plot.crestObj | R Documentation |
Plot the reconstructions and their uncertainties if they exist.
## S3 method for class 'crestObj' plot( x, climate = x$parameters$climate, uncertainties = x$parameters$uncertainties, optima = TRUE, add_modern = FALSE, simplify = FALSE, xlim = NA, ylim = NA, pt.cex = 0.8, pt.lwd = 0.8, pt.col = ifelse(simplify, "black", "white"), col.hiatus = "white", save = FALSE, width = 5.51, height = 5.51, as.png = FALSE, png.res = 300, filename = "Reconstruction.pdf", col = viridis::viridis(125)[26:125], ... )
x |
A |
climate |
The climate variables to plot (default is all the reconstructed variables from x) |
uncertainties |
A (vector of) threshold value(s) indicating the error bars that should be calculated (default are the values stored in x). |
optima |
A boolean to indicate whether to plot the optimum ( |
add_modern |
Adds the modern climate values to the plot. |
simplify |
A boolean to indicate if the full distribution of uncertainties
should be plotted ( |
xlim |
the x limits (x1, x2) of the plot. Note that The default value, |
ylim |
the y limits of the plot. |
pt.cex |
The size of the points (default 0.8). |
pt.lwd |
The thickness of the lines (default 0.8). |
pt.col |
The colour of the points and lines. |
col.hiatus |
A colour for the hiatus(es) of the record (default white) |
save |
A boolean to indicate if the diagram should be saved as a pdf file.
Default is |
width, height |
The dimensions of the pdf file (default 5.51in ~14cm). |
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). |
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
|
col |
A colour gradient. |
... |
other graphical parameters (see |
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" ) reconstr <- loo(reconstr) ## End(Not run) ## example using pre-saved reconstruction obtained with the previous command. data(reconstr) plot(reconstr) plot(reconstr, climate='bio1', simplify = TRUE)
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