predPlot: Plot predicted values for presences and absences, optionally...

In modEvA: Model Evaluation and Analysis

Plot predicted values for presences and absences, optionally classified according to a prediction threshold.

Description

This function plots predicted values separated into observed presences and absences and (optionally and by default) coloured according to whether they are above or below a given prediction threshold. The plot imitates (with permission from the author) one of the graphical outputs of the 'summary' of models built with the embarcadero package (Carlson, 2020), but it can be applied to other types of models or to a set of observed and predicted values, and it allows specifying a user-defined threshold.

Usage

predPlot(model = NULL, obs = NULL, pred = NULL, thresh = "preval", pbg = FALSE,
main = "Classified predicted values", legend.pos = "n", pch = 1, cex = 0.5,
col = c("black", "grey"), na.rm = TRUE, rm.dup = FALSE, interval = 0.01,
quant = 0)

Arguments

model	a binary-response model object of class "glm", "gam", "gbm", "randomForest" or "bart". If this argument is provided, 'obs' and 'pred' will be extracted with mod2obspred. Alternatively, you can input the 'obs' and 'pred' arguments instead of 'model'.
obs	alternatively to 'model' and together with 'pred', a numeric vector of observed presences (1) and absences (0) of a binary response variable. Alternatively (and if 'pred' is a 'SpatRaster'), a two-column matrix or data frame containing, respectively, the x (longitude) and y (latitude) coordinates of the presence points, in which case the 'obs' vector will be extracted with ptsrast2obspred. This argument is ignored if 'model' is provided.
pred	alternatively to 'model' and together with 'obs', a vector with the corresponding predicted values of presence probability, habitat suitability, environmental favourability or alike. Must be of the same length and in the same order as 'obs'. Alternatively (and if 'obs' is a set of point coordinates), a 'SpatRaster' map of the predicted values for the entire evaluation region, in which case the 'pred' vector will be extracted with ptsrast2obspred. This argument is ignored if 'model' is provided.
thresh	threshold value to separate predicted presences from predicted absences in 'pred'; can be "preval" (the default), to use the prevalence (i.e. proportion of presences) in 'obs'; or any real number between 0 and 1; or any of the options available on modEvAmethods("getThreshold") – see Details in getThreshold for their description. This value, if not NA or NULL, will be used to draw a vertical line on the plot and to colour the points (predicted values) according to whether they fall above or below the threshold.
pbg	logical value to pass to inputMunch indicating whether to use presence/background (rather than presence/absence) data. Default FALSE.
main	Main title for the plot.
legend.pos	character value specifying the position for the legend on the plot. Can be "bottomleft", "bottom", "bottomright", "topleft", "left", "top", "topright", "right", "center", or NA or "n" for no legend (the default). Partial argument matching is used.
pch	plotting character for the presences and absences (see par).
cex	relative size of the plotting character (see par).
col	vector of length 2 indicating the colours with which to plot predicted presences and absences (points above and below the threshold), respectively. If 'thresh' is NA or NULL, all points will have the first of the specified colours.
na.rm	Logical value indicating whether missing values should be ignored in computations. Defaults to TRUE.
rm.dup	If TRUE and if 'pred' is a SpatRaster and if there are repeated points within the same pixel, a maximum of one point per pixel is used to compute the presences. See examples in ptsrast2obspred. The default is FALSE.
interval	Argument to pass to optiThresh indicating the interval between the thresholds to test, if 'thresh' implies optimizing a threshold-based measure. The default is 0.01. Smaller values may provide more precise results but take longer to compute.
quant	Numeric value indicating the proportion of presences to discard if thresh="MTP" (minimum training presence). With the default value 0, MTP will be the threshold at which all observed presences are classified as such; with e.g. quant=0.05, MTP will be the threshold at which 5% presences will be classified as absences.

Value

This function outputs a plot as per 'Description'.

Note

Points are jittered randomly along the y axis to minimize visual overlap. So, each run of 'predPlot' (unless you use set.seed first) will produce a different arrangement of points for the same data, although their x-axis values are faithful.

Author(s)

A. Marcia Barbosa

References

Carlson C.J. (2020) embarcadero: Species distribution modelling with Bayesian additive regression trees in R. Methods in Ecology and Evolution, 11: 850-858.

See Also

predDensity, plotGLM

Examples

# load sample models:
data(rotif.mods)

# choose a particular model to play with:
mod <- rotif.mods$models[[1]]

predPlot(model = mod)

predPlot(model = mod, thresh = 0.5)


# you can first select a threshold optimized according to a particular metric:

## Not run: 
threshold <- optiThresh(mod, measures = "TSS", optimize = "each")
threshold <- threshold$optimals.each[ , "threshold"]
threshold
predPlot(model = mod, thresh = threshold)

## End(Not run)

# you can also use 'predPlot' with vectors of observed and predicted values
# instead of a model object:

presabs <- mod$y
prediction <- mod$fitted.values

predPlot(obs = presabs, pred = prediction)

predPlot(obs = presabs, pred = prediction, thresh = 0.5)


# 'obs' can also be a table of presence point coordinates
# and 'pred' a SpatRaster of predicted values

modEvA documentation built on Oct. 30, 2024, 1:06 a.m.