plot.predict.downscale: Plotting of downscaled occupancy at fine grain sizes

In downscale: Downscaling Species Occupancy

Description

A simple plotting function of predict.downscale objects. Occupancy is plotted against grain size (cell area) in log-log space. Observed occupancy at large grain sizes are plotted in black, and occupancies predicted through predict.downscale plotted in red.

Usage

## S3 method for class 'predict.downscale'
plot(x, xlim = NULL, ylim = NULL,
     xlab = NULL, ylab = NULL, main = NULL, lwd.obs = NULL, lwd.pred = NULL,
     col.obs = NULL, col.pred = NULL, ...)

Arguments

x	Output object from predict.downscale and of class predict.downscale
xlim, ylim	limits of axes. Defaults to minimum and maximum of data.
xlab, ylab, main	axis labels and title.
lwd.obs, lwd.pred	line width of observed and predicted occupancies (default = 2).
col.obs, col.pred	line and point colours of observed (default = black) and predicted (default = red) occupancies.
...	arguments, including graphical parameters passed to other methods.

Author(s)

Charles Marsh <[e-mail]>.

See Also

See predict.downscale and hui.downscale for generating predict.downscale objects.

Examples

## example species data
data.file <- system.file("extdata", "atlas_data.txt", package = "downscale")
atlas.data <- read.table(data.file, header = TRUE)

## upgrain data (using All Occurrences threshold)
occupancy <- upgrain(atlas.data,
                     cell.width = 10,
                     scales = 3,
                     method = "All_Sampled",
                     plot = FALSE)

## Logistic model
logis <- downscale(occupancies = occupancy,
                   model = "Logis")

## predict occupancies at fine scales
logis.pred <- predict(logis,
                      new.areas = c(1, 5, 25, 100, 400, 1600, 6400))

## plot predictions
plot(logis.pred)

## change some of the plotting arguments
plot(logis.pred,
     col.obs = "blue",
     pch = 16,
     ylim = c(0.01, 0.7))

downscale documentation built on May 2, 2019, 5:24 p.m.