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Colin Beale

2007-Jan-26 09:58 UTC

[R] Using functions within functions (environment problems)

Hi everyone,

I've been having difficulty writing wrapper functions for some
functions where those same functions include other functions with
eval()
calls where the environment is specified. A very simple example using
function lmer from lme4:

lmerWrapper <- function(formula, data, family = gaussian, method
c("REML",
    "ML", "PQL", "Laplace", "AGQ"),
control = list(), start = NULL,
    subset, weights, na.action, offset, contrasts = NULL, model TRUE,

    ...)
{

    xNew <- runif(0,1, length(data[,1]))
    fNew <- sample(1:4, length(data[,1]), replace = T)
    data <- as.data.frame(cbind(data, xNew, fNew))
    formula <- update(formula, .~. + xNew + (1|fNew))
    out <- lmer (formula = formula, data = data, family = family,
method         method, weights = weights, control = control, start = start,
        subset = subset, na.action = na.action, offset = offset,
        contrasts = contrasts, model = model)
}

dat <- data.frame(Y = rnorm(100), X1 = rnorm(100), X2 = rnorm(100), 
        F1 = as.factor(sample(1:4, 400, replace = T)))
test <- lmerWrapper (Y ~ X1 + X2 + (1|F1), data = dat)


This function attempts to create two new variables, add these to the
data.frame and modify the formula for include these two new variables,
and then fit this expanded model using lmer. Clearly the example is
silly, but it illustrates the problem as it fails with the error:

Error in eval(expr, envir, enclos) : object "xNew" not found

because a function within lmer (lmerFrames) makes an eval call where
the environment is specified as the .GlobalEnv which doesn't contain
xNew - it needs to be looking in the environment from which it was
called rather than going right back to the root. In a more general
context, I might like to create a function where I don't specify a new
data.frame in the wrapper, but want the function to search the back
down
the search path for each component, finding xNew in the environment of
the wrapper function and X1 in the .GlobalEnv. Is there a general
solution to this? Or do I need to create a modified lmer function that
calls a modified lmerFrames function where I specify the environment
differently? There's quite a lot in the archives dealing with
environments and search paths, but I'm either not understanding how to
apply the wisdom therein, or not finding the specific answer to my
problem, and I should say that I have this problem with more than just
the lmer function.

Thanks for any pointers,

Colin
> sessionInfo()R version 2.4.1 (2006-12-18) 
i386-pc-mingw32 

locale:
LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
Kingdom.1252;LC_MONETARY=English_United
Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252

attached base packages:
[1] "stats"     "graphics"  "grDevices"
"datasets"  "tcltk"
"utils"
    "methods"   "base"     

other attached packages:
      debug    mvbutils        lme4      Matrix     lattice   
svSocket
       svIO      R2HTML      svMisc       svIDE 
    "1.1.0"     "1.1.1" "0.9975-10" 
"0.9975-8"   "0.14-16"
"0.9-5"
    "0.9-5"      "1.58"     "0.9-5"    
"0.9-5"




Dr. Colin Beale
Spatial Ecologist
The Macaulay Institute
Craigiebuckler
Aberdeen
AB15 8QH
UK

Tel: 01224 498245 ext. 2427
Fax: 01224 311556
Email: c.beale at macaulay.ac.uk 



-- 
Please note that the views expressed in this e-mail are those of the
sender and do not necessarily represent the views of the Macaulay
Institute. This email and any attachments are confidential and are
intended solely for the use of the recipient(s) to whom they are
addressed. If you are not the intended recipient, you should not read,
copy, disclose or rely on any information contained in this e-mail, and
we would ask you to contact the sender immediately and delete the email
from your system. Thank you.
Macaulay Institute and Associated Companies, Macaulay Drive,
Craigiebuckler, Aberdeen, AB15 8QH.

