plot_scatterPDFs: Plot the pdf optima and uncertainty ranges in a climate...

In mchevalier2/crestr: A Probabilistic Approach to Reconstruct Past Climates Using Palaeoecological Datasets

Plot the pdf optima and uncertainty ranges in a climate biplot

Description

Plot the pdf optima and uncertainty ranges in a climate biplot

Usage

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]]),
  add_modern = FALSE,
  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.
add_modern	A boolean to add the location and the modern climate values to the plot (default FALSE).
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

## 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)
dat <- plot_scatterPDFs(reconstr, save=FALSE,
                 taxanames=c(reconstr$inputs$taxa.name[c(2,4,5,1)]))
dat

mchevalier2/crestr documentation built on Feb. 14, 2025, 6:31 p.m.