diff --git a/vignettes/data_mashups.Rmd b/vignettes/data_mashups.Rmd index d131222a..1ec15efb 100644 --- a/vignettes/data_mashups.Rmd +++ b/vignettes/data_mashups.Rmd @@ -12,6 +12,9 @@ vignette: > \usepackage[utf8]{inputenc} --- + + + ## Combining data from OToL and other sources. One of the major goals of `rotl` is to help users combine data from other @@ -300,7 +303,7 @@ tr <- tol_induced_subtree(ott_ids = ott_in_tree) plot(tr) ``` -![plot of chunk subtree](figure/subtree-1.png) +![plot of chunk subtree](fig-vignettes-subtree-1.png) ### Connect your data to the tips of your tree @@ -363,7 +366,7 @@ And now we can plot the data and the tree together plot(tree_data) ``` -![plot of chunk unnamed-chunk-1](figure/unnamed-chunk-1-1.png) +![plot of chunk unnamed-chunk-1](fig-vignettes-unnamed-chunk-1-1.png) ## Find external data associated with studies, trees and taxa from Open Tree diff --git a/vignettes/data_mashups.Rmd.orig b/vignettes/data_mashups.Rmd.orig index 31c9b796..4c229540 100644 --- a/vignettes/data_mashups.Rmd.orig +++ b/vignettes/data_mashups.Rmd.orig @@ -12,6 +12,11 @@ vignette: > \usepackage[utf8]{inputenc} --- +```{r setup, include=FALSE} +knitr::opts_chunk$set(fig.path = "fig-vignettes-") +``` + + ## Combining data from OToL and other sources. One of the major goals of `rotl` is to help users combine data from other diff --git a/vignettes/fig-vignettes-birds_in_a_tree-1.png b/vignettes/fig-vignettes-birds_in_a_tree-1.png new file mode 100644 index 00000000..11f38b89 Binary files /dev/null and b/vignettes/fig-vignettes-birds_in_a_tree-1.png differ diff --git a/vignettes/fig-vignettes-eggs_in_a_funnel-1.png b/vignettes/fig-vignettes-eggs_in_a_funnel-1.png new file mode 100644 index 00000000..66e5c877 Binary files /dev/null and b/vignettes/fig-vignettes-eggs_in_a_funnel-1.png differ diff --git a/vignettes/fig-vignettes-subtree-1.png b/vignettes/fig-vignettes-subtree-1.png new file mode 100644 index 00000000..599040cd Binary files /dev/null and b/vignettes/fig-vignettes-subtree-1.png differ diff --git a/vignettes/fig-vignettes-unnamed-chunk-1-1.png b/vignettes/fig-vignettes-unnamed-chunk-1-1.png new file mode 100644 index 00000000..140a194a Binary files /dev/null and b/vignettes/fig-vignettes-unnamed-chunk-1-1.png differ diff --git a/vignettes/fig-vignettes-unnamed-chunk-16-1.png b/vignettes/fig-vignettes-unnamed-chunk-16-1.png new file mode 100644 index 00000000..991dad36 Binary files /dev/null and b/vignettes/fig-vignettes-unnamed-chunk-16-1.png differ diff --git a/vignettes/fig-vignettes-unnamed-chunk-3-1.png b/vignettes/fig-vignettes-unnamed-chunk-3-1.png new file mode 100644 index 00000000..de5a3888 Binary files /dev/null and b/vignettes/fig-vignettes-unnamed-chunk-3-1.png differ diff --git a/vignettes/fig-vignettes-unnamed-chunk-8-1.png b/vignettes/fig-vignettes-unnamed-chunk-8-1.png new file mode 100644 index 00000000..899f3f27 Binary files /dev/null and b/vignettes/fig-vignettes-unnamed-chunk-8-1.png differ diff --git a/vignettes/make-vignettes.R b/vignettes/make-vignettes.R index bde51524..fb470915 100644 --- a/vignettes/make-vignettes.R +++ b/vignettes/make-vignettes.R @@ -7,20 +7,9 @@ make_vignettes <- function() { knitr::knit(x, output = y) } ) - ## clean figure directory if it exists - if (dir.exists("vignettes/figure")) { - unlink("vignettes/figure/", recursive = TRUE, force = TRUE) - } - ## recreate the directory - dir.create("vignettes/figure") ## move the figures - figures <- list.files("figure", pattern = "\\.png$", full.names = TRUE) + figures <- list.files(".", pattern = "fig-vignettes-.