View source: R/crest.reconstruct.R
crest.reconstruct | R Documentation |
This function fits the climate response of the selected taxa to the selected climate variables.
crest.reconstruct( x, presenceThreshold = 0, taxWeight = "normalisation", uncertainties = c(0.5, 0.95), skip_for_loo = FALSE, verbose = TRUE )
x |
A |
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 |
verbose |
A boolean to print non-essential comments on the terminal
(default |
A crestObj
object containing the reconstructions and
all the associated data.
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)
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