sdm (version 1.2-32)

roc: plot ROC curves

Description

Plot the Receiver Operating Characteristics (ROC) curve with AUC statistic in the legend.

Usage

roc(x,p=NULL,species=NULL,method=NULL,replication=NULL,run=NULL,
     wtest=NULL,smooth=FALSE,legend=TRUE,...)
     
getRoc(x,p,...)

Value

an object of class matrix

Arguments

x

Either sdmModels, or sdmEvaluate object; or a numeric vector including observed binary values of species occurrence

p

if x is sdmModels, p is an optional vector with model ID number(s) that should be plotted (NULL (default means all models)); if x is a numeric vector, p is a vector with the same length including the predicted values

species

the name of species should be specified (required if x is sdmModels containing models for several species)

method

a character vector with the name of modelling methods that one need to get the roc plot for (if NULL [default], all methods in the object are considered); only if x is sdmModels

replication

a character vector with the name of replication methods (i.e., 'sub','cv','boot') that one need to get the roc plot for

run

if x is sdmModels, and the models are fitted through a replication procedure, run specifies which runs of the partitioning (replications) are required; if NULL, all are considered

wtest

evaluation for which test datasets are required, maximum 2 names from 'training', 'test.dep', 'test.indep' (i.e., evaluation for training data, dependent test dataset, and independent test dataset, respectively)

smooth

logical, specified whether the ROC curves should be smoothed through a spline procedure

legend

logical, specified whether a legend including AUC statistic is required on the plot

...

additional arguments passed to plot function

Author

Babak Naimi

https://www.r-gis.net/

https://www.biogeoinformatics.org/

Details

roc generates the plots of roc curves, and getRoc generate the values of ROC

References

Naimi, B., Araujo, M.B. (2016) sdm: a reproducible and extensible R platform for species distribution modelling, Ecography, 39:368-375, DOI: 10.1111/ecog.01881

Examples

if (FALSE) {
file <- system.file("external/model.sdm", package="sdm")

m <- read.sdm(file) # a sdmModels Object (fitted using sdm function)

roc(m)

roc(m,1) # for the first model

roc(m, 1:2)

roc(m,method = 'glm',smooth = T) # only for models fitted using glm method & with smoothed curve


}