Cca Analysis: Error in rowSums(X): 'X' Must Be Numeric
I Try to Do a Ca Analysis from the Vegan Package. This Is the Code I Use: Install. Packages("Vegan") Library(Vegan) Plots
I try to do a CA analysis from the vegan package.
This is the code I use:
install.packages("vegan")
library(vegan)
plots <- c("plotA", "plotB", "plotC", "plotD", "plotE")
animal1 <- c(2,7,4,8,1)
animal2 <- c(4,3,7,1,0)
animal3 <- c(8,5,0,1,3)
animal4 <- c(2,2,9,5,2)
animal5 <- c(1,6,9,8,7)
animalData <- data.frame (plots, animal1, animal2, animal3, animal4, animal5)
attach(animalData)
animalData.ca <- cca(animalData)
But then, I always get an error:
Error in rowSums(X) : 'x' must be numeric
I know that the labels are a factor and the analysis works if I delete the first column. But then the analysis creates own labels and I cannot use mine. Is there a way to get my own labels (plotA, plotB etc. ) included?
1 Answer
You need to have the plots variable stored as the rownames attribute of the animalData data frame, not as a variable in the actual data.
You want:
library(vegan)
plots <- c("plotA", "plotB", "plotC", "plotD", "plotE")
animal1 <- c(2,7,4,8,1)
animal2 <- c(4,3,7,1,0)
animal3 <- c(8,5,0,1,3)
animal4 <- c(2,2,9,5,2)
animal5 <- c(1,6,9,8,7)
animalData <- data.frame(animal1, animal2, animal3, animal4, animal5)
rownames(animalData) <- plots
animalData now should look like this:
> animalData
animal1 animal2 animal3 animal4 animal5
plotA 2 4 8 2 1
plotB 7 3 5 2 6
plotC 4 7 0 9 9
plotD 8 1 1 5 8
plotE 1 0 3 2 7
Then for the CA
animalData.ca <- cca(animalData)
which works:
> animalData.ca
Call: cca(X = animalData)
Inertia Rank
Total 0.3793
Unconstrained 0.3793 4
Inertia is mean squared contingency coefficient
Eigenvalues for unconstrained axes:
CA1 CA2 CA3 CA4
0.219528 0.099206 0.055572 0.005018
Plotting this object results in
plot(animalData.ca, type = "text", scaling = 3)
which as you can see, has used the attribute data from the animalData data frame.
Also, don't attach() data sets like this; it isn't required and is in fact dangerous as the data are not attached, but an independent copy.
James Sterling reports on renewable energy developments, climate policy, ecological conservation, and green tech innovations around the globe.
