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)], 'Taxon'),
col=c('darkblue', 'firebrick3'))
#> Warning: PDFs are not available for all taxa names ('Taxon').

#> $Range = 50% #> bio1_tol_inf bio1_tol_sup bio1_range #> Taxon1 23.00601 25.33066 2.324649 #> Taxon2 23.64729 25.81162 2.164329 #> Taxon4 18.35671 22.20441 3.847695 #> Taxon5 18.11623 22.52505 4.408818 #> #>$Range = 95%