plot_combinedPDFs: Plot representing how the 'pdfs' combine to produce the...

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

Plot representing how the pdfs combine to produce the reconstruction.

Description

Plot representing how the pdfs combine to produce the reconstruction.

Usage

plot_combinedPDFs(
  x,
  ages = range(x$inputs$x),
  samples = which(x$inputs$x >= min(ages) & x$inputs$x <= max(ages)),
  climate = x$parameters$climate[1],
  optima = TRUE,
  xlim = NA,
  only.present = FALSE,
  only.selected = FALSE,
  col = crestr::colour_theme(1),
  save = FALSE,
  filename = "samplePDFs.pdf",
  as.png = FALSE,
  png.res = 300,
  width = 7.48,
  height = 5
)

Arguments

x	A crestObj generated by the crest.reconstruct or crest functions.
ages	An age range to subset the samples to plot. By default, all the samples will be selected.
samples	The list of sample indexes for which the plot should be plotted. All samples will be plotted by default.
climate	The climate variable to use to plot the variable. Default is first variable (x$parameters$climate\[1\]).
optima	A boolean to indicate whether to plot the optimum (TRUE) or the mean (FALSE) estimates.
xlim	The climate range to plot the pdfs on. Default is the full range used to fit the pdfs (x$modelling$xrange).
only.present	A boolean to only add the names of the taxa recorded in the sample (default FALSE).
only.selected	A boolean to only add the names of the selected taxa (default FALSE).
col	A range of colour values to colour the pdfs. Colours will be recycled to match the number of taxa.
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 'samplePDFs.pdf'.
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).
width	The width of the output file in inches (default 7.48in ~ 19cm).
height	The height of the output file in inches (default 5in ~ 12.7cm).

Value

No return value, this function is used to plot.

Examples

## Not run: 
  data(crest_ex)
  data(crest_ex_pse)
  data(crest_ex_selection)
  reconstr <- crest(
    df = crest_ex, pse = crest_ex_pse, taxaType = 0,
    climate = c("bio1", "bio12"), bin_width = c(2, 20),
    shape = c("normal", "lognormal"),
    selectedTaxa = crest_ex_selection, dbname = "crest_example",
    leave_one_out = FALSE
   )

## End(Not run)
## example using pre-saved reconstruction obtained with the previous command.
data(reconstr)
plot_combinedPDFs(reconstr, ages=c(6,9), climate='bio12')

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