knitr::opts_chunk$set(fig.height = 5, fig.width = 10, fig.align = 'center')
In this guide, we'll dive into the technique of subsetting or cropping a PresenceAbsence
object.
To accomplish this task, we'll use the lets.subsetPAM
function. Just let the function know which species you want to keep and provide the PresenceAbsence
object as input.
# Package library(letsR) # Data data("PAM") names <- PAM$Species_name[1:20] # keep only the first 20 names PAM_subset <- lets.subsetPAM(PAM, names) par(mfrow = c(1, 2)) plot(PAM, main = "All species") plot(PAM_subset, main = "Subset")
You might also find it useful to crop your PresenceAbsence
object to a specific region using a shapefile. The lets.pamcrop
function offers a straightforward method to achieve this. For instance, let's crop our Presence-Absence Matrix (PAM) to the borders of Brazil.
data(wrld_simpl) # World map data(PAM) Brazil <- wrld_simpl[wrld_simpl$NAME == "Brazil", ] # Brazil (polygon) PAM_crop <- lets.pamcrop(PAM, Brazil, remove.sp = TRUE) par(mfrow = c(1, 2)) plot(PAM, main = "South America") plot(PAM_crop, xlab = "Longitude", ylab = "Latitude", main = "Phyllomedusa species richness (Brazil crop)") plot(sf::st_geometry(wrld_simpl), add = TRUE)
To cite letsR in publications use: Bruno Vilela and Fabricio Villalobos (2015). letsR: a new R package for data handling and analysis in macroecology. Methods in Ecology and Evolution. DOI: 10.1111/2041-210X.12401
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