From dcc270381f70c1d1b76a3a146e14515482fc3d9a Mon Sep 17 00:00:00 2001 From: Dong Xi <38050865+xidongdxi@users.noreply.github.com> Date: Fri, 8 Nov 2024 11:32:33 -0500 Subject: [PATCH] transfer to openpharma updated links and version --- DESCRIPTION | 6 +++--- NEWS.md | 5 +++++ R/graph_create.R | 2 +- README.Rmd | 26 ++++++++++++++++++++------ README.md | 35 ++++++++++++++++++++++++++--------- _pkgdown.yml | 2 +- codemeta.json | 14 +++++++------- inst/CITATION | 4 ++-- man/graph_create.Rd | 2 +- man/graphicalMCP-package.Rd | 4 ++-- 10 files changed, 68 insertions(+), 32 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 8be8f9e..eae88f5 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Type: Package Package: graphicalMCP Title: Graphical Multiple Comparison Procedures -Version: 0.2.5 +Version: 0.2.6 Authors@R: c( person("Dong", "Xi", , "dong.xi1@gilead.com", role = c("aut", "cre")), person("Ethan", "Brockmann", , "ethan.brockmann@atorusresearch.com", role = "aut"), @@ -15,8 +15,8 @@ Description: Multiple comparison procedures (MCPs) control the familywise error implementation of graphical MCPs which allow mixed types of tests. It also includes power simulations and visualization of graphical MCPs. License: Apache License (>= 2) -URL: https://gilead-biostats.github.io/graphicalMCP/ -BugReports: https://github.com/Gilead-BioStats/graphicalMCP/issues +URL: https://github.com/openpharma/graphicalMCP +BugReports: https://github.com/openpharma/graphicalMCP/issues Depends: R (>= 4.1.0) Imports: diff --git a/NEWS.md b/NEWS.md index 8d30aee..008cf9c 100644 --- a/NEWS.md +++ b/NEWS.md @@ -41,3 +41,8 @@ * Updated adjust_weights_parametric_util.Rd * Resubmission for first CRAN release + +# graphicalMCP 0.2.6 + +* Github repo transferred to openpharma +* Submission for CRAN release diff --git a/R/graph_create.R b/R/graph_create.R index 5d9c4a8..2c26e64 100644 --- a/R/graph_create.R +++ b/R/graph_create.R @@ -101,7 +101,7 @@ #' H3 = c(0, 1, 0, 0), #' H4 = c(1, 0, 0, 0) #' ) -#' \dontrun{ +#' \try{ #' g <- graph_create(hypotheses, transitions) #' } #' diff --git a/README.Rmd b/README.Rmd index 2f21120..97d4b0e 100644 --- a/README.Rmd +++ b/README.Rmd @@ -17,11 +17,15 @@ knitr::opts_chunk$set( +[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) [![CRAN status](https://www.r-pkg.org/badges/version/graphicalMCP)](https://cran.r-project.org/package=graphicalMCP) +[![CRAN monthly downloads](https://cranlogs.r-pkg.org/badges/graphicalMCP)](https://cranlogs.r-pkg.org/badges/graphicalMCP) +[![CRAN total downloads](https://cranlogs.r-pkg.org/badges/grand-total/graphicalMCP)](https://cranlogs.r-pkg.org/badges/grand-total/graphicalMCP) + -# graphicalMCP +# graphicalMCP # Introduction @@ -29,11 +33,21 @@ Graphical approaches for multiple comparison procedures (MCPs) are a general fra # Installation -`graphicalMCP` is currently not on CRAN but can be installed from GitHub using the following code: +### Release -```{r eval = FALSE} +You can install the current release version from *CRAN* with: + +```{r cran-installation, eval = FALSE} +install.packages("graphicalMCP") +``` + +### Development + +You can install the current development version from *GitHub* with: + +```{r github-installation, eval = FALSE} # install.packages("pak") -pak::pak("Gilead-BioStats/graphicalMCP") +pak::pak("openpharma/graphicalMCP") ``` # Documentation @@ -46,7 +60,7 @@ pak::pak("Gilead-BioStats/graphicalMCP") - see `vignette("graph-examples")` for common multiple comparison procedures