BiodiversityR

Preserving Biodiversity: An Integrated Approach Using R and the IUCN Red List for Rhinella Granulosa species

Overview

This R code is part of a biodiversity project and aims to assess habitat suitability for different species based on land-use data. The code involves loading spatial data, rasterizing species range shapes, reclassifying land-use, and calculating suitable habitats.

Setup

setwd("C:/Users/Asus/Desktop/biodiversityproject1")
load("redlist_practical.Rdata")
library(maptools)
library(raster)
library(rgdal)
library(sp)
library(Rcpp)

Data Import

lu2005 = raster("landuse_2005.tif")
lu2012 = raster("landuse_2012.tif")
lu_fut = raster("lu_fut.tif")
renelosa = readShapePoly("a3070.shp")

Exploring Data

plot(lu2005)
plot(lu2012)
plot(lu_fut)
plot(renelosa)
plot(renelosa, add = TRUE)

Rasterizing Species Range

renelosa.r = rasterize(renelosa, lu2012, field = 1)
plot(renelosa.r)

Reclassification

reclass = read.delim("reclass_renelosa.txt")
rcl = data.frame(reclass[, c(1, 3)])
suitability2012 = reclassify(lu2012, rcl = rcl)
plot(suitability2012)

Calculating Suitable Habitat

suit_2012_renelosa = suitability2012 * renelosa.r
plot(suit_2012_renelosa)
a = area(suit_2012_renelosa)
zonal(a, suit_2012_renelosa, "sum")

Saving Progress

save.image("redlist_practical.Rdata")

New Species Analysis

renelosa = readShapePoly("a3070.shp")
renelosa.r = rasterize(renelosa, lu2012, field = 1)
reclass = read.delim("reclass_renelosa.txt")
rcl = data.frame(reclass[, 2:3])
suitability2012 = reclassify(lu2012, rcl = rcl)
suit_2012_SPECIESNAME = suitability2012 * SPECIESNAME.r  # replace SPECIESNAME with the actual species name
plot(suit_2012_SPECIESNAME)
a = area(suit_2012_SPECIESNAME)
zonal(a, suit_2012_SPECIESNAME, "sum")

Repeat the above steps for 2005 and future projections.

Future Suitability

suitability_future = reclassify(lu.fut, rcl = rcl)
suit_future_SPECIESNAME = suitability_future * SPECIESNAME.r  # replace SPECIESNAME with the actual species name
plot(suit_future_SPECIESNAME)

Additional Steps

save.image("redlist_practical.Rdata")

This code can be used as a guide for analyzing habitat suitability for multiple species in different time periods.
Please note that I made a few assumptions, such as the existence of a variable SPECIESNAME.r which needs to be replaced with the actual rasterized species range data. Make sure to replace placeholders like SPECIESNAME with the correct names in your data.

AnitaVafaei/BiodiversityR