crest.reconstruct: Reconstruct climate from fossil data

In mchevalier2/crestr: A Probabilistic Approach to Reconstruct Past Climates Using Palaeoecological Datasets

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
)

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).

Value

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

Examples

data(crest_ex_pse)
data(crest_ex_selection)
data(crest_ex)
## Not run: 
  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)

## End(Not run)

mchevalier2/crestr documentation built on Feb. 14, 2025, 6:31 p.m.