+\\.png$", full.names = TRUE) res_mv <- file.rename(figures, file.path("vignettes", figures)) stopifnot(all(res_mv)) - - ## remove base directory - unlink("figure", recursive = TRUE, force = TRUE) - - ## returns TRUE is everything worked - invisible(!dir.exists("figure")) + TRUE } diff --git a/vignettes/meta-analysis.Rmd b/vignettes/meta-analysis.Rmd index 73b79dff..c9362e27 100644 --- a/vignettes/meta-analysis.Rmd +++ b/vignettes/meta-analysis.Rmd @@ -12,6 +12,8 @@ vignette: > %\VignetteEncoding{UTF-8} --- + + ## Phylogenetic Comparative Methods The development of phylogenetic comparative methods has made phylogenies and @@ -106,7 +108,7 @@ plot(1 / sqrt(egg_data$VZr), egg_data$Zr, ) ``` -![plot of chunk eggs_in_a_funnel](figure/eggs_in_a_funnel-1.png) +![plot of chunk eggs_in_a_funnel](fig-vignettes-eggs_in_a_funnel-1.png) In order to use this data later on we need to first convert it to a standard `data.frame`. We can also convert the `animal` column (the species names) to @@ -317,7 +319,7 @@ tr <- tol_induced_subtree(ott_id(taxa)[is_in_tree(ott_id(taxa))]) plot(tr, show.tip.label = FALSE) ``` -plot of chunk birds_in_a_tree +plot of chunk birds_in_a_tree There are a few things to note here. First, the tree has no branch lengths. At present this is true for the whole of the Open Tree synthetic tree. Some diff --git a/vignettes/meta-analysis.Rmd.orig b/vignettes/meta-analysis.Rmd.orig index fccbf338..b0d410f7 100644 --- a/vignettes/meta-analysis.Rmd.orig +++ b/vignettes/meta-analysis.Rmd.orig @@ -12,6 +12,10 @@ vignette: > %\VignetteEncoding{UTF-8} --- +```{r setup, include=FALSE} +knitr::opts_chunk$set(fig.path = "fig-vignettes-") +``` + ## Phylogenetic Comparative Methods The development of phylogenetic comparative methods has made phylogenies and diff --git a/vignettes/rotl.Rmd b/vignettes/rotl.Rmd index ce848a8a..03700910 100644 --- a/vignettes/rotl.Rmd +++ b/vignettes/rotl.Rmd @@ -12,6 +12,8 @@ vignette: > \usepackage[utf8]{inputenc} --- + + `rotl` provides an interface to the Open Tree of Life (OTL) API and allows users to query the API, retrieve parts of the Tree of Life and integrate these parts with other R packages. @@ -143,7 +145,7 @@ my_tree <- tol_induced_subtree(ott_ids = resolved_names$ott_id) plot(my_tree, no.margin = TRUE) ``` -![plot of chunk unnamed-chunk-3](figure/unnamed-chunk-3-1.png) +![plot of chunk unnamed-chunk-3](fig-vignettes-unnamed-chunk-3-1.png) ## FAQ @@ -366,7 +368,7 @@ mono_tree <- tol_subtree(ott_id = ott_id(mono_id)) plot(mono_tree) ``` -![plot of chunk unnamed-chunk-8](figure/unnamed-chunk-8-1.png) +![plot of chunk unnamed-chunk-8](fig-vignettes-unnamed-chunk-8-1.png) ### How do I find trees from studies focused on my favourite taxa? @@ -666,4 +668,4 @@ tr <- tol_induced_subtree(ott_id(taxa)) plot(tr) ``` -![plot of chunk unnamed-chunk-16](figure/unnamed-chunk-16-1.png) +![plot of chunk unnamed-chunk-16](fig-vignettes-unnamed-chunk-16-1.png) diff --git a/vignettes/rotl.Rmd.orig b/vignettes/rotl.Rmd.orig index eaa87d1e..be575051 100644 --- a/vignettes/rotl.Rmd.orig +++ b/vignettes/rotl.Rmd.orig @@ -12,6 +12,10 @@ vignette: > \usepackage[utf8]{inputenc} --- +```{r setup, include=FALSE} +knitr::opts_chunk$set(fig.path = "fig-vignettes-") +``` + `rotl` provides an interface to the Open Tree of Life (OTL) API and allows users to query the API, retrieve parts of the Tree of Life and integrate these parts with other R packages.