Plot the pdf optima and uncertainty ranges in a climate biplot

plot_scatterPDFs(
x,
climate = x$parameters$climate[1:2],
taxanames = x$input$taxa.name,
uncertainties = x$parameters$uncertainties,
xlim = range(x$modelling$climate_space[, climate[1]]),
ylim = range(x$modelling$climate_space[, climate[2]]),
save = FALSE,
filename = "scatterPDFs.pdf",
width = 5.51,
height = 5.51,
as.png = FALSE,
png.res = 300
)

Arguments

x

A crestObj generated by either the crest.calibrate, crest.reconstruct or crest functions.

climate

Names of the two climate variables to be used to generate the plot. By default plot. By default the first two variables are included.

taxanames

A list of taxa to use for the plot (default is all the recorded taxa).

uncertainties

A (vector of) threshold value(s) indicating the error bars that should be calculated (default are the values stored in x).

xlim,

ylim The climate range to plot the data. Default is the full range of the observed climate space.

ylim

the y limits of the plot.

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)
dat <- plot_scatterPDFs(reconstr, save=FALSE,
taxanames=c(reconstr$inputs$taxa.name[c(2,4,5,1)], 'Taxon'))
#> Warning: PDFs are not available for all taxa names ('Taxon').

dat
#> $Range = 50% #> bio1_tol_inf bio1_tol_sup bio1_range bio12_tol_inf bio12_tol_sup #> Taxon2 23.64729 25.81162 2.164329 247.49499 531.4629 #> Taxon4 18.35671 22.20441 3.847695 669.53908 841.4830 #> Taxon5 18.11623 22.52505 4.408818 57.31463 169.3387 #> Taxon1 23.00601 25.33066 2.324649 565.33066 752.9058 #> bio12_range #> Taxon2 283.9679 #> Taxon4 171.9439 #> Taxon5 112.0240 #> Taxon1 187.5752 #> #>$Range = 95%
#>        bio1_tol_inf bio1_tol_sup bio1_range bio12_tol_inf bio12_tol_sup
#> Taxon2     21.56313     27.97595   6.412826     127.65531     1021.2425
#> Taxon4     14.50902     25.97194  11.462926     536.67335     1047.2946
#> Taxon5     13.86774     26.85371  12.985972      20.84168      458.5170
#> Taxon1     20.68136     27.73547   7.054108     429.85972      995.1904
#>        bio12_range
#> Taxon2    893.5872
#> Taxon4    510.6212
#> Taxon5    437.6754
#> Taxon1    565.3307
#>