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xfer_userEnvs Transfer model to user specified area and time

xfer_userEnvs.Rd

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.

See also

predict, xfer_time xfer_userExtent

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{
## 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)
} # }