map.plot: Plot maps showing predictions for a given set of climate...

In MarkJBrewer/plateau: Fit plateau climate envelopes in species distribution models for presence/absence data

Description

map.plot plots the fitted maps of "climate suitability" for a given set of climate variable values. Can also be use to plot maps of the presence/absence data.

Usage

map.plot(inputs, plot.type = "Prediction", x.clim.new, x.nonclim.new = NULL,
  x.factor.new = NULL, coordinates, species.name = "", scenario.name = "",
  save.PDF = FALSE, file.name)

Arguments

inputs	If plot.type has value "Prediction", then inputs contains a fitted model object as output by fit.glm.env or fit.bugs.env. If plot.type has value "Presence", then inputs should be a numeric vector of length n and containing 0's and 1's (or FALSE and TRUE) marking absence and presence respectively. The "Prediction" form is used for plotting shaded predictions for fitted climate envelope models; the "Presence" form is used for making simple presence/absence plots. For presence/absence plots, x.clim.new, and other similar arguments are ignored.
plot.type	A string to indicate what kind of map to plot; takes values "Prediction" (the default) or "Presence". (In fact, any string not identical to "Prediction" will lead to a Presence plot.)
x.clim.new	A matrix, having the same columns as inputs$x.clim, and containing the points in climate space at which to evaluate the envelope and produce predictions in space.
x.nonclim.new	The n by p2 matrix of non-climate covariates for prediction, only to be specified if a corresponding x.nonclim element exists in inputs (default NULL).
x.factor.new	The n by p3 matrix of non-climate factors for prediction, only to be specified if a corresponding x.factor element exists in inputs (default NULL).
coordinates	An n by 2 matrix or list or data frame, having elements (or columns) long and lat for longitude and latitude respectively.
species.name	The pretty name of the species for plotting.
scenario.name	The name of the scenario (and year) for plotting.
save.PDF	Logical to indicate whether to save as PDF (default FALSE).
file.name	If save.PDF is TRUE, the name of the pdf file; if missing, this is created using the species and scenario names (if available).

Value

Map of predictions of "climate suitability".

See Also

link{envelope.plot}

MarkJBrewer/plateau documentation built on May 7, 2019, 3:35 p.m.