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I am using the pvclust package in R to get hierarchical clustering dendrograms with p-values.

I want to use the "Ward" clustering and the "Euclidean" distance method. Both work fine with my data when using hclust. In pvclust however I keep getting the error message "invalid clustering method". The problem apparently results from the "ward" method, because other methods such as "average" work fine, as does "euclidean" on its own.

This is my syntax and the resulting error message:

result <- pvclust(t(data2007num), method.hclust="ward", method.dist="euclidean", nboot=100)

Bootstrap (r = 0.5)... 
Error in hclust(distance, method = method.hclust) : invalid clustering method

My data matrix has the following form (28 countries x 20 policy dimensions): 

    X1 X2 X3 X4 X5 X6 X7 X8 X9 X10 Y1 Y2 Y3 Y4 Y5  Y6 Y7 Y8 Y9 Y10
AUT  2  3  4  2  1  1  4  3  2   2  2  3  3  4  4 2.0  5  4  0   3
GER  3  5  3  2  1  3  2  4  4   5  4  0  4  5  4 3.0  5  5  3   2
SWE  5  5  1  5  4  3  1  4  4   5  3  4  5  2  4 3.0  3  3  5   0
NLD  4  4  2  3  2  1  0  4  4   0  4  4  4  2  2 4.0  4  4  2   5
ESP  3  4  1  4  5  0  3  2  4   1  4  3  3  1  2 3.0  2  2  0   2
ITA  3  2  0  3  1  1  3  3  5   5  4  2  4  1  1 2.0  0  2  0   2
FRA  3  2  1  3  1  2  4  2  5   2  3  2  3  3  5 4.0  1  2  0   3
DNK  5  2  1  3  4  4  2  4  3   0  4  4  2  3  5 2.0  5  4  5   3
GRE  3  3  2  5  2  1  3  2  2   2  3  2  3  0  2 3.0  0  1  0   2
CHE  5  4  3  3  4  3  2  3  4   1  4  4  2  1  1 3.0  5  4  0   3
BEL  3  2  3  1  4  2  4  2  2   2  3  3  3  1  5 2.0  2  3  2   0
CZE  2  4  3  3  2  2  1  2  5   2  3  1  4  1  2 3.0  1  4  0   2
POL  3  3  4  4  0  1  3  3  2   2  4  2  2  0  3 4.0  2  2  0   3
IRL  3  1  2  1  4  3  2  1  5   4  3  2  2  1  3 2.0  0  1  1   2
LUX  2  1  2  5  3  2  2  5  4   2  2  4  3  2  4 3.0  2  3  0   1
HUN  1  3  2  3  2  1  4  3  5   4  2  3  4  3  3 2.0  3  2  4   2
PRT  3  2  3  5  4  1  4  1  5   5  3  2  2  1  2 2.0  1  1  1   1
AUS  4  1  2  1  2  3  1  1  1   5  4  5  3  1  2 3.0  1  3  5   1
CAN  1  1  1  1  4  1  0  1  1   5  1  1  3  3  2 2.0  1  2  5   4
FIN  5  4  4  3  2  3  2  3  3   3  2  2  4  3  3 3.0  4  4  5   2
GBR  3  1  2  1  2  3  1  1  2   5  4  4  4  3  1 2.0  1  3  5   5
JPN  4  1  0  1  2  2  0  2  5   4  3  1  1  3  3 2.0  2  4  5   3
KOR  3  3  0  1  2  1  0  0  1   4  0  1  1  2  3 2.0  1  2  1   3
MEX  0  3  4  0  3  2  5  2  3   5  2  2  0  0  0 0.0  0  1  0   3
NZL  5  1  2  1  2  3  1  1  5   2  3  5  2  2  2 0.5  0  0  3   3
NOR  5  3  2  4  2  4  2  5  4   2  4  5  4  2  4 4.0  5  4  5   0
SVK  1  4  3  2  4  2  1  2  5   2  3  2  4  2  2 3.0  0  2  0   3
USA  3  0  1  3  2  4  0  3  0   1  0  0  3  4  1 2.0  1  1  5   4

I tried to used "ward" with the dataset provided by the pvclust package (lung) as well as other data provided in R (such as Boston in the MASS package, without any success. Does anyone now a solution or if the "ward" method was disabled inpvclust?

Thomas75
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  • It works for me. Please provide the `sessionInfo()` when you get the error. –  Jul 08 '15 at 10:11
  • Thank you, this was a helpful hint! Originally I was using R version 3.0.3 (2014-03-06) Platform: x86_64-w64-mingw32/x64 (64-bit); I now tried an older distribution - R version 2.15.1 (2012-06-22) Platform: i386-pc-mingw32/i386 (32-bit) - and it worked fine. – Thomas75 Jul 13 '15 at 06:59
  • Does it work with an upgraded version of R? –  Jul 13 '15 at 07:04
  • I'll look into that, currently however I cannot upgrade R on my workstation (admin rights...). – Thomas75 Jul 17 '15 at 08:18

0 Answers0