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gamlss-dev / gamlss2

gamlss2: GAMLSS Infrastructure for Flexible Distributional Regression
https://gamlss-dev.github.io/gamlss2/
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Vignette Templates #6

Open freezenik opened 1 month ago

freezenik commented 1 month ago

I just added vignette templates in the gamlss2/vignettes folder. I have several topics, which I thought could be assigned to:

If you have other topics in mind, please post them here. I put all vignettes in .Rbuildignore for the moment and at them when they are ready. All vignettes are then shown on the website https://gamlss-dev.github.io/gamlss2/.

mstasinopoulos commented 1 month ago

Dear Niki and All

Thanks for your templates

i) For me it will be easier to make them in quarto. This because I use quarto for a year and I think I have solved most of the problem associated with it.

ii) I try to recompile gamlss2 with the vignettes but It give an error

--- re-building ‘random.Rmd’ using rmarkdown --- finished re-building ‘random.Rmd’

--- re-building ‘s+pb.Rmd’ using rmarkdown Error: processing vignette 's+pb.Rmd' failed with diagnostics: Failed to locate ‘weave’ output file ‘s+pb.pdf’ or ‘s+pb.html’ for vignette with name ‘s+pb’ and engine ‘knitr::rmarkdown’. The following files exist in working directory ‘/private/var/folders/2s/77r_lrjx2ll5jv1ykl58dw_40000gn/T/RtmpD8TKYK/Rbuildcc4440b71c1b/gamlss2/vignettes’: ‘families.Rmd’ (552 bytes), ‘gamlss2.R’ (476 bytes), ‘gamlss2.Rmd’ (2318 bytes), ‘gamlss2.bib’ (1059 bytes), ‘gamlss2.html’ (1.49725e+06 bytes), ‘random.R’ (101 bytes), ‘random.Rmd’ (545 bytes), ‘random.html’ (1.24618e+06 bytes), ‘s+pb.R’ (101 bytes), ‘s+pb.Rmd’ (606 bytes), ‘s+pb.html’ (1.24628e+06 bytes), ‘selection.Rmd’ (603 bytes), ‘spatial.Rmd’ (549 bytes), ‘topmodels.Rmd’ (556 bytes) --- failed re-building ‘s+pb.Rmd’

Any clue why? It looks the problem is s+pb (I wander if it is the + in the name)

iiI) How big the vignette should be? Up to 5-6 pages maybe? Or can be more detailed? My feeling is that it should be small with other extra documentation in the web cite.

Thanks

Mikis

On 27 Sep 2024, at 10:36, Nikolaus Umlauf @.***> wrote:

I just added vignette templates in the gamlss2/vignette folder. I have several topics, which I thought could be assigned to:

random.Rmd https://github.com/gamlss-dev/gamlss2/blob/main/vignettes/random.Rmd, @gillheller https://github.com/gillheller + @rigbyr https://github.com/rigbyr spatial.Rmd https://github.com/gamlss-dev/gamlss2/blob/main/vignettes/spatial.Rmd, @tkneib https://github.com/tkneib s+pb.Rmd https://github.com/gamlss-dev/gamlss2/blob/main/vignettes/s%2Bpb.Rmd, @mstasinopoulos https://github.com/mstasinopoulos topmodels.Rmd https://github.com/gamlss-dev/gamlss2/blob/main/vignettes/topmodels.Rmd, @zeileis https://github.com/zeileis selection https://github.com/gamlss-dev/gamlss2/blob/main/vignettes/selection.Rmd, @mstasinopoulos https://github.com/mstasinopoulos + @freezenik https://github.com/freezenik families.Rmd https://github.com/gamlss-dev/gamlss2/blob/main/vignettes/families.Rmd, @freezenik https://github.com/freezenik If you have other topics in mind, please post them here. I put all vignettes in .Rbuildignore https://github.com/gamlss-dev/gamlss2/blob/main/.Rbuildignore for the moment and at them when they are ready.

— Reply to this email directly, view it on GitHub https://github.com/gamlss-dev/gamlss2/issues/6, or unsubscribe https://github.com/notifications/unsubscribe-auth/AE7QN7QLQPP4SPKTIJITVV3ZYUDGLAVCNFSM6AAAAABO6SMO6GVHI2DSMVQWIX3LMV43ASLTON2WKOZSGU2TEMRSHA3DKMA. You are receiving this because you were mentioned.

mstasinopoulos commented 1 month ago

In connection with the name of the vignette

I rename thefile s_pb.Rmd and seems to compiled

Thanks

Mikis

On 27 Sep 2024, at 10:41, Nikolaus Umlauf @.***> wrote:

Assigned #6 https://github.com/gamlss-dev/gamlss2/issues/6 to @mstasinopoulos https://github.com/mstasinopoulos.

— Reply to this email directly, view it on GitHub https://github.com/gamlss-dev/gamlss2/issues/6#event-14426867006, or unsubscribe https://github.com/notifications/unsubscribe-auth/AE7QN7Q32W4XUMVO7RO4563ZYUDZ3AVCNFSM6AAAAABO6SMO6GVHI2DSMVQWIX3LMV45UABCJFZXG5LFIV3GK3TUJZXXI2LGNFRWC5DJN5XDWMJUGQZDMOBWG4YDANQ. You are receiving this because you were assigned.

zeileis commented 1 month ago

If we want to do qmd instead of Rmd we can easily re-name the files. Then, instead of the output: in the YAML, we should use format:. For example:

format: 
  html:
    html-math-method: mathjax
    toc: true
    number-sections: true

The result in the altdoc page will look very similar.

In principle, it's also possible and mix the vignettes and have some in Rmd and some in qmd. But, if possible, it's eaiser if we are consistent.

mstasinopoulos commented 1 month ago

Thanks

Achim for showing how to transfer to quarto

Here is my modify .qmd version if one wands to compere it with the original .Rmd one.

Thanks

Mikis



On 30 Sep 2024, at 02:42, Achim Zeileis @.***> wrote:

If we want to do qmd instead of Rmd we can easily re-name the files. Then, instead of the output: in the YAML, we should use format:. For example:

format: html: html-math-method: mathjax toc: true number-sections: true The result in the altdoc page will look very similar.

In principle, it's also possible and mix the vignettes and have some in Rmd and some in qmd. But, if possible, it's eaiser if we are consistent.

— Reply to this email directly, view it on GitHub https://github.com/gamlss-dev/gamlss2/issues/6#issuecomment-2381654348, or unsubscribe https://github.com/notifications/unsubscribe-auth/AE7QN7UM2KYVYT2QUXQKJCDZZCF4TAVCNFSM6AAAAABO6SMO6GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGOBRGY2TIMZUHA. You are receiving this because you were mentioned.