Bricklemyer, Ross S wrote:> I am attempting to write a routine where I can run PAM (partition around
mediods) on a dataset containing multiple soil cores and PCA spectral data from
several depths per core. I want to run PAM on each individual core, so I need
to group the data by core to run the analysis. Below is an example of my data
structure:
>
> Lab.id PC1 PC2 PC3
> MAT057.2.5 2.438454966 -1.011182986 -3.040881377
> MAT057.7.5 10.69120648 4.767694892 -1.719466898
> MAT057.12.5 8.215852171 4.645793327 0.974020242
> MAT057.17.5 10.00422215 3.516213164 2.586742695
> MAT057.22.5 18.49165113 5.143031557 0.472636009
> MAT057.27.5 18.31255522 4.255319595 0.802902692
> MAT057.35 11.75818601 -0.325388031 3.445673092
> MAT057.45 6.043984786 -3.297325975 3.075221644
>
> The MAT057 is the core code and the values following the period refer to
the sampling depths. There are many cores in the dataset and I want to automate
the analysis so that it will grab data with the same core code and run PAM. Any
ideas on what the R code would look like for that?
>
> Ross
>
Looks like these aren't really row names but a variable called Lab.id.
Look into things like
sub("\\..*$", "", Lab.id)
or maybe
sapply(strsplit(Lab.id, "\\."), "[[", 1)
(if Lab.id is a factor, you need first to transform using as.character
in the 2nd version)> *******************************************************************
> Ross Bricklemyer
> Dept. of Crop and Soil Sciences
> Washington State University
> 291D Johnson Hall
> PO Box 646420
> Pullman, WA 99164-6420
> Work: 509.335.3661
> Cell/Home: 406.570.8576
> Fax: 509.335.8674
> Email: rsb at wsu.edu
>
>
>
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>
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