xfer_time: xfer_time Transfer model to a new time

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

xfer_time Transfer model to a new time

Description

Function transfers the model generated in previous components to a new time and area using provided layers.

Usage

xfer_time(
  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 must be 1.
envs	environmental layers of different time 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	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. The area of transfer is user provided in the map of the GUI and the transfer time user selected. The model will be transferred to the new area and time 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 xferTime. The first is a RasterBrick or 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 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"))
occsEnvs <- m@occs
bgEnvs <- m@bg
envsFut <- list.files(path = system.file('extdata/wc/future',
                                         package = "wallace"),
                      full.names = TRUE)
envsFut <- raster::stack(envsFut)
modXfer <- xfer_time(evalOut = m, curModel = 1,
                     envs = envsFut, alg = 'maxent.jar',
                     xfExt = polyExt, clamp = FALSE, outputType = 'cloglog')

## End(Not run)

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