transfer to openpharma

updated links and version
openpharma · Nov 8, 2024 · dcc2703 · dcc2703
1 parent ec0ee2c
commit dcc2703
Show file tree

Hide file tree

Showing 10 changed files with 68 additions and 32 deletions.
diff --git 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", , "[email protected]", role = c("aut", "cre")),
     person("Ethan", "Brockmann", , "[email protected]", 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
@@ -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
@@ -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
@@ -17,23 +17,37 @@ knitr::opts_chunk$set(
 
 <!-- badges: start -->
 
+[![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)
+<!-- [![Code Coverage](https://raw.githubusercontent.com/openpharma/graphicalMCP/_xml_coverage_reports/data/main/badge.svg)](https://openpharma.github.io/graphicalMCP/latest-tag/coverage-report/) -->
 
 <!-- badges: end -->
 
-# graphicalMCP <a href="https://gilead-biostats.github.io/graphicalMCP/"><img src="man/figures/logo.png" align="right" height="139" /></a>
+# graphicalMCP <a href="https://openpharma.github.io/graphicalMCP/"><img src="man/figures/logo.png" align="right" height="139" /></a>
 
 # Introduction
 
 Graphical approaches for multiple comparison procedures (MCPs) are a general framework to control the family-wise error rate strongly at a pre-specified significance level $0<\alpha<1$. This approach includes many commonly used MCPs as special cases and is transparent in visualizing MCPs for better communications. `graphicalMCP` is designed to design and analyze graphical MCPs in a flexible, informative and efficient way.
 
 # 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
@@ -2,12 +2,20 @@
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 <!-- badges: start -->
 
+[![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)
+<!-- [![Code Coverage](https://raw.githubusercontent.com/openpharma/graphicalMCP/_xml_coverage_reports/data/main/badge.svg)](https://openpharma.github.io/graphicalMCP/latest-tag/coverage-report/) -->
 
 <!-- badges: end -->
 
-# graphicalMCP <a href="https://gilead-biostats.github.io/graphicalMCP/"><img src="man/figures/logo.png" align="right" height="139" /></a>
+# graphicalMCP <a href="https://openpharma.github.io/graphicalMCP/"><img src="man/figures/logo.png" align="right" height="139" /></a>
 
 # 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
@@ -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
@@ -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) <doi:10.1002/bimj.201000239>, Lu (2016) <doi:10.1002/sim.6985>, and Xi et al. (2017) <doi:10.1002/bimj.201600233>. 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
@@ -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
diff --git a/man/graphicalMCP-package.Rd b/man/graphicalMCP-package.Rd