From 05802bba7b500cc7d86dfd8c0da2e48fce3c367c Mon Sep 17 00:00:00 2001 From: Puzzled-Face Date: Fri, 2 Aug 2024 10:38:31 +0000 Subject: [PATCH 01/10] Allow zero follow-up times in DataDA objects. --- DESCRIPTION | 2 +- R/Data-validity.R | 2 +- man/crmPackExample.Rd | 2 +- man/crmPackHelp.Rd | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 2df846ee1..43530657a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: crmPack Title: Object-Oriented Implementation of CRM Designs -Version: 2.0.0.9158 +Version: 2.0.0 Authors@R: c( person("Daniel", "Sabanes Bove", , "daniel.sabanes_bove@rconis.com", role = c("aut", "cre")), person("Wai", "Yin Yeung", , "winnie.yeung@roche.com", role = "aut"), diff --git a/R/Data-validity.R b/R/Data-validity.R index 08a0ffee8..665af9a4b 100644 --- a/R/Data-validity.R +++ b/R/Data-validity.R @@ -182,7 +182,7 @@ v_data_da <- function(object) { } v$check( test_numeric(object@u, upper = object@Tmax, len = object@nObs, any.missing = FALSE) && - all(object@u > 0), + all(object@u >= 0), "u must be of type double, nObs length, non-negative and not greater than Tmax" ) v$check( diff --git a/man/crmPackExample.Rd b/man/crmPackExample.Rd index 72f1988f9..167e2e274 100644 --- a/man/crmPackExample.Rd +++ b/man/crmPackExample.Rd @@ -14,6 +14,6 @@ Calling this helper function should open the example.pdf document, residing in the doc subfolder of the package installation directory. } \author{ -Daniel Sabanes Bove \email{sabanesd@roche.com} +Daniel Sabanes Bove \email{sabanesd@rconis.com} } \keyword{documentation} diff --git a/man/crmPackHelp.Rd b/man/crmPackHelp.Rd index d8023e40f..4c10756d4 100644 --- a/man/crmPackHelp.Rd +++ b/man/crmPackHelp.Rd @@ -14,6 +14,6 @@ This convenience function opens your browser with the help pages for crmPack. } \author{ -Daniel Sabanes Bove \email{sabanesd@roche.com} +Daniel Sabanes Bove \email{sabanesd@rconis.com} } \keyword{documentation} From afa05516a00bd209a3dc1fa01de2e9c49ec2ac3e Mon Sep 17 00:00:00 2001 From: Puzzled-Face Date: Fri, 2 Aug 2024 10:58:51 +0000 Subject: [PATCH 02/10] Fix version number in NEWS.md and update test results to reflect changed reporting labels/slot names. --- NEWS.md | 2 +- tests/testthat/_snaps/Design-methods.md | 32 ++++++++++++------------- 2 files changed, 17 insertions(+), 17 deletions(-) diff --git a/NEWS.md b/NEWS.md index 050b241c4..194234bb2 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# Version 2.0.0.9158 +# Version 2.0.0 * **Note: This release (1.0 -> 2.0) signifies a major breaking revamp of the package.** Users are advised to carefully review the release notes and documentation for detailed information on the changes and any necessary updates to their existing code. * Implemented `knit_print` methods for almost all `crmPack` classes to improve rendering in Markdown and Quarto documents. See the vignette for more details. * Provided basic support for ordinal CRM models. See the vignette for more details. diff --git a/tests/testthat/_snaps/Design-methods.md b/tests/testthat/_snaps/Design-methods.md index 51a305cc9..dda5a1b36 100644 --- a/tests/testthat/_snaps/Design-methods.md +++ b/tests/testthat/_snaps/Design-methods.md @@ -605,7 +605,7 @@ result Output An object of class "PseudoDualSimulations" - Slot "fitEff": + Slot "fit_eff": [[1]] [[1]]$theta1 [1] -4.20662 @@ -619,13 +619,13 @@ - Slot "FinalGstarEstimates": + Slot "final_gstar_estimates": [1] 146.2479 - Slot "FinalGstarAtDoseGrid": + Slot "final_gstar_at_dose_grid": [1] 125 - Slot "FinalGstarCIs": + Slot "final_gstar_cis": [[1]] [[1]]$lower [1] 75.03531 @@ -635,16 +635,16 @@ - Slot "FinalGstarRatios": + Slot "final_gstar_ratios": [1] 3.798815 - Slot "FinalOptimalDose": + Slot "final_optimal_dose": [1] 137.5996 - Slot "FinalOptimalDoseAtDoseGrid": + Slot "final_optimal_dose_at_dose_grid": [1] 125 - Slot "sigma2est": + Slot "sigma2_est": [1] 0.1616952 Slot "fit": @@ -765,7 +765,7 @@ result Output An object of class "PseudoDualSimulations" - Slot "fitEff": + Slot "fit_eff": [[1]] middle lower upper 1 -0.3079474 -0.8521410 0.08196096 @@ -782,13 +782,13 @@ 12 1.6915134 1.2623492 2.22318756 - Slot "FinalGstarEstimates": + Slot "final_gstar_estimates": [1] 300 - Slot "FinalGstarAtDoseGrid": + Slot "final_gstar_at_dose_grid": [1] 225 - Slot "FinalGstarCIs": + Slot "final_gstar_cis": [[1]] [[1]]$lower [1] 300 @@ -798,16 +798,16 @@ - Slot "FinalGstarRatios": + Slot "final_gstar_ratios": [1] 1 - Slot "FinalOptimalDose": + Slot "final_optimal_dose": [1] 62.78087 - Slot "FinalOptimalDoseAtDoseGrid": + Slot "final_optimal_dose_at_dose_grid": [1] 50 - Slot "sigma2est": + Slot "sigma2_est": [1] 0.2648646 Slot "fit": From 1d0b03dcea53dc3852a70facf41a1a0bf05ca529 Mon Sep 17 00:00:00 2001 From: Puzzled-Face Date: Fri, 2 Aug 2024 12:14:54 +0000 Subject: [PATCH 03/10] Fix new pkgdown errors. --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 43530657a..2f647df84 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -33,7 +33,7 @@ Description: Implements a wide range of model-based dose escalation new models, escalation or stopping rules. Further details are presented in Sabanes Bove et al. (2019) . License: GPL (>= 2) -URL: https://github.com/openpharma/crmPack +URL: https://github.com/openpharma/crmPack, https://github.com/openpharma/crmPack BugReports: https://github.com/openpharma/crmPack/issues Depends: ggplot2 (>= 2.0.0), From 0d02e6ecda0d1729b96524bda4c9f34392e0b612 Mon Sep 17 00:00:00 2001 From: Puzzled-Face Date: Tue, 10 Sep 2024 09:20:23 +0000 Subject: [PATCH 04/10] update error message for invalid DataDA --- R/Data-validity.R | 2 +- tests/testthat/test-Data-validity.R | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/R/Data-validity.R b/R/Data-validity.R index 665af9a4b..9c9748855 100644 --- a/R/Data-validity.R +++ b/R/Data-validity.R @@ -183,7 +183,7 @@ v_data_da <- function(object) { v$check( test_numeric(object@u, upper = object@Tmax, len = object@nObs, any.missing = FALSE) && all(object@u >= 0), - "u must be of type double, nObs length, non-negative and not greater than Tmax" + "u must be of type double, nObs length, non-negative, not missing and not greater than Tmax" ) v$check( test_numeric(object@t0, lower = 0, len = object@nObs, any.missing = FALSE, sorted = TRUE), diff --git a/tests/testthat/test-Data-validity.R b/tests/testthat/test-Data-validity.R index 21fcf5b9c..b4ae84d00 100644 --- a/tests/testthat/test-Data-validity.R +++ b/tests/testthat/test-Data-validity.R @@ -242,7 +242,7 @@ test_that("v_data_da: error for u of wrong length and values", { expect_equal( v_data_da(object), - "u must be of type double, nObs length, non-negative and not greater than Tmax" # nolintr + "u must be of type double, nObs length, non-negative, not missing and not greater than Tmax" # nolintr ) }) From f02a4d1ec56f27ab26de04ab6127bdaf4fac13be Mon Sep 17 00:00:00 2001 From: Puzzled-Face Date: Tue, 10 Sep 2024 11:01:26 +0000 Subject: [PATCH 05/10] Fix URL in DESCRIPTION --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 2f647df84..6aafcde77 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -33,7 +33,7 @@ Description: Implements a wide range of model-based dose escalation new models, escalation or stopping rules. Further details are presented in Sabanes Bove et al. (2019) . License: GPL (>= 2) -URL: https://github.com/openpharma/crmPack, https://github.com/openpharma/crmPack +URL: https://github.com/openpharma/crmPack, https://github.io/openpharma/crmPack BugReports: