Plot CAST classes — plot • CAST

Generic plot function for CAST Classes

A plotting function for a forward feature selection result. Each point is the mean performance of a model run. Error bars represent the standard errors from cross validation. Marked points show the best model from each number of variables until a further variable could not improve the results. If type=="selected", the contribution of the selected variables to the model performance is shown.

Density plot of nearest neighbor distances in geographic space or feature space between training data as well as between training data and prediction locations. Optional, the nearest neighbor distances between training data and test data or between training data and CV iterations is shown. The plot can be used to check the suitability of a chosen CV method to be representative to estimate map accuracy.

Plot the DI/LPD and errormetric from Cross-Validation with the modeled relationship

Usage

# S3 method for class 'trainDI'
plot(x, ...)

# S3 method for class 'aoa'
plot(x, samplesize = 1000, variable = "DI", ...)

# S3 method for class 'nndm'
plot(x, type = "strict", stat = "ecdf", ...)

# S3 method for class 'knndm'
plot(x, type = "strict", stat = "ecdf", ...)

# S3 method for class 'ffs'
plot(
  x,
  plotType = "all",
  palette = rainbow,
  reverse = FALSE,
  marker = "black",
  size = 1.5,
  lwd = 0.5,
  pch = 21,
  ...
)

# S3 method for class 'geodist'
plot(x, unit = "m", stat = "density", ...)

# S3 method for class 'errorModel'
plot(x, ...)

Arguments

x: errorModel, see DItoErrormetric
...: other params
samplesize: numeric. How many prediction samples should be plotted?
variable: character. Variable for which to generate the density plot. 'DI' or 'LPD'
type: String, defaults to "strict" to show the original nearest neighbour distance definitions in the legend. Alternatively, set to "simple" to have more intuitive labels.
stat: "density" for density plot or "ecdf" for empirical cumulative distribution function plot.
plotType: character. Either "all" or "selected"
palette: A color palette
reverse: Character. Should the palette be reversed?
marker: Character. Color to mark the best models
size: Numeric. Size of the points
lwd: Numeric. Width of the error bars
pch: Numeric. Type of point marking the best models
unit: character. Only if type=="geo" and only applied to the plot. Supported: "m" or "km".

Value

a ggplot

Author

Marvin Ludwig, Hanna Meyer

Carles Milà

Examples

if (FALSE) { # \dontrun{
data(splotdata)
splotdata <- st_drop_geometry(splotdata)
ffsmodel <- ffs(splotdata[,6:16], splotdata$Species_richness, ntree = 10)
plot(ffsmodel)
#plot performance of selected variables only:
plot(ffsmodel,plotType="selected")
} # }