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
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diff --git a/vignettes/ggplot-phylo-plot-2-1.png b/vignettes/ggplot-phylo-plot-2-1.png
index 4e92264..7c4fcb1 100644
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diff --git a/vignettes/ggplot-phylo-plot-3-1.png b/vignettes/ggplot-phylo-plot-3-1.png
index 93c08b8..850b6e8 100644
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diff --git a/vignettes/ggplot-phylo-plot-4-1.png b/vignettes/ggplot-phylo-plot-4-1.png
index 2c7fc0b..e088ce4 100644
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