R devel - Mar 2004 - termplot has problems with a single term (fix included) (PR#6675)

The bug exists on R-1.9.0-alpha compiled the 10/3.

Termplot has a problem if either the model only contains a single term
or if asked to plot a single term. In addition there are problems with
the option se = TRUE.

Analysis: termplot starts with 

  terms <- if (is.null(terms)) 
    predict(model, type = "terms", se = se)
  else predict(model, type = "terms", se = se, terms = terms)
  n.tms <- ncol(tms <- as.matrix(if (se) 
                                 terms$fit
  else terms))

In this case terms is now a matrix of fitted values, with a single
column for each term in the model or in the terms argument. Because
the predict function returns a vector if called with a single term,
the matrix tms has no column names. This maskes the lines
  nmt <- colnames(tms)
  cn <- parse(text = nmt)
fail.

Solution: manually add the column names in case the number of columns
of tms == 1. Beware that the terms argument is overwritten in the
first line of the function (Is that a good style? Perhaps the body of
the function needs another name for the terms object defined in the
very first line). This means we manually need to save the terms name
first (code below)

Fixing this bug uncovers another one: in case of a single term in the
model formula, and with the option se = TRUE, the terms objects
consists of a list with elements fit and se.fit. In the code above
explicit care is taken to ensure that the fit element is a matrix by
using 
  tms <- as.matrix(if (se) terms$fit
                   else terms)
The element se.fit needs to be a matrix as well. I suggest a final fix
to be

{
*  terms.names <- terms
   terms <- if (is.null(terms)) 
     predict(model, type = "terms", se = se)
   else predict(model, type = "terms", se = se, terms = terms)
   n.tms <- ncol(tms <- as.matrix(if (se) 
                                  terms$fit
   else terms))
*  if(n.tms==1)
*    colnames(tms) <- if(is.null(terms)) attr(model$terms,
"term.labels")
*                        else terms.names
*  if(se)
*    terms$se.fit <- as.matrix(terms$se.fit)

* = added line.


The fix above is somewhat ugly. Perhaps (as mentioned above) the
object terms needs renaming (terms.something?), in which case the
first line is redundant.
-- 
Kasper Daniel Hansen, Research Assistent
Department of Biostatistics, University of Copenhagen

On Thu, 18 Mar 2004 k.hansen@biostat.ku.dk wrote:
> The bug exists on R-1.9.0-alpha compiled the 10/3.
>
> Termplot has a problem if either the model only contains a single term
> or if asked to plot a single term. In addition there are problems with
> the option se = TRUE.
I can't reproduce this in either R-devel or 1.8.1, and termplot hasn't
changed since January.

I do
example(termplot)
termplot(model, terms="z")
termplot(model, terms="z", se=TRUE)
termplot(model, terms=1)
termplot(model, terms="ns(x, 6)")
termplot(model, terms="ns(x, 6)", se=TRUE)
termplot(model, terms=2)

mm<-glm(y~x)
termplot(mm)
termplot(mm,se=TRUE)
mm<-glm(y~x-1)
termplot(mm)
termplot(mm,se=TRUE)

without any error messages.  I also note that termplot() doesn't
(anymore) start with the line you say it starts with, though it did until
January.

Could you provide an example?

	-thomas
> Analysis: termplot starts with
>
>   terms <- if (is.null(terms))
>     predict(model, type = "terms", se = se)
>   else predict(model, type = "terms", se = se, terms = terms)
>   n.tms <- ncol(tms <- as.matrix(if (se)
>                                  terms$fit
>   else terms))
>
> In this case terms is now a matrix of fitted values, with a single
> column for each term in the model or in the terms argument. Because
> the predict function returns a vector if called with a single term,
> the matrix tms has no column names. This maskes the lines
>   nmt <- colnames(tms)
>   cn <- parse(text = nmt)
> fail.
>
> Solution: manually add the column names in case the number of columns
> of tms == 1. Beware that the terms argument is overwritten in the
> first line of the function (Is that a good style? Perhaps the body of
> the function needs another name for the terms object defined in the
> very first line). This means we manually need to save the terms name
> first (code below)
>
> Fixing this bug uncovers another one: in case of a single term in the
> model formula, and with the option se = TRUE, the terms objects
> consists of a list with elements fit and se.fit. In the code above
> explicit care is taken to ensure that the fit element is a matrix by
> using
>   tms <- as.matrix(if (se) terms$fit
>                    else terms)
> The element se.fit needs to be a matrix as well. I suggest a final fix
> to be
>
> {
> *  terms.names <- terms
>    terms <- if (is.null(terms))
>      predict(model, type = "terms", se = se)
>    else predict(model, type = "terms", se = se, terms = terms)
>    n.tms <- ncol(tms <- as.matrix(if (se)
>                                   terms$fit
>    else terms))
> *  if(n.tms==1)
> *    colnames(tms) <- if(is.null(terms)) attr(model$terms,
"term.labels")
> *                        else terms.names
> *  if(se)
> *    terms$se.fit <- as.matrix(terms$se.fit)
>
> * = added line.
>
>
> The fix above is somewhat ugly. Perhaps (as mentioned above) the
> object terms needs renaming (terms.something?), in which case the
> first line is redundant.
> --
> Kasper Daniel Hansen, Research Assistent
> Department of Biostatistics, University of Copenhagen
>
> ______________________________________________
> R-devel@stat.math.ethz.ch mailing list
> https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
>
Thomas Lumley			Assoc. Professor, Biostatistics
tlumley@u.washington.edu	University of Washington, Seattle