accuracy: Calculate Classification Accuracy

In rRDP: Interface to the RDP Classifier

Description

Calculate the classification accuracy at a given phylogenetic level.

Usage

accuracy(actual, predicted, rank)
confusionTable(actual, predicted, rank)

Arguments

actual	data.frame with the actual classification hierarchy.
predicted	data.frame with the predicted classification hierarchy.
rank	rank at which the accuracy should be evaluated.

Value

The accuracy or a confusion table.

Examples

seq <- readRNAStringSet(system.file("examples/RNA_example.fasta",
	package="rRDP"))

### decode the actual classification
actual <- decode_Greengenes(names(seq))
  
### use RDP to predict the classification
pred <- predict(rdp(), seq)  

### calculate accuracy
confusionTable(actual, pred, "genus")  
accuracy(actual, pred, "genus")

rRDP documentation built on Nov. 8, 2020, 6:39 p.m.