Add method for Fischer's exact test

[rempsyc]

Add full support for Fischer's exact test: closes #351

---

# load packages
library(report)
packageVersion("report")
#> [1] '0.5.7.11'

# Create data and fischer test object
TeaTasting <-
  matrix(c(3, 1, 1, 3),
         nrow = 2,
         dimnames = list(Guess = c("Milk", "Tea"),
                         Truth = c("Milk", "Tea")))
x <- fisher.test(TeaTasting, alternative = "greater")

report(x)
#> Effect sizes were labelled following Funder's (2019) recommendations.
#> 
#> The Fisher's Exact Test for Count Data testing the association between the
#> variables of the TeaTasting dataset suggests that the effect is statistically
#> not significant, and large (odds ratio = 6.41, 95% CI [0.31, Inf], p = 0.243;
#> Adjusted Cramer's v = 0.35, 95% CI [0.00, 1.00])

^{Created on 2023-09-30 with reprex v2.0.2}

[codecov]

Codecov Report

Merging #395 (75ef67a) into main (da67740) will decrease coverage by 0.03%.
The diff coverage is 75.64%.

❗ Current head 75ef67a differs from pull request most recent head ecaabb4. Consider uploading reports for the commit ecaabb4 to get more accurate results

@@            Coverage Diff             @@
##             main     #395      +/-   ##
==========================================
- Coverage   73.81%   73.78%   -0.03%     
==========================================
  Files          48       49       +1     
  Lines        3425     3494      +69     
==========================================
+ Hits         2528     2578      +50     
- Misses        897      916      +19     

Files	Coverage Δ
R/report.htest.R	92.02% <100.00%> (+0.35%)	⬆️
R/report_htest_fisher.R	71.21% <71.21%> (ø)

... and 1 file with indirect coverage changes

[IndrajeetPatil]

Can you please also clean the newly found lints?

[rempsyc]

Can you please also clean the newly found lints?

@IndrajeetPatil I ran the tests locally and found no problems with the lints with the changed files after downloading today's version of lintr from github. Then I triggered the tests on GHA and again it seems both lint workflows pass. So is it OK?

[rempsyc]

Ok there are snapshots failing now (is that what you meant?). On R-devel, it seems that Message is now printed as <simpleMessage>, e.g.,

- Message <simpleMessage>
+ Message

And so my understanding is that it is not currently possible to satisfy both R-devel and R-latest with snapshots. In those cases, should I suppress messages?

[IndrajeetPatil]

This is not about the R version. The change is coming from testthat 3.2.0 release.

…

On Sun 22. Oct 2023 at 19:20, Rémi Thériault ***@***.***> wrote: Ok there are snapshots failing now (is that what you meant?). On R-devel, it seems that Message is now printed as <simpleMessage>, e.g., - Message <simpleMessage> + Message And so my understanding is that it is not currently possible to satisfy both R-devel and R-latest with snapshots. In those cases, should I suppress messages? — Reply to this email directly, view it on GitHub <#395 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACWOHFJBT2ACRXVSIO7MSVTYAVIVXAVCNFSM6AAAAAA5NTHZOKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONZUGE2TAMJSGM> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[rempsyc]

Oh nice, amazing, thank you. Then updating testthat to latest now I am able to update the snapshots correctly locally :)

[rempsyc]

Ok so I fixed snapshots, but check-random-test-order and test-coverage are still failing.

For check-random-test-order, this is strange because the file contains a single test_that() call... I think I remember seeing a similar discussion at some point in our other repos...

For test-coverage, the issue seems to be with rstan::stan_model, so not sure what is going on and cannot replicate locally (where all tests pass). I even ran the workflow covr::codecov(quiet = FALSE) and that too works, so not sure what to do here.

That's after installing all latest easystats packages with easystats::install_latest() and also updating all my other packages to their latest version.

[rempsyc]

Ok, all tests are passing now, I think I can merge after approval :)

[IndrajeetPatil]

Thanks!