Greetings, I just used the indicspecies package in R to evaluate the contribution of several thousand 'species' (in this case approximate sequence variants) to four unique riverine biomes (flies, rock swabs, retreat, silk net). The test runs well. However, I would like to export the ASV names, stat, and p-values to a flat file. From what I can tell, R does tests of abundance/contributions, and then places the information i'm interested in into 'Groups' with different names. Example, all ASVs contributing to the group 'fly', group 'swab' (and several other groupings). I can see what i am interested in by using the summary function on the R console on the output of multipatt.
New to biostars (and can't seem to attach my R output). regardless, i'm using R version 4.1 (on osx high sierra), indispecies installed using install.packages("indispecies"). what i want to accomplish is the same regardless of data-set, so the toy with indicspecies works just as well. From 'https://www.rdocumentation.org/packages/indicspecies/versions/1.7.9/topics/multipatt'
>library(stats)
>data(wetland) ## Loads species data
>wetkm = kmeans(wetland, centers=3) ## Creates three clusters using kmeans
## Runs the combination analysis using IndVal.g as statistic
>wetpt = multipatt(wetland, wetkm$cluster, control = how(nperm=999))
## Lists those species with significant association to one combination
>summary(wetpt)
And now, what i would like to do is convert the output of the 'summary(wetpt)' function to a tab delimited file, where with the 'stat', 'p-value' as columns, and 'species' as rows.
