diff --git a/vignettes/a-getting-started.Rmd b/vignettes/a-getting-started.Rmd index a93bf8a..79b8f4a 100644 --- a/vignettes/a-getting-started.Rmd +++ b/vignettes/a-getting-started.Rmd @@ -9,7 +9,7 @@ vignette: > **Authors:** Lewis A. Jones & William Gearty -**Last updated:** 2024-01-23 +**Last updated:** 2024-04-23 @@ -53,8 +53,8 @@ citation("rphylopic") ``` ## To cite rphylopic in publications, use the following citation: ## -## Gearty, W. and Jones, L.A. 2023. rphylopic: An R package for fetching, transforming, and visualising PhyloPic -## silhouettes. Methods in Ecology and Evolution, 14(11), 2700-2708. doi: 10.1111/2041-210X.14221. +## Gearty, W. and Jones, L.A. 2023. rphylopic: An R package for fetching, transforming, and visualising PhyloPic silhouettes. +## Methods in Ecology and Evolution, 14(11), 2700-2708. doi: 10.1111/2041-210X.14221. ## ## A BibTeX entry for LaTeX users is ## diff --git a/vignettes/b-advanced-ggplot.Rmd b/vignettes/b-advanced-ggplot.Rmd index a03b30d..6bba6c3 100644 --- a/vignettes/b-advanced-ggplot.Rmd +++ b/vignettes/b-advanced-ggplot.Rmd @@ -9,7 +9,7 @@ vignette: > **Authors:** William Gearty & Lewis A. Jones -**Last updated:** 2024-01-23 +**Last updated:** 2024-04-23 @@ -164,7 +164,7 @@ ggplot(penguins_subset) + labels = c("Female", "Male")) + facet_wrap(~species, ncol = 1) + theme_bw(base_size = 15) + - theme(legend.position = c(0.9, 0.9)) + theme(legend.position.inside = c(0.9, 0.9)) ```
@@ -402,7 +402,7 @@ revts(ggtree(vertebrate.tree, size = 1)) %<+% vertebrate_data + scale_x_continuous(breaks = seq(-500, 0, 100), labels = seq(500, 0, -100), limits = c(-500, 0)) + - coord_geo_polar(dat = "periods") + + coord_geo_radial(dat = "periods") + theme(line = element_line(linewidth = 1), axis.text.r = element_text(size = 5, hjust = -0.5, vjust = -1.5)) ``` diff --git a/vignettes/b-advanced-ggplot.Rmd.orig b/vignettes/b-advanced-ggplot.Rmd.orig index ef31a81..d1b1739 100644 --- a/vignettes/b-advanced-ggplot.Rmd.orig +++ b/vignettes/b-advanced-ggplot.Rmd.orig @@ -136,7 +136,7 @@ ggplot(penguins_subset) + labels = c("Female", "Male")) + facet_wrap(~species, ncol = 1) + theme_bw(base_size = 15) + - theme(legend.position = c(0.9, 0.9)) + theme(legend.position.inside = c(0.9, 0.9)) ``` Now that's a nice figure! @@ -166,7 +166,7 @@ tetrapods <- subset(tetrapods, genus == "Diplocaulus") Now, let's plot those occurrences on a world map. `{ggplot2}` and it's built-in function `map_data()` make this a breeze. Note that we use `alpha = 0.75` in case there are multiple occurrences in the same place. That way, the darker the fill color, the more occurrences in that geographic location. -```{r ggplot-geog-plot-1, fig.height = 3.5} +```{r ggplot-geog-plot-1, fig.height = 3.5, warning = FALSE} # Get map data world <- st_as_sf(map("world", fill = TRUE, plot = FALSE)) world <- st_wrap_dateline(world) @@ -312,7 +312,7 @@ revts(ggtree(vertebrate.tree, size = 1)) %<+% vertebrate_data + scale_x_continuous(breaks = seq(-500, 0, 100), labels = seq(500, 0, -100), limits = c(-500, 0)) + - coord_geo_polar(dat = "periods") + + coord_geo_radial(dat = "periods") + theme(line = element_line(linewidth = 1), axis.text.r = element_text(size = 5, hjust = -0.5, vjust = -1.5)) ``` diff --git a/vignettes/c-advanced-base.Rmd b/vignettes/c-advanced-base.Rmd index 614ff71..36bf297 100644 --- a/vignettes/c-advanced-base.Rmd +++ b/vignettes/c-advanced-base.Rmd @@ -9,7 +9,7 @@ vignette: > **Authors:** William Gearty & Lewis A. Jones -**Last updated:** 2024-01-23 +**Last updated:** 2024-04-23 diff --git a/vignettes/ggplot-penguin-plot-6-1.png b/vignettes/ggplot-penguin-plot-6-1.png index f845fb4..1889731 100644 Binary files a/vignettes/ggplot-penguin-plot-6-1.png and b/vignettes/ggplot-penguin-plot-6-1.png differ diff --git a/vignettes/ggplot-phylo-plot-2-1.png b/vignettes/ggplot-phylo-plot-2-1.png index 4e92264..7c4fcb1 100644 Binary files a/vignettes/ggplot-phylo-plot-2-1.png and b/vignettes/ggplot-phylo-plot-2-1.png differ diff --git a/vignettes/ggplot-phylo-plot-3-1.png b/vignettes/ggplot-phylo-plot-3-1.png index 93c08b8..850b6e8 100644 Binary files a/vignettes/ggplot-phylo-plot-3-1.png and b/vignettes/ggplot-phylo-plot-3-1.png differ diff --git a/vignettes/ggplot-phylo-plot-4-1.png b/vignettes/ggplot-phylo-plot-4-1.png index 2c7fc0b..e088ce4 100644 Binary files a/vignettes/ggplot-phylo-plot-4-1.png and b/vignettes/ggplot-phylo-plot-4-1.png differ