predict.rivpacs: Use a RIVPACS model to calculate metrics

In jasonelaw/RIVPACS: Fit RIVPACS type models and calculate metrics from RIVPACS predictions

Use a RIVPACS model to calculate metrics

Description

This function predicts the expected number of taxa for a site or sample based on a RIVPACS model.

Usage

## S3 method for class 'rivpacs'
predict(object, newdata, cutoff = 0.05, outlier.probs = c(0.01, 0.05), ...)

Arguments

newdata	a biodiversity object
cutoff	a probability; taxa with a group occurrence probability < cutoff will not be used to calculate metrics.
outlier.probs	p-value thresholds to report which data points are outliers. Only used if method used to fit the RIVPACS model was 'lda'
x	a RIVPACS model

Details

If newdata is missing, fitted values for the data used to fit the model will be returned.

Value

a matrix of RIVPACS metrics

jasonelaw/RIVPACS documentation built on Sept. 27, 2022, 6:34 p.m.