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fmichonneau · Jan 23, 2024 · c3c179f · c3c179f
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -17,3 +17,4 @@ README.*
 ^appveyor\.yml$
 ^\.github/workflows/R-CMD-check\.yaml$
 ^\.github$
+^README\.Rmd$
diff --git a/README.Rmd b/README.Rmd
@@ -1,15 +1,27 @@
+---
+output: github_document
+---
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>",
+  fig.path = "man/figures/README-",
+  out.width = "100%"
+)
+```
+
+# phylobase
+
 <!-- badges: start -->
-[![Build Status](https://travis-ci.org/fmichonneau/phylobase.png?branch=master)](https://travis-ci.org/fmichonneau/phylobase)
-[![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/fmichonneau/phylobase?branch=master&svg=true)](https://ci.appveyor.com/project/fmichonneau/phylobase)
+[![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)
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 ![](http://cranlogs.r-pkg.org/badges/phylobase)
 [![CRAN version](http://www.r-pkg.org/badges/version/phylobase)](http://cran.r-project.org/package=phylobase)
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 <!-- badges: end -->
 
-# phylobase
-
 ## About this package
 
 `phylobase` provides classes and methods to easily associate, manipulate,
@@ -38,7 +50,6 @@ can be downloaded from CRAN.
 
 ```{r, eval=FALSE}
 install.packages("phylobase")
-library(phylobase)
 ```
 
 ### Development version
@@ -49,8 +60,7 @@ installed using the [`devtools`](http://cran.r-project.org/package=devtools)
 package.
 
 ```{r, eval=FALSE}
-library(devtools)
-install_github("phylobase", "fmichonneau")
+pak::install_github("fmichonneau/phylobase")
 library(phylobase)
 ```
 

diff --git a/README.md b/README.md
@@ -1,156 +1,203 @@
 
-[![Build Status](https://travis-ci.org/fmichonneau/phylobase.png?branch=master)](https://travis-ci.org/fmichonneau/phylobase) [![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/fmichonneau/phylobase?branch=master&svg=true)](https://ci.appveyor.com/project/fmichonneau/phylobase) [![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) [![Research software impact](http://depsy.org/api/package/cran/phylobase/badge.svg)](http://depsy.org/package/r/phylobase)
+<!-- README.md is generated from README.Rmd. Please edit that file -->
 
-phylobase
-=========
+# phylobase
 
-About this package
-------------------
+<!-- badges: start -->
 
-`phylobase` provides classes and methods to easily associate, manipulate, explore, and plot phylogenetic trees and data about the species they include. The goal of this package is to provide a base set of tools likely to be shared by all packages designed for phylogenetic analysis. This standardization will benefit both *end-users* by allowing them to move results across packages and keep data associated with the phylogenetic trees; and *developers* by focusing on method development instead of having to rewrite the base functions.
+[![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)
+<!-- badges: end -->
 
--   Authors: R Hackathon et al. (alphabetically: Ben Bolker, Marguerite Butler, Peter Cowan, Damien de Vienne, Dirk Eddelbuettel, Mark Holder, Thibaut Jombart, Steve Kembel, Francois Michonneau, David Orme, Brian O'Meara, Emmanuel Paradis, Jim Regetz, Derrick Zwickl)
+## About this package
+
+`phylobase` provides classes and methods to easily associate,
+manipulate, explore, and plot phylogenetic trees and data about the
+species they include. The goal of this package is to provide a base set
+of tools likely to be shared by all packages designed for phylogenetic
+analysis. This standardization will benefit both *end-users* by allowing
+them to move results across packages and keep data associated with the
+phylogenetic trees; and *developers* by focusing on method development
+instead of having to rewrite the base functions.
+
+-   Authors: R Hackathon et al. (alphabetically: Ben Bolker, Marguerite
+    Butler, Peter Cowan, Damien de Vienne, Dirk Eddelbuettel, Mark
+    Holder, Thibaut Jombart, Steve Kembel, Francois Michonneau, David
+    Orme, Brian O’Meara, Emmanuel Paradis, Jim Regetz, Derrick Zwickl)
 -   Maintainer: Francois Michonneau
--   Licence: GPL (&gt;= 2)
--   Issues, bug reports, feature requests, discussion: <http://github.com/fmichonneau/phylobase/issues>
+-   Licence: GPL (\>= 2)
+-   Issues, bug reports, feature requests, discussion:
+    <http://github.com/fmichonneau/phylobase/issues>
 
