update generated files

Author: fmichonneau

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: rotl
 Title: Interface to the 'Open Tree of Life' API
-Version: 3.1.0
+Version: 3.1.1
 Authors@R: 
     c(person(given = "Francois",
              family = "Michonneau",
@@ -52,4 +52,4 @@ X-schema.org-isPartOf: https://ropensci.org
 X-schema.org-keywords: metadata, ropensci, phylogenetics,
     independant-contrasts, biodiversity
 X-schema.org-relatedLink: https://codemeta.github.io/codemetar
-RoxygenNote: 7.2.1
+RoxygenNote: 7.3.3

NEWS.md

@@ -1,3 +1,7 @@
+# rotl 3.1.1
+
+* Update formatting of the documentation to solve CRAN checks (#148 by @villegar).
+
 # rotl 3.1.0
 
 ## Breaking change

README.Rmd

@@ -10,11 +10,11 @@ opts_knit$set(upload.fun = imgur_upload)
 
 <!-- badges: start -->
 [![R-CMD-check](https://github.com/ropensci/rotl/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ropensci/rotl/actions/workflows/R-CMD-check.yaml)
-[![codecov.io](https://app.codecov.io/github/ropensci/rotl?branch=master)](https://app.codecov.io/github/ropensci/rotl?branch=master)
 [![](https://www.r-pkg.org/badges/version/rotl)](https://www.r-pkg.org/pkg/rotl)
 [![CRAN RStudio mirror downloads](https://cranlogs.r-pkg.org/badges/rotl)](https://www.r-pkg.org/pkg/rotl)
 [![](https://badges.ropensci.org/17_status.svg)](https://github.com/ropensci/software-review/issues/17)
 [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
+[![Codecov test coverage](https://codecov.io/gh/ropensci/rotl/graph/badge.svg)](https://app.codecov.io/gh/ropensci/rotl)
 <!-- badges: end -->
 
 

README.md

@@ -2,14 +2,15 @@
 <!-- badges: start -->
 
 [![R-CMD-check](https://github.com/ropensci/rotl/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ropensci/rotl/actions/workflows/R-CMD-check.yaml)
-[![codecov.io](https://app.codecov.io/github/ropensci/rotl?branch=master)](https://app.codecov.io/github/ropensci/rotl?branch=master)
 [![](https://www.r-pkg.org/badges/version/rotl)](https://www.r-pkg.org/pkg/rotl)
 [![CRAN RStudio mirror
 downloads](https://cranlogs.r-pkg.org/badges/rotl)](https://www.r-pkg.org/pkg/rotl)
 [![](https://badges.ropensci.org/17_status.svg)](https://github.com/ropensci/software-review/issues/17)
 [![Project Status: Active – The project has reached a stable, usable
 state and is being actively
 developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
+[![Codecov test
+coverage](https://codecov.io/gh/ropensci/rotl/graph/badge.svg)](https://app.codecov.io/gh/ropensci/rotl)
 <!-- badges: end -->
 
 # rotl: An R interface to Open Tree API <img src="man/figures/logo.svg" align="right" />
@@ -48,17 +49,17 @@ remotes::install_github("ropensci/rotl")
 
 There are three vignettes:
 
--   Start by checking out the “How to use `rotl`?” by typing:
-    `vignette("rotl", package="rotl")` after installing the package.
+- Start by checking out the “How to use `rotl`?” by typing:
+  `vignette("rotl", package="rotl")` after installing the package.
 
--   Then explore how you can use `rotl` with other packages to combine
-    your data with trees from the Open Tree of Life project by typing:
-    `vignette("data_mashups", package="rotl")`.
+- Then explore how you can use `rotl` with other packages to combine
+  your data with trees from the Open Tree of Life project by typing:
+  `vignette("data_mashups", package="rotl")`.
 
--   The vignette “Using the Open Tree Synthesis in a comparative
-    analysis” demonstrates how you can reproduce an analysis of a
-    published paper by downloading the tree they used, and data from the
-    supplementary material: `vignette("meta-analysis", package="rotl")`.
+- The vignette “Using the Open Tree Synthesis in a comparative analysis”
+  demonstrates how you can reproduce an analysis of a published paper by
+  downloading the tree they used, and data from the supplementary
+  material: `vignette("meta-analysis", package="rotl")`.
 
 The vignettes are also available from CRAN: [How to use
 `rotl`?](https://cran.r-project.org/package=rotl/vignettes/rotl.html),
@@ -88,12 +89,12 @@ apes <- c("Pongo", "Pan", "Gorilla", "Hoolock", "Homo")
     ## 3       gorilla     Gorilla             FALSE     1 417969      FALSE
     ## 4       hoolock     Hoolock             FALSE     1 712902      FALSE
     ## 5          homo        Homo             FALSE     1 770309      FALSE
-    ##            flags number_matches
-    ## 1                             2
-    ## 2 sibling_higher              2
-    ## 3 sibling_higher              1
-    ## 4                             1
-    ## 5 sibling_higher              1
+    ##                               flags number_matches
+    ## 1                                                2
+    ## 2                    sibling_higher              2
+    ## 3                    sibling_higher              1
+    ## 4                                                1
+    ## 5 extinct_inherited, sibling_higher              1
 
 Now we can get the tree with just those tips:
 
@@ -111,7 +112,7 @@ tr <- tol_induced_subtree(ott_ids = ott_id(resolved_names))
 plot(tr)
 ```
 
-![](https://i.imgur.com/0tnzsFv.png)<!-- -->
+![](https://i.imgur.com/m9pusZk.png)<!-- -->
 
 The code above can be summarized in a single pipe:
 
@@ -131,7 +132,7 @@ c("Pongo", "Pan", "Gorilla", "Hoolock", "Homo") %>%
     ## mrcaott83926ott3607689, mrcaott83926ott3607732, mrcaott770295ott3607719,
     ## mrcaott770295ott3607692, Ponginae ott1082538, Hylobatidae ott166544
 
-![](https://i.imgur.com/ww5PZ6B.png)<!-- -->
+![](https://i.imgur.com/6o95mvV.png)<!-- -->
 
 ## Citation and Manuscript