bgplot: Plotting of a biogeographic partitioning

In adamkocsis/obigeo: Occurrence-based biogeography

Plotting of a biogeographic partitioning

Description

The function takes a single time slice from a grouping output and plots a geographic rendering.

Usage

bgplot(
  bdat,
  map = NULL,
  lng = NULL,
  lat = NULL,
  colors = NULL,
  labels = NULL,
  cell = "rownames",
  circles = TRUE,
  icosa = NULL,
  xlim = c(-180, 180),
  ylim = c(-90, 90),
  xlab = "longitude",
  ylab = "latitude",
  alpha = 0.5,
  between = NULL,
  fademap = 0.5,
  map.args = NULL,
  border = "gray50",
  grid.args = NULL,
  lab.args = NULL,
  axes = TRUE,
  asp = 1,
  add = FALSE
)

Arguments

bdat	(data.frame) Biogeographic partitioning.
map	(SpatialPolygons, SpatialPolygonsDataFrame, RasterLayer) A map object, plottable with mapplot.
colors	(character) Variable name of the colors.
labels	(character) Variable name of the labels.
cell	(character) Where is the cell information? "rownames" or column name.
circles	(logical) Should the Equator and the 30 degree latitudinal circles be plotted?
icosa	(hexagrid) or trigrid Optional argument, a grid from the icosa package (if cells of such grid are used). Otherise the biogeographic regions will be indicated with circles (not yet?).
xlim	(numeric) the standard argument of plot() - not tested yet!
ylim	(numeric) the standard argument of plot() - not tested yet!
xlab	(character) the standard argument of plot() - not tested yet!
ylab	(character) the standard argument of plot() - not tested yet!
alpha	(numeric) Numeric value between 0 and 1 indicating the opacity of the partitioning.
between	(expression) code to be executed between the map drawing and the plotting of the partitioning.
fademap	(numeric) Numeric value between 0 and 1 indicating the opacity of the map.
map.args	(list) Additional arguments passed to the mapplot function to render the maps.
grid.args	(logical) Additional arguments to plot the grid itself.
lab.args	(logical) Additional arguments to plot the labels with the text function.
axes	(logical) Should the default axes be plotted?
asp	(numeric) Same as in par(). Defaults to 1 (fixed aspect ratio).
add	(logical) Should the plot be added to another plot?

Details

Option B. coorindates go to bdat, triggering

Examples

# Partition the Cenozoic 6 benthic subset of the Paleobiology Database
oneC6 <- bgpart(ceno6,bin=NULL, tax="trinomen", cell="icos", ocq=10, base="network", method="infomap")
# The used grid for plotting
library(icosa)
hex <- hexagrid(c(4,3), sp=TRUE)
# land polygons and colors for a nice plot
data(land)
bgplot(oneC6, map=land, colors="col", icosa=hex, labels="grouping")

adamkocsis/obigeo documentation built on Oct. 14, 2024, 8:46 a.m.