similar to: Problem building rmarkdown vignettes with child

Dear Duncan, Thank you, got it working with your advice. I did placed the child markdown documents into inst/ParametrizedReportsChild And this is the code in the main vignette by which I include them: child_docs <- "Grp2Analysis_MissingInOneCondtion.Rmd_t" if(!sum(NAinfo$nrProteins > 0) > 0){ child_docs <- "Grp2Analysis_Empty.Rmd_t" } child_docs <-

Dear List, I am working on moving some Rmarkdown reports into the vignettes folder of a package. While I was able to solve to problem of parametrized reports in vignettes folder thanks to your invaluable help (Thank you), I am now struggling with the following problem. One of the reports which I am moving to vignettes includes the following code : ```{r} child_docs <-

On 10/07/2018 11:44 AM, Witold E Wolski wrote: > Dear List, > > I am working on moving some Rmarkdown reports into the vignettes > folder of a package. While I was able to solve to problem of > parametrized reports in vignettes folder thanks to your invaluable > help (Thank you), I am now struggling with the following problem. > > > One of the reports which I am

Hello, This is a problem I posted about already some time ago: https://stat.ethz.ch/pipermail/r-devel/2018-September/076786.html Finally, I did had some time to create a minimal package to reproduce the problem that vignettes with child can not be build. https://github.com/wolski/RmarkdownVignetteProblem The problem basically is that while all the vignettes can be build by running

Dear Duncan, Following your advice (Thank you for it) I did include into the vignettes params: configuration: !r get(data(sample_analysis)) data: !r get(data(skylineconfig)) And everything seemed (see below) to work fine. devtools::build_vignettes() builds the vignettes. Runs with NO error. By this the .Rmd file, html file and corresponding .R files is being placed into the inst/doc

So far you haven't provided a reproducible example yet. I wonder what exactly the object `sample_analysis` is. Sounds like it is an environment. If that is the case, devtools::build_vignettes() will tangle (for the meaning of "tangle", see ?tools::buildVignette) your vignette into an invalid R script. Environments cannot be represented via dput(), so knitr's purl() (eventually

On 09/07/2018 8:49 AM, Witold E Wolski wrote: > Dear Duncan, > > Following your advice (Thank you for it) I did include into the vignettes > params: > configuration: !r get(data(sample_analysis)) > data: !r get(data(skylineconfig)) > > And everything seemed (see below) to work fine. > devtools::build_vignettes() builds the vignettes. > > Runs with NO

Dear Yihui, Thank you for the valuable questions. sample_analysis is a "tibble" while configuration is an "R6" class. But I also have parametrized reports where I pass R reference classes as arguments. This is the Rmd yaml params part corresponding to the error message. params: configuration: !r get(data(skylineconfig)) data: !r get(data(sample_analysis)) Might the R6

Hello, Thank you for the questions as well as remaining me of the default parameters in the yaml session. Indeed this seems to be the solution. But how would I assign package data as a default parameter? So originally I thought to render the markdown with : <code> data(sample_analysis) data(skylineconfig) x <- rmarkdown::render("report.Rmd", output_format =

Suppose I have a file (named "tmp.rmd") containing: --- title: Test --- ```{r example, echo=FALSE, results='asis'} tmp <- data.frame(a=1:5, b=letters[1:5]) print( knitr::kable(tmp, row.names=FALSE)) ``` And I render it with: rmarkdown::render('tmp.rmd', output_format=c('html_document','pdf_document')) I get two files: tmp.pdf tmp.html Is

Hi Dan, Hi All, I read the below post. I am wondering how do I know which "keys" are available, e.g. "core.r" and "pre". Where kind I find the definition of what can be adjusted and which "words" to use? Kind regards Georg > Gesendet: Donnerstag, 08. Juni 2017 um 16:16 Uhr > Von: "Nordlund, Dan (DSHS/RDA)" <NordlDJ at

Hola, cuando ejecuto Rmarkdown los gráficos plotly no salen. No hay ningún error pero en el resultado final no se obtiene nada. Si ejecuto plotly desde R los gráficos primero salen en blanco y es necesario "recargar" para poderlo ver, si lo inspeccionas no sale nada. El equipo en el que me pasa esto es: platform x86_64-w64-mingw32 arch x86_64 os mingw32

Buenas noches: Estoy realizando un documento rmarkdown donde realiza un modelo de random forest con la librería H2O, el problema lo tengo cuando lo compilo con knit a pdf, ya que en el documento me sale con rayas con el porcentaje de entrenamiento que lleva. ¿Alguien sabe como eliminarlas para que no aparezca en el documento en pdf? [cid:image001.png en 01D49FC5.4D2AEEE0] Muchas Gracias. Un

Although it is not an elegant solution, but if your output format is HTML, you can add an arbitrary empty HTML element like <span id="foo"></span> before your code chunk. Then you can jump to this <span> via a link like "see [this code chunk](#foo)". Regards, Yihui -- https://yihui.name On Tue, Aug 29, 2017 at 1:30 PM, Roy Mendelssohn - NOAA Federal

Buenas, he intentado varias veces instalar knitr y Rmarkdown tanto desde Rstudio como desde la terminal de Ubuntu usando diferentes codigos y en nunca consegui q lo instalara. el error q tira es el siguiente: Warning in install.packages : installation of package ?/tmp/RtmpavyTWw/downloaded_packages/stringr_1.0.0.tar.gz? had non-zero exit status Alguien me podria ayudar, porq estoy dejando

Hola, colegas, compañeros y maestros. Es una tontería... que no atino a preguntarsela bien a Google. Tengo unos datos a los que si en consola les digo: > sum(dtk$V9) [1] 37790 devuelve. Pero si eso mismo se lo digo en RMarkdown con código on line, lease `r sum(dtk$V9)` me devuelve un numero horroroso: 3.77910^{4} entre el texto Qué, para colmo, ocupa más carácteres que el que no me imprime.

Hello, When evaluating different learning methods for a categorization problem with the (really useful!) caret package, I'm getting confusing results from the Kappa computation. The data is about 20,000 rows and a few dozen columns, and the categories are quite asymmetrical, 4.1% in one category and 95.9% in the other. When I train a ctree model as: model <- train(dat.dts,

Buenas noches, Escribo este mail porque tengo un problema con rmarkdown, estoy creando un informe y me iba bien al generarlo como pdf, de repente me sale el siguiente error y no sé como solucionarlo: pandoc.exe: Error producing PDF from TeX sourceError: pandoc document conversion failed with error 43Además: Warning message:comando ejecutado '"C:/Program

Are you sure that you want to read in the output_file in text <- readLines(output_file, warn = FALSE)? best regards, Heinz Thierry Onkelinx wrote/hat geschrieben on/am 06.09.2017 11:41: > Dear all, > > I'm trying to write a post_processor() for a custom rmarkdown format. The > goal of the post_processor() is to modify the latex file before it is > compiled. For some

Buenas tardes, Al tratar de hacer en rstudio documentos pdf, word o html con un archivo rmd me sale un mensaje tal que así: "Rendering R Markdown documents requires updated versions of the following packages: knitr, rmarkdown. Do you want to install these packages now?" He probado a reinstalar esos paquetes (que ya tenía instalados) pero cuando vuelvo a aplicar knit to pdf,