R：基本功能无法使用Caper包中的对象

Question

I'm running a phylogenetic analysis using the caper package, where the regression function (which uses phylogeneticaly independent contrasts) is crunch . The crunch function uses an object internal to the caper package called caic .

The model is started via:

crunchMod <- crunch(y ~ f(x), data = comparison)

When I run summary(crunchMod) I am given a format identical to that of a summary produced from the lm() function.

However, in an attempt to begin checking model assumptions by entering rstandard(crunchMod) , I receive the following error:

Error in UseMethod("rstandard") : 
no applicable method for 'rstandard' applied to an object of class "caic"

Reading through http://cran.r-project.org/web/packages/caper/vignettes/caper.pdf on pages 19-20, I find that plot(crunchMod) uses a wrapper to enable the checking of regression assumptions. However, these are graphical checks for:

residuals vs Fitted values
standardized residuals vs theoretical quantities [QQ plot]
sqrt(standardized residuals) vs fitted values [Scale-location]
standardized residuals vs leverage).

Does anyone know how to access the standardized residuals using my own wrapper, or allow me to access p-values instead of the graphical images?

Answer 1

This one is pretty simple, but only after going round in circles for a while with that second if() statement in crunch(). Looking at the summary method for caic , it's just a subset of the entire summary / model

> summary.caic
function (object, ...) 
{
    summary(object$mod, ...)
}
<environment: namespace:caper>

You can see the names of the entire model show there are useful statistics in the rest of it.

names(summary(crunchMod))
# [1] "call"          "terms"         "residuals"     "coefficients" 
# [5] "aliased"       "sigma"         "df"            "r.squared"    
# [9] "adj.r.squared" "fstatistic"    "cov.unscaled" 

Note that only the mod section inherits from lm() You can check out all the inheritence of the crunchMod objects with

> sapply(crunchMod, is)
$contrast.data
[1] "list"   "vector"

$mod
[1] "lm"       "oldClass"

$data
[1] "comparative.data"