View source: R/plot.violinPDFS.R
plot_violinPDFs | R Documentation |
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 )
x |
A |
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 |
save |
A boolean to indicate if the diagram should be saved as a pdf file.
Default is |
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
|
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 |
png.res |
The resolution of the png file (default 300 pixels per inch). |
A table with the climate tolerances of all the taxa
## Not run: 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") ) ## End(Not run) ## 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')) lapply(ranges, head)
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