Species distribution modeling using the functions system.time() and bioclim(): Convert a GADM vector file into raster file format

Problem Outline:

I am attempting to do some species distribution modeling using the function bioclim(). My map of Sri Lanka (Image 1: see below) was extracted from GADM resources, which I understand is a vector object.

For the bioclim() function to work, you need to use this format:

Usage

bioclim(x, p.....)

Arguments:

x Raster*object or matrix

p two column matrix or SpatialPoints object

I am quite new in regards to producing maps and doing species distribution modeling in R. After spending a lot of hours researching, I have tried my very best figure out how to rasterize this GADM vector object into raster file format to be inputted into the bioclim() function. I have been following these species distribution exercises in order to construct a species distribution model for GPS points which constitute the latitude/longitude points for blue whales that were recorded during field surveys.

Aim

The code below was used to produce a map of Sri Lanka (see image 1) with associated GPS points, and my aim is to produce a species distribution model using the function bioclim() and then display the probability bar onto a separate map (see image 2).

The aim of the model is to illustrate the probability of detecting blue whales within particular locations in Sri Lankan waters. Image 2 is the desired output.

After many attempts, I have finally produced code that works, but I am experiencing problems rasterizing the GADM vector object into raster format using the function system.time() and running the bioclim() model. Please see the 2 error message below.

If anyone can help me solve this problem, I cannot express my gratitude.

I cannot publish the data but I have provided a mini data frame below:

Many thanks in advance.

Error messages:

##Error message when I run the system.time() function to rasterize the GADM vector object into a raster file

Error in .getPutVals(p, field, npol, mask) : invalid value for field
Timing stopped at: 0.003 0 0.004

##Error message when I run the bioclim() model

        Error in (function (classes, fdef, mtable)  : 
      unable to find an inherited method for function ‘bioclim’ for signature ‘"SpatialPolygonsDataFrame", "missing"’

R-code:

###Open Packages

library("sp")
library("rgdal")
library("raster")
library("maptools")
library("rgdal")
library("dismo")
library("spatialEco")
library("ggplot2")
library("dplyr")
library("maps")
library("ggspatial")
library("GADMTools")
library("maps")

##Mini dataframe for Blue.whale.new

Blue.whale.new <- data.frame(longitude = c(80.5, 80.5, 80.5, 80.5, 80.4, 80.4, 80.5, 80.5, 80.4),
                         latitude = c(5.84, 5.82, 5.85, 5.85, 5.89, 5.82, 5.82, 5.84, 5.83))

    ###Uploading the map from GADM resources

    ##Plotting the map of Sri Lanka
    dev.new()

    bioclim1.data <- getData('GADM', country='LKA', level=1)

    ####Get boudnign box of Sri Lanka shape file
    bb=bioclim1.data@bbox

    # Determine geographic extent of our data
    max.lat <- ceiling(max(Blue.whale$latitude))
    min.lat <- floor(min(Blue.whale$latitude))
    max.lon <- ceiling(max(Blue.whale$longitude))
    min.lon <- floor(min(Blue.whale$longitude))
    geographic.extent <- extent(x = c(min.lon, max.lon, min.lat, max.lat))

    #####Plot map
    dev.new()

    plot(bioclim1.data, 
         xlim = c(min(c(min.lon,bb[1,1])), max(c(max.lon,bb[1,2]))),
         ylim = c(min(c(min.lat,bb[2,1])), max(c(max.lat,bb[2,2]))),
         axes = TRUE, 
         col = "grey95")

    # Add the points for individual observation
    points(x = Blue.whale$longitude, 
           y = Blue.whale$latitude, 
           col = "olivedrab", 
           pch = 15, 
           cex = 0.50)

    ###Building a model and visualising results

    ##Crop bioclim data to geographic extent of blue whales
    bioclim.data.blue.whale<-crop(x=bioclim1.data, y=geographic.extent)

    ###Rasterize the GADM Formatinto raster format

    ##Define Rasterlayer object
    r.raster<-raster()

    ##Define raster layer extent
    extent(r.raster)<-extent(bioclim1.data)

    # Rasterize
      system.time(bioclim1.data <- rasterize(bioclim1.data, r.raster))

    Error in .getPutVals(p, field, npol, mask) : invalid value for field
Timing stopped at: 0.003 0 0.004

    ##Build species distribution model

    Blue.whale.model<-bioclim(x=bioclim1.data, y=Blue.whale_New)

Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘bioclim’ for signature ‘"SpatialPolygonsDataFrame", "data.frame"’

R-code I plan to run once this error message issue is solved:

# Predict presence from model
predict.presence <- dismo::predict(object = Blue.whale.model, x = bioclim1.data, ext = geographic.extent)

# Plot base map
plot(bioclim1.data, 
     xlim = c(min(c(min.lon,bb[1,1])), max(c(max.lon,bb[1,2]))),
     ylim = c(min(c(min.lat,bb[2,1])), max(c(max.lat,bb[2,2]))),
     axes = TRUE, 
     col = "grey95")

# Add model probabilities
plot(predict.presence, add = TRUE)

# Redraw those country borders
plot(bioclim1.data, add = TRUE, border = "grey5")

# Add original observations
points(Blue.whale_New$longitude, Blue.whale_New$latitude, col = "olivedrab", pch = 20, cex = 0.75)
box()

Image 1

Image 2 (Example of desired output):