Update vignettes

palaeoverse · Apr 23, 2024 · b8e395a · b8e395a
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diff --git 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
@@ -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))
 ```
 
 <div class="figure">
@@ -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
@@ -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
@@ -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
diff --git a/vignettes/ggplot-phylo-plot-2-1.png b/vignettes/ggplot-phylo-plot-2-1.png
diff --git a/vignettes/ggplot-phylo-plot-3-1.png b/vignettes/ggplot-phylo-plot-3-1.png
diff --git a/vignettes/ggplot-phylo-plot-4-1.png b/vignettes/ggplot-phylo-plot-4-1.png
Original file line number	Diff line number	Diff line change
Expand Up		@@ -9,7 +9,7 @@ vignette: >

		Authors: William Gearty & Lewis A. Jones

		Last updated: 2024-01-23
		Last updated: 2024-04-23



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