-Installation
-------------
+## Installation
 
 ### Stable version
 
-The stable version (the minor and patch version numbers are even, e.g., 0.6.8) can be downloaded from CRAN.
+The stable version (the minor and patch version numbers are even, e.g.,
+0.6.8) can be downloaded from CRAN.
 
 ``` r
 install.packages("phylobase")
-library(phylobase)
 ```
 
 ### Development version
 
-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.
+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.
 
 ``` r
-library(devtools)
-install_github("phylobase", "fmichonneau")
+pak::install_github("fmichonneau/phylobase")
 library(phylobase)
 ```
 
 ### Getting started
 
 `phylobase` comes with example data sets `geospiza` and `geospiza_raw`.
 
--   `geospiza` is a `phylo4d` object (the `phylobase` class that holds together a phylogenetic tree and associated data, the `phylo4` class is for phylogenetic trees only).
--   `geospiza_raw` is a list that contains the tree `geospiza_raw$tree` (as an `ape::phylo` object) and the data `geospiza_raw$data` (as a `data.frame`) that were used to build the `geospiza` object.
+-   `geospiza` is a `phylo4d` object (the `phylobase` class that holds
+    together a phylogenetic tree and associated data, the `phylo4` class
+    is for phylogenetic trees only).
+-   `geospiza_raw` is a list that contains the tree `geospiza_raw$tree`
+    (as an `ape::phylo` object) and the data `geospiza_raw$data` (as a
+    `data.frame`) that were used to build the `geospiza` object.
 
-Now we'll take the data from and merge it with the tree. However, since is included in the tree but not in the data set, we will initially run into some trouble:
+Now we’ll take the data from and merge it with the tree. However, since
+is included in the tree but not in the data set, we will initially run
+into some trouble:
 
 ``` r
 data(geospiza_raw)
 g1 <- as(geospiza_raw$tree, "phylo4")
 geodata <- geospiza_raw$data
 g2 <- phylo4d(g1, geodata)
+#> Error in formatData(phy = x, dt = tip.data, type = "tip", ...): The following nodes are not found in the dataset:  olivacea
 ```
 
-    ## Error in formatData(phy = x, dt = tip.data, type = "tip", ...): The following nodes are not found in the dataset:  olivacea
-
-To deal with *G. olivacea* missing from the data, we have a few choices. The easiest is to use `missing.data="warn"` to allow `R` to create the new object with a warning (you can also use `missing.data="OK"` to proceed without warnings):
+To deal with *G. olivacea* missing from the data, we have a few choices.
+The easiest is to use `missing.data="warn"` to allow `R` to create the
+new object with a warning (you can also use `missing.data="OK"` to
+proceed without warnings):
 
 ``` r
 g2 <- phylo4d(g1, geodata, missing.data="warn")
-```
-
-    ## Warning in formatData(phy = x, dt = tip.data, type = "tip", ...): The
-    ## following nodes are not found in the dataset: olivacea
-
-``` r
+#> Warning in formatData(phy = x, dt = tip.data, type = "tip", ...): The following
+#> nodes are not found in the dataset: olivacea
 head(g2)
+#>           label node ancestor edge.length node.type    wingL  tarsusL  culmenL
+#> 1    fuliginosa    1       24     0.05500       tip 4.132957 2.806514 2.094971
+#> 2        fortis    2       24     0.05500       tip 4.244008 2.894717 2.407025
+#> 3  magnirostris    3       23     0.11000       tip 4.404200 3.038950 2.724667
+#> 4   conirostris    4       22     0.18333       tip 4.349867 2.984200 2.654400
+#> 5      scandens    5       21     0.19250       tip 4.261222 2.929033 2.621789
+#> 6    difficilis    6       20     0.22800       tip 4.224067 2.898917 2.277183
+#> 7       pallida    7       25     0.08667       tip 4.265425 3.089450 2.430250
+#> 8      parvulus    8       27     0.02000       tip 4.131600 2.973060 1.974420
+#> 9    psittacula    9       27     0.02000       tip 4.235020 3.049120 2.259640
+#> 10       pauper   10       26     0.03500       tip 4.232500 3.035900 2.187000
+#> 11   Platyspiza   11       18     0.46550       tip 4.419686 3.270543 2.331471
+#> 12        fusca   12       17     0.53409       tip 3.975393 2.936536 2.051843
+#> 13 Pinaroloxias   13       16     0.58333       tip 4.188600 2.980200 2.311100
+#> 14     olivacea   14       15     0.88077       tip       NA       NA       NA
+#> 15         <NA>   15        0          NA      root       NA       NA       NA
+#> 16         <NA>   16       15     0.29744  internal       NA       NA       NA
+#> 17         <NA>   17       16     0.04924  internal       NA       NA       NA
+#> 18         <NA>   18       17     0.06859  internal       NA       NA       NA
+#> 19         <NA>   19       18     0.13404  internal       NA       NA       NA
+#> 20         <NA>   20       19     0.10346  internal       NA       NA       NA
+#>       beakD   gonysW
+#> 1  1.941157 1.845379
+#> 2  2.362658 2.221867
+#> 3  2.823767 2.675983
+#> 4  2.513800 2.360167
+#> 5  2.144700 2.036944
+#> 6  2.011100 1.929983
+#> 7  2.016350 1.949125
+#> 8  1.873540 1.813340
+#> 9  2.230040 2.073940
+#> 10 2.073400 1.962100
+#> 11 2.347471 2.282443
+#> 12 1.191264 1.401186
+#> 13 1.547500 1.630100
+#> 14       NA       NA
+#> 15       NA       NA
+#> 16       NA       NA
+#> 17       NA       NA
+#> 18       NA       NA
+#> 19       NA       NA
+#> 20       NA       NA
 ```
 
