Performs the leave-one-out analysis

Source: R/crest.leave_one_out.R

Repeat the reconstructions by removing one taxon at a time.

loo(x, climate = x$parameters$climate, verbose = TRUE)

Arguments

x

a crestObj produced by the crest.reconstruct or crest functions.

climate

A vector of the climate variables to extract. See accClimateVariables for the list of accepted values.

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

if (FALSE) {
  data(crest_ex)
  data(crest_ex_pse)
  data(crest_ex_selection)
  reconstr <- crest(
    df = crest_ex, pse = crest_ex_pse, taxaType = 0,
    climate = c("bio1", "bio12"), bin_width = c(2, 20),
    shape = c("normal", "lognormal"),
    selectedTaxa = crest_ex_selection, dbname = "crest_example"
  )
  reconstr <- loo(reconstr)
}
## example using pre-saved reconstruction obtained with the previous command.
data(reconstr)
lapply(reconstr$reconstructions$bio12$loo, head)
#> $Taxon1
#>         optima      mean
#> [1,]    0.0000    0.0000
#> [2,]    0.0000    0.0000
#> [3,]    0.0000    0.0000
#> [4,]    0.0000    0.0000
#> [5,]    0.0000    0.0000
#> [6,] -182.3647 -197.7712
#> 
#> $Taxon2
#> [1] NA
#> 
#> $Taxon3
#> [1] NA
#> 
#> $Taxon4
#>         optima      mean
#> [1,] -164.1283 -183.5160
#> [2,]    0.0000    0.0000
#> [3,]    0.0000    0.0000
#> [4,]    0.0000    0.0000
#> [5,] -375.1503 -373.2838
#> [6,]    0.0000    0.0000
#> 
#> $Taxon5
#>        optima     mean
#> [1,] 489.7796 408.2192
#> [2,]   0.0000   0.0000
#> [3,]   0.0000   0.0000
#> [4,]   0.0000   0.0000
#> [5,] 278.7575 218.4514
#> [6,] 375.1503 310.0513
#> 
plot_loo(reconstr)