Plot representing how the pdfs combine to produce the reconstruction.

Plot representing how the pdfs combine to produce the reconstruction.

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

if (FALSE) {
  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
   )
}
## example using pre-saved reconstruction obtained with the previous command.
data(reconstr)
plot_combinedPDFs(reconstr, ages=c(6,9), climate='bio12')