[R] Linking in R package documentation
I have two straightforward questions about linking in the man pages for R
packages:
First, is it possible to link from within parts of the documentation that are
not the \seealso section? For example, I would like to have something like:
\arguments{
\item{correlation}{an optional \code{corStruct} object describing the
within-group correlation structure; the available classes are given in
\link{\code{corClasses}}}
}
When the package is compiled, the word corClasses is blue and underlines, but
nothing happens when you click on it.
Second, how do I link to a function of the same name in another package? I
thought I could use something like:
\seealso{\code{\link[nlme]{ranef}}}
but that gives a Page Not Found.
Thank you in advance!
Rebecca
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Re: [R] \dQuote in packages
Thank you! (That was easy to fix.)
How does one deal with quoting (in \reference)? The following line causes
problems:
\references{Sela, Rebecca J., and Simonoff, Jeffrey S., \dQuote{RE-EM Trees: A
New Data Mining Approach for Longitudinal Data}.}
The error given is:
Warning in parse_Rd(./man/predict.Rd, encoding = unknown) :
./man/predict.Rd:28: unknown macro '\dquote'
*** error on file ./man/predict.Rd
Error : ./man/predict.Rd:28: Unrecognized macro \dquote
The manual for writing R packages said I should not just use the character .
What should I be using here?
Thanks again!
Rebecca
- Original Message -
From: Uwe Ligges lig...@statistik.tu-dortmund.de
To: Rebecca Sela rs...@stern.nyu.edu
Cc: r-help r-help@r-project.org
Sent: Friday, July 10, 2009 8:17:44 PM GMT -05:00 US/Canada Eastern
Subject: Re: [R] \dQuote in packages
Rebecca Sela wrote:
Here is one Rd file with problems, now inline so that it can be read:
\name{simpleREEMdata}
\docType{data}
\alias{simpleREEMdata}
\title{Sample Data for RE-EM trees}
\description{
This data set is consists of a panel of 50 individuals with 12 observations
per individual. The data is based on a regression tree with an initial split
based on a dummy variable (\code{D}) and a second split based on time in the
branch where \code{D=1}. The observations include both randomly generated
individual-specific effects and observation-specific errors.
}
\format{
The data has 600 rows and 5 columns. The columns are:
insert here:
\itemize{
\item{\code{Y}}{the target variable}
\item{\code{t}}{a numeric predictor (time)}
\item{\code{D}}{a catergorical predictor with two levels, 0 and 1}
\item{\code{ID}}{the identifier for each individual}
\item{\code{X}}{another covariate (which is intentionally unrelated to the
target variable)}
insert here:
}
or in other words, you need an itemize environment in order to use \item
within \format, see the manual Writing R Extensions.
Best,
Uwe
}
\references{Sela, Rebecca J., and Simonoff, Jeffrey S., \dQuote{RE-EM Trees:
A New Data Mining Approach for Longitudinal Data}.}
\keyword{datasets}
Thanks again for your help!
Rebecca
- Original Message -
From: Uwe Ligges lig...@statistik.tu-dortmund.de
To: Rebecca Sela rs...@stern.nyu.edu
Cc: r-help r-help@r-project.org
Sent: Thursday, July 9, 2009 6:05:46 AM GMT -05:00 US/Canada Eastern
Subject: Re: [R] \dQuote in packages
Rebecca,
the attachments have been stripped off by the mailing list.
Rebecca Sela wrote:
That's good to know. I have attached three Rd files that gave errors
(others gave identical errors). I would love to know what is wrong with
them.
I'm using 2.1.1 because that is what is installed on the Linux computer I
have access to. (I haven't bothered figuring out how to assemble a package
in Windows.)
You should *really* upgrade! That version is outdated for several years now.
How to do it on Windows: See the R Installation and Administration
manual with its corresponding section.
Best,
Uwe
Thank you for your help!
Rebecca
- Original Message -
From: Uwe Ligges lig...@statistik.tu-dortmund.de
To: Rebecca Sela rs...@stern.nyu.edu
Cc: r-help r-help@r-project.org
Sent: Wednesday, July 8, 2009 6:11:33 PM GMT -05:00 US/Canada Eastern
Subject: Re: [R] \dQuote in packages
The difference you are experiencing is the new Rd2 parser that is more
picky now (but also prevents to produce wrong documentation files).
