New to R, trying to use agnes, but can't load my ditance matrix
On Mon, Jun 27, 2011 at 3:43 AM, Karen R. Khar <karen.khar at gmail.com> wrote:
Hi, I'm mighty new to R. I'm using it on Windows. I'm trying to cluster using a distance matrix I created from the data on my own and called it D10.dist. I loaded the cluster package. Then tried the following command...
agnes("E:D10.dist", diss = TRUE, metric = "euclidean", stand = FALSE,
method = "average", par.method, keep.diss = n < 1000, keep.data = !diss)
And it responded...
Error in agnes("E:D10.dist", diss = TRUE, metric = "euclidean", stand =
FALSE, :
x is not and cannot be converted to class dissimilarity
At a guess, you need to actually import D10.dist into R. It looks like you're trying to give agnes() a string that contains the path to the file, but agnes() just sees that as a string, and of course can't figure out what to do with it.
D10.dist has the following data... D1 ? ? ?0 D2 ? ? ?0.608392 ? ? ? ?0 D3 ? ? ?0.497451 ? ? ? ?0.537662 ? ? ? ?0 D4 ? ? ?0.634548 ? ? ? ?0.393343 ? ? ? ?0.537426 ? ? ? ?0 D5 ? ? ?0.558785 ? ? ? ?0.543399 ? ? ? ?0.632221 ? ? ? ?0.726633 ? ? ? ?0 D6 ? ? ?0.659483 ? ? ? ?0.701778 ? ? ? ?0.741425 ? ? ? ?0.668624 ? ? ? ?0.655914 ? ? ? ?0 D7 ? ? ?0.603012 ? ? ? ?0.659173 ? ? ? ?0.571776 ? ? ? ?0.687599 ? ? ? ?0.383712 ? ? ? ?0.683948 ? ? ? ?0 D8 ? ? ?0.611919 ? ? ? ?0.665357 ? ? ? ?0.526453 ? ? ? ?0.715093 ? ? ? ?0.457496 ? ? ? ?0.698213 ? ? ? ?0.317039 ? ? ? ?0 D9 ? ? ?0.41501 0.652117 ? ? ? ?0.552011 ? ? ? ?0.68969 0.485988 ? ? ? ?0.702738 ? ? ? ?0.42819 0.442598 ? ? ? ?0 D10 ? ? 0.376512 ? ? ? ?0.600607 ? ? ? ?0.517857 ? ? ? ?0.673515 ? ? ? ?0.530421 ? ? ? ?0.667736 ? ? ? ?0.537025 ? ? ? ?0.48062 0.240559 ? ? ? ?0
If you can convince whatever software you used to write out a full symmetric matrix instead of a lower-triangular matrix, you can easily use read.table() to import it.
I would appreciate any suggestions. Please assume I know virtually nothing about R.
Then Karen, my first suggestion is that you read one of the many excellent intro to R guides available online. Sarah
Sarah Goslee http://www.functionaldiversity.org