Add TIGER

[cchen22]

@marouenbg I have updated the "TIGER.R" file in the "R" folder and added two example data files, "expr.rda" and "prior.rda," to the "data" folder. Please let me know if these changes are sufficient?

[marouenbg]

Thanks @cchen22 , can you please run devtools::document() at the root of the netZoo folder and upload the generated files?

[cchen22]

@marouenbg The situation is more complex than I initially thought. I have now documented everything and successfully tested the "example(TIGER)" on my end. However, an error message indicates that the "cmdstanr" R package needs to be installed. I'm unsure about the best course of action, as it requires two steps outlined in my ReadMe file

1. Install the "cmdstanr" package by running the command: install.packages("cmdstanr", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
2. Install cmdstan by running the command: cmdstanr::install_cmdstan()

Please advise on how to proceed. Thank you!

[marouenbg]

Oh I see, can you add the package in the depends section here: https://github.com/netZoo/netZooR/blob/master/DESCRIPTION#L24

[marouenbg]

Does it work on your end after adding it to the dependencies?

[cchen22]

Does it work on your end after adding it to the dependencies?

No. ERROR: dependency 'cmdstanr' is not available for package 'netZooR'

[marouenbg]

OK remove it from description and try running this function at the root of netZooR https://mc-stan.org/rstantools/reference/use_rstan.html and upload the new updated files to this PR

[cchen22]

OK remove it from description and try running this function at the root of netZooR https://mc-stan.org/rstantools/reference/use_rstan.html and upload the new updated files to this PR

This appears to be a pipeline for rstan, not for cmdstanr. Unfortunately, these are two separate packages... When I created TIGER, I searched for a solution to this question but had no luck. However, I came across a potentially useful repository: https://github.com/rok-cesnovar/misc/tree/master/democmdstanr. I will examine it and inform you later.

[marouenbg]

You can also add a remotes section in description like so Remotes: stan-dev/cmdstanr

[cchen22]

You can also add a remotes section in description like so Remotes: stan-dev/cmdstanr

I finally applied this method and added a .onLoad function to check and install stan when netZooR is loaded. On my end cmdstanr can be successfully installed and example(TIGER) works fine. However, I encountered some error messages that don't appear to be related to Stan. Could you share your thoughts on this? Thanks!

[marouenbg]

OK, I am on it now.

[marouenbg]

@cchen22 The issues you mentioned were fixed. Let me know how it goes.

[codecov[bot]]

Codecov Report

Patch coverage has no change and project coverage change: -0.09 :warning:

Comparison is base (e6c9280) 41.52% compared to head (7bd555e) 41.43%.

:exclamation: Current head 7bd555e differs from pull request most recent head 5d33f21. Consider uploading reports for the commit 5d33f21 to get more accurate results

Additional details and impacted files

```diff @@ Coverage Diff @@ ## devel #283 +/- ## ========================================== - Coverage 41.52% 41.43% -0.09% ========================================== Files 21 22 +1 Lines 2786 2792 +6 ========================================== Hits 1157 1157 - Misses 1629 1635 +6 ``` | [Impacted Files](https://app.codecov.io/gh/netZoo/netZooR/pull/283?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=netZoo) | Coverage Δ | | |---|---|---| | [R/TIGER.R](https://app.codecov.io/gh/netZoo/netZooR/pull/283?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=netZoo#diff-Ui9USUdFUi5S) | `0.00% <0.00%> (ø)` | | | [R/zzz.R](https://app.codecov.io/gh/netZoo/netZooR/pull/283?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=netZoo#diff-Ui96enouUg==) | `0.00% <0.00%> (ø)` | |

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[cchen22]

@marouenbg Well done! I've noticed that there are two warnings regarding my example datasets "prior.rda" and "expr.rda". I'm curious about how you document your previous datasets in netZooR, such as the one named "small1976.rda". Did you use the method by Hadley?

[marouenbg]

Hi @cchen22 yep, here is how that data file was documented in CONDOR.R https://github.com/netZoo/netZooR/blob/81cb072fd4f3e1b47b99ef2ce67d1cad6a83bde1/R/CONDOR.R#L1032

[cchen22]

Hi @cchen22 yep, here is how that data file was documented in CONDOR.R

https://github.com/netZoo/netZooR/blob/81cb072fd4f3e1b47b99ef2ce67d1cad6a83bde1/R/CONDOR.R#L1032

OK, I'll add the dataset document. Anything else I need to do before merging?

[marouenbg]

Thanks @cchen22 , this should be fine for this iteration, we will add tests in a new PR.

[marouenbg]

Also, make sure to update docs with devtools, like you did earlier devtools::document()

[marouenbg]

@cchen22 everything looks good, merging now. Fantastic work! Please use Tiger from the netZooR distribution so that you use the same version used by others which makes it easier to replicate bugs etc...

[marouenbg]

Hi @cchen22 , would it be possible to update the TIGER vignette using netZooR code? Thank you!

[cchen22]

Hi @cchen22 , would it be possible to update the TIGER vignette using netZooR code? Thank you!

Sure! But do you want me to start a new PR?

[marouenbg]

Yes, here please https://github.com/netZoo/netbooks

[marouenbg]

Hello @cchen22, would it be possible to add a small description of TIGER in the readme file through a new pull request? Thank you https://github.com/netZoo/netZooR/blob/devel/README.md