xfer_userEnvs: xfer_userEnvs Transfer model to user specified area and time

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

xfer_userEnvs Transfer model to user specified area and time

Description

The function transfers the model generated in previous components to user uploaded environmental variables.

Usage

xfer_userEnvs(
  evalOut,
  curModel,
  envs,
  xfExt,
  alg,
  outputType = NULL,
  clamp = NULL,
  logger = NULL,
  spN = NULL
)

Arguments

evalOut	ENMevaluate output from previous module and using any of the available algorithms.
curModel	if algorithm is maxent, model selected by user as best or optimal, in terms of feature class and regularization multiplier (e.g 'L_1'). Otherwise it must be 1.
envs	user provided environmental layers (in raster format) to be used for transferring.
xfExt	extent of the area to transfer the model. This must be provided by the user as a shapefile or as a SpatialPolygons object.
alg	modeling algorithm used in the model component. Can be one of: 'BIOCLIM', 'maxent.jar' or 'maxnet'.
outputType	output type to be used when algorithm is maxnet or maxent.jar.
clamp	logical. Whether transfer will be of clamped or unclamped model.
logger	Stores all notification messages to be displayed in the Log Window of Wallace GUI. Insert the logger reactive list here for running in shiny, otherwise leave the default NULL.
spN	character. Used to obtain species name for logger messages.

Details

This functions allows transferring the model created in previous components to a new time and area provided by the user. The transferring time and area is user-provided. The model will be transferred to the new time and area as long as the environmental variables provided are available for the area and match the variables used for model building. This function returns a list including the cropped environmental variables used for transferring and the transferred model.

Author(s)

Jamie Kass <[e-mail]>

Andrea Paz <[e-mail]>

Gonzalo E. Pinilla-Buitrago <[e-mail]>

Bethany A. Johnson <[e-mail]>

See Also

predict, xfer_time xfer_userExtent

Examples

## Not run: 
## extent to transfer
# set coordinates
longitude <- c(-71.58400, -78.81300, -79.34034, -69.83331, -66.47149, -66.71319,
               -71.11931)
latitude <- c(13.18379, 7.52315, 0.93105, -1.70167, 0.98391, 6.09208, 12.74980)
# generate matrix
selCoords <- matrix(c(longitude, latitude), byrow = FALSE, ncol = 2)
polyExt <- sp::SpatialPolygons(list(sp::Polygons(list(sp::Polygon(selCoords)),
                                                 ID = 1)))
# load model
m <- readRDS(system.file("extdata/model.RDS",
                         package = "wallace"))
envsFut <- list.files(path = system.file('extdata/wc/future',
                                         package = "wallace"),
                      full.names = TRUE)
envsFut <- raster::stack(envsFut)
### run function
modXfer <- xfer_userEnvs(evalOut = m, curModel = 1, envs = envsFut,
                         outputType = "cloglog", alg = "maxent.jar",
                         clamp = FALSE, xfExt = polyExt)

## End(Not run)

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