> * Simulation time: 0.388 secs
+#> * Simulation time: 0.413 secs
 #> * Base random seed: 67890
 #> * Credible interval width: 95%
 #> * Number of posterior draws: 5000

cran-comments.md

@@ -1,13 +1,8 @@
-## Resubmission
-
-This is a resubmission of a minor release, fixing a moved URL and an invalid
-file URI in a function documentation. Comments for original submission below.
-
 ## Release summary
 
-This is a minor patch release updating documentation, adding limited new
-functionality, and updating an internal function due to updates to the
-`&&`-function in R >= 4.2.0.
+This is a minor patch release triggered by a CRAN request for updates to the
+package documentation to only use HTML5, which also includes minor bugfixes to
+print methods and messages in the setup_trial function.
 
 ## R CMD check results