If you make the code of the Rd available, someone might be able to help.
Are you really under R-2.1.1 ??? That is really ancient!
Best,
Uwe Ligges
Rebecca Sela wrote:
I am in the process of submitting a package to CRAN. R CMD check ran
successfully on the package on my local computer, using R version 2.1.1.
However, on the computers for CRAN (with version 2.10.0), the following
errors occurred:
Warning in parse_Rd(./man/predict.Rd, encoding = unknown) :
./man/predict.Rd:28: unknown macro '\dquote'
*** error on file ./man/predict.Rd
Error : ./man/predict.Rd:28: Unrecognized macro \dquote
Warning in parse_Rd(./man/print.Rd, encoding = unknown) :
./man/print.Rd:17: unexpected UNKNOWN '\sideeffects'
Warning in parse_Rd(./man/simpleREEMdata.Rd, encoding = unknown) :
./man/simpleREEMdata.Rd:10: unknown macro '\item'
Are \dquote, \sideeffects, and \item not supported in newer versions of R?
Is there some underlying problem that I should fix that makes these show up?
Thank you very much.
Rebecca
__
R-help@r-project.org 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.
__
R-help@r
Re: [R] \dQuote in packages
Here is one Rd file with problems, now inline so that it can be read:
\name{simpleREEMdata}
\docType{data}
\alias{simpleREEMdata}
\title{Sample Data for RE-EM trees}
\description{
This data set is consists of a panel of 50 individuals with 12 observations per
individual. The data is based on a regression tree with an initial split based
on a dummy variable (\code{D}) and a second split based on time in the branch
where \code{D=1}. The observations include both randomly generated
individual-specific effects and observation-specific errors.
}
\format{
The data has 600 rows and 5 columns. The columns are:
\item{\code{Y}}{the target variable}
\item{\code{t}}{a numeric predictor (time)}
\item{\code{D}}{a catergorical predictor with two levels, 0 and 1}
\item{\code{ID}}{the identifier for each individual}
\item{\code{X}}{another covariate (which is intentionally unrelated to the
target variable)}
}
\references{Sela, Rebecca J., and Simonoff, Jeffrey S., \dQuote{RE-EM Trees: A
New Data Mining Approach for Longitudinal Data}.}
\keyword{datasets}
Thanks again for your help!
Rebecca
- Original Message -
From: Uwe Ligges lig...@statistik.tu-dortmund.de
To: Rebecca Sela rs...@stern.nyu.edu
Cc: r-help r-help@r-project.org
Sent: Thursday, July 9, 2009 6:05:46 AM GMT -05:00 US/Canada Eastern
Subject: Re: [R] \dQuote in packages
Rebecca,
the attachments have been stripped off by the mailing list.
Rebecca Sela wrote:
That's good to know. I have attached three Rd files that gave errors (others
gave identical errors). I would love to know what is wrong with them.
I'm using 2.1.1 because that is what is installed on the Linux computer I
have access to. (I haven't bothered figuring out how to assemble a package
in Windows.)
You should *really* upgrade! That version is outdated for several years now.
How to do it on Windows: See the R Installation and Administration
manual with its corresponding section.
Best,
Uwe
Thank you for your help!
Rebecca
- Original Message -
From: Uwe Ligges lig...@statistik.tu-dortmund.de
To: Rebecca Sela rs...@stern.nyu.edu
Cc: r-help r-help@r-project.org
Sent: Wednesday, July 8, 2009 6:11:33 PM GMT -05:00 US/Canada Eastern
Subject: Re: [R] \dQuote in packages
The difference you are experiencing is the new Rd2 parser that is more
picky now (but also prevents to produce wrong documentation files).
If you make the code of the Rd available, someone might be able to help.
Are you really under R-2.1.1 ??? That is really ancient!
Best,
Uwe Ligges
Rebecca Sela wrote:
I am in the process of submitting a package to CRAN. R CMD check ran
successfully on the package on my local computer, using R version 2.1.1.
