update links

R/checkdata.R

@@ -18,7 +18,7 @@
 ##' \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{http://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

README.Rmd

@@ -17,9 +17,9 @@ knitr::opts_chunk$set(
 
 <!-- badges: start -->
 [![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](http://codecov.io/github/fmichonneau/phylobase/coverage.svg?branch=master)](http://codecov.io/github/fmichonneau/phylobase?branch=master)
-![](http://cranlogs.r-pkg.org/badges/phylobase)
-[![CRAN version](http://www.r-pkg.org/badges/version/phylobase)](http://cran.r-project.org/package=phylobase)
+[![codecov.io](https://codecov.io/github/fmichonneau/phylobase/coverage.svg?branch=master)](https://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)
 <!-- badges: end -->
 
 ## About this package
@@ -39,7 +39,7 @@ focusing on method development instead of having to rewrite the base functions.
 - Maintainer: Francois Michonneau
 - Licence: GPL (>= 2)
 - Issues, bug reports, feature requests, discussion:
-  http://github.com/fmichonneau/phylobase/issues
+  https://github.com/fmichonneau/phylobase/issues
 
 ## Installation
 
@@ -56,7 +56,7 @@ install.packages("phylobase")
 
 The development version (the patch version number is odd, e.g., 0.6.9) is
 available on GitHub (https://github.com/fmichonneau/phylobase), and can be
-installed using the [`devtools`](http://cran.r-project.org/package=devtools)
+installed using the [`devtools`](https://cran.r-project.org/package=devtools)
 package.
 
 ```{r, eval=FALSE}
@@ -106,7 +106,7 @@ head(g2)
 
 `phylobase` has a robust parser for NEXUS files (it uses the NEXUS Class Library
 from Paul Lewis and Mark Holder,
-[NCL](http://sourceforge.net/projects/ncl/files/)). It can be used to import
+[NCL](https://sourceforge.net/projects/ncl/files/)). It can be used to import
 simultaneously tree and species data.
 
 ```{r}

README.md

@@ -6,9 +6,9 @@
 <!-- badges: start -->
 
 [![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](http://codecov.io/github/fmichonneau/phylobase/coverage.svg?branch=master)](http://codecov.io/github/fmichonneau/phylobase?branch=master)
-![](http://cranlogs.r-pkg.org/badges/phylobase) [![CRAN
-version](http://www.r-pkg.org/badges/version/phylobase)](http://cran.r-project.org/package=phylobase)
+[![codecov.io](https://codecov.io/github/fmichonneau/phylobase/coverage.svg?branch=master)](https://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)
 <!-- badges: end -->
 
 ## About this package
@@ -29,7 +29,7 @@ instead of having to rewrite the base functions.
 -   Maintainer: Francois Michonneau
 -   Licence: GPL (\>= 2)
 -   Issues, bug reports, feature requests, discussion:
-    <http://github.com/fmichonneau/phylobase/issues>
+    <https://github.com/fmichonneau/phylobase/issues>
 
 ## Installation
 
@@ -47,7 +47,7 @@ install.packages("phylobase")
 The development version (the patch version number is odd, e.g., 0.6.9)
 is available on GitHub (<https://github.com/fmichonneau/phylobase>), and
 can be installed using the
-[`devtools`](http://cran.r-project.org/package=devtools) package.
+[`devtools`](https://cran.r-project.org/package=devtools) package.
 
 ``` r
 pak::install_github("fmichonneau/phylobase")
@@ -137,7 +137,7 @@ head(g2)
 
 `phylobase` has a robust parser for NEXUS files (it uses the NEXUS Class
 Library from Paul Lewis and Mark Holder,
-[NCL](http://sourceforge.net/projects/ncl/files/)). It can be used to
+[NCL](https://sourceforge.net/projects/ncl/files/)). It can be used to
 import simultaneously tree and species data.
 
 ``` r

vignettes/phylobase.Rmd

@@ -802,9 +802,9 @@ separately with `tdata(x,"tip")`, `tdata(x,"internal")` or
 `tdata(x,"all")`. There is no separate slot for edge data, but these can
 be stored as node data associated with the descendant node.
 
-[^1]: <http://ape.mpl.ird.fr/>
+[^1]: <https://emmanuelparadis.github.io/ape_development.html>
 
-[^2]: see <http://en.wikipedia.org/wiki/Tree_traversal> for more
+[^2]: see <https://en.wikipedia.org/wiki/Tree_traversal> for more
     information on orderings. (`ape`'s "pruningwise" is "bottom-up"
     ordering).
 

vignettes/phylobase.Rmd.orig

@@ -622,9 +622,9 @@ separately with `tdata(x,"tip")`, `tdata(x,"internal")` or
 `tdata(x,"all")`. There is no separate slot for edge data, but these can
 be stored as node data associated with the descendant node.
 
-[^1]: <http://ape.mpl.ird.fr/>
+[^1]: <https://emmanuelparadis.github.io/ape_development.html>
 
-[^2]: see <http://en.wikipedia.org/wiki/Tree_traversal> for more
+[^2]: see <https://en.wikipedia.org/wiki/Tree_traversal> for more
     information on orderings. (`ape`'s "pruningwise" is "bottom-up"
     ordering).