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Welcome to the manual for the epm R package!

What is the epm package and what can it do?

The R package epm (short for EcoPhyloMapper) allows one to combine individual species' geographic ranges into a self-contained R object that includes a full accounting of which species occur in each grid cell. The epmGrid object also has the ability to contain morphological and phylogenetic data.

This provides us with the ability to calculate various metrics on a cell by cell basis. These metrics could be taxonomic, using the species occurrence data, morphological and/or phylogenetic. We can also calculate turnover metrics based on neighborhoods of cells by employing a moving window average.

The epm package will ultimately be hosted on CRAN, but for the time being, you can install it from this Github repository by running the following: remotes::install_github('ptitle/epm')

Although not required, the epm package is enhanced by the presence of the R packages data.table, tmap and spdep. It is recommended that you install these as well.

Table of contents

1. Creating epmGrid objects

• Main demo

• • What is an epmGrid object?
• • Creating an epmGrid object from range polygons
• • • Preparing range polygons from SpatialPolygons objects (instead of sf objects)
• • A brief description of the options
• • Creating epmGrid objects from point occurrences
• • Creating the epmGrid object
• • Adding trait or phylogenetic data

• in-depth exploration of options in createEPMgrid()

• • polygon-to-grid conversion method
• • handling of small-ranged species
• • specifying the extent -- multiple options
• • providing a cutoff for species inclusion
• • matching your epmGrid object to an existing raster object

2. Diversity metrics

3. Plotting

4. Exporting data

5. Saving epmGrid objects