xfer_time Transfer model to a new time

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.

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.

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.

Author

Jamie Kass <jamie.m.kass@gmail.com>

Andrea Paz <paz.andreita@gmail.com>

Gonzalo E. Pinilla-Buitrago <gepinillab@gmail.com>

Bethany A. Johnson <bjohnso005@citymail.cuny.edu>

Examples

if (FALSE) { # \dontrun{
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')
} # }