[R] New to R, trying to use agnes, but can't load my ditance matrix

[Sarah Goslee]

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