[Rd] Should there be a confint.mlm ?
steven pav
@h@bbychef @ending from gm@il@com
Sun Jul 22 06:58:41 CEST 2018
I would welcome the fixes suggested by Martin. I did not think my
implementation was pretty, but didn't want to suggest a bugfix without
submitting code.
Regarding the idea of a `stderr` function, I am all for potential
efficiency gains, but I suspect that in many situations `vcov` is the
result of a matrix inversion. This might mean an 'efficient computation of
only the diagonal of the inverse of a matrix' function would be required to
achieve widespread use. (I am not aware of the algorithm for that, but I am
ignorant.)
Again, thanks for patching `confint.lm`.
On Fri, Jul 20, 2018 at 9:06 AM, Martin Maechler <maechler using stat.math.ethz.ch
> wrote:
> >>>>> steven pav
> >>>>> on Thu, 19 Jul 2018 21:51:07 -0700 writes:
>
> > It seems that confint.default returns an empty data.frame
> > for objects of class mlm. For example:
>
> > It seems that confint.default returns an empty data.frame for objects of
> > class mlm.
>
> Not quite: Note that 'mlm' objects are also 'lm' objects, and so
> it is confint.lm() which is called here and fails.
>
> > For example:
> >
> > ```
> > nobs <- 20
> > set.seed(1234)
> > # some fake data
> > datf <-
> > data.frame(x1=rnorm(nobs),x2=runif(nobs),y1=rnorm(nobs),y2=rnorm(nobs))
> > fitm <- lm(cbind(y1,y2) ~ x1 + x2,data=datf)
> > confint(fitm)
> > # returns:
> > 2.5 % 97.5 %
> > ```
> >
> > I have seen proposed workarounds on stackoverflow and elsewhere, but
> > suspect this should be fixed in the stats package.
>
> I agree.
> It may be nicer to tweak confint.lm() instead though.
>
> I'm looking into doing that.
>
> > A proposed implementation would be:
> >
> > ```
> > # I need this to run the code, but stats does not:
> > format.perc <- stats:::format.perc
>
> or better (mainly for esthetical reasons), use
>
> environment(confint.mlm) <- asNamespace("stats")
>
> after defining confint.mlm [below]
>
> > # compute confidence intervals for mlm object.
> > confint.mlm <- function (object, level = 0.95, ...) {
> > cf <- coef(object)
> > ncfs <- as.numeric(cf)
> > a <- (1 - level)/2
> > a <- c(a, 1 - a)
> > fac <- qt(a, object$df.residual)
> > pct <- format.perc(a, 3)
> > ses <- sqrt(diag(vcov(object)))
> ^^^^^^^^^^^^^^^^^^^^^^^^
> BTW --- and this is a diversion --- This is nice mathematically
> (and used in other places, also in "base R" I think)
> but in principle is a waste: Computing a full
> k x k matrix and then throwing away all but the length-k
> diagonal ...
> In the past I had contemplated but never RFC'ed or really
> implemented a stderr() generic with default method
>
> stderr.default <- function(object) sqrt(diag(vcov(object)))
>
> but allow non-default methods to be smarter and hence more efficient.
>
> > ci <- ncfs + ses %o% fac
> > setNames(data.frame(ci),pct)
> > }
> >
> > # returning to the example above,
> > confint(fitm)
> > # returns:
> > 2.5 % 97.5 %
> > y1:(Intercept) -1.2261 0.7037
> > y1:x1 -0.5100 0.2868
> > y1:x2 -2.7554 0.8736
> > y2:(Intercept) -0.6980 2.2182
> > y2:x1 -0.6162 0.5879
> > y2:x2 -3.9724 1.5114
> > ```
>
> I'm looking into a relatively small patch to confint.lm()
> *instead* of the confint.mlm() above
>
> Thank you very much, Steven, for your proposal!
> I will let you (and the R-devel audience) know the outcome.
>
> Best regards,
> Martin Maechler
> ETH Zurich and R Core Team
>
> > --
> >
> > --sep
> >
> > [[alternative HTML version deleted]]
> >
>
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