However, on the computers for CRAN (with version 2.10.0), the following
errors occurred:
Warning in parse_Rd(./man/predict.Rd, encoding = unknown) :
./man/predict.Rd:28: unknown macro '\dquote'
*** error on file ./man/predict.Rd
Error : ./man/predict.Rd:28: Unrecognized macro \dquote
Warning in parse_Rd(./man/print.Rd, encoding = unknown) :
./man/print.Rd:17: unexpected UNKNOWN '\sideeffects'
Warning in parse_Rd(./man/simpleREEMdata.Rd, encoding = unknown) :
./man/simpleREEMdata.Rd:10: unknown macro '\item'
Are \dquote, \sideeffects, and \item not supported in newer versions of R?
Is there some underlying problem that I should fix that makes these show up?
Thank you very much.
Rebecca
__
R-help@r-project.org 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.
__
R-help@r-project.org 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.
__
R-help@r-project.org 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.
[R] \dQuote in packages
I am in the process of submitting a package to CRAN. R CMD check ran successfully on the package on my local computer, using R version 2.1.1. However, on the computers for CRAN (with version 2.10.0), the following errors occurred: Warning in parse_Rd(./man/predict.Rd, encoding = unknown) : ./man/predict.Rd:28: unknown macro '\dquote' *** error on file ./man/predict.Rd Error : ./man/predict.Rd:28: Unrecognized macro \dquote Warning in parse_Rd(./man/print.Rd, encoding = unknown) : ./man/print.Rd:17: unexpected UNKNOWN '\sideeffects' Warning in parse_Rd(./man/simpleREEMdata.Rd, encoding = unknown) : ./man/simpleREEMdata.Rd:10: unknown macro '\item' Are \dquote, \sideeffects, and \item not supported in newer versions of R? Is there some underlying problem that I should fix that makes these show up? Thank you very much. Rebecca __ R-help@r-project.org 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.
Re: [R] \dQuote in packages
That's good to know. I have attached three Rd files that gave errors (others gave identical errors). I would love to know what is wrong with them. I'm using 2.1.1 because that is what is installed on the Linux computer I have access to. (I haven't bothered figuring out how to assemble a package in Windows.) Thank you for your help! Rebecca - Original Message - From: Uwe Ligges lig...@statistik.tu-dortmund.de To: Rebecca Sela rs...@stern.nyu.edu Cc: r-help r-help@r-project.org Sent: Wednesday, July 8, 2009 6:11:33 PM GMT -05:00 US/Canada Eastern Subject: Re: [R] \dQuote in packages The difference you are experiencing is the new Rd2 parser that is more picky now (but also prevents to produce wrong documentation files). If you make the code of the Rd available, someone might be able to help. Are you really under R-2.1.1 ??? That is really ancient! Best, Uwe Ligges Rebecca Sela wrote: I am in the process of submitting a package to CRAN. R CMD check ran successfully on the package on my local computer, using R version 2.1.1. However, on the computers for CRAN (with version 2.10.0), the following errors occurred: Warning in parse_Rd(./man/predict.Rd, encoding = unknown) : ./man/predict.Rd:28: unknown macro '\dquote' *** error on file ./man/predict.Rd Error : ./man/predict.Rd:28: Unrecognized macro \dquote Warning in parse_Rd(./man/print.Rd, encoding = unknown) : ./man/print.Rd:17: unexpected UNKNOWN '\sideeffects' Warning in parse_Rd(./man/simpleREEMdata.Rd, encoding = unknown) : ./man/simpleREEMdata.Rd:10: unknown macro '\item' Are \dquote, \sideeffects, and \item not supported in newer versions of R? Is there some underlying problem that I should fix that makes these show up? Thank you very much. Rebecca __ R-help@r-project.org 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. __ R-help@r-project.org 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.
[R] Problems with subsets in NLME
I am trying to estimate models with subsets using the NLME package. However, I am getting an error in the case below (among others): subset - c(rep(TRUE, 107), FALSE) fm2 - lme(distance ~ age + Sex, data = Orthodont, random = ~ 1, subset=subset) Error in xj[i] : invalid subscript type 'closure' fm2 - lme(distance ~ age + Sex, data = Orthodont, random = ~ 1, subset=1:107) The second estimation works. Does anyone know if there is another work-around? (I have also e-mailed the package maintainers, but one of the e-mails bounced, so I am trying this list as well.) Thank you! Rebecca -- Rebecca Sela IOMS/Statistics Group Stern School of Business New York University __ R-help@r-project.org 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.
