GBIF and IUCN Red List

stangandaho · stangandaho · commit d82d2273ff80 · 2025-11-25T16:14:33.000+01:00
diff --git a/vignettes/GBIF-and-IUCN-Red-List.Rmd b/vignettes/GBIF-and-IUCN-Red-List.Rmd
@@ -24,14 +24,14 @@ The workflow combines spatial filtering of occurrence data with automated querie
 
 We begin by loading the required packages. The `rgbif` package provides access to GBIF data, `redlist` interfaces with the IUCN Red List API, and `sf` handles spatial operations. The `dplyr` and `ggplot2` packages support data manipulation and visualization respectively.
 
-```{r setup, echo=FALSE, warning=FALSE, message=FALSE}
+```{r setup, warning=FALSE, message=FALSE}
 # Define required packages
 packages <- c("rgbif", "redlist", "sf", "dplyr", "ggplot2")
 
 # Install missing packages and load all
 for (pkg in packages) {
   if (!requireNamespace(pkg, quietly = TRUE)) {
-    install.packages(pkg, repos = "https://packagemanager.posit.co/cran/latest")
+    install.packages(pkg, repos = "https://packagemanager.posit.co/cran/latest", dependencies = TRUE)
   }
   library(pkg, character.only = TRUE)
 }

Original file line number	Diff line number	Diff line change
`@@ -24,14 +24,14 @@ The workflow combines spatial filtering of occurrence data with automated querie`
`24`	`24`
`25`	`25`	We begin by loading the required packages. The `rgbif` package provides access to GBIF data, `redlist` interfaces with the IUCN Red List API, and `sf` handles spatial operations. The `dplyr` and `ggplot2` packages support data manipulation and visualization respectively.
`26`	`26`
`27`		-```{r setup, echo=FALSE, warning=FALSE, message=FALSE}
	`27`	+```{r setup, warning=FALSE, message=FALSE}
`28`	`28`	`# Define required packages`
`29`	`29`	`packages <- c("rgbif", "redlist", "sf", "dplyr", "ggplot2")`
`30`	`30`
`31`	`31`	`# Install missing packages and load all`
`32`	`32`	`for (pkg in packages) {`
`33`	`33`	`if (!requireNamespace(pkg, quietly = TRUE)) {`
`34`		`- install.packages(pkg, repos = "https://packagemanager.posit.co/cran/latest")`
	`34`	`+ install.packages(pkg, repos = "https://packagemanager.posit.co/cran/latest", dependencies = TRUE)`
`35`	`35`	`}`
`36`	`36`	`library(pkg, character.only = TRUE)`
`37`	`37`	`}`