[Bioc-devel] EXTERNAL: LazyData: false and accessing data in the YAML section of an Rmd document
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 argument of the `render` function.
Therefore, I thought about the following code, which unfortunately
Errors with BiocCheck.
```{r data-fonfig, include=FALSE}
evalAll <- is.null(params$data)
if(!evalAll ){
data <- params$data
}
```
```{r eval = evalAll}
data(data_ionstar, package = "prolfqua")
data <- data_ionstar$data
```
Running BiocCheck produces:
* Checking library calls...
Error in eval(x, envir = envir) : object 'evalAll' not found
Best regards
Witek
On 19/11/2021 17:00, McDavid, Andrew wrote:
How about in the YAML:
params:
??configuration: NULL
??project_conf: NULL
??data: NULL
Then in the first chunk something like:
```{r data-config}
if(is.null(params$data)){
data(data_ionstar, package = "prolfqua")
?data = ?data_ionstar
configuration = data$filtered()$config
}
```
You can use a more ornate expression for these parameters when rendering
otherwise `rmarkdown::render()`, which I suppose you could call from a
Makefile if needed when rendering package the vignettes.
Andrew McDavid
Biostatistics and Computational Biology
University of Rochester Medical Center
On Nov 19, 2021, at 6:00 AM, bioc-devel-request at r-project.org <mailto:bioc-devel-request at r-project.org> wrote: If anyone wonders, why do I need it. By this I can reuse the vignette with a different dataset.