[R] Error: package/namespace load failed
I am writing my first R package, and I have been getting the following series of errors when I run R CMD check: * checking S3 generic/method consistency ... WARNING Error: package/namespace load failed for 'REEMtree' Call sequence: 2: stop(gettextf(package/namespace load failed for '%s', libraryPkgName(package)), call. = FALSE, domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Execution halted See section 'Generic functions and methods' of the 'Writing R Extensions' manual. * checking replacement functions ... WARNING Error: package/namespace load failed for 'REEMtree' Call sequence: 2: stop(gettextf(package/namespace load failed for '%s', libraryPkgName(package)), call. = FALSE, domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Execution halted In R, the argument of a replacement function which corresponds to the right hand side must be named 'value'. * checking foreign function calls ... WARNING Error: package/namespace load failed for 'REEMtree' Call sequence: 2: stop(gettextf(package/namespace load failed for '%s', libraryPkgName(package)), call. = FALSE, domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Execution halted See section 'System and foreign language interfaces' of the 'Writing R Extensions' manual. * checking Rd files ... OK * checking for missing documentation entries ... ERROR Error: package/namespace load failed for 'REEMtree' (Everything is OK up to this point.) Looking around online, I have found references to this error when there is compiled C or Fortran code, but I have none of that in my code. I imagine this is a simple problem (perhaps with my NAMESPACE file), but I don't know what it is. (The text of the NAMESPACE file is at the bottom of this e-mail.) Thank you in advance for your help! Rebecca NAMESPACE file: useDynLib(REEMtree) export(AutoCorrelationLRtest, FixedEffectsTree, RandomEffectsTree, LMEpredict, PredictionTest, RandomEffectsTree, RMSE, simpleREEMdata, REEMtree, FEEMtree) import(nlme) import(rpart) S3method(is,REEMtree) S3method(logLik,REEMtree) S3method(plot,REEMtree) S3method(predict,REEMtree) S3method(print, REEMtree) S3method(ranef,REEMtree) S3method(tree,REEMtree) S3method(is,FEEMtree) S3method(logLik,FEEMtree) S3method(plot,FEEMtree) S3method(predict,FEEMtree) S3method(print, FEEMtree) S3method(tree,FEEMtree) useDynLib(REEMtree) export(AutoCorrelationLRtest, FixedEffectsTree, RandomEffectsTree, LMEpredict, PredictionTest, RandomEffectsTree, RMSE, simpleREEMdata, REEMtree, FEEMtree) import(nlme) import(rpart) S3method(is,REEMtree) S3method(logLik,REEMtree) S3method(plot,REEMtree) S3method(predict,REEMtree) S3method(print, REEMtree) S3method(ranef,REEMtree) S3method(tree,REEMtree) S3method(is,FEEMtree) S3method(logLik,FEEMtree) S3method(plot,FEEMtree) S3method(predict,FEEMtree) S3method(print, FEEMtree) S3method(tree,FEEMtree) __ R-help@r-project.org 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.
