Responding to CRAN review

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
 Version: 0.1.0
-Date: 2022-10-04 13:40:57 UTC
-SHA: 4b7c4ca4b9938b7f463f0e5cdda0f615c02b2d18
+Date: 2022-10-24 15:38:45 UTC
+SHA: ac55a7f7e2e5f95cecbf60d64ecba12435523788

README.md

@@ -1,3 +1,4 @@
+
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
 # mtdesign
@@ -8,7 +9,6 @@
 status](https://www.r-pkg.org/badges/version/mtdesign)](https://CRAN.R-project.org/package=mtdesign)
 [![Test
 Coverage](https://raw.githubusercontent.com/openpharma/mtdesign/_xml_coverage_reports/data/main/badge.svg)](https://github.com/openpharma/mtdesign/blob/_xml_coverage_reports/data/main/coverage.xml)
-
 <!-- badges: end -->
 
 ## Introduction
@@ -34,7 +34,7 @@ You can install the development version of `mtdesign` from
 
 ## Set up vignette environment
 
-```r
+``` r
 # By policy, on CRAN, use only two cores, no matter how many are available.
 if (requireNamespace("parallel", quietly = TRUE)) {
   maxCores <- parallel::detectCores()
@@ -51,7 +51,7 @@ interest but those with a response rate of at least 25% are worthy of
 further development. A Simon’s 2-stage design to seek an efficacy signal
 with a significance level of 5% and a power of 80% is required.
 
-```r
+``` r
 library(mtdesign)
 library(knitr)
 library(dplyr)
@@ -72,7 +72,7 @@ simonDesign %>%
 ```
 
 | nTotal | nStage1 | rTotal | rFutility | Type1 | Type2 | PETNull | AveSizeNull | Criterion |
-| -----: | ------: | -----: | --------: | ----: | ----: | ------: | ----------: | :-------- |
+|-------:|--------:|-------:|----------:|------:|------:|--------:|------------:|:----------|
 |     17 |       9 |      2 |         0 | 0.047 | 0.188 |    0.63 |        12.0 | optimal   |
 |     16 |      12 |      2 |         0 | 0.043 | 0.199 |    0.54 |        13.8 | minimax   |
 
@@ -83,7 +83,7 @@ the power level achieved is 100% - 18.8% = 81.2%.
 
 The power curves for both designs are easily plotted.
 
-```r
+``` r
 powerPlot(simonDesign)
 ```
 
@@ -92,7 +92,7 @@ powerPlot(simonDesign)
 Obtaining the equivalent Mander & Thompson designs requires only a small
 change to the calls.
 
-```r
+``` r
 manderDesign <- obtainDesign(
   p0 = 0.05,
   p1 = 0.25,
@@ -107,14 +107,13 @@ manderDesign %>%
 ```
 
 | nTotal | nStage1 | rTotal | rFutility | rSuccess | Type1 | Type2 | PETNull | PETAlt | AveSizeNull | AveSizeAlt | Criterion   |
-| -----: | ------: | -----: | --------: | -------: | ----: | ----: | ------: | -----: | ----------: | ---------: | :---------- |
+|-------:|--------:|-------:|----------:|---------:|------:|------:|--------:|-------:|------------:|-----------:|:------------|
 |     17 |       9 |      2 |         0 |        2 | 0.047 |  0.19 |    0.64 |   0.47 |        11.9 |         NA | optimalNull |
 |     16 |      12 |      2 |         0 |        2 | 0.043 |  0.20 |    0.56 |   0.64 |        13.8 |         NA | minimaxNull |
 |     17 |       9 |      2 |         0 |        2 | 0.047 |  0.19 |    0.64 |   0.47 |        11.9 |         NA | optimalAlt  |
 |     16 |      12 |      2 |         0 |        2 | 0.043 |  0.20 |    0.56 |   0.64 |        13.8 |         NA | minimaxAlt  |
 
-```r
-
+``` r
 powerPlot(manderDesign)
 ```
 
@@ -128,7 +127,7 @@ stage design is 0/9 2/17. That’s close to n<sub>1</sub> = 8, n = 16. Is
 there a (slightly) sub-optimal design that has n<sub>1</sub> = 8, n =
 16?
 
