From e18a7f40b799c960b81214346982083c6955e531 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fran=C3=A7ois=20Michonneau?= Date: Mon, 29 Jan 2024 14:28:19 +0100 Subject: [PATCH] redocument --- .Rbuildignore | 3 ++- README.Rmd | 4 ++-- README.md | 4 ++-- man/checkPhylo4.Rd | 2 +- 4 files changed, 7 insertions(+), 6 deletions(-) diff --git a/.Rbuildignore b/.Rbuildignore index ae24a8c..9a47cbb 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -17,4 +17,5 @@ cleanup ^\.github/workflows/R-CMD-check\.yaml$ ^\.github$ ^figure$ -^README\.html$ \ No newline at end of file +^README\.html$ +^CRAN-SUBMISSION$ diff --git a/README.Rmd b/README.Rmd index 6c76da5..da87589 100644 --- a/README.Rmd +++ b/README.Rmd @@ -17,9 +17,9 @@ knitr::opts_chunk$set( [![R-CMD-check](https://github.com/fmichonneau/phylobase/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/fmichonneau/phylobase/actions/workflows/R-CMD-check.yaml) -[![codecov.io](https://codecov.io/github/fmichonneau/phylobase/coverage.svg?branch=master)](https://codecov.io/github/fmichonneau/phylobase?branch=master) +[![codecov.io][(https://app.codecov.io/github/fmichonneau/phylobase?branch=master)](https://app.codecov.io/github/fmichonneau/phylobase?branch=master) ![](https://cranlogs.r-pkg.org/badges/phylobase) -[![CRAN version](https://www.r-pkg.org/badges/version/phylobase)](http://cran.r-project.org/package=phylobase) +[![CRAN version](https://www.r-pkg.org/badges/version/phylobase)](https://cran.r-project.org/package=phylobase) ## About this package diff --git a/README.md b/README.md index ba8cc93..ddf9d10 100644 --- a/README.md +++ b/README.md @@ -6,9 +6,9 @@ [![R-CMD-check](https://github.com/fmichonneau/phylobase/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/fmichonneau/phylobase/actions/workflows/R-CMD-check.yaml) -[![codecov.io](https://codecov.io/github/fmichonneau/phylobase/coverage.svg?branch=master)](https://codecov.io/github/fmichonneau/phylobase?branch=master) +\[\[codecov.io\]\[()\]() ![](https://cranlogs.r-pkg.org/badges/phylobase) [![CRAN -version](https://www.r-pkg.org/badges/version/phylobase)](http://cran.r-project.org/package=phylobase) +version](https://www.r-pkg.org/badges/version/phylobase)](https://cran.r-project.org/package=phylobase) ## About this package diff --git a/man/checkPhylo4.Rd b/man/checkPhylo4.Rd index 9414282..c69c5c3 100644 --- a/man/checkPhylo4.Rd +++ b/man/checkPhylo4.Rd @@ -25,7 +25,7 @@ These functions are only intended to be called by other phylobase functions. \code{checkTree}. The rules for \code{phylo4} objects essentially follow those for \code{phylo} objects from the \code{ape} package, which are in turn defined in -\url{https://ape-package.ird.fr/misc/FormatTreeR_24Oct2012.pdf}. +\url{https://emmanuelparadis.github.io/misc/FormatTreeR.pdf}. These are essentially that: \itemize{ \item if the tree has edge lengths defined, the number of edge lengths must match the number of edges; \item the number of tip labels must match the number of