[R] knncat broken on R 2.14?

Thu Feb 2 02:09:08 CET 2012

Hi,

Until recently I was using the knncat classifier function of 
knncat on an old computer (2.12, Mac OS X 10.4), and 
everything worked great.

However, now that I have updated to R 2.14.1 (on Mac OS X 
10.7), knncat seems broken.  Problems:

1. It seems to output verbose output by default, and 
regardless of whether I put 0 or 1 into the verbose option.

2. It seems to just predict everything to be class "0".

3. I can see this problem even when running the example 
script under ?knncat.

Given example from ?knncat, and expected behavior:
=======================
library(knncat)

library(MASS) # Load data set
syncat <- knncat (synth.tr, classcol=3)

## Not run: syncat
Train set misclass rate: 12.8
synpred <- predict (syncat, synth.tr, synth.te, 
train.classcol=3,
                     newdata.classcol=3)
table (synpred, synth.te$yc)

synpred 0   1
       0 460  91
       1  40 409
=======================

Actual behavior:
==========================================
 > library(MASS) # Load data set
 > syncat <- knncat (synth.tr, classcol=3)

Global U:

              [,1]        [,2]        [,3]        [,4] 
   [,5]
[1,] 3.20705e+02  1.91438e+02  1.51645e+02  1.20514e+02 
8.21981e+01
[2,] 1.91438e+02  1.14799e+02  9.09814e+01  7.22355e+01 
4.92108e+01
[3,] 1.51645e+02  9.09814e+01  7.21094e+01  5.72461e+01 
3.89942e+01
[4,] 1.20514e+02  7.22355e+01  5.72461e+01  4.54553e+01 
3.09702e+01
[5,] 8.21981e+01  4.92108e+01  3.89942e+01  3.09702e+01 
2.11076e+01
[6,] 5.57264e+01  3.34476e+01  2.65108e+01  2.10446e+01 
1.43334e+01
[7,] 2.51586e+01  1.52490e+01  1.20991e+01  9.58523e+00 
6.51199e+00
[8,] 1.45272e+01  8.85590e+00  7.03089e+00  5.56357e+00 
3.77419e+00
[9,] 8.30201e+00  5.07964e+00  4.03440e+00  3.19007e+00 
2.16202e+00
[10,] 3.36454e+00  2.07002e+00  1.64502e+00  1.29931e+00 
8.79344e-01

              [,6]        [,7]        [,8]        [,9] 
   [,10]
[1,] 5.57264e+01  2.51586e+01  1.45272e+01  8.30201e+00 
3.36454e+00
[2,] 3.34476e+01  1.52490e+01  8.85590e+00  5.07964e+00 
2.07002e+00
[3,] 2.65108e+01  1.20991e+01  7.03089e+00  4.03440e+00 
1.64502e+00
[4,] 2.10446e+01  9.58523e+00  5.56357e+00  3.19007e+00 
1.29931e+00
[5,] 1.43334e+01  6.51199e+00  3.77419e+00  2.16202e+00 
8.79344e-01
[6,] 9.74699e+00  4.45226e+00  2.58857e+00  1.48583e+00 
6.06140e-01
[7,] 4.45226e+00  2.07551e+00  1.22083e+00  7.05915e-01 
2.91111e-01
[8,] 2.58857e+00  1.22083e+00  7.22786e-01  4.19620e-01 
1.74066e-01
[9,] 1.48583e+00  7.05915e-01  4.19620e-01  2.44220e-01 
1.01671e-01
[10,] 6.06140e-01  2.91111e-01  1.74066e-01  1.01671e-01 
4.25445e-02

Global W:

              [,1]        [,2]        [,3]        [,4] 
   [,5]
[1,] 3.68224e+02  2.36787e+02  1.93972e+02  1.58837e+02 
1.12597e+02
[2,] 2.36787e+02  1.58549e+02  1.32054e+02  1.09539e+02 
7.88945e+01
[3,] 1.93972e+02  1.32054e+02  1.11021e+02  9.27903e+01 
6.74442e+01
[4,] 1.58837e+02  1.09539e+02  9.27903e+01  7.82101e+01 
5.74745e+01
[5,] 1.12597e+02  7.88945e+01  6.74442e+01  5.74745e+01 
4.31835e+01

[...etc...lots of undesired detailed/verbose output, then...]

 > syncat
Training set misclass rate: 50%

 > synpred <- predict (syncat, synth.tr, synth.te, 
train.classcol=3,
+                     newdata.classcol=3)

 > table (synpred, synth.te$yc)

synpred   0   1
       0 500 500
==========================================

Any help would be much appreciated!

Cheers,
Nick

PS computer details
=====================
knncat is version 1.1.11
=====================

==========================================
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==========================================

-- 
====================================================
Nicholas J. Matzke
Ph.D. Candidate, Graduate Student Researcher

Huelsenbeck Lab
Center for Theoretical Evolutionary Genomics
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Department of Integrative Biology
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