Re: [R] Checking a (new) package - examples require other package functions
After adding the right functions to the NAMESPACE file, I am now getting a different error: Error: package/namespace load failed for 'REEMtree' Call sequence: 2: stop(gettextf(package/namespace load failed for '%s', libraryPkgName(package)), call. = FALSE, domain = NA) 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE) Execution halted I have attached the NAMESPACE file in case that is where the problem is. Thanks again for your help! Rebecca - Original Message - From: Duncan Murdoch murd...@stats.uwo.ca To: Rebecca Sela rs...@stern.nyu.edu Cc: r-help r-help@r-project.org Sent: Thursday, May 14, 2009 6:57:21 AM GMT -05:00 US/Canada Eastern Subject: Re: [R] Checking a (new) package - examples require other package functions On 13/05/2009 2:38 PM, Rebecca Sela wrote: I am creating an R package. I ran R CMD check on the package, and everything passed until it tried to run the examples. Then, the result was: * checking examples ... ERROR Running examples in REEMtree-Ex.R failed. The error most likely occurred in: ### * AutoCorrelationLRtest flush(stderr()); flush(stdout()) ### Name: AutoCorrelationLRtest ### Title: Test for autocorrelation in the residuals of a RE-EM tree ### Aliases: AutoCorrelationLRtest ### Keywords: htest tree models ### ** Examples # Estimation without autocorrelation simpleEMresult-RandomEffectsTree(Y~D+t+X, data=simpleREEMdata, random=~1|ID, simpleREEMdata$ID) Error: couldn't find function RandomEffectsTree Execution halted The function RandomEffectsTree is defined in the R code for the package. How can I refer to other functions from the package in examples? (I have the Writing R-extensions PDF, so it would be enough to point me to the right page, if the answer is in there and I just missed it.) You should not need to do anything special to make package functions visible, as long as they would be visible to a normal user. (Functions not exported in the NAMESPACE file won't be visible in the examples.) Are you sure you have a function with that exact name? It could be a typo somewhere, e.g. RandomEffectTree or RandomeffectsTree. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Checking a (new) package - examples require other package functions
I am creating an R package. I ran R CMD check on the package, and everything passed until it tried to run the examples. Then, the result was: * checking examples ... ERROR Running examples in REEMtree-Ex.R failed. The error most likely occurred in: ### * AutoCorrelationLRtest flush(stderr()); flush(stdout()) ### Name: AutoCorrelationLRtest ### Title: Test for autocorrelation in the residuals of a RE-EM tree ### Aliases: AutoCorrelationLRtest ### Keywords: htest tree models ### ** Examples # Estimation without autocorrelation simpleEMresult-RandomEffectsTree(Y~D+t+X, data=simpleREEMdata, random=~1|ID, simpleREEMdata$ID) Error: couldn't find function RandomEffectsTree Execution halted The function RandomEffectsTree is defined in the R code for the package. How can I refer to other functions from the package in examples? (I have the Writing R-extensions PDF, so it would be enough to point me to the right page, if the answer is in there and I just missed it.) Thanks! Rebecca __ R-help@r-project.org 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.
[R] DLM and matrices with 0 eigenvalues
I am using DLM to fit a state space model. The covariance matrix of states (W) is given by: a 0 a 0 0 0 0 0 a 0 a 0 0 0 0 0 where a is a parameter to be estimated. Even though the matrix is positive semidefinite, sometimes DLM gives me an error that W is not a valid variance matrix. As far as I can tell, the reason is that one of R's computed eigenvalues is very slightly negative (something like -5E-17). Is there a way to work around this? Thanks! Rebecca __ R-help@r-project.org 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.
[R] Three questions about DSE
I have been using the dse1 and dse2 packages to estimate a model in which the underlying state is an ARMA(2,2) and the observed variables are equal to the state plus noise. I am describing this model using a state space model. First, in estimation, is there a way to restrict two of the estimated coefficients to be equal to each other? In order to desribe an ARMA(2,2) model using a state space model, I must restrict the innovation variance to have its two non-zero elements equal to each other, and I haven't figured out how to do that. Second, I am using the smoother to extract the signal using the code in the attached file. The estimated value of the signal in the last period is 0, but all the estimated values are right. Is there something I am missing here? Finally, sometimes the smoother fails, but the filtered version of the signal is fine. (That will not be the case with the attached code.) Is there a known reason why this sometimes occurs? Thank you in advance for all of your help! Rebecca -- Rebecca Sela Doctoral Candidate Statistics Group/IOMS Stern School of Business__ R-help@r-project.org 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.
[R] LME prediction - object not subsettable?
I fit a random effects linear model to data, and then tried to use it to predict, but I got this error: predict(lmeObject, newdata, level=0) Error in eval(mCall$fixed)[-2] : object is not subsettable This is a new error for me. It still occurs if I change the level to 1 or if I change the data for prediction back to the original dataset to which the lme model was fitted. Can anyone help? Thank you in advance! Rebecca __ R-help@r-project.org 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.
