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### confusionMatrix.R (2014-11-13)
###
### Compute Confusion Matrix
###
### Copyright 2014 Korbinian Strimmer
###
###
### This file is part of the `crossval' library for R and related languages.
### It is made available under the terms of the GNU General Public
### License, version 3, or at your option, any later version,
### incorporated herein by reference.
###
### This program is distributed in the hope that it will be
### useful, but WITHOUT ANY WARRANTY; without even the implied
### warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
### PURPOSE. See the GNU General Public License for more
### details.
###
### You should have received a copy of the GNU General Public
### License along with this program; if not, write to the Free
### Software Foundation, Inc., 59 Temple Place - Suite 330, Boston,
### MA 02111-1307, USA
confusionMatrix = function(actual, predicted, negative="control")
{
idx.null = (actual==negative)
idx.alternative = !idx.null
# True Positives ("hit")
# example: predicted is cancer, and actual is cancer
TP = sum( predicted[idx.alternative] != negative )
# True Negatives ("correct rejection")
# example:predict is control, and actual is control
TN = sum( predicted[idx.null] == negative )
# False Positives ("false alarm", Type I error)
# example: predicted is cancer, and actual is control
FP = sum( predicted[idx.null] != negative )
# False Negatives ("miss", Type II error)
# example: predicted is control, and actual is cancer
FN = sum( predicted[idx.alternative] == negative )
cm = c(FP, TP, TN, FN)
names(cm) = c("FP", "TP", "TN", "FN")
attr(cm, "negative") = negative
return ( cm )
}
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