R help - Oct 2005 - LaTex error when creating DVI version when compiling package

Dear Listers,

I got this message when compiling a package:

* creating pgirmess-manual.tex ... OK
* checking pgirmess-manual.text ... ERROR
LaTex errors when creating DVI version.
This typically indicates Rd problems.

The message is quite explicit but I struggled a lot before understanding 
that the trouble comes from a single file "selMod.rd" among 44 topics.
Even though I have checked it ten times and even rewrite it on 
prompt(selMod), I cannot find out what is wrong with it.

Can somebody used with LaTex and the format of R *.rd file have a quick 
look to the attached contents and tell me if he can detect some obvious 
faulty writing?

Thanks in advance,

Patrick



\name{selMod}
\alias{selMod}
\alias{selMod.lm}
\alias{selMod.glm}
\alias{selMod.list}

\title{ Model selection according to information theoretic methods }
\description{
 Handles lm, glm and list of models lm, glm, lme and nlme objects and 
provides parameters to compare models according to Anderson et al. (1998)
}
\usage{
    selMod(aModel, Order = "AICc", ...) group method

    selMod.lm(aModel, Order = "AICc", dropNull = FALSE, selconv=TRUE,
...)
    selMod.list(aModel, Order = "AICc", ...)
}

\arguments{
  \item{aModel}{ a lm or glm model or a list of lm or glm models }
  \item{dropNull}{ if TRUE, drops the simplest model (e.g. 'y~1')  }
  \item{Order}{ if set to "AICc" (default) sort the models on this 
parameter, otherwise "AIC" is allowed }
  \item{selconv}{ if TRUE (default) keep the models for which 
convergence is obtained (glm object only) and with no anova singularity 
(lm and glm) }
  \item{...}{ other parameters to be passed as arguments (not used here) }
}

\details{
  This function provides parameters used in the information theoretic 
methods for model comparisons. lm and glm objects can be passed directly 
as the upper scope of term addition (all terms added).
  Every model from 'y~1' is computed adding one term at a time until the
upper scope model is derived. A list of user specified lm, glm, lme or 
nlme objects can alternately be passed.
}

\value{
 A list with the following items:
  \item{AIC}{a data.frame including LL, the maximized log-likelihood; K 
the number of estimated parameters; N2K, number of observations/K; AIC, 
the Akaike index criterion; deltAIC, the difference between AIC and the 
lowest AIC value; w_i, the Akaike weights; AICc, the second order Akaike 
criterion; deltAICc, the difference between AICc and the lowest AICc 
value; w_ic, the AICc weights }
  \item{models}{the list of models}
}
\references{
    Anderson, D.R., Link, W.A., Johnson, D.H. and Burnham, K.P. (2001). 
Suggestions for presenting the results of data analyses. Journal of 
Wildlife Management, 65, 373-378; Burnham, K.P. and Anderson, D.R. 
(2002) Model Selection and Multimodel Inference: a Practical 
Information-Theoretic Approach, 2nd edn., Springer-Verlag, New York. 353 pp
 }
\author{ Patrick Giraudoux and David Pleydell: pgiraudo at univ-fcomte.fr, 
dpleydel at univ-fcomte.fr }

\seealso{ \code{\link{AIC}},\code{\link{logLik}} }
\examples{
 library(MASS)
 anorex.1 <- lm(Postwt ~ Prewt*Treat, data = anorexia)
 selMod(anorex.1)
 anorex.2 <- glm(Postwt ~ Prewt*Treat, family=gaussian,data = anorexia)
 selMod(anorex.2)
 anorex.3<-lm(Postwt ~ Prewt+Treat, data = anorexia)
 selMod(list(anorex.1,anorex.2,anorex.3))
}
\keyword{ models }

On Sat, 29 Oct 2005, Patrick Giraudoux wrote:
> Dear Listers,
> 
> I got this message when compiling a package:
> 
> * creating pgirmess-manual.tex ... OK
> * checking pgirmess-manual.text ... ERROR
> LaTex errors when creating DVI version.
> This typically indicates Rd problems.
> 
> The message is quite explicit but I struggled a lot before understanding 
> that the trouble comes from a single file "selMod.rd" among 44
topics.
> Even though I have checked it ten times and even rewrite it on 
> prompt(selMod), I cannot find out what is wrong with it.
> 
> Can somebody used with LaTex and the format of R *.rd file have a quick 
> look to the attached contents and tell me if he can detect some obvious 
> faulty writing?
The general answer is to look through the (often very long) *.log file in 
the *.Rcheck directory until you find the problem. That will typically 
give you a line number in the *.tex file, which shows not only where the 
error occurred, but the *.log file entry often shows what it is. My 
typical errors are using LaTeX special symbols, and most often having 
unprotected $ and _. I see quite a lot of _ below in \value{}, so I'd try 
\_ there first.