-    ##           label node ancestor edge.length node.type    wingL  tarsusL
-    ## 1    fuliginosa    1       24     0.05500       tip 4.132957 2.806514
-    ## 2        fortis    2       24     0.05500       tip 4.244008 2.894717
-    ## 3  magnirostris    3       23     0.11000       tip 4.404200 3.038950
-    ## 4   conirostris    4       22     0.18333       tip 4.349867 2.984200
-    ## 5      scandens    5       21     0.19250       tip 4.261222 2.929033
-    ## 6    difficilis    6       20     0.22800       tip 4.224067 2.898917
-    ## 7       pallida    7       25     0.08667       tip 4.265425 3.089450
-    ## 8      parvulus    8       27     0.02000       tip 4.131600 2.973060
-    ## 9    psittacula    9       27     0.02000       tip 4.235020 3.049120
-    ## 10       pauper   10       26     0.03500       tip 4.232500 3.035900
-    ##     culmenL    beakD   gonysW
-    ## 1  2.094971 1.941157 1.845379
-    ## 2  2.407025 2.362658 2.221867
-    ## 3  2.724667 2.823767 2.675983
-    ## 4  2.654400 2.513800 2.360167
-    ## 5  2.621789 2.144700 2.036944
-    ## 6  2.277183 2.011100 1.929983
-    ## 7  2.430250 2.016350 1.949125
-    ## 8  1.974420 1.873540 1.813340
-    ## 9  2.259640 2.230040 2.073940
-    ## 10 2.187000 2.073400 1.962100
-    ##  [ reached getOption("max.print") -- omitted 10 rows ]
-
 ### Importing data
 