illustrated using `graphicalMCP` - see `vignette("generate-closure")` for rationales to generate the closure and the weighting strategy of a graph - see `vignette("comparisons")` for comparisons to other R packages -- To view vignettes in R after properly installing `graphicalMCP` from GitHub, we can build vignettes by `devtools::install(build_vignettes = TRUE)`, and then use `browseVignettes("graphicalMCP")` to view the full list of vignettes +- To view vignettes in R after properly installing `graphicalMCP`, we can build vignettes by `devtools::install(build_vignettes = TRUE)`, and then use `browseVignettes("graphicalMCP")` to view the full list of vignettes # Related work @@ -60,6 +74,6 @@ Built upon these packages, we hope to implement graphical MCPs in a more general Along with the authors and contributors, thanks to the following people for their suggestions and inspirations on the package: -Frank Bretz, Willi Maurer, Ekkehard Glimm, Nan Chen, Jeremy Wildfire, Spencer Childress, Colleen McLaughlin, Matt Roumaya, Chelsea Dickens, and Ron Yu +Frank Bretz, Willi Maurer, Ekkehard Glimm, Nan Chen, Jeremy Wildfire, Spencer Childress, Colleen McLaughlin, Matt Roumaya, Chelsea Dickens, Nan Xiao, Keaven Anderson, and Ron Yu We owe a debt of gratitude to the authors of [gMCP](https://cran.r-project.org/package=gMCP) for their pioneering work, without which this package would not be nearly as extensive as it is. diff --git a/README.md b/README.md index c7cd47d..21e0ad6 100644 --- a/README.md +++ b/README.md @@ -2,12 +2,20 @@ +[![Project Status: Active – The project has reached a stable, usable +state and is being actively +developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) [![CRAN status](https://www.r-pkg.org/badges/version/graphicalMCP)](https://cran.r-project.org/package=graphicalMCP) +[![CRAN monthly +downloads](https://cranlogs.r-pkg.org/badges/graphicalMCP)](https://cranlogs.r-pkg.org/badges/graphicalMCP) +[![CRAN total +downloads](https://cranlogs.r-pkg.org/badges/grand-total/graphicalMCP)](https://cranlogs.r-pkg.org/badges/grand-total/graphicalMCP) + -# graphicalMCP +# graphicalMCP # Introduction @@ -21,12 +29,21 @@ efficient way. # Installation -`graphicalMCP` is currently not on CRAN but can be installed from GitHub -using the following code: +### Release + +You can install the current release version from *CRAN* with: + +``` r +install.packages("graphicalMCP") +``` + +### Development + +You can install the current development version from *GitHub* with: ``` r # install.packages("pak") -pak::pak("Gilead-BioStats/graphicalMCP") +pak::pak("openpharma/graphicalMCP") ``` # Documentation @@ -46,10 +63,10 @@ pak::pak("Gilead-BioStats/graphicalMCP") the closure and the weighting strategy of a graph - see `vignette("comparisons")` for comparisons to other R packages -- To view vignettes in R after properly installing `graphicalMCP` from - GitHub, we can build vignettes by - `devtools::install(build_vignettes = TRUE)`, and then use - `browseVignettes("graphicalMCP")` to view the full list of vignettes +- To view vignettes in R after properly installing `graphicalMCP`, we + can build vignettes by `devtools::install(build_vignettes = TRUE)`, + and then use `browseVignettes("graphicalMCP")` to view the full list + of vignettes # Related work @@ -70,7 +87,7 @@ for their suggestions and inspirations on the package: Frank Bretz, Willi Maurer, Ekkehard Glimm, Nan Chen, Jeremy Wildfire, Spencer Childress, Colleen McLaughlin, Matt Roumaya, Chelsea