-```r
+``` r
 x <- createGrid(p0 = 0.05, p1 = 0.25, alpha = 0.05, beta = 0.2, mander = FALSE)
 
 y <- x %>% filter(nStage1 == 8, nTotal == 16)
@@ -147,7 +146,7 @@ if (nrow(z) == 0) {
 
 No, there isn’t. How close can we get?
 
-```r
+``` r
 z1 <- y %>% augmentGrid()
 
 bestSize <- z1 %>%
@@ -162,13 +161,12 @@ bestSize %>%
 ```
 
 | nTotal | nStage1 | rTotal | rFutility | Type1 | Type2 | PETNull | AveSizeNull |
-| -----: | ------: | -----: | --------: | ----: | ----: | ------: | ----------: |
+|-------:|--------:|-------:|----------:|------:|------:|--------:|------------:|
 |     16 |       8 |      2 |         0 | 0.039 | 0.229 |    0.66 |        10.7 |
 
 Best sub-optimal design with required significance level
 
-```r
-
+``` r
 bestPower <- z1 %>%
   filter(Type2 < Beta) %>%
   slice_min(Type1)
@@ -182,7 +180,7 @@ bestPower %>%
 ```
 
 | nTotal | nStage1 | rTotal | rFutility | Type1 | Type2 | PETNull | AveSizeNull |
-| -----: | ------: | -----: | --------: | ----: | ----: | ------: | ----------: |
+|-------:|--------:|-------:|----------:|------:|------:|--------:|------------:|
 |     16 |       8 |      1 |         0 | 0.151 | 0.127 |    0.66 |        10.7 |
 
 Best sub-optimal design with required power
@@ -198,7 +196,7 @@ level.
 The power curve for each of these designs can be compared with that for
 the globally optimal design.
 
-```r
+``` r
 plotData1 <- simonDesign %>%
   filter(Criterion == "optimal") %>%
   bind_rows(list(bestSize, bestPower))
@@ -211,15 +209,15 @@ powerPlot(plotData1)
 
 The `mtdesign` package consists of three main functions:
 
-* `createGrid` creates the grid (of nStage1, rFutility, nTotal and
-  rTotal for Simon’s design or nStage1, rFutility, rSuccess, nTotal and
-  rTotal for a Mander & Thompson design) over which the brute force
-  search for the required design(s) is conducted
-* `augmentGrid`takes a grid created by `createGrid` and adds columns for
-  probability of early termination, Type 1 error, Type 2 error and
-  expected sample size to it.
-* `obtainDesign` takes an augmented grid and identifies the optimal and
-  minimax designs
+-   `createGrid` creates the grid (of nStage1, rFutility, nTotal and
+    rTotal for Simon’s design or nStage1, rFutility, rSuccess, nTotal
+    and rTotal for a Mander & Thompson design) over which the brute
+    force search for the required design(s) is conducted
+-   `augmentGrid`takes a grid created by `createGrid` and adds columns
+    for probability of early termination, Type 1 error, Type 2 error and
+    expected sample size to it.
+-   `obtainDesign` takes an augmented grid and identifies the optimal
+    and minimax designs
 
 ## Error and warning messages and logging
 
@@ -244,13 +242,13 @@ attempt to speed up the evaluation of candidate designs.
 The `augmentGrid` function allows users some control over the
 parallelisation process:
 
-* The `parallel` parameter defaults to `TRUE` and defines whether or not
-  paralellisation is to be used.
-* The `cores` parameter specifies how many cores are to be used. The
-  default value, `NA` tells `mtdesign` to use all available (as defined
-  by `parallel::detectCores()`), cores.
-* The `minChunkSize` determines the smallest grid of candidate designs
-  that will trigger paralellisation. The default value is `100000`.
+-   The `parallel` parameter defaults to `TRUE` and defines whether or
+    not paralellisation is to be used.
+-   The `cores` parameter specifies how many cores are to be used. The
+    default value, `NA` tells `mtdesign` to use all available (as
+    defined by `parallel::detectCores()`), cores.
+-   The `minChunkSize` determines the smallest grid of candidate designs
+    that will trigger paralellisation. The default value is `100000`.
 
