Plot the pdfs as violins

plot_violinPDFs(
  x,
  climate = x$parameters$climate[1],
  taxanames = x$input$taxa.name,
  col = viridis::viridis(20),
  ylim = range(x$modelling$xrange[[climate]]),
  save = FALSE,
  filename = "violinPDFs.pdf",
  width = 7.48,
  height = 5,
  as.png = FALSE,
  png.res = 300
)

Arguments

x: A crestObj generated by either the crest.calibrate, crest.reconstruct or crest functions.
climate: Climate variables to be used to generate the plot. By default all the variables are included.
taxanames: A list of taxa to use for the plot (default is all the recorded taxa).
col: A vector of colours that will be linearly interpolated to give a unique colour to each taxon.
ylim: The climate range to plot the pdfs on. Default is the full range used to fit the pdfs (x$modelling$xrange)
save: A boolean to indicate if the diagram should be saved as a pdf file. Default is FALSE.
filename: An absolute or relative path that indicates where the diagram should be saved. Also used to specify the name of the file. Default: the file is saved in the working directory under the name 'violinPDFs.pdf'.
width: The width of the output file in inches (default 7.48in ~ 19cm).
height: The height of the output file in inches (default 3in ~ 7.6cm per variables).
as.png: A boolean to indicate if the output should be saved as a png. Default is FALSE and the figure is saved as a pdf file.
png.res: The resolution of the png file (default 300 pixels per inch).

Value

A table with the climate tolerances of all the taxa

Examples

if (FALSE) {
  data(crest_ex_pse)
  data(crest_ex_selection)
  reconstr <- crest.get_modern_data(
    pse = crest_ex_pse, taxaType = 0,
    climate = c("bio1", "bio12"),
    selectedTaxa = crest_ex_selection, dbname = "crest_example"
  )
  reconstr <- crest.calibrate(reconstr,
    geoWeighting = TRUE, climateSpaceWeighting = TRUE,
    bin_width = c(2, 20), shape = c("normal", "lognormal")
  )
}
## example using pre-saved reconstruction obtained with the previous command.
data(reconstr)
ranges <- plot_violinPDFs(reconstr, save=FALSE, ylim=c(5,35),
                taxanames=c(reconstr$inputs$taxa.name[c(2,4,5,1)]),
                col=c('darkblue', 'firebrick3'))

lapply(ranges, head)
#> $`Range = 50%`
#>        bio1_tol_inf bio1_tol_sup bio1_range
#> Taxon1     23.00601     25.33066   2.324649
#> Taxon2     23.64729     25.81162   2.164329
#> Taxon4     18.35671     22.20441   3.847695
#> Taxon5     18.11623     22.52505   4.408818
#> 
#> $`Range = 95%`
#>        bio1_tol_inf bio1_tol_sup bio1_range
#> Taxon1     20.68136     27.73547   7.054108
#> Taxon2     21.56313     27.97595   6.412826
#> Taxon4     14.50902     25.97194  11.462926
#> Taxon5     13.86774     26.85371  12.985972
#>