View source: R/plot.combinedPDFS.R
plot_combinedPDFs | R Documentation |
pdfs
combine to produce the reconstruction.Plot representing how the pdfs
combine to produce the reconstruction.
plot_combinedPDFs( x, samples = 1:length(x$inputs$x), 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 )
x |
A |
samples |
The list of samples 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 ( |
optima |
A boolean to indicate whether to plot the optimum ( |
xlim |
The climate range to plot the pdfs on. Default is the full range
used to fit the |
only.present |
A boolean to only add the names of the taxa recorded in
the sample (default |
only.selected |
A boolean to only add the names of the selected taxa
(default |
col |
A range of colour values to colour 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
|
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). |
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). |
No return value, this function is used to plot.
## 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, samples=1:4, climate='bio12')
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