Dickens, -and Ron Yu +Nan Xiao, Keaven Anderson, and Ron Yu We owe a debt of gratitude to the authors of [gMCP](https://cran.r-project.org/package=gMCP) for their pioneering diff --git a/_pkgdown.yml b/_pkgdown.yml index b9ea367..10ad583 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -1,4 +1,4 @@ -url: https://gilead-biostats.github.io/graphicalMCP/ +url: https://openpharma.github.io/graphicalMCP/ template: bootstrap: 5 diff --git a/codemeta.json b/codemeta.json index a4d5f3d..6cf624a 100644 --- a/codemeta.json +++ b/codemeta.json @@ -4,10 +4,10 @@ "identifier": "graphicalMCP", "description": "Multiple comparison procedures (MCPs) control the familywise error rate in clinical trials. Graphical MCPs include many commonly used procedures as special cases; see Bretz et al. (2011) , Lu (2016) , and Xi et al. (2017) . This package is a low-dependency implementation of graphical MCPs which allow mixed types of tests. It also includes power simulations and visualization of graphical MCPs.", "name": "graphicalMCP: Graphical Multiple Comparison Procedures", - "codeRepository": "https://github.com/Gilead-BioStats/graphicalMCP", - "issueTracker": "https://github.com/Gilead-BioStats/graphicalMCP/issues", + "codeRepository": "https://github.com/openpharma/graphicalMCP", + "issueTracker": "https://github.com/openpharma/graphicalMCP/issues", "license": "Apache License 2", - "version": "0.2.5", + "version": "0.2.6", "programmingLanguage": { "@type": "ComputerLanguage", "name": "R", @@ -330,10 +330,10 @@ } ], "name": "{graphicalMCP}: Graphical multiple comparison procedures", - "url": "https://github.com/Gilead-BioStats/graphicalMCP" + "url": "https://github.com/openpharma/graphicalMCP" } ], - "relatedLink": "https://gilead-biostats.github.io/graphicalMCP/", - "releaseNotes": "https://github.com/Gilead-BioStats/graphicalMCP/blob/master/NEWS.md", - "readme": "https://github.com/Gilead-BioStats/graphicalMCP/blob/main/README.md" + "relatedLink": "https://github.com/openpharma/graphicalMCP", + "releaseNotes": "https://github.com/openpharma/graphicalMCP/blob/master/NEWS.md", + "readme": "https://github.com/openpharma/graphicalMCP/blob/main/README.md" } diff --git a/inst/CITATION b/inst/CITATION index 3f5bd8f..342738f 100644 --- a/inst/CITATION +++ b/inst/CITATION @@ -4,7 +4,7 @@ bibentry( "manual", title = "{graphicalMCP}: Graphical multiple comparison procedures", author = as.person("Dong Xi and Ethan Brockmann"), - edition = "version 0.2.5", + edition = "version 0.2.6", year = 2024, - url = "https://github.com/Gilead-BioStats/graphicalMCP" + url = "https://CRAN.R-project.org/package=graphicalMCP" ) diff --git a/man/graph_create.Rd b/man/graph_create.Rd index 7b339a1..146d4c9 100644 --- a/man/graph_create.Rd +++ b/man/graph_create.Rd @@ -101,7 +101,7 @@ transitions <- rbind( H3 = c(0, 1, 0, 0), H4 = c(1, 0, 0, 0) ) -\dontrun{ +\try{ g <- graph_create(hypotheses, transitions) } diff --git a/man/graphicalMCP-package.Rd b/man/graphicalMCP-package.Rd index 07f8c69..55fb61a 100644 --- a/man/graphicalMCP-package.Rd +++ b/man/graphicalMCP-package.Rd @@ -13,8 +13,8 @@ Multiple comparison procedures (MCPs) control the familywise error rate in clini \seealso{ Useful links: \itemize{ - \item \url{https://gilead-biostats.github.io/graphicalMCP/} - \item Report bugs at \url{https://github.com/Gilead-BioStats/graphicalMCP/issues} + \item \url{https://github.com/openpharma/graphicalMCP} + \item Report bugs at \url{https://github.com/openpharma/graphicalMCP/issues} } }