pdf.allplot: Export a pdf with one or more species maps.
In forestgeo/ctfs: Tools for the Analysis of Forest Dynamics

Description Usage Arguments See Also

Export a pdf with one or more species maps. If singlefile=TRUE, all maps will be in one big pdf, otherwise, a pdf for every species is created. The file exported will be named with Map.pdf in the path name given.

This calls the map() function for all species in the splitdata list; it is designed for all species from a plot (default is all species from the BCI plot).

pdf.allplot(splitdata = bci.split6, spplist = bci.spptable,
  elev = ctfs.elev$bci$mat, plotdim = c(1000, 500), cutoff = c(10,
  100, 300, 3000), topoint = 2, bw = FALSE, topoclr = "gray80",
  bty = "o", plotside = 9, h = 8, w = 10, size = c(0.3, 0.45,
  0.65), deadtree = FALSE, symbols = NULL, legsize = 0.75,
  legpos = c(plotdim[1]/2, 1.16 * plotdim[2]), export = TRUE,
  singlefile = TRUE, path = "/home/condit/data/maps/bci/")

`spplist`	A table with species codes and Latin names can be submitted as well, so that the full genus-species is added to plot. This must have species codes as row names. It should be the CTFS R format species table (eg, bciex::bci_species). It can be set to NULL if not available, then only the species code (as submitted) appears on the map.
`plotdim`	The x and y dimensions of the plot.
`cutoff`	Diameter breaks for changing size of plotting points.
`topoint`	Interval for topolines, if elevdata are submitted.
`bw`	If TRUE, only black, white, and grays are used.
`topoclr`	Color of topolines.
`bty`	Type of box to appear around species name. The default, 'n', means no box; set to 'o'to see the box.
`plotside`	The vertical dimension (inches) of the map.
`h, w`	A number giving the height and width.
`size`	The size of plotting points, to match the number of diameter breaks. If NULL, a default set is assigned. This can require fiddling, as big points do not work for really abundant species, and small points for rare species.
`deadtree`	Set NULL to map all trees, alive and dead; TRUE for dead only, FALSE for live only (relies on status in the R table).
`symbols`	A vector of symbols, one per species. Can be anything accepted by R for pch (plot character in the function plot()). If NULL, defaults are assigned.
`legsize`	For the species name, whether to include, where to place, and font size. Try the defaults first before fiddling, or just set addlegend=FALSE to remove.
`legpos`	For the species name, whether to include, where to place, and font size. Try the defaults first before fiddling, or just set addlegend=FALSE to remove.
`export`	`export = "no"`, does nothing, so the next graph uses the default R device. With this option, the size of the graph cannot have been set larger than the default size, which is usually 7 inches. `export = "unix"`, a new graphics window in unix, size `h` and width `w`, will be opened allowing you to alter the size of the output. `export = "windows"`, or `export = "mac"` are similar to `export = "unix"` but for windows and mac. `export = format` exports the graph to a specific file format: "pdf", "png", "jpg", "bmp", "emf".