Gabor Grothendieck

2007-Jan-26 11:05 UTC

head link

[R] Using functions within functions (environment problems)

Check out this post and the entire thread to which it belongs:

http://finzi.psych.upenn.edu/R/Rhelp02a/archive/67474.html

On 1/26/07, Colin Beale <c.beale at macaulay.ac.uk>
wrote:> Hi everyone,
>
> I've been having difficulty writing wrapper functions for some
> functions where those same functions include other functions with
> eval()
> calls where the environment is specified. A very simple example using
> function lmer from lme4:
>
> lmerWrapper <- function(formula, data, family = gaussian, method >
c("REML",
>    "ML", "PQL", "Laplace", "AGQ"),
control = list(), start = NULL,
>    subset, weights, na.action, offset, contrasts = NULL, model > TRUE,
>
>    ...)
> {
>
>    xNew <- runif(0,1, length(data[,1]))
>    fNew <- sample(1:4, length(data[,1]), replace = T)
>    data <- as.data.frame(cbind(data, xNew, fNew))
>    formula <- update(formula, .~. + xNew + (1|fNew))
>    out <- lmer (formula = formula, data = data, family = family,
> method >        method, weights = weights, control = control, start =
start,
>        subset = subset, na.action = na.action, offset = offset,
>        contrasts = contrasts, model = model)
> }
>
> dat <- data.frame(Y = rnorm(100), X1 = rnorm(100), X2 = rnorm(100),
>        F1 = as.factor(sample(1:4, 400, replace = T)))
> test <- lmerWrapper (Y ~ X1 + X2 + (1|F1), data = dat)
>
>
> This function attempts to create two new variables, add these to the
> data.frame and modify the formula for include these two new variables,
> and then fit this expanded model using lmer. Clearly the example is
> silly, but it illustrates the problem as it fails with the error:
>
> Error in eval(expr, envir, enclos) : object "xNew" not found
>
> because a function within lmer (lmerFrames) makes an eval call where
> the environment is specified as the .GlobalEnv which doesn't contain
> xNew - it needs to be looking in the environment from which it was
> called rather than going right back to the root. In a more general
> context, I might like to create a function where I don't specify a new
> data.frame in the wrapper, but want the function to search the back
> down
> the search path for each component, finding xNew in the environment of
> the wrapper function and X1 in the .GlobalEnv. Is there a general
> solution to this? Or do I need to create a modified lmer function that
> calls a modified lmerFrames function where I specify the environment
> differently? There's quite a lot in the archives dealing with
> environments and search paths, but I'm either not understanding how to
> apply the wisdom therein, or not finding the specific answer to my
> problem, and I should say that I have this problem with more than just
> the lmer function.
>
> Thanks for any pointers,
>
> Colin
>
> > sessionInfo()
> R version 2.4.1 (2006-12-18)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
> Kingdom.1252;LC_MONETARY=English_United
> Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
>
> attached base packages:
> [1] "stats"     "graphics"  "grDevices"
"datasets"  "tcltk"
> "utils"
>    "methods"   "base"
>
> other attached packages:
>      debug    mvbutils        lme4      Matrix     lattice
> svSocket
>       svIO      R2HTML      svMisc       svIDE
>    "1.1.0"     "1.1.1" "0.9975-10" 
"0.9975-8"   "0.14-16"
> "0.9-5"
>    "0.9-5"      "1.58"     "0.9-5"    
"0.9-5"
>
>
>
>
> Dr. Colin Beale
> Spatial Ecologist
> The Macaulay Institute
> Craigiebuckler
> Aberdeen
> AB15 8QH
> UK
>
> Tel: 01224 498245 ext. 2427
> Fax: 01224 311556
> Email: c.beale at macaulay.ac.uk
>
>
>
> --
> Please note that the views expressed in this e-mail are those of the
> sender and do not necessarily represent the views of the Macaulay
> Institute. This email and any attachments are confidential and are
> intended solely for the use of the recipient(s) to whom they are
> addressed. If you are not the intended recipient, you should not read,
> copy, disclose or rely on any information contained in this e-mail, and
> we would ask you to contact the sender immediately and delete the email
> from your system. Thank you.
> Macaulay Institute and Associated Companies, Macaulay Drive,
> Craigiebuckler, Aberdeen, AB15 8QH.
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

Prof Brian Ripley

2007-Jan-26 12:12 UTC

head link

[R] Using functions within functions (environment problems)

I don't think your subject line is relevant.  You do not have 'functions
within functions': lmerFrames is not within lmer.  (You seem to be 
confusing functions within and calls from.)

Your example does not work (did you test it?).  When the erroneous runif 
call is corrected (it gives a result of length 0), I get a different error 
about 'weights', and indeed you have not specified 'weights' nor
'subset'
nor 'na.action' nor 'offset'.

