Update deprecated syntax for future rstan compatibility

[andrjohns]

Now that rstan 2.26 is available on CRAN we need to update the deprecated syntax in your package's Stan models, otherwise it will fail to install with an upcoming version of RStan.

The following updates have been made:

• New array syntax
• _cdf functions using conditional | notation (i.e., _cdf(y |x))
  • The current CRAN rstan has a bug in recognising this in _cdf functions, so I've updated your syntax to work on the log scale with the respective _lcdf function. This will let your package be compatible with the current and future parser, and is also more numerically stable with extreme values (bonus!)

More information about the deprecated and removed syntax in Stan can be found here:

• https://mc-stan.org/docs/functions-reference/deprecated-functions.html
• https://mc-stan.org/docs/functions-reference/removed-functions.html

If you could merge and submit to CRAN soon, it would be greatly appreciated.

Let me know if you have any questions about these changes.

Thanks!

[github-actions]

This is how benchmark results would change (along with a 95% confidence interval in relative change) if 0b473b3 is merged into main:

•   :ballot_box_with_check:default: 44.5s -> 46.8s [-13.95%, +24.13%]
•   :ballot_box_with_check:no_delays: 45.7s -> 50.4s [-0.51%, +20.9%]
•   :ballot_box_with_check:random_walk: 14.4s -> 14.6s [-8%, +10.98%]
•   :ballot_box_with_check:stationary: 26.5s -> 28.2s [-2.71%, +15.79%]
•   :ballot_box_with_check:uncertain: 1.08m -> 1.15m [-5.03%, +16.71%]
  Further explanation regarding interpretation and methodology can be found in the documentation.

[sbfnk]

Thanks! Exciting to see the rstan update on CRAN. I had a look at the failing checks and as far as I can see it seem to be due to this issue I just opened on rstan.

[andrjohns]

Thanks! Exciting to see the rstan update on CRAN. I had a look at the failing checks and as far as I can see it seem to be due to this issue I just opened on rstan.

Thanks for flagging! I've opened a PR with a fix and I'll let you know when it's made it to CRAN

[seabbs]

As we aren't testing stan code on CRAN (just on our CI) and that is what we use expose_stan_functions() for we should be able to update on CRAN/merge this without waiting on that PR fix. We would need to temporarily pause CI checks of the stan code in order to do this (to avoid CI checks failing on main).

That does leave on outstanding issue which is causing R-CMD-as-CRAN-check to fail which is the estimate_truncation example erroring - will check this out today to see what the issue is.

[sbfnk]

@andrjohns can you rebase to main / merge to see if the as-cran-check is fixed by #454?

[github-actions]

This is how benchmark results would change (along with a 95% confidence interval in relative change) if 1dc754d is merged into main:

•   :ballot_box_with_check:default: 44.6s -> 46.2s [-10.62%, +18%]
•   :ballot_box_with_check:no_delays: 49.4s -> 48.5s [-17.18%, +13.69%]
•   :ballot_box_with_check:random_walk: 15s -> 15.2s [-10.02%, +12.91%]
•   :ballot_box_with_check:stationary: 29.1s -> 29s [-6.6%, +5.66%]
•   :ballot_box_with_check:uncertain: 1.15m -> 1.22m [-4.5%, +16.81%]
  Further explanation regarding interpretation and methodology can be found in the documentation.

[sbfnk]

CRAN checks passing so merging for CRAN submission as discussed