MIAmaxent (version 0.4.0)

testAUC: Calculate model AUC with test data.

Description

For a given model, testAUC calculates the Area Under the Curve (AUC) of the Receiver Operating Characteristic (ROC) as a threshold-independent measure of binary classification performance. This function is intended to be used with occurence data that is independent from the data used to train the model, to obtain an unbiased measure of model performance.

Usage

testAUC(data, transformation, model)

Arguments

data

Data frame containing test occurrence data in the first column and corresponding explanatory variables in subsequent columns. The test data should be coded as: 1/0/NA, representing presence, absence, and unknown. See readData.

transformation

Full pathway of the 'transformation.Rdata' file containing the transformations used to build the model. This file is saved as a result of the deriveVars function. Equivalently, the second item in the list returned by deriveVars can be used directly.

model

Full pathway of the '.lambdas' file of the model in question. This file is saved as a result of selectEV.

Value

In addition to returning the testAUC value, graphical output showing the corresponding ROC plot is produced. The point along the ROC curve where the discrimination threshold is PRO = 1 is shown for reference.

Examples

## Not run: ------------------------------------
# AUC <- testAUC(testdat,
#    transformation = "D:/path/to/modeling/directory/deriveVars/transformations.Rdata",
#    model = "D:/path/to/modeling/directory/selectEV/round/model/1.lambdas")
## ---------------------------------------------

sp1pa <- toydata_sp1po
sp1pa$RV[is.na(sp1pa$RV)] <- 0
sp1pa[, 1] <- sample(sp1pa$RV, 40)
auc <- testAUC(sp1pa, toydata_dvs$transformations,
   system.file("extdata/sommerfeltia", "1.lambdas", package = "MIAmaxent"))
auc

## Not run: ------------------------------------
# From vignette:
# grasslandAUC <- testAUC(grasslandPA, transformation = grasslandDVs[[2]],
#    model = system.file("extdata", "1.lambdas", package = "MIAmaxent"))
# grasslandAUC
## ---------------------------------------------