From 00ca67f04a1fb718cda0367549e7ea3b11c5b8c8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fran=C3=A7ois=20Michonneau?= Date: Wed, 24 Jan 2024 16:19:17 +0100 Subject: [PATCH] update links --- R/checkdata.R | 2 +- README.Rmd | 12 ++++++------ README.md | 12 ++++++------ man/checkPhylo4.Rd | 2 +- vignettes/fig-vignettes-plotvcvphylo-1.png | Bin 14575 -> 17626 bytes vignettes/phylobase.Rmd | 4 ++-- vignettes/phylobase.Rmd.orig | 4 ++-- 7 files changed, 18 insertions(+), 18 deletions(-) diff --git a/R/checkdata.R b/R/checkdata.R index 2a55a20..9f5a076 100644 --- a/R/checkdata.R +++ b/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 diff --git a/README.Rmd b/README.Rmd index 770341a..6c76da5 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](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) ## 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} diff --git a/README.md b/README.md index 4843307..ba8cc93 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](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) ## 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: - + ## 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 (), 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 diff --git a/man/checkPhylo4.Rd b/man/checkPhylo4.Rd index a5f6c78..9414282 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{http://ape-package.ird.fr/misc/FormatTreeR_24Oct2012.pdf}. +\url{https://ape-package.ird.fr/misc/FormatTreeR_24Oct2012.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 diff --git a/vignettes/fig-vignettes-plotvcvphylo-1.png b/vignettes/fig-vignettes-plotvcvphylo-1.png index 065af06c653b2b34a26015d87dfff7fe222f7c6b..3bbab514def0c2ba1c3dc604f2fdf8b08ff4847f 100644 GIT binary patch literal 17626 zcmcJ%byQXD+Aq9RL_|sHE7zc4Pt z-!MNmy92*nw|%7PfI!^9NBz3gH{pGXK+qs$A4oiNjbEE^5f3?`zP7m#zdz}LVLl~Y zpC&1N7i+?ZkWBr7v-N(3QCbH}^h*;Rj|a+X?X5Qn9~u*wGmoAGBdN!Gtm0L=mj-6e zj&l|Sx_6GeDGusRjuRK$utPdcZXpojx{ls_@C9lDlCL3>`O!oWh$h;_ONcwz5;zEP zI}CROB1o#|3gQWc9~HuP8h00gAPD@|OU0`VGh|-B&g7^cYiRc(uoH`Gis*%xeCOef zONfj6WyGm1Nsqb%69KFDV(X_28=? zTZ+U!MsJK9*AcOA+Qamtc{@65#UE6CEp->d;2o0F(Ptumb-V`Ulfi{ zOoW7lbar$cPN*}@5Uo;^+I4NUex$`md%EY^kSq7;hl56c;*J?y+UWz6u6X8q_txg- zjLpn6>WfQCN|KX(!*re4)bn)g?CkIe32$TgDQ0?jcqEB>X+3=!j`VUOD=I3&#Ke5T z`SB+=9V^qYI+50__Fz_~OM2Mn*;~XE@Pg 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There is no separate slot for edge data, but these can be stored as node data associated with the descendant node. -[^1]: +[^1]: -[^2]: see for more +[^2]: see for more information on orderings. (`ape`'s "pruningwise" is "bottom-up" ordering). diff --git a/vignettes/phylobase.Rmd.orig b/vignettes/phylobase.Rmd.orig index c9aa6eb..f4d3aee 100644 --- a/vignettes/phylobase.Rmd.orig +++ b/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]: +[^1]: -[^2]: see for more +[^2]: see for more information on orderings. (`ape`'s "pruningwise" is "bottom-up" ordering).