Re: [Bioc-devel] EXTERNAL: LazyData: false and accessing data in the YAML section of an Rmd document

2021-11-22 Thread Witold Wolski
Dear Andrew, Thanks for your suggestion. Loading the data explicitly in the markdown instead of the YAML section - appeals to me. It is desirable to show the code in the vignette if the vignette loads it. However, I would like not to display the code if I pass the data using the params

Re: [Bioc-devel] EXTERNAL: LazyData: false and accessing data in the YAML section of an Rmd document

2021-11-19 Thread McDavid, Andrew
How about in the YAML: params: configuration: NULL project_conf: NULL data: NULL Then in the first chunk something like: ```{r data-config} if(is.null(params$data)){ data(data_ionstar, package = "prolfqua") data = data_ionstar configuration = data$filtered()$config } ``` You can use a

Re: [Bioc-devel] EXTERNAL: LazyData: false and accessing data in the YAML section of an Rmd document

2021-11-18 Thread Witold Wolski
I guess I failed to explain: In the yaml section of the rmarkdown I can only use a single R expression; i.e., I can not write: ``` configuration: !r data('somedata', package="xyz"); somedata$uvw ``` because these are two expressions. I could write: xyz::somedata$uvw So to rephrase my

Re: [Bioc-devel] EXTERNAL: LazyData: false and accessing data in the YAML section of an Rmd document

2021-11-18 Thread Marcel Ramos
Hi Witold, I am not sure what the use case is for loading data in the yaml header. If you're swapping out data for your vignettes, perhaps your introduction chunks could contain the code to load the data. In any case, I recommend that you use `data("dataset", package = "package")` to load the