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 abundanceSimulateWorld_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 forOM
objects. It returns a data frame with hindcast and forecast predicitons or you can pass in newdata.print
method forOM
objects. Typesim
and basic info about the simulation is shown. Full information is insim$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.