AfricaBirdData/ABAP

Code for downloading and working with data from the African Bird Atlas Project # ABAP This packages provides functionality to access, download, and manipulate data from the African Bird Atlas Project. It is possible to download these same data using the ABAP API, but being able to pull these data straight into R, in a standard format, should make them more accessible, easier to analyse, and eventually make our analyses more reliable and reproducible. There is another package named `CWAC` that provides similar functionality, but now to download count data from the Coordinated Waterbird Counts project. In addition, there is a companion package the `ABDtools` package, which adds the functionality necessary to annotate different data formats (points and polygons) with environmental information from the Google Earth Engine data catalog. ## INSTRUCTIONS TO INSTALL To install `ABAP` from GitHub using the remotes package, run: ``` r install.packages("remotes") remotes::install_github("AfricaBirdData/ABAP") ``` ## DOWNLOAD ABAP DATA FOR A SPECIES A typical workflow entails defining a region and a species of interest, e.g. say we are interested in the occupancy of the African Black Duck in the North West province of South Africa: First find the ABAP code for the species: ``` r library(ABAP) library(sf) #> Linking to GEOS 3.10.2, GDAL 3.4.1, PROJ 8.2.1; sf_use_s2() is TRUE library(dplyr, warn.conflicts = FALSE) # We can search for all duck species ducks # A tibble: 1 × 1 #> Spp #> #> 1 95 ``` With our code (95) we can download the data recorded for the region of interest: ``` r my_det_data % sample(10) # We can now subset those pentads from the original data det_data_sel % st_as_sf(coords = c("lon", "lat"), crs = 4326) %>% # this is WGS84 st_bbox() %>% st_as_sfc() # Extract pentads within your polygon my_pentads % filter(Pentad %in% my_pentads[,"pentad"]) # Plots plot(st_geometry(nw_pentads), axes = TRUE, lwd = 0.1, cex.axis = 0.7) plot(st_geometry(my_pentads), add = TRUE, col = "red", lwd = 0.1) plot(st_geometry(my_pol), add …