goodness.cca

[sjankin]

Hi I was running a CCA model, calling goodness() afterwards returns an error "Error in diag(w) %*% CA^2 %*% diag(eig) : non-conformable arguments".

Replicable code below:

Data:
data.zip

Code:

library(vegan)
library(readr)

#Example works fine
data(dune)
data(dune.env)
mod <- cca(dune ~ A1 + Management + Condition(Moisture), data=dune.env)
goodness(mod, addprevious = TRUE)

#Error message
words <- read_csv("words.csv")
env <- read_csv("env.csv")
cca <- cca(words ~ Idealpoint, data = env)

goodness(cca, addprevious = TRUE)
#Error in diag(w) %*% CA^2 %*% diag(eig) : non-conformable arguments

[jarioksa]

This is a bug. I'll fix it asap.

The bug can be triggered with standard vegan data:

library(vegan)
data(dune, dune.env)
# these both fail
goodness(cca(dune ~ A1, dune.env))
goodness(rda(dune ~ A1, dune.env))

The error appears when constraints have rank=1. It looks like one of the classic R gotchas: what happens with diag(x) when x is a one-element vector?

[jarioksa]

Fixed with 07f1857. Thanks for reporting the bug.

[sjankin]

That's great. Thanks for dealing with it so quickly. Are you going to push to CRAN an update?

[sjankin]

Hi Jari, The build directly from GitHub is failing. So I used a local source with updated goodness.cca.R function, and I am still getting the same error message. Using the example data and code I submitted earlier:

source("goodness.cca.R")
words <- read_csv("words.csv")
env <- read_csv("env.csv")
cca <- cca(words ~ Idealpoint, data = env)
goodness.cca(cca, addprevious = TRUE)

Error in diag(w) %*% CCA^2 %*% diag(object$CCA$eig) : 
non-conformable arguments 
4 is.data.frame(x) 
3 rowSums(diag(w) %*% CCA^2 %*% diag(object$CCA$eig)) 
2 inertcomp(object, display = display) at goodness.cca.R#42
1 goodness.cca(cca, addprevious = TRUE) 

[jarioksa]

You also need to upgrade the inertcomp() function that is called from goodness.cca and has the same flaw in handling diag(x). The inertcomp function was fixed in the same commit as goodness.cca.

If you upgrade these functions by sourcing, you may also need to take care that they are in the vegan environment and replace the original functions that were locked into vegan namespace when loading vegan:

source("goodness.cca.R")
source("inertcomp.R")
environment(goodness.cca) <- enviroment(dbrda) # or any function in vegan NAMESPACE
environment(inertcomp) <- environment(dbrda)
assignInNamespace("goodness.cca", goodness.cca, "vegan")
assignInNamespace("inertcomp", inertcomp, "vegan")

You may not need all these tricks, but sometimes you do -- depends on the kind of functions.

About inability to build vegan from github: do you have C and Fortran compilers?

[sjankin]

Ok, perfect. My mistake with the Fortran compiler.

One small thing, the "choices" option is not functional any more? (Just running from my earlier example data/code, but with 2.5 version)

goodness(cca, display="sites", choices=c(1,2,3))
goodness(cca, display="species", choices=c(1,2,3))

This produces contributes only for the constrained dimension (CCA1).

[gavinsimpson]

It looks like choices isn't used anywhere in the code since the original goodness.cca was replaced by goodness2.cca. Previously we had:

    if (!missing(choices)) 
        vexp <- vexp[, choices, drop = FALSE]

It's not immediately clear to me what choices did or where it fit in the newer version of the code, so I'll leave that to @jarioksa but I'll file a new issue to trick this bug, be it in documentation or code.