search for: sample_analysi

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 called by...

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 directory. However, when I did want to check...

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 = "html_document", params = list(data = sample_analysis, configuration = skylineconfig),envir = new.env()) <code> I do not think I can wri...

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(da...

On 09/07/2018 3:24 PM, Witold E Wolski wrote: > 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 g...

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 error. By this the .Rmd file, html file and corresponding > .R files is being placed into the inst/doc directory....

...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 = "html_document", > params = list(data = sample_analysis, > configuration = > skylineconfig),envir = new.env()) > <co...

...l as to use the package parameter in data made it work, with all devtools::install,check,build and build_vignettes as well as with R CMD ... etc. But most importantly it also still works with: rmarkdown::render("vignettes/tr_srm_summary.Rmd", params=list(configuration=skylineconfig, data=sample_analysis )) THANK YOU. This is how my vignette header looks (see below) and it works. --- title: "Titel" author: "WEW at FGCZ.ETHZ.CH" date: "`r Sys.Date()`" output: pdf_document: default html_document: default params: configuration: !r quote(get(data(skylineconfi...

Hello, I have a package which includes some parameterized r-markdown report which I would also like to build as package vignettes. Is there a way to run the parameterized vignette creation with the package build or package check? Thank you -- Witold Eryk Wolski