Benchmark Data Sets and Functions for Marine Species Distribution Modelling

A collection of marine species benchmark data sets and functions for species distribution modelling (ecological niche modelling).


MIT License Build Status Coverage Status R code for downloading and working with the Marine SPEcies and Environmental Data (MarineSPEED.org) benchmark dataset.

Installation:

devtools::install_github("samuelbosch/marinespeed")

Example usage:

library(marinespeed)

## list of all species
species <- list_species()
View(species)

## count number of occurrences for all species 
get_occ_count <- function(speciesname, occ) {
  nrow(occ)
}
record_counts <- lapply_species(get_occ_count)
print(sum(unlist(record_counts)))

## plot first 2 folds for the first 10 species
plot_occurrences <- function(speciesname, data, k) {
   title <- paste0(speciesname, " (fold = ", k, ")")
   plot(data$occurrence_train[,c("longitude", "latitude")], pch=".", 
        col="blue", main = title)
   points(data$occurrence_test[,c("longitude", "latitude")], pch=".", 
          col="red")
}

# plot training (blue) and test (red) occurrences of the first 2 disc folds 
# for the first 10 species
species <- list_species()
lapply_kfold_species(plot_occurrences, species=species[1:10,],
                     fold_type = "disc", k = 1:2)

News

MarineSPEED 0.1.0

Initial release of the MarineSPEED package.

Reference manual

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install.packages("marinespeed")

0.1.0 by Samuel Bosch, a year ago


http://www.samuelbosch.com/p/marinespeed.html


Report a bug at https://github.com/samuelbosch/marinespeed/issues


Browse source code at https://github.com/cran/marinespeed


Authors: Samuel Bosch [aut, cre]


Documentation:   PDF Manual  


GPL (>= 3) license


Imports stats, utils, graphics, grDevices, geosphere, sp, bit

Suggests biomod2, dismo, FNN, testthat, knitr, rmarkdown


See at CRAN