update,Stacked.SDM-method {SSDM}

Update a previous SSDM

Description

Update a previous SSDM with new occurrence data. The function takes as inputs updated or new occurrence data from one species, previous environmental variables, and an S4 Stacked.SDM class object containing a previously built SSDM.

Usage

## S4 method for signature 'Stacked.SDM'
update(
  object,
  Occurrences,
  Env,
  Xcol = "Longitude",
  Ycol = "Latitude",
  Pcol = NULL,
  Spname = NULL,
  name = stack@name,
  save = FALSE,
  path = getwd(),
  thresh = 1001,
  tmp = FALSE,
  verbose = TRUE,
  GUI = FALSE,
  ...
)

Arguments

object

Stacked.SDM. The previously built SSDM.

Occurrences

data frame. New or updated occurrence table (can be processed first by load_occ).

Env

raster object. Environment raster object (can be processed first by load_var).

Xcol

character. Name of the column in the occurrence table containing Latitude or X coordinates.

Ycol

character. Name of the column in the occurrence table containing Longitude or Y coordinates.

Pcol

character. Name of the column in the occurrence table specifying whether a line is a presence or an absence. A value of 1 is presence and value of 0 is absence. If NULL presence-only dataset is assumed.

Spname

character. Name of the new or updated species.

name

character. Optional name given to the final SSDM produced, by default it's the name of the previous SSDM.

save

logical. If set to true, the model is automatically saved.

path

character. Name of the path to the directory to contain the saved SSDM.

thresh

numeric. A single integer value representing the number of equal interval threshold values between 0 and 1.

tmp

logical. If set to true, the habitat suitability map of each algorithm is saved in a temporary file to release memory. But beware: if you close R, temporary files will be deleted To avoid any loss you can save your model with save.model.

verbose

logical. If set to true, allows the function to print text in the console.

GUI

logical. Don't take that argument into account (parameter for the user interface).

...

additional parameters for the algorithm modelling function (see details below).

Value

an S4 Stacked.SDM class object viewable with the plot.model function.

See Also

stack_modelling to build SSDMs.

Examples

## Not run: 
update(stack, Occurrences, Env, Spname = 'NewSpecie')

## End(Not run)