crestr (version 1.2.1)

crest.reconstruct: Reconstruct climate from fossil data

Description

This function fits the climate response of the selected taxa to the selected climate variables.

Usage

crest.reconstruct(
  x,
  presenceThreshold = 0,
  taxWeight = "normalisation",
  uncertainties = c(0.5, 0.95),
  skip_for_loo = FALSE,
  verbose = TRUE
)

Value

A crestObj object containing the reconstructions and all the associated data.

Arguments

x

A crestObj produced by the crest.calibrate function.

presenceThreshold

All values above that threshold will be used in the reconstruction (e.g. if set at 1, all percentages below 1 will be set to 0 and the associated presences discarded). Default is 0.

taxWeight

One value among the following: 'originalData', 'presence/absence', 'percentages' or 'normalisation' (default).

uncertainties

A (vector of) threshold value(s) indicating the error bars that should be calculated (default both 50 and 95% ranges).

skip_for_loo

A boolean that tells the loo function to skip parts and fasten the process. Not for users, always leave to FALSE.

verbose

A boolean to print non-essential comments on the terminal (default TRUE).

Examples

data(crest_ex_pse)
data(crest_ex_selection)
data(crest_ex)
if (FALSE) {
  x <- crest.get_modern_data( df = crest_ex,
    pse = crest_ex_pse, taxaType = 0,
    climate = c("bio1", "bio12"),
    selectedTaxa = crest_ex_selection, dbname = "crest_example",
    verbose = FALSE
  )
  x <- crest.calibrate(x,
    geoWeighting = TRUE, climateSpaceWeighting = TRUE,
    bin_width = c(2, 50), shape = c("normal", "lognormal"),
    verbose = FALSE
  )
  x <- crest.reconstruct(x,
    verbose = FALSE)
  plot(x)
}