[R] False convergence in LME
I tried to use LME (on a fairly large dataset, so I am not including it), and I got this error message: Error in lme.formula(formula(paste(c(toString(TargetName), as.factor(nodeInd)), : nlminb problem, convergence error code = 1 message = false convergence (8) Is there any way to get more information or to get the potentially wrong estimates from LME? (Also, the page in the NLMINB documentation, http://netlib.bell-labs.com/cm/cs/cstr/153.pdf, has errors in it, which makes it harder to check on what is happening.) Thank you in advance! Rebecca __ R-help@r-project.org 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.
[R] Predicting a single observatio using LME
When I use a model fit with LME, I get an error if I try to use predict with a dataset consisting of a single line. For example, using this data: simpledata Y t D ID 1 -1.464740870 1 0 1 2 1.222911373 2 0 1 3 -0.605996798 3 0 1 4 0.155692707 4 0 1 5 3.849619772 1 0 2 6 4.289213902 2 0 2 7 2.369407737 3 0 2 8 2.249052533 4 0 2 9 0.920044316 1 0 3 10 2.003262622 2 0 3 11 0.003833438 3 0 3 12 1.578300927 4 0 3 13 -0.842322442 1 1 4 14 -0.657256158 2 1 4 15 1.504491575 3 1 4 16 2.896007045 4 1 4 17 0.990505440 1 1 5 18 2.722942793 2 1 5 19 4.395861278 3 1 5 20 4.849296475 4 1 5 21 3.049616421 1 1 6 22 2.874405962 2 1 6 23 4.359511097 3 1 6 24 6.165419699 4 1 6 This happened: testLME - lme(Y~t+D,data=simpledata,random=~1|ID) predict(testLME, simpledata[1,]) Error in val[revOrder, level + 1] : incorrect number of dimensions This has occurred with other datasets as well. Is this a bug in the code, or am I doing something wrong? (Also, is there a way to parse a formula of a type given to random? For example, given ~1+t|ID, I'd like to be able to extract all the variable names to the left of | and to the right of |, the way one can with a normal formula.) Thanks in advance! Rebecca __ R-help@r-project.org 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.
[R] Extracting variables from random effects formulas
I would like to be able to extract the names of the variables in a formula that specifies random effects. For example, given: random = ~ 1+year | st_name I'd like to be able to get year and st_name out of random. Neither terms(random) nor random[2] seems to work. Is there a way to get variable names out? Thanks in advance! Rebecca __ R-help@r-project.org 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.
[R] NLMINB convergence codes
According to the R documentation for NLMINB, the returned value of convergence is 0 for successful convergence. When I got another code (1), I looked up the PDF that linked from the documentation (http://netlib.bell-labs.com/cm/cs/cstr/153.pdf), which said that a return code under 3 was impossible. Is there other documentation that gives the correct meanings of the NLMINB convergence codes in the R implementation? Thanks! Rebecca __ R-help@r-project.org 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.
[R] NaN as a parameter in NLMINB optimization
I am trying to optimize a likelihood function using NLMINB. After running without a problem for quite a few iterations (enough that my intermediate output extends further than I can scroll back), it tries a vector of parameter values NaN. This has happened with multiple Monte Carlo datasets, and a few different (but very similar) likelihood functions. (They are complicated, but I can send them to someone if desired.) Is this something that can happen with NLMINB, perhaps because of a 0/0 in the gradient calculations? Or is it unique to my code? Thanks in advance! Rebecca -- Rebecca Sela Statistics Department/IOMS Stern School of Business New York University __ R-help@r-project.org 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.
[R] Disentagling formulas
I am writing a program in which I would like to take in a formula, change the response (Y) variable into something else, and then pass the formula, with the new Y variable to another function. That is, I am starting with formula - Y~X1+X2+X3 and I'd like to do something like Y - formula$Y newY - f(Y) lm(newY~X1+X2+X3) So far, it seems that my only option will be a very complicated sequence of steps involving match.call(). Is there a simpler way to change the response variable in a formula? Thanks in advance! Rebecca -- Rebecca Sela Statistics Department Stern School of Business New York University __ R-help@r-project.org 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.
