About

MarineSPEED is a benchmark dataset for presence-only species distribution modelling. It contains a collection of 514 marine species linked to environmental data for the 71 current climate layers of Bio-ORACLE and MARSPEC.

R package "marinespeed"

An R package for downloading and working with MarineSPEED is available on CRAN and on GitHub. For more information see the R package documentation, the README or contact me at mail@samuelbosch.com .

# Installation from CRAN
install.packages("marinespeed")
# or from GitHub
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)

Direct download

You can also directly download all MarineSPEED data with the following links.

• species data
  • species.csv.gz
  • traits.csv.gz
  • occurrences.zip
  • occurrences_raw.zip
• random_background.zip
• targetgroup_background.zip
• random folds
  • random_species_5cv_folds.csv.gz
  • random_background_5cv_folds.csv.gz
  • targetgroup_background_5cv_folds.csv.gz
• pseudo-disc (spatial) folds
  • pseudodisc_species_5cv_folds.csv.gz
  • pseudodisc_background_5cv_folds.csv.gz
• grid (spatial) 4-fold
  • grid_species_4cv_folds.csv.gz
  • grid_background_4cv_folds.csv.gz
• grid (spatial) 9-fold
  • grid_species_9cv_folds.csv.gz
  • grid_background_9cv_folds.csv.gz