Convert roxygen2 comments to markdown

[Bisaloo]

No description provided.

[codecov]

Codecov Report

Merging #115 (dcb3f27) into master (84361d9) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master     #115   +/-   ##
=======================================
  Coverage   48.44%   48.44%           
=======================================
  Files          18       18           
  Lines        1348     1348           
=======================================
  Hits          653      653           
  Misses        695      695           

Impacted Files	Coverage Δ
R/absolute_error.R	86.66% <ø> (ø)
R/bias.R	87.93% <ø> (ø)
R/eval_forecasts.R	66.07% <ø> (ø)
R/eval_forecasts_binary.R	100.00% <ø> (ø)
R/eval_forecasts_continuous_integer.R	69.64% <ø> (ø)
R/eval_forecasts_helper.R	100.00% <ø> (ø)
R/interval_score.R	95.45% <ø> (ø)
R/pairwise-comparisons.R	42.36% <ø> (ø)
R/pit.R	56.09% <ø> (ø)
R/plot.R	0.00% <ø> (ø)
... and 3 more

---

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[seabbs]

nice stuff. A few comments. I see some issues in the check which will look at shortly.

[seabbs]

is %% correct markdown here?

[Bisaloo]

Hmm, I seem to remember that %% is the correct way to escape % in LaTeX rather than \% but I cannot find any source for this so I might have invented it 🤷 😅.

Anyways, it seems that % doesn't need to be escape in markdown and that both \% and %% produce extra characters:

testfile <- tempfile(fileext = ".md")

write(
r"(
10%
20\%
30%%
)",
testfile
)

knitr::knit(testfile, output = stdout())
#> processing file: /tmp/RtmpPqcVnl/file301a18fe1273.md
#> 
#> 10%
#> 20\%
#> 30%%
#> A connection with                            
#> description "output"        
#> class       "textConnection"
#> mode        "wr"            
#> text        "text"          
#> opened      "opened"        
#> can read    "no"            
#> can write   "yes"

^{Created on 2021-08-04 by the reprex package (v2.0.0.9000)}

Thanks for making me check!

[seabbs]

I've never read this and perhaps explains why my documentation is shocking: https://cran.r-project.org/web/packages/roxygen2/vignettes/rd-formatting.html

Key bits of the failing check:

Warning:   prepare_Rd: man/range_example_data_wide.Rd:19: unknown macro '\item'
196
  prepare_Rd: man/range_example_data_wide.Rd:20: unknown macro '\item'
197
214
  prepare_Rd: man/range_example_data_wide.Rd:40: unexpected section header '\usage'
215
  prepare_Rd: man/range_example_data_wide.Rd:43: unexpected section header '\description'
216
  prepare_Rd: man/range_example_data_wide.Rd:47: unexpected section header '\keyword'
217
  prepare_Rd: man/range_example_data_wide.Rd:48: unexpected END_OF_INPUT '
218
  '
219
  checkRd: (5) range_example_data_wide.Rd:0-68: Must have a \description
220

Warning:   Package unavailable to check Rd xrefs: ‘surveillance’
225
  Missing link or links in documentation object 'ae_median_quantile.Rd':
226
    ‘absolute_error’
227
230
❯ checking for code/documentation mismatches ... WARNING
231
Warning:   Data codoc mismatches from documentation object 'range_example_data_wide':
232
  Variables in data frame 'range_example_data_wide'
233
    Code: creation_date geography horizon lower_0 lower_10 lower_20
234
          lower_30 lower_40 lower_50 lower_60 lower_70 lower_80 lower_90
235
          model true_value upper_0 upper_10 upper_20 upper_30 upper_40
236
          upper_50 upper_60 upper_70 upper_80 upper_90 value_date
237
          value_desc value_type
238
    Docs: creation_date geography horizon lower_0 model true_value
239
          value_date value_desc value_type
240

Mainly moving from \ to @ I think

[nikosbosse]

Thank you both for working on this! I'll review when I'm back from my holidays, but please feel free to merge anything you see fit! Hugo Gruson ***@***.***> schrieb am Mi., 4. Aug. 2021, 11:54:

…

***@***.**** commented on this pull request. ------------------------------ In R/pairwise-comparisons.R <#115 (comment)> : > @@ -53,8 +52,8 @@ #' #' eval <- scoringutils::eval_forecasts(scoringutils::range_example_data_long) #' pairwise <- pairwise_comparison(eval, summarise_by = c("model")) -#' @author Nikos Bosse ***@***.***} -#' @author Johannes Bracher, ***@***.***} +#' @author Nikos Bosse \email{nikosbosse@@gmail.com} +#' @author Johannes Bracher, \email{johannes.bracher@@kit.edu} Yep :), https://roxygen2.r-lib.org/articles/rd-formatting.html#links-1 (can't find the official source right now). As far as I know, it works well with a single @ in most cases. But this is the 'correct' syntax if we want to follow the rules. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#115 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AJBYFLJMDKMSI4JHPVRKSKTT3EE4BANCNFSM5A35QOMA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&utm_campaign=notification-email> .

[Bisaloo]

The solution for failing tests would be to either:

• removing the link to surveillance::permutationTest()
• add the permutation package to Suggests

Both solutions seem as good from a technical point of view. I'd say it depends if you want to advertise the surveillance package or not. So I leave the choice to you.