Re: [Rd] [R-sig-ME] lmer error: number of observations <= number of random effects

Dear Srinidhi, You are trying to fit 1 random intercept and 2 random slopes per individual, while you have at most 3 observations per individual. You simply don't have enough data to fit the random slopes. Reduce the random part to (1|ID). Best regards, Thierry ir. Thierry Onkelinx Statis

[Rd] bug in utils:::format.person

── package * version date (UTC) lib source cli 3.6.1 2023-03-23 [1] CRAN (R 4.3.0) fortunes 1.5-4 2016-12-29 [1] CRAN (R 4.3.0)

[Rd] install.packages() and Additional_repositories

u accept a patch to amend this? If so, should install.packages() use the `Additional_repositories` when listed? Or should that be based on an extra argument? E.g. additional_repos = FALSE (default). Best regards, Thierry ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid / Gov

Re: [Rd] order of operations

IMHO this is just bad practice. Whether the result is guaranteed or not, doesn't matter. ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid / Government of Flanders INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND FOREST Team Biometrie & Kwali

Re: [Rd] sorting bug in R-devel?

Dear Peter, Thanks for the feedback on the locale. Is there a better alternative for the C locale? One that yields a consistent and stable sorting independent of the R version and OS. Best regards, Thierry ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid / Government of

[Rd] sorting bug in R-devel?

"a'" "a'b" "a'b'c" "|" [29] "\200" "\265" "\340" "\347" "\351" ## Ubuntu 18.04 R 4.0.3 [1] "\ta" "\na" "\"NA\"&quo

[Rd] change in sorting?

t;, locale = "C") return( c( ctype = old_ctype, collate = old_collate, time = old_time, monetary = old_monetary ) ) } ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid / Government of Flanders INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTI

Re: [Rd] Hard memory limit of 16GB under Windows?

when you get a similar error message. Best regards, ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid / Government of Flanders INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND FOREST Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance t

Re: [Rd] Cryptic error message from namespaceExport

g: INLA is a very large package. The old version is 87 MB, the new one 250 MB Best regards, ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid / Government of Flanders INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND FOREST Team Biometrie & Kwaliteitszor

[Rd] Cryptic error message from namespaceExport

ribed above. Is the possible to improve this error message? The current message is misleading as neither packages contain the string ".__C__inla" Best regards, ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid / Government of Flanders INSTITUUT VOOR NATUUR- EN BOSONDERZO

Re: [Rd] Fwd: Bug Reporting

;) > end - start Time difference of 1 days > as.integer(end) - as.integer(start) [1] 86400 Best regards, ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid / Government of Flanders INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND FOREST Team Biomet

Re: [Rd] Function I mean not to export keeps being documented in a manual?

Dear Marta, Add the @noRd tag to the Roxygen documentation of the function. Best regards, ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid / Government of Flanders INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND FOREST Team Biometrie & Kwaliteits

Re: [Rd] problematic dev.off() after running examples without plots

Dear Martin, Thanks for the feedback. After some more digging, I found that the problem was caused by a function which we imported from another package. That function closes open devices as a side-effect. Best regards, ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid

[Rd] problematic dev.off() after running examples without plots

least one example which has some plot. Is there a better solution? We are using R 3.5.1 Best regards, ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid / Government of Flanders INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND FOREST Team Biometrie

Re: [Rd] build package with unicode (farsi) strings

Dear Farid, Try using the ASCII notation. letters_fa <- c("\u0627", "\u0641"). The full code table is available at https://www.utf8-chartable.de Best regards, ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid / Government of Flanders INSTITUUT VOOR

Re: [Rd] CRAN indices out of whack (for at least macOS)

Another benefit of Winston's proposal is that it make it easy to install specific package versions from source. For the time being I'm using a construct like https://github.com/inbo/Rstable/blob/master/cran_install.sh to generate a Docker image. Best regards, ir. Thierry Onkelinx S

Re: [Rd] resolving a names conflict

Dear Terry, Why not have the required code in survival and use importFrom(survival, gchol) in bdsmatrix? Since you maintain both, that shouldn't be too complicated. Best regards, ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid / Government of Flanders INSTITUUT VOOR NATUU

Re: [Rd] new function to tools/utils package: dependencies based on DESCRIPTION file

Dear Jan, Similar functionality is available in devtools::dev_package_deps() Best regards, ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance Kliniekstraat

Re: [Rd] vignette/knitr help

required to compile vignettes. Best regards, ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance Kliniekstraat 25 1070 Anderlecht Belgium To call in the statistician afte

