Calculate Classification Accuracy

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Description

Calculate the classification accuracy at a given phylogenetic level.

Usage

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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

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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")