From bolker at ufl.edu  Wed Oct 21 05:57:18 2009
From: bolker at ufl.edu (Bolker,Benjamin Michael)
Date: Tue, 20 Oct 2009 23:57:18 -0400
Subject: [Rd] odd evaluation within correlation argument of glmmPQL
Message-ID: <AC6F23A2BA13C347A59BDCBCFF41E27B5F538D4640@UFEXCH-MBXCL03.ad.ufl.edu>


  [I think I've seen this reported before but can't locate it any more.
I believe this oddity (glitch? feature?) is behind a query that
Jean-Baptiste Ferdy asked a year ago 
<http://finzi.psych.upenn.edu/Rhelp08/2008-October/176449.html>]

  It appears that glmmPQL looks in the global workspace, not
within the data frame specified by the "data" argument, for
the variables specified in the "form" argument of spatial
correlation structures provided to the "correlation" argument.
This is potentially confusing/dangerous, because you can easily
(1) get an error saying that the variable is not found (the least
dangerous and confusing), (2) get an error saying the variable
is of the wrong length, if there is a variable with a matching
name but the wrong length in the global environment,
(3) get completely misled if there is a *different* variable with
a matching name in the global environment with the right
length (in which case glmmPQL will ignore the element in the data
frame you specified and use the one from the global environment).

  The following patch (to MASS 7.3-3, retrieved from CRAN src/contrib
2.10.0 directory) appears to fix the problem.  A quick look suggests that
the same version of MASS is in 2.11.0 as well.

*** glmmPQL.R.orig	2009-10-20 23:48:38.000000000 -0400
--- glmmPQL.R	2009-10-20 23:51:33.000000000 -0400
***************
*** 39,44 ****
--- 39,47 ----
      off <- attr(Terms, "offset")
      if(length(off<- attr(Terms, "offset"))) allvars <-
          c(allvars, as.character(attr(Terms, "variables"))[off+1])
+     ## add variables in correlation formula, if any
+     if (!missing(correlation) && !is.null(attr(correlation,"formula")))
+       allvars <- c(allvars,all.vars(attr(correlation,"formula")))
      ## substitute back actual formula (rather than a variable name)
      Call$fixed <- eval(fixed); Call$random <- eval(random)
      m$formula <- as.formula(paste("~", paste(allvars, collapse="+")))

 code below shows the problem.

    Ben Bolker


## set up data
set.seed(1001)
d = data.frame(x = runif(100),
  y = runif(100),
  z = rpois(100,2),
  f = factor(rep(letters[1:20],each=5)))

library(MASS)
## without correlation structure: fine
glmmPQL(z~1,random=~1|f,data=d,family="poisson")

## with correlation structure,
##   but x and y not defined outside of 'd'
glmmPQL(z~1,random=~1|f,data=d,
        correlation=corExp(form=~x+y),
        family="poisson")
## Error in eval(expr, envir, enclos) : object 'x' not found

x = y = runif(10)
glmmPQL(z~1,random=~1|f,data=d,
        correlation=corExp(form=~x+y),
        family="poisson")
## Error in ...
##   variable lengths differ (found for 'f')

## this is what we probably wanted
x = d$x
y = d$y
glmmPQL(z~1,random=~1|f,data=d,
        correlation=corExp(form=~x+y),
        family="poisson")

## this is dangerous!
x = y = runif(100)
glmmPQL(z~1,random=~1|f,data=d,
        correlation=corExp(form=~x+y),
        family="poisson")

## proof that glmmPQL really is looking
## outside of the data frame for its
## correlation variables ...
x = y = rep(0,100)
glmmPQL(z~1,random=~1|f,data=d,
        correlation=corExp(form=~x+y),
        family="poisson")
## Error in getCovariate.corSpatial(object, data = data) : 
##   Cannot have zero distances in "corSpatial"



> sessionInfo()
R version 2.9.2 (2009-08-24) 
i486-pc-linux-gnu 

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  grid      methods  
[8] base     

other attached packages:
[1] nlme_3.1-95   MASS_7.2-49   reshape_0.8.3 plyr_0.1.9    proto_0.3-8  

loaded via a namespace (and not attached):
[1] ggplot2_0.8.4   lattice_0.17-26


[Rd] odd evaluation within correlation argument of glmmPQL
Bolker,Benjamin Michael