envfit, R, writing output in a tab-delimited format

[tonybert]

Greetings, I was wondering if anyone had any experience in writing the output of envfit in the R function to a tab-delimited file format. I performed envfit on a matrix of 16S rRNA OTUs over an nmds result, and would now like to filter the results, but find the R output difficult to use on its own, and can't seem get it write to a file.

thanks,

-tony

[cliffbeall]

I work these things out using the str() function in R-

Consider an example envfit object made by using the provided commands:

> data(varespec)
> data(varechem)
> library(MASS)
> ord <- metaMDS(varespec)
(skipped output)
> (fit <- envfit(ord, varechem, perm = 999))
(skipped output)

Then you can do:

> str(fit)
List of 3
 $ vectors  :List of 5
  ..$ arrows      : num [1:14, 1:2] -0.0573 0.6197 0.7665 0.6852 0.6325 ...
  .. ..- attr(*, "dimnames")=List of 2
  .. .. ..$ : chr [1:14] "N" "P" "K" "Ca" ...
  .. .. ..$ : chr [1:2] "NMDS1" "NMDS2"
  .. ..- attr(*, "decostand")= chr "normalize"
  ..$ r           : Named num [1:14] 0.254 0.194 0.181 0.412 0.427 ...
  .. ..- attr(*, "names")= chr [1:14] "N" "P" "K" "Ca" ...
  ..$ permutations: int 999
  ..$ pvals       : num [1:14] 0.061 0.099 0.13 0.003 0.002 0.137 0.001 0.002 0.001 0.11 .
(note: skipped longer output)

That shows a long output, but the whole thing is a list of 3 items. The first one of those is called "$vectors" and is in turn a list of 5 items. If what you're looking to write to a file are the list items $arrows, $r, and $pvals,
you can make them into a dataframe like:

df <- data.frame((fit$vectors)$arrows, (fit$vectors)$r, (fit$vectors)$pvals)

Then you can write that to a file with write.table().