From 6a1853b47c41f6bafe4407a17209636325d273cb Mon Sep 17 00:00:00 2001 From: Marius Thomas Date: Tue, 13 Oct 2026 14:18:21 +0200 Subject: [PATCH 01/10] update contributors section in readme --- README.Rmd | 2 +- README.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/README.Rmd b/README.Rmd index fe61a0e..9ec5506 100644 --- a/README.Rmd +++ b/README.Rmd @@ -100,7 +100,7 @@ as listed in the `DESCRIPTION` file. ### Other authors and substantial contributors -- Ludger Sandig — Vignettes +- Ludger Sandig — Vignettes, testthat framework - Marius Thomas — Bayesian MCP-mod, various updates to code, docs, and tests - Daniel Sabanes Bove — powMCTInterim implementation, longitudinal data vignette - Carina Miller - Time-to-event vignette diff --git a/README.md b/README.md index 82198b9..400acd9 100644 --- a/README.md +++ b/README.md @@ -132,7 +132,7 @@ package authors and maintainers as listed in the `DESCRIPTION` file. ### Other authors and substantial contributors -- Ludger Sandig — Vignettes +- Ludger Sandig — Vignettes, testthat framework - Marius Thomas — Bayesian MCP-mod, various updates to code, docs, and tests - Daniel Sabanes Bove — powMCTInterim implementation, longitudinal data From 17841dd58017d9a2f49a110bd9a64b515d558739 Mon Sep 17 00:00:00 2001 From: Marius Thomas Date: Tue, 13 Oct 2026 14:20:58 +0200 Subject: [PATCH 02/10] fix issue with structure in test --- tests/testsMCT.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/testsMCT.R b/tests/testsMCT.R index a2305a2..0e1cadc 100644 --- a/tests/testsMCT.R +++ b/tests/testsMCT.R @@ -260,7 +260,7 @@ exm2<-c(0.05,5) expo<-0.2 quad<--0.6 beta<-c(0.05,4) -data.sim <- structure(list(X = structure(1:4, .Label = c("0", "10", "20", "40"), class = "factor"), +data.sim <- structure(list(X = structure(1:4, levels = c("0", "10", "20", "40"), class = "factor"), dose = c(0L, 10L, 20L, 40L), Estimate = c(0.266942236, 3.792703657, 14.69084734, 17.71179102), Cov1 = c(3.685607913, 0.595285049, 0.651289991, 0.742901538), From 1ac62b53bbe0fb177bfb76bfbef446cc1efb2d2c Mon Sep 17 00:00:00 2001 From: Marius Thomas Date: Tue, 13 Oct 2026 14:30:58 +0200 Subject: [PATCH 03/10] update NEWS --- NEWS.md | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index 29cee38..308b9b3 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,9 @@ -# DoseFinding (development version) +# DoseFinding 1.4-2 +* Added vignette illustrating analysis of time-to-event data (#9. thanks to Carina Miller for her work on this) +* added contributors section to readme (#40) +* plot.DRMod now also works correctly when arguments are provided as expressions (#51) +* updated link for github installation (#44) +* Rdpack is now used to handle references (#43) # DoseFinding 1.4-1 * Added powMCTInterim function to implement conditional/predictive power From 9788fae406d4f23681f8c9eda4e9d74250495b4a Mon Sep 17 00:00:00 2001 From: Marius Thomas Date: Tue, 13 Oct 2026 16:34:28 +0200 Subject: [PATCH 04/10] update cran-comments.md --- cran-comments.md | 6 ------ 1 file changed, 6 deletions(-) diff --git a/cran-comments.md b/cran-comments.md index 84d238a..837203a 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,9 +1,3 @@ -## 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 From 3a9be484c332939d35cf846f2d7eed226f4483b4 Mon Sep 17 00:00:00 2001 From: Marius Thomas Date: Wed, 14 Oct 2026 13:35:12 +0200 Subject: [PATCH 05/10] update Description for release --- DESCRIPTION | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index a8413fc..ba02123 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: DoseFinding Type: Package Title: Planning and Analyzing Dose Finding Experiments -Version: 1.4-1.9000 -Date: 2025-07-08 +Version: 1.4-2 +Date: 2026-10-14 Authors@R: c( person("Bjoern", "Bornkamp", email = "bjoern.bornkamp@novartis.com", comment = c(ORCID = "0000-0002-6294-8185"), role = c("aut")), From a00b62300e0828770122844bd31f3306fae9ac7a Mon Sep 17 00:00:00 2001 From: Marius Thomas Date: Thu, 15 Oct 2026 17:32:47 +0200 Subject: [PATCH 06/10] fix dead links, reduce time that tte vignette runs --- CRAN-SUBMISSION | 3 +++ inst/REFERENCES.bib | 2 +- vignettes/analysis_normal.Rmd | 2 +- vignettes/time_to_event_data.Rmd | 2 +- 4 files changed, 6 insertions(+), 3 deletions(-) create mode 100644 CRAN-SUBMISSION diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION new file mode 100644 index 0000000..c46a268 --- /dev/null +++ b/CRAN-SUBMISSION @@ -0,0 +1,3 @@ +Version: 1.4-2 +Date: 2026-10-14 11:40:21 UTC +SHA: 3a9be484c332939d35cf846f2d7eed226f4483b4 diff --git a/inst/REFERENCES.bib b/inst/REFERENCES.bib index 65ee814..14bb1cd 100644 --- a/inst/REFERENCES.bib +++ b/inst/REFERENCES.bib @@ -31,7 +31,7 @@ @article{biesheuvel2002 number={1}, pages={101--116}, year={2002}, - doi = {10.1002/1521-4036(200201)44:13.0.CO;2-H}, + doi = {10.1002/1521-4036(200201)44:1<101::AID-BIMJ101>3.0.CO;2-H}, publisher={Wiley Online Library} } diff --git a/vignettes/analysis_normal.Rmd b/vignettes/analysis_normal.Rmd index 67847de..15cf2b2 100644 --- a/vignettes/analysis_normal.Rmd +++ b/vignettes/analysis_normal.Rmd @@ -21,7 +21,7 @@ There is a separate vignette with details on [sample size and power calculation] We will use data from @verkindre2010, who actually use a cross-over design and utilize MCP-Mod in a supportive analysis. More information can be found at the corresponding -[clinicaltrials.gov page](https://www.clinicaltrials.gov/study/NCT00501852) +[clinicaltrials.gov page](https://clinicaltrials.gov/study/NCT00501852) and on the R help page `?glycobrom`. The main purpose @verkindre2010 was to provide safety and efficacy data on Glycopyrronium Bromide (NVA237) diff --git a/vignettes/time_to_event_data.Rmd b/vignettes/time_to_event_data.Rmd index 91f666f..db51b18 100644 --- a/vignettes/time_to_event_data.Rmd +++ b/vignettes/time_to_event_data.Rmd @@ -672,7 +672,7 @@ sampSizeMCT_TTE <- function(mods, Now we can calculate how many patients we would need to recruit to achieve an average power of 80%, assuming we would recruit for 2 years and we would end the study after 4 years. ```{r} -sampSizeMCT_TTE(mods, alpha = 0.025, alRatio = alRatio, end_rec = 2, end_stu = 4, targPow = 0.8, lowerN = 100, upperN = 500) +sampSizeMCT_TTE(mods, alpha = 0.025, alRatio = alRatio, end_rec = 2, end_stu = 4, targPow = 0.8, lowerN = 100, upperN = 00) ``` From a13bdc5c38c4f8385dc514c88d570b7e74d651c8 Mon Sep 17 00:00:00 2001 From: Marius Thomas Date: Thu, 15 Oct 2026 17:44:19 +0200 Subject: [PATCH 07/10] speed up tte vignette --- vignettes/time_to_event_data.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vignettes/time_to_event_data.Rmd b/vignettes/time_to_event_data.Rmd index db51b18..26e09ca 100644 --- a/vignettes/time_to_event_data.Rmd +++ b/vignettes/time_to_event_data.Rmd @@ -672,7 +672,7 @@ sampSizeMCT_TTE <- function(mods, Now we can calculate how many patients we would need to recruit to achieve an average power of 80%, assuming we would recruit for 2 years and we would end the study after 4 years. ```{r} -sampSizeMCT_TTE(mods, alpha = 0.025, alRatio = alRatio, end_rec = 2, end_stu = 4, targPow = 0.8, lowerN = 100, upperN = 00) +sampSizeMCT_TTE(mods, alpha = 0.025, alRatio = alRatio, end_rec = 2, end_stu = 4, targPow = 0.8, lowerN = 100, upperN = 300) ``` From 6d95c3e23f5f622b139612d4c019de8aee0dab52 Mon Sep 17 00:00:00 2001 From: Marius Thomas Date: Fri, 16 Oct 2026 16:17:56 +0200 Subject: [PATCH 08/10] CRAN submission file and comments --- CRAN-SUBMISSION | 4 ++-- cran-comments.md | 5 +++++ 2 files changed, 7 insertions(+), 2 deletions(-) diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION index c46a268..380ed67 100644 --- a/CRAN-SUBMISSION +++ b/CRAN-SUBMISSION @@ -1,3 +1,3 @@ Version: 1.4-2 -Date: 2026-10-14 11:40:21 UTC -SHA: 3a9be484c332939d35cf846f2d7eed226f4483b4 +Date: 2026-10-15 15:54:19 UTC +SHA: a13bdc5c38c4f8385dc514c88d570b7e74d651c8 diff --git a/cran-comments.md b/cran-comments.md index 837203a..6079244 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,3 +1,8 @@ +## Resubmission +This is a resubmission. In this version I have made the following updates + * fixed broken links + * made changes to one vignette to speed up checks + ## R CMD check results 0 errors | 0 warnings | 0 notes From 0372715b732d75fc8bc6f6e6d72495e2cee2deec Mon Sep 17 00:00:00 2001 From: MThomas91 Date: Fri, 16 Oct 2026 16:24:47 +0200 Subject: [PATCH 09/10] remove submission file --- CRAN-SUBMISSION | 3 --- 1 file changed, 3 deletions(-) delete mode 100644 CRAN-SUBMISSION diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION deleted file mode 100644 index 380ed67..0000000 --- a/CRAN-SUBMISSION +++ /dev/null @@ -1,3 +0,0 @@ -Version: 1.4-2 -Date: 2026-10-15 15:54:19 UTC -SHA: a13bdc5c38c4f8385dc514c88d570b7e74d651c8 From 3844a8545fd56e87c0219b07bbb92323fc905a33 Mon Sep 17 00:00:00 2001 From: MThomas91 Date: Fri, 16 Oct 2026 16:26:08 +0200 Subject: [PATCH 10/10] update to dev version --- DESCRIPTION | 2 +- NEWS.md | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index ba02123..032ea1f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: DoseFinding Type: Package Title: Planning and Analyzing Dose Finding Experiments -Version: 1.4-2 +Version: 1.4-2.9000 Date: 2026-10-14 Authors@R: c( person("Bjoern", "Bornkamp", email = "bjoern.bornkamp@novartis.com", diff --git a/NEWS.md b/NEWS.md index 308b9b3..a50e92e 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,5 @@ +# DoseFinding (development version) + # DoseFinding 1.4-2 * Added vignette illustrating analysis of time-to-event data (#9. thanks to Carina Miller for her work on this) * added contributors section to readme (#40)