The following does work for me:

lmerWrapper <- function(formula, data, ...)
{

     xNew <- runif(length(data[,1]))
     fNew <- sample(1:4, length(data[,1]), replace = TRUE)
     data <- as.data.frame(cbind(data, xNew, fNew))
     formula <- update(formula, .~. + xNew + (1|fNew))
     out <- lmer (formula = formula, data = data, ...)
}

dat <- data.frame(Y = rnorm(100), X1 = rnorm(100), X2 = rnorm(100),
         F1 = as.factor(sample(1:4, 400, replace = T)))
test <- lmerWrapper (Y ~ X1 + X2 + (1|F1), data = dat)

so whatever your actual problem is, it is it seems not about finding xNew.


There is one potential problem I spotted.  One of the places a standard 
model-fitting function will look for variables is in the environment of 
'formula'.  This is an argument, and update.formula changes the 
environment, so it is possible that old (rather than additional) variables 
could disappear from view.


On Fri, 26 Jan 2007, Colin Beale wrote:
> Hi everyone,
>
> I've been having difficulty writing wrapper functions for some
> functions where those same functions include other functions with
> eval()
> calls where the environment is specified. A very simple example using
> function lmer from lme4:
>
> lmerWrapper <- function(formula, data, family = gaussian, method >
c("REML",
>    "ML", "PQL", "Laplace", "AGQ"),
control = list(), start = NULL,
>    subset, weights, na.action, offset, contrasts = NULL, model > TRUE,
>
>    ...)
> {
>
>    xNew <- runif(0,1, length(data[,1]))
>    fNew <- sample(1:4, length(data[,1]), replace = T)
>    data <- as.data.frame(cbind(data, xNew, fNew))
>    formula <- update(formula, .~. + xNew + (1|fNew))
>    out <- lmer (formula = formula, data = data, family = family,
> method >        method, weights = weights, control = control, start =
start,
>        subset = subset, na.action = na.action, offset = offset,
>        contrasts = contrasts, model = model)
> }
>
> dat <- data.frame(Y = rnorm(100), X1 = rnorm(100), X2 = rnorm(100),
>        F1 = as.factor(sample(1:4, 400, replace = T)))
> test <- lmerWrapper (Y ~ X1 + X2 + (1|F1), data = dat)
>
>
> This function attempts to create two new variables, add these to the
> data.frame and modify the formula for include these two new variables,
> and then fit this expanded model using lmer. Clearly the example is
> silly, but it illustrates the problem as it fails with the error:
>
> Error in eval(expr, envir, enclos) : object "xNew" not found
>
> because a function within lmer (lmerFrames) makes an eval call where
> the environment is specified as the .GlobalEnv which doesn't contain
> xNew - it needs to be looking in the environment from which it was
> called rather than going right back to the root. In a more general
> context, I might like to create a function where I don't specify a new
> data.frame in the wrapper, but want the function to search the back
> down
> the search path for each component, finding xNew in the environment of
> the wrapper function and X1 in the .GlobalEnv. Is there a general
> solution to this? Or do I need to create a modified lmer function that
> calls a modified lmerFrames function where I specify the environment
> differently? There's quite a lot in the archives dealing with
> environments and search paths, but I'm either not understanding how to
> apply the wisdom therein, or not finding the specific answer to my
> problem, and I should say that I have this problem with more than just
> the lmer function.
>
> Thanks for any pointers,
>
> Colin
>
>> sessionInfo()
> R version 2.4.1 (2006-12-18)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
> Kingdom.1252;LC_MONETARY=English_United
> Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
>
> attached base packages:
> [1] "stats"     "graphics"  "grDevices"
"datasets"  "tcltk"
> "utils"
>    "methods"   "base"
>
> other attached packages:
>      debug    mvbutils        lme4      Matrix     lattice
> svSocket
>       svIO      R2HTML      svMisc       svIDE
>    "1.1.0"     "1.1.1" "0.9975-10" 
"0.9975-8"   "0.14-16"
> "0.9-5"
>    "0.9-5"      "1.58"     "0.9-5"    
"0.9-5"
>
>
>
>
> Dr. Colin Beale
> Spatial Ecologist
> The Macaulay Institute
> Craigiebuckler
> Aberdeen
> AB15 8QH
> UK
>
> Tel: 01224 498245 ext. 2427
> Fax: 01224 311556
> Email: c.beale at macaulay.ac.uk
>
>
>
>
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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