inst/shiny/modules/envs_worldclim.md

In wallace: A Modular Platform for Reproducible Modeling of Species Niches and Distributions

Module: WorldClim Bioclimatic Variables

BACKGROUND

The WorldClim project provides bioclimatic variables for the Earth's land surfaces for all continents except Antarctica. Monthly data from weather stations were spatially interpolated using elevation as a covariate; subsequently, 19 bioclimatic variables were derived, reflecting various aspects of temperature and precipitation (Fick & Hijmans 2017). The descriptions of each variable are listed below, taken from the WorldClim website, where more details can be found.

BIO1 = Annual Mean Temperature BIO2 = Mean Diurnal Range (Mean of monthly (max temp - min temp)) BIO3 = Isothermality (BIO2/BIO7) ( 100) BIO4 = Temperature Seasonality (standard deviation 100) BIO5 = Max Temperature of Warmest Month BIO6 = Min Temperature of Coldest Month BIO7 = Temperature Annual Range (BIO5-BIO6) BIO8 = Mean Temperature of Wettest Quarter BIO9 = Mean Temperature of Driest Quarter BIO10 = Mean Temperature of Warmest Quarter BIO11 = Mean Temperature of Coldest Quarter BIO12 = Annual Precipitation BIO13 = Precipitation of Wettest Month BIO14 = Precipitation of Driest Month BIO15 = Precipitation Seasonality (Coefficient of Variation) BIO16 = Precipitation of Wettest Quarter BIO17 = Precipitation of Driest Quarter BIO18 = Precipitation of Warmest Quarter BIO19 = Precipitation of Coldest Quarter

IMPLEMENTATION

This module relies on the R package geodata (Hijmans et al. 2024) to download WorldClim v2.1 bioclimatic variables from the WorldClim server (Fick and Hijmans 2017). Wallace makes all four resolutions of the data available (10 arcmin ≈ 20 km, 5 arcmin ≈ 10 km, 2.5 arcmin ≈ 5 km, and 30 arcsec ≈ 1 km).

The finest-grain WorldClim dataset (30 arcsec) can only be downloaded by separate 30 x 30 degree tiles in the current implementation of dismo (1.1-1), so Wallace uses the current center of the map display as the tile reference for this resolution. This means that analyses with 30 arcsec climatic data using the current version of Wallace are restricted to the extent of a single tile. To visualize the tile, check the “30 arcsec tile” box in the bottom left corner of the map. This will let the user see if the occurrences are all contained within the tile or whether they extend beyond it. When running locally, the dataset is downloaded to the Wallace folder (which can take substantial time), but Wallace will use the downloaded data for later runs when the same resolution is selected.

The “Batch” option will load the environmental variables selected at the chosen resolution for all the species that have occurrence data uploaded.

REFERENCES

Fick, S.E., & Hijmans, R.J. (2017). WorldClim 2: new 1-km spatial resolution climate surfaces for global land areas. International Journal of Climatology, 37(12), 4302-4315. DOI: 10.1002/joc.5086

Hijmans, R.J., et al. (2024). geodata: Download Geographic Data. R package version 0.6-2. CRAN

wallace documentation built on Sept. 11, 2024, 9:16 p.m.