Update links with urlchecker::url_update()

ropensci · Dec 19, 2023 · 99ed393 · 99ed393
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diff --git a/NEWS.md b/NEWS.md
@@ -360,7 +360,7 @@ create_lambda_param(value = 1.2, estimate = TRUE)
 
 ### MINOR IMPROVEMENTS
 
-  * Follow all [rOpenSci packaging guidelines](https://github.com/ropensci/onboarding/blob/master/packaging_guide.md)
+  * Follow all [rOpenSci packaging guidelines](https://github.com/ropensci/software-review/blob/master/packaging_guide.md)
 
 ### BUG FIXES
 

diff --git a/README.md b/README.md
@@ -1,14 +1,14 @@
 # babette
 
-[![Peer Review Status](https://badges.ropensci.org/209_status.svg)](https://github.com/ropensci/onboarding/issues/209)
+[![Peer Review Status](https://badges.ropensci.org/209_status.svg)](https://github.com/ropensci/software-review/issues/209)
 [![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/babette)](https://cran.r-project.org/package=babette)
 [![](http://cranlogs.r-pkg.org/badges/grand-total/babette)]( https://CRAN.R-project.org/package=babette)
 [![](http://cranlogs.r-pkg.org/badges/babette)](https://CRAN.R-project.org/package=babette)
 
-Branch   |[![GitHub Actions logo](man/figures/GitHubActions.png)](https://github.com/ropensci/babette/actions)|[![Codecov logo](man/figures/Codecov.png)](https://www.codecov.io)
+Branch   |[![GitHub Actions logo](man/figures/GitHubActions.png)](https://github.com/ropensci/babette/actions)|[![Codecov logo](man/figures/Codecov.png)](https://about.codecov.io/)
 ---------|----------------------------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------
-`master` |![R-CMD-check](https://github.com/ropensci/babette/workflows/R-CMD-check/badge.svg?branch=master)   |[![codecov.io](https://codecov.io/github/ropensci/babette/coverage.svg?branch=master)](https://codecov.io/github/ropensci/babette/branch/master)
-`develop`|![R-CMD-check](https://github.com/ropensci/babette/workflows/R-CMD-check/badge.svg?branch=develop)  |[![codecov.io](https://codecov.io/github/ropensci/babette/coverage.svg?branch=develop)](https://codecov.io/github/ropensci/babette/branch/develop)
+`master` |![R-CMD-check](https://github.com/ropensci/babette/workflows/R-CMD-check/badge.svg?branch=master)   |[![codecov.io](https://codecov.io/github/ropensci/babette/coverage.svg?branch=master)](https://app.codecov.io/github/ropensci/babette/branch/master)
+`develop`|![R-CMD-check](https://github.com/ropensci/babette/workflows/R-CMD-check/badge.svg?branch=develop)  |[![codecov.io](https://codecov.io/github/ropensci/babette/coverage.svg?branch=develop)](https://app.codecov.io/github/ropensci/babette/branch/develop)
 
 [![DOI](https://zenodo.org/badge/118616108.svg)](https://zenodo.org/badge/latestdoi/118616108)
 
@@ -48,7 +48,7 @@ See:
  * [lumier](https://github.com/ropensci/lumier): R Shiny app to help create the R function call needed
  * [examples](https://github.com/richelbilderbeek/babette_examples): examples tested by Travis CI and AppVeyor
  * [article](https://besjournals.onlinelibrary.wiley.com/doi/abs/10.1111/2041-210X.13032), in 'Methods in Ecology and Evolution'
- * [Methods.blog post: The babette R Package: How to Sooth the Phylogenetic BEAST2](https://methodsblog.wordpress.com/2018/06/25/babette-beast2/)
+ * [Methods.blog post: The babette R Package: How to Sooth the Phylogenetic BEAST2](https://methodsblog.com/2018/06/25/babette-beast2/)
  * [rOpenSci blog post: Call BEAST2 for Bayesian evolutionary analysis from R](https://ropensci.org/blog/2020/01/28/babette/)
  * [pre-print article](https://doi.org/10.1101/271866), in bioRxiv
  * ['babette' YouTube channel](https://www.youtube.com/watch?v=nA-0-Fc95xY&list=PLu8_ZyzXyRDFIRx-kdDI5Q6xVr-HnY7TB)
@@ -95,12 +95,12 @@ Sure, just add an Issue. Or send an email.
 
