cca per groups and row.names - r

Question

I am somewhat new to R, so forgive my basic questions.
I perform a CCA on a full dataset (358 sites, 40 abiotic parameters, 100 species observation).
library(vegan)
env <- read.table("env.txt", header = TRUE, sep = "\t", dec = ",")
otu <- read.table(otu.txt", header = TRUE, sep = "\t", dec = ",")
cca <- cca(otu~., data=env)
cca.plot <- plot(cca, choices=c(1,2))
vif.cca(cca)
ccared <- cca(formula = otu ~EnvPar1,2,n, data = env)
ccared.plot <- plot(ccared, choices=c(1,2))
orditorp(ccared.plot, display="sites")
This works without using sample names in the first columns (initially, the first column containing numeric samples names got interpreted as a variable, so i used tables without that information. When i add site names to the plot via orditorp, it gives "row.name=n" in the plot.)
I want to use my sample names, however. I tried row.names=1 on both tables with sample name information:
envnames <- read.table("envwithnames.txt", header = TRUE, row.names=1, sep = "\t", dec = ",")
otunames <- read.table("otuwithnames.txt", header = TRUE, row.names=1, sep = "\t", dec = ",")
, and any combination of env/otu/envnames/otunames. cca worked out well in any case, but any plot command yielded
plot.ccarownames <- plot(cca(ccarownames, choices=c(1,2)))
Error in rowSums(X) : 'x' must be numeric
My second problem is connected to that: The 358 sites are grouped into 6 groups (4x60,2x59). The complete matrix has this information inferred as an extra column.
Since i couldnt work out the row name problem, i am even more stuck with nominal data, anyhow.
The original matrix contains a first column (sample names, numeric, but can be easily transformed to nominal) and second one (group identity, nominal), followed by biological observations.
What i would like to have:
A CCA containing all six groups that is coloring sites per group.
A CCA containing only data for one group (without manual
construction of individual input tables)
CCA plots that are using my original sample names.
Any help is appreciated! Really, i am stuck with it since yesterday morning :/

Answer 1

I'm using cca() from vegan myself and I have some of your own problems, however I've been able to at least solve your original "row names" problem. I'm doing a CCA analysis on data from 41 soils, with 334 species and 39 environmental factors.
In my case I used
rownames(MyDataSet) <- MyDataSet$ObservationNamesColumn
(I used default names such as MyDataSet for the sake of example here)
However I still had environmental factors which weren't numerical (such as soil texture). You could try checking for non numerical factors in case you have a mistake in your original dataset or an abiotic factor which is not interpreted as numerical for any other reason. To do this you can either use the command str(MyDataSet) which tells you the nature of each of your variable, or lapply(MyDataSet, class) which also tells you the same but in a different output.
In case you have abiotic factors which are not numerical (again, such as texture) and you want to remove them, you can do so by creating a whole new dataset using only the numerical variables (you will still keep your observation names as they were defined as row names), this is rather easy to do and can be done using something similar to this:
MyDataSet.num <- MyDataSet[,sapply(MyDataSet, is.numeric)]
This creates a new data set which has the same rows as the original but only columns (variables) with numeric values. You should be able then to continue your work using this new data set.
I am very new to both R programming and statistics (I'm a microbiologist) but I hope this helps!