Add indentation when `knit_print()` stopping rule list

[fenguoerbian]

Summary

knit_print() is a convenient way of rendering reader-friendly output of crmPack objects in Rmd report. But I see some improvement in the way of knit_print.StoppingList().

Currently there is no indentation added to the rendered stopping rule list. So if there are nested stopping rule list, they will all be at the same level, such as what is shown in the vignette, or an example as follows:

tmp_stop <- crmPack::.DefaultDesign()@stopping
#> Registered S3 method overwritten by 'crmPack':
#>   method       from  
#>   print.gtable gtable

crmPack:::knit_print.StoppingAny(tmp_stop) |>
    cat()
#> If any of the following rules are `TRUE`:
#