 ## Dependencies
 
-Branch                                          |[![GitHub Actions logo](man/figures/GitHubActions.png)](https://github.com/ropensci/babette/actions) `master`|[![GitHub Actions logo](man/figures/GitHubActions.png)](https://github.com/ropensci/babette/actions) `develop`|[![Codecov logo](man/figures/Codecov.png)](https://www.codecov.io) `master`                                                                       |[![Codecov logo](man/figures/Codecov.png)](https://www.codecov.io) `develop`
+Branch                                          |[![GitHub Actions logo](man/figures/GitHubActions.png)](https://github.com/ropensci/babette/actions) `master`|[![GitHub Actions logo](man/figures/GitHubActions.png)](https://github.com/ropensci/babette/actions) `develop`|[![Codecov logo](man/figures/Codecov.png)](https://about.codecov.io/) `master`                                                                       |[![Codecov logo](man/figures/Codecov.png)](https://about.codecov.io/) `develop`
 ------------------------------------------------|-------------------------------------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------
-[beautier](https://github.com/ropensci/beautier)|![R-CMD-check](https://github.com/ropensci/beautier/workflows/R-CMD-check/badge.svg?branch=master)           |![R-CMD-check](https://github.com/ropensci/beautier/workflows/R-CMD-check/badge.svg?branch=develop)           |[![codecov.io](https://codecov.io/github/ropensci/beautier/coverage.svg?branch=master)](https://codecov.io/github/ropensci/beautier/branch/master)|[![codecov.io](https://codecov.io/github/ropensci/beautier/coverage.svg?branch=develop)](https://codecov.io/github/ropensci/beautier/branch/develop)
-[beastier](https://github.com/ropensci/beastier)|![R-CMD-check](https://github.com/ropensci/beastier/workflows/R-CMD-check/badge.svg?branch=master)           |![R-CMD-check](https://github.com/ropensci/beastier/workflows/R-CMD-check/badge.svg?branch=develop)           |[![codecov.io](https://codecov.io/github/ropensci/beastier/coverage.svg?branch=master)](https://codecov.io/github/ropensci/beastier/branch/master)|[![codecov.io](https://codecov.io/github/ropensci/beastier/coverage.svg?branch=develop)](https://codecov.io/github/ropensci/beastier/branch/develop)
-[mauricer](https://github.com/ropensci/mauricer)|![R-CMD-check](https://github.com/ropensci/mauricer/workflows/R-CMD-check/badge.svg?branch=master)           |![R-CMD-check](https://github.com/ropensci/mauricer/workflows/R-CMD-check/badge.svg?branch=develop)           |[![codecov.io](https://codecov.io/github/ropensci/mauricer/coverage.svg?branch=master)](https://codecov.io/github/ropensci/mauricer/branch/master)|[![codecov.io](https://codecov.io/github/ropensci/mauricer/coverage.svg?branch=develop)](https://codecov.io/github/ropensci/mauricer/branch/develop)
-[tracerer](https://github.com/ropensci/tracerer)|![R-CMD-check](https://github.com/ropensci/tracerer/workflows/R-CMD-check/badge.svg?branch=master)           |![R-CMD-check](https://github.com/ropensci/tracerer/workflows/R-CMD-check/badge.svg?branch=develop)           |[![codecov.io](https://codecov.io/github/ropensci/tracerer/coverage.svg?branch=master)](https://codecov.io/github/ropensci/tracerer/branch/master)|[![codecov.io](https://codecov.io/github/ropensci/tracerer/coverage.svg?branch=develop)](https://codecov.io/github/ropensci/tracerer/branch/develop)
+[beautier](https://github.com/ropensci/beautier)|![R-CMD-check](https://github.com/ropensci/beautier/workflows/R-CMD-check/badge.svg?branch=master)           |![R-CMD-check](https://github.com/ropensci/beautier/workflows/R-CMD-check/badge.svg?branch=develop)           |[![codecov.io](https://codecov.io/github/ropensci/beautier/coverage.svg?branch=master)](https://app.codecov.io/github/ropensci/beautier/branch/master)|[![codecov.io](https://codecov.io/github/ropensci/beautier/coverage.svg?branch=develop)](https://app.codecov.io/github/ropensci/beautier/branch/develop)
+[beastier](https://github.com/ropensci/beastier)|![R-CMD-check](https://github.com/ropensci/beastier/workflows/R-CMD-check/badge.svg?branch=master)           |![R-CMD-check](https://github.com/ropensci/beastier/workflows/R-CMD-check/badge.svg?branch=develop)           |[![codecov.io](https://codecov.io/github/ropensci/beastier/coverage.svg?branch=master)](https://app.codecov.io/github/ropensci/beastier/branch/master)|[![codecov.io](https://codecov.io/github/ropensci/beastier/coverage.svg?branch=develop)](https://app.codecov.io/github/ropensci/beastier/branch/develop)
+[mauricer](https://github.com/ropensci/mauricer)|![R-CMD-check](https://github.com/ropensci/mauricer/workflows/R-CMD-check/badge.svg?branch=master)           |![R-CMD-check](https://github.com/ropensci/mauricer/workflows/R-CMD-check/badge.svg?branch=develop)           |[![codecov.io](https://codecov.io/github/ropensci/mauricer/coverage.svg?branch=master)](https://app.codecov.io/github/ropensci/mauricer/branch/master)|[![codecov.io](https://codecov.io/github/ropensci/mauricer/coverage.svg?branch=develop)](https://app.codecov.io/github/ropensci/mauricer/branch/develop)
+[tracerer](https://github.com/ropensci/tracerer)|![R-CMD-check](https://github.com/ropensci/tracerer/workflows/R-CMD-check/badge.svg?branch=master)           |![R-CMD-check](https://github.com/ropensci/tracerer/workflows/R-CMD-check/badge.svg?branch=develop)           |[![codecov.io](https://codecov.io/github/ropensci/tracerer/coverage.svg?branch=master)](https://app.codecov.io/github/ropensci/tracerer/branch/master)|[![codecov.io](https://codecov.io/github/ropensci/tracerer/coverage.svg?branch=develop)](https://app.codecov.io/github/ropensci/tracerer/branch/develop)
 
 ## Windows
 
@@ -114,9 +114,9 @@ Package                                                                       |
 
 ## Related packages
 
-Package                                     |[![Codecov logo](man/figures/Codecov.png)](https://www.codecov.io)
+Package                                     |[![Codecov logo](man/figures/Codecov.png)](https://about.codecov.io/)
 --------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------
-[lumier](https://github.com/ropensci/lumier)|[![codecov.io](https://codecov.io/github/ropensci/lumier/coverage.svg?branch=master)](https://codecov.io/github/ropensci/lumier/branch/master)
+[lumier](https://github.com/ropensci/lumier)|[![codecov.io](https://codecov.io/github/ropensci/lumier/coverage.svg?branch=master)](https://app.codecov.io/github/ropensci/lumier/branch/master)
 
 ## External links