 #### From NEXUS files
 
-`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 simultaneously tree and species data.
+`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 simultaneously tree and species data.
 
 ``` r
 myrmeFile <- system.file("nexusfiles/treeWithDiscreteData.nex", package="phylobase")
 myrme <- readNexus(file=myrmeFile)
 head(myrme)
+#>                      label node ancestor edge.length node.type        time
+#> 1   Myrmecocystussemirufus    1       27    1.724765       tip     diurnal
+#> 2   Myrmecocystusplacodops    2       27    1.724765       tip     diurnal
+#> 3      Myrmecocystusmendax    3       26    4.650818       tip     diurnal
+#> 4    Myrmecocystuskathjuli    4       28    1.083870       tip     diurnal
+#> 5    Myrmecocystuswheeleri    5       28    1.083870       tip     diurnal
+#> 6     Myrmecocystusmimicus    6       30    2.708942       tip     diurnal
+#> 7     Myrmecocystusdepilis    7       30    2.708942       tip     diurnal
+#> 8    Myrmecocystusromainei    8       32    2.193845       tip     diurnal
+#> 9  Myrmecocystusnequazcatl    9       32    2.193845       tip     diurnal
+#> 10       Myrmecocystusyuma   10       31    4.451425       tip crepuscular
+#> 11   Myrmecocystuskennedyi   11       23    6.044804       tip     diurnal
+#> 12 Myrmecocystuscreightoni   12       22   10.569191       tip crepuscular
+#> 13  Myrmecocystussnellingi   13       33    2.770378       tip crepuscular
+#> 14 Myrmecocystustenuinodis   14       33    2.770378       tip crepuscular
+#> 15  Myrmecocystustestaceus   15       20   12.300701       tip crepuscular
+#> 16  Myrmecocystusmexicanus   16       34    5.724923       tip   nocturnal
+#> 17   Myrmecocystuscfnavajo   17       35    2.869547       tip   nocturnal
+#> 18     Myrmecocystusnavajo   18       35    2.869547       tip   nocturnal
+#> 19                    <NA>   19        0          NA      root        <NA>
+#> 20                    <NA>   20       19    1.699299  internal        <NA>
+#>         subgenus
+#> 1   Endiodioctes
+#> 2   Endiodioctes
+#> 3   Endiodioctes
+#> 4   Endiodioctes
+#> 5   Endiodioctes
+#> 6   Endiodioctes
+#> 7   Endiodioctes
+#> 8   Endiodioctes
+#> 9   Endiodioctes
+#> 10  Eremnocystus
+#> 11  Endiodioctes
+#> 12  Eremnocystus
+#> 13  Eremnocystus
+#> 14  Eremnocystus
+#> 15 Myrmecocystus
+#> 16 Myrmecocystus
+#> 17 Myrmecocystus
+#> 18 Myrmecocystus
+#> 19          <NA>
+#> 20          <NA>
 ```
 
-    ##                      label node ancestor edge.length node.type        time
-    ## 1   Myrmecocystussemirufus    1       27    1.724765       tip     diurnal
-    ## 2   Myrmecocystusplacodops    2       27    1.724765       tip     diurnal
-    ## 3      Myrmecocystusmendax    3       26    4.650818       tip     diurnal
-    ## 4    Myrmecocystuskathjuli    4       28    1.083870       tip     diurnal
-    ## 5    Myrmecocystuswheeleri    5       28    1.083870       tip     diurnal
-    ## 6     Myrmecocystusmimicus    6       30    2.708942       tip     diurnal
-    ## 7     Myrmecocystusdepilis    7       30    2.708942       tip     diurnal
-    ## 8    Myrmecocystusromainei    8       32    2.193845       tip     diurnal
-    ## 9  Myrmecocystusnequazcatl    9       32    2.193845       tip     diurnal
-    ## 10       Myrmecocystusyuma   10       31    4.451425       tip crepuscular
-    ## 11   Myrmecocystuskennedyi   11       23    6.044804       tip     diurnal
-    ## 12 Myrmecocystuscreightoni   12       22   10.569191       tip crepuscular
-    ## 13  Myrmecocystussnellingi   13       33    2.770378       tip crepuscular
-    ## 14 Myrmecocystustenuinodis   14       33    2.770378       tip crepuscular
-    ##         subgenus
-    ## 1   Endiodioctes
-    ## 2   Endiodioctes
-    ## 3   Endiodioctes
-    ## 4   Endiodioctes
-    ## 5   Endiodioctes
-    ## 6   Endiodioctes
-    ## 7   Endiodioctes
-    ## 8   Endiodioctes
-    ## 9   Endiodioctes
-    ## 10  Eremnocystus
-    ## 11  Endiodioctes
-    ## 12  Eremnocystus
-    ## 13  Eremnocystus
-    ## 14  Eremnocystus
-    ##  [ reached getOption("max.print") -- omitted 6 rows ]
-
 #### From NeXML
 
 ``` r
 library(RNeXML)
-```
-
-    ## Loading required package: ape
-
-    ## 
-    ## Attaching package: 'ape'
-
-    ## The following object is masked from 'package:phylobase':
-    ## 
-    ##     edges
-
-``` r
+#> Loading required package: ape
+#> 
+#> Attaching package: 'ape'
+#> The following object is masked from 'package:phylobase':
+#> 
+#>     edges
 nxmlFile <- system.file("nexmlfiles/comp_analysis.xml", package="phylobase")
 nxml <- nexml_read(nxmlFile)
 nxmlEx <- phylo4(nxml)