Roger

> 
> Thanks in advance,
> 
> Patrick
> 
> 
> 
> \name{selMod}
> \alias{selMod}
> \alias{selMod.lm}
> \alias{selMod.glm}
> \alias{selMod.list}
> 
> \title{ Model selection according to information theoretic methods }
> \description{
>  Handles lm, glm and list of models lm, glm, lme and nlme objects and 
> provides parameters to compare models according to Anderson et al. (1998)
> }
> \usage{
>     selMod(aModel, Order = "AICc", ...) group method
> 
>     selMod.lm(aModel, Order = "AICc", dropNull = FALSE,
selconv=TRUE, ...)
>     selMod.list(aModel, Order = "AICc", ...)
> }
> 
> \arguments{
>   \item{aModel}{ a lm or glm model or a list of lm or glm models }
>   \item{dropNull}{ if TRUE, drops the simplest model (e.g. 'y~1') 
}
>   \item{Order}{ if set to "AICc" (default) sort the models on
this
> parameter, otherwise "AIC" is allowed }
>   \item{selconv}{ if TRUE (default) keep the models for which 
> convergence is obtained (glm object only) and with no anova singularity 
> (lm and glm) }
>   \item{...}{ other parameters to be passed as arguments (not used here) }
> }
> 
> \details{
>   This function provides parameters used in the information theoretic 
> methods for model comparisons. lm and glm objects can be passed directly 
> as the upper scope of term addition (all terms added).
>   Every model from 'y~1' is computed adding one term at a time
until the
> upper scope model is derived. A list of user specified lm, glm, lme or 
> nlme objects can alternately be passed.
> }
> 
> \value{
>  A list with the following items:
>   \item{AIC}{a data.frame including LL, the maximized log-likelihood; K 
> the number of estimated parameters; N2K, number of observations/K; AIC, 
> the Akaike index criterion; deltAIC, the difference between AIC and the 
> lowest AIC value; w_i, the Akaike weights; AICc, the second order Akaike 
> criterion; deltAICc, the difference between AICc and the lowest AICc 
> value; w_ic, the AICc weights }
>   \item{models}{the list of models}
> }
> \references{
>     Anderson, D.R., Link, W.A., Johnson, D.H. and Burnham, K.P. (2001). 
> Suggestions for presenting the results of data analyses. Journal of 
> Wildlife Management, 65, 373-378; Burnham, K.P. and Anderson, D.R. 
> (2002) Model Selection and Multimodel Inference: a Practical 
> Information-Theoretic Approach, 2nd edn., Springer-Verlag, New York. 353 pp
>  }
> \author{ Patrick Giraudoux and David Pleydell: pgiraudo at univ-fcomte.fr, 
> dpleydel at univ-fcomte.fr }
> 
> \seealso{ \code{\link{AIC}},\code{\link{logLik}} }
> \examples{
>  library(MASS)
>  anorex.1 <- lm(Postwt ~ Prewt*Treat, data = anorexia)
>  selMod(anorex.1)
>  anorex.2 <- glm(Postwt ~ Prewt*Treat, family=gaussian,data = anorexia)
>  selMod(anorex.2)
>  anorex.3<-lm(Postwt ~ Prewt+Treat, data = anorexia)
>  selMod(list(anorex.1,anorex.2,anorex.3))
> }
> \keyword{ models }
> 
> ______________________________________________
> 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
> 
-- 
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, Helleveien 30, N-5045 Bergen,
Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43
e-mail: Roger.Bivand at nhh.no

Thanks both.... Explanations perfectly clear. Also you make me discover 
there was a 'pgirmess-manual.log', with error lines detected and 
commented, indeed... (shame on me!!!) which would have been of great 
help during the past decade... The misuse of _ should be the origin.

I should manage with, now.

Thank again,

Patrick
>The general answer is to look through the (often very long) *.log file in 
>the *.Rcheck directory until you find the problem. That will typically 
>give you a line number in the *.tex file, which shows not only where the 
>error occurred, but the *.log file entry often shows what it is. My 
>typical errors are using LaTeX special symbols, and most often having 
>unprotected $ and _. I see quite a lot of _ below in \value{}, so I'd
try
>\_ there first.
>
>Roger
>

Berwin A Turlach a 侀crit :
>G'day Patrick
>
>  
>
>>>>>>"PG" == Patrick Giraudoux
<patrick.giraudoux@univ-fcomte.fr> writes:
>>>>>>            
>>>>>>
>
>    PG> \value{ A list with the following items: \item{AIC}{a
>    PG> data.frame including LL, the maximized log-likelihood; K the
>    PG> number of estimated parameters; N2K, number of observations/K;
>    PG> AIC, the Akaike index criterion; deltAIC, the difference
>    PG> between AIC and the lowest AIC value; w_i, the Akaike weights;
>w_i is LaTeX notation for "w subscript i" and needs to be inside a
>maths environment otherwise there will be a LaTeX error.  Change this
>to, e.g. \eqn{w_i}
>
>    PG> AICc, the second order Akaike criterion; deltAICc, the
>    PG> difference between AICc and the lowest AICc value; w_ic, the
>w_ic is LaTeX notation for "w subscript i followed by c".  This
needs
>to be insite a maths environment to avoid a LaTeX error.  But I
>presume that your intention is actuall "w subscript {ic}", thus
change
>this to, e.g. \eqn{w_{ic}}
>
>HTH.
>
>Cheers,
>
>        Berwin
>
>PS:  Would make life simple for checker if you sent along the .log
>     file in future. :)
>
>  
>
	[[alternative HTML version deleted]]