xfer_area: xfer_area Transfer model to a new area

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

xfer_area Transfer model to a new area

Description

Function transfers the model generated in previous components to a new user drawn area.

Usage

xfer_area(
  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'). Else must be 1.
envs	environmental layers to be used for transferring the model. They must match the layers used for generating the model in the model component.
xfExt	extent of the area to transfer the model. This is defined by the user in the map of the GUI and is provided as a SpatialPolygons object.
alg	character. 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 transfers the model created in previous components to a new area. The area of transfer is user provided in the map of the GUI. The model will be transferred to the new area as long as the environmental variables are available for the area. This function returns a list including the cropped environmental variables used for transferring and the transferred model.

Value

A list of two elements: xferExt and xferArea. The first is a RasterBrick or a RasterStack of the environmental variables cropped to the area of transfer. The second element is a raster of the transferred model with the specified output type.

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_userEnvs

Examples

## Not run: 
envs <- envs_userEnvs(rasPath = list.files(system.file("extdata/wc",
                                           package = "wallace"),
                      pattern = ".tif$", full.names = TRUE),
                      rasName = list.files(system.file("extdata/wc",
                                           package = "wallace"),
                      pattern = ".tif$", full.names = FALSE))
# extent of transfer
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)
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"))
modXfer <- xfer_area(evalOut = m, curModel = 1, envs,
                     outputType = 'cloglog', alg = 'maxent.jar',
                     clamp = TRUE, xfExt = polyExt)

## End(Not run)

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