 The `parallel` package is required for parallelisation. If
 parallelisation is both needed (ie the grid size exceeds `minChunkSize`)
@@ -264,36 +262,36 @@ more rows, a warning is produced.
 If, when installing or using the `mtdesign` package, you get an error
 regarding a syntax error in an`.hpp` file, similar to the following
 
-```r
+``` r
 .../BH/include/boost/math/tools/fraction.hpp:84:48: error: ‘long double’ is not a class, struct, or union type using value_type = typename T::value_type;
 ```
 
 the issue is most likely a mismatch between the g++ compiler being used
 and the headers supplied by the `BH` package. There are only two
 solutions that I know of:
 
-* Upgrade g++
-* Downgrade the version of the `BH` package you are using. The
-  appropriate package version depends on the version of the g++ compiler
-  you are using.
+-   Upgrade g++
+-   Downgrade the version of the `BH` package you are using. The
+    appropriate package version depends on the version of the g++
+    compiler you are using.
 
 ## References
 
 <div id="refs" class="references csl-bib-body hanging-indent">
 
 <div id="ref-LOGGER" class="csl-entry">
 
-Daróczi, Gergely. 2021. _Logger: A Lightweight, Modern and Flexible
-Logging Utility_. <https://daroczig.github.io/logger/>.
+Daróczi, Gergely. 2021. *Logger: A Lightweight, Modern and Flexible
+Logging Utility*. <https://daroczig.github.io/logger/>.
 
 </div>
 
 <div id="ref-MANDER" class="csl-entry">
 
 Mander, AP, and Thompson, SG. 2010. “Two-Stage Designs Optimal Under the
 Alternative Hypothesis for Phase II Cancer Clinical Trials.”
-_Contemporary Clinical Trials_ 31 (6): 572–78.
-<https://doi.org/><https://doi.org/10.1016/j.cct.2010.07.008>.
+*Contemporary Clinical Trials* 31 (6): 572–78.
+https://doi.org/<https://www.doi.org/10.1016/j.cct.2010.07.008>.
 
 </div>
 
@@ -307,8 +305,8 @@ Functions.” Software. <https://CRAN.R-project.org/package=clinfun>.
 <div id="ref-SIMON" class="csl-entry">
 
 Simon, R. 1989. “Optimal Two-Stage Designs for Phase II Clinical
-Trials.” _Controlled Clinical Trials_ 10 (1): 1–10.
-<https://doi.org/><https://doi.org/10.1016/0197-2456(89)90015-9>.
+Trials.” *Controlled Clinical Trials* 10 (1): 1–10.
+https://doi.org/<https://www.doi.org/10.1016/0197-2456(89)90015-9>.
 
 </div>
 

cran-comments.md

@@ -1,3 +1,6 @@
+## Fourth resubmission
+In README.md, I have changed "https://doi.org/..." to "https://www.doi.org/...".  I was confused by the request to change "http://" to "https://" since the URLs already use "https://". If the change is not what was expected, please clarify.
+
 ## Third resubmission
 In DESCRIPTION, I have:
 * Amended the date record to `Date: 2022-10-04`.

mtdesign.bib

@@ -8,7 +8,7 @@ @Article{SIMON
   volume  = {10},
   number  = {1},
   pages   = {1-10},
-  doi     = {https://doi.org/10.1016/0197-2456(89)90015-9},
+  doi     = {https://www.doi.org/10.1016/0197-2456(89)90015-9},
 }
 
 @Article{MANDER,
@@ -19,7 +19,7 @@ @Article{MANDER
   volume  = {31},
   number  = {6},
   pages   = {572-578},
-  doi     = {https://doi.org/10.1016/j.cct.2010.07.008},
+  doi     = {https://www.doi.org/10.1016/j.cct.2010.07.008},
 }
 
 @Misc{CLINFUN,