roc {sdm}

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,...)

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

Details

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

Value

an object of class matrix

Author(s)

Babak Naimi [e-mail]

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

https://www.biogeoinformatics.org/

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

## Not run: 
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



## End(Not run)