README.md

In eeholmes/WRAP: WRAP Location Study

WRAP Package

To install

library(devtools)
install_github("eeholmes/WRAP", dependencies=TRUE)

Overview and help files

To see all the functions with links to their help files, use

library(WRAP)
help(package="WRAP")

Vignettes

There are detailed vignettes that show how to fit models and make a variety of plots. To open links to the vignettes in a browser use:

browseVignettes(package="WRAP")

To find the Rmd files for these vignettes, look in the vignettes folder.

Functions

The simulation functions are

• SimulateWorld() This is the function that generates temperature dependent species distribution and abundance
• SimulateWorld_ROMS() This function uses temperature data from ROMS to generate species distribution and abundance.
• SimulateWorld_ROMS_TrophicInteraction() This function uses temperature and chl-a to build suitability for two species, and generate distribution and abundance for one species.

To run the simulations using ROMS data, you need the ROMS data. It is assumed that you have these data in a folder called "Rasters_2d_monthly" in your working directory. That can be changed. See ?SimulateWorld_ROMS. The simulation functions return a OM object. There is a

• predict method for OM objects. It returns a data frame with hindcast and forecast predicitons or you can pass in newdata.
• print method for OM objects. Type sim and basic info about the simulation is shown. Full information is in sim$meta.

The functions to fit a SDM from a grid of covariates and abundances is

• gam_sdm
• brt_sdm
• mlp_sdm

The predict function will take a SDM and make hindcast and forecast predictions.

The functions to plot are

• plot_abund
• plot_pres
• plot_cog
• plot_grid
• plot for OM and POM objects

ROMS data

The rasters in the package were created from netcdf files using the script Create_ROMS_Rasters.R in the doc\ROMSdata folder. Most users do not need to use this code.

eeholmes/WRAP documentation built on Feb. 18, 2021, 10:51 a.m.