Re: [Rd] vignette/knitr help

Dear Mick, Note that both knitr and rmarkdown are listed under Suggests: both are required to compile the vignette. Installing rmarkdown should solve the problem. If not, please provide more information. OS, R version, digest version, ... Best regards, ir. Thierry Onkelinx Instituut voor natuur

Re: [Rd] (no) circular dependency

age C with all the common functions. Then A and B import those functions from C. Best regards, ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance Kliniekstraat 25 10

Re: [Rd] install.packages() fails with drat repository on networkdrive

)) if(length(res0) & !inherits(res0, "try-error")) rownames(res0) <- res0[, "Package"] works around this problem. Best regards, Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie &am

[Rd] install.packages() fails with drat repository on networkdrive

attached base packages: character(0) other attached packages: [1] drat_0.1.0.1 loaded via a namespace (and not attached): [1] graphics_3.2.3 tools_3.2.3 utils_3.2.3 grDevices_3.2.3 stats_3.2.3 datasets_3.2.3 methods_3.2.3 base_3.2.3 fortunes_1.5-3 Best regards, ir. Thierry O

Re: [Rd] Best way to implement optional functions?

Roxygen2 documents imported and re-exported functions. See http://www.r-bloggers.com/roxygen2-5-0-0/ Best regards, ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie & Kwaliteitszorg / team Biometrics & Quality A

Re: [Rd] reverse object creation

Dear Bo, Please keep the mailing list in cc. Your function only works properly with a data.frame in which all variables are characters. dput() will preserve the structure of the object and works with all R objects. Best regards, ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek

Re: [Rd] reverse object creation

Dear Bo, I think that you are looking for dput() Best regards, ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance Kliniekstraat 25 1070 Anderlecht Belgium To cal

Re: [Rd] authorship and citation

Dear Adrian, Have a look at the DESCRIPTION of the RODBC package. One of the authors was contributing from 1999 to 2002. I have the feeling that your situation is similar. Best regards, ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team

Re: [Rd] User Input

If you use S4 objects then have a look at ?setValidity Best regards, Thierry Op 11-jul.-2015 04:11 schreef "Glenn Schultz" : > All, > > I have a package BondLab, all variables are passed to the models via Cusip > objects. > > The only variables input by the user are > settlement date, > price or

Re: [Rd] Problem with adding slots to S4 object

Dear Michael, Thank you very much for your reply. It helped me to solve the problem and increased my understanding of S4 objects. I've updated the github repository in case someone else might be interested. Best regards, Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonde

Re: [Rd] Problem with adding slots to S4 object

30 0.00 0.00 ".getClassFromCache" 0.08 0.04 0.08 0.04 "getClassDef"0.08 0.04 0.00 0.00 "initialize" 0.08 0.04 0.00 0.00 "new"0

Re: [Rd] Print output during long tests?

Dear Toby, Have you tried adding output to the tests with the context() function? Best regards, Thierry Op 4 mei 2015 18:28 schreef "Toby Hocking" : I am the author of R package animint which uses testthat for unit tests. This means that there is a single test file (animint/tests/testthat.R) a

[Rd] Problem with adding slots to S4 object

m I using the virual classes in the wrong way? Best regards, ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance Kliniekstraat 25 1070 Anderlecht Belgium To call in th

Re: [Rd] robust updating methods

( https://github.com/ThierryO/testlme4/blob/master/tests/testthat/test_fit_model.R fails). Directly calculating the confidence intervals in the same function is an acceptable solution for my work. Thank you for this solution. Best regards, Thierry ir. Thierry Onkelinx Instituut voor natuur- en

Re: [Rd] vignette checking woes

I think that you need to check how MatrixModels imports sparse.model.matrix(). If MatrixModels depends on Matrix, then you are probably forced to depend on MatrixModels. ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie

Re: [Rd] vignette checking woes

Dear Roger, How is Matrix loaded? If you use sparse.model.matrix() inside a function from your package you need to declare it as Matrix::sparse.model.matrix() Best regards, ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie

Re: [Rd] robust updating methods

int() of a model as returned by a function fails. It even fails when I try to calculate the confint() inside the same function as the glmer() call (see the fit_model_ci function). Best regards, Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature

[Rd] normalizePath output depends on existence of directory

LC_TIME=Dutch_Belgium.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] fortunes_1.5-2 tools_3.1.2 Best regards, ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / R

Re: [Rd] Bug in rnorm? (PR#12016)

That's not a bug. It's FAQ 7.31 Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest Cel biometrie, methodologie en kwaliteitszorg / Section