https://github.com/openpharma/crmPack/issues Depends: ggplot2 (>= 2.0.0), From 33345f014502c89f381ee484e9b5271b751ad5c6 Mon Sep 17 00:00:00 2001 From: Puzzled-Face Date: Tue, 10 Sep 2024 12:19:43 +0000 Subject: [PATCH 06/10] Fix URL in DESCRIPTION --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 6aafcde77..2aba866ea 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -33,7 +33,7 @@ Description: Implements a wide range of model-based dose escalation new models, escalation or stopping rules. Further details are presented in Sabanes Bove et al. (2019) . License: GPL (>= 2) -URL: https://github.com/openpharma/crmPack, https://github.io/openpharma/crmPack +URL: https://github.com/openpharma/crmPack, https://pages.github.com/openpharma/crmPack BugReports: https://github.com/openpharma/crmPack/issues Depends: ggplot2 (>= 2.0.0), From 3b6e087caf6f44e5dd3a3d830f937df0eafe579e Mon Sep 17 00:00:00 2001 From: Puzzled-Face Date: Tue, 10 Sep 2024 12:55:45 +0000 Subject: [PATCH 07/10] Fix URL in DESCRIPTION --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 2aba866ea..faf3a323a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -33,7 +33,7 @@ Description: Implements a wide range of model-based dose escalation new models, escalation or stopping rules. Further details are presented in Sabanes Bove et al. (2019) . License: GPL (>= 2) -URL: https://github.com/openpharma/crmPack, https://pages.github.com/openpharma/crmPack +URL: https://github.com/openpharma/crmPack, https://openpharma.github.io/crmPack BugReports: https://github.com/openpharma/crmPack/issues Depends: ggplot2 (>= 2.0.0), From 295e283f9d5bbb172673380908ccbc8e5121e7ca Mon Sep 17 00:00:00 2001 From: Puzzled-Face Date: Tue, 10 Sep 2024 12:59:56 +0000 Subject: [PATCH 08/10] Fix URL: in DESCRIPTION --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index faf3a323a..8e8a2d401 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -33,7 +33,7 @@ Description: Implements a wide range of model-based dose escalation new models, escalation or stopping rules. Further details are presented in Sabanes Bove et al. (2019) . License: GPL (>= 2) -URL: https://github.com/openpharma/crmPack, https://openpharma.github.io/crmPack +URL: https://github.com/openpharma/crmPack, https://openpharma.github.io/crmPack/ BugReports: https://github.com/openpharma/crmPack/issues Depends: ggplot2 (>= 2.0.0), From 2a20040602a8ea6d04be69db9ab7db2852689d3c Mon Sep 17 00:00:00 2001 From: Puzzled-Face Date: Tue, 10 Sep 2024 13:30:36 +0000 Subject: [PATCH 09/10] Bump --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 8e8a2d401..1657211f3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -32,7 +32,7 @@ Description: Implements a wide range of model-based dose escalation form in the S4 class system, making it very flexible for adaptation to new models, escalation or stopping rules. Further details are presented in Sabanes Bove et al. (2019) . -License: GPL (>= 2) +License: GPL (>= 2) URL: https://github.com/openpharma/crmPack, https://openpharma.github.io/crmPack/ BugReports: https://github.com/openpharma/crmPack/issues Depends: From 7fef255ac86f9b2ba9199f24942b7ca0949f1f7d Mon Sep 17 00:00:00 2001 From: John Kirkpatrick <133956382+Puzzled-Face@users.noreply.github.com> Date: Mon, 30 Sep 2024 09:26:47 +0100 Subject: [PATCH 10/10] Update DESCRIPTION --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 4386b2ee9..1657211f3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: crmPack Title: Object-Oriented Implementation of CRM Designs -Version: 2.0.0.9160 +Version: 2.0.0 Authors@R: c( person("Daniel", "Sabanes Bove", , "daniel.sabanes_bove@rconis.com", role = c("aut", "cre")), person("Wai", "Yin Yeung", , "winnie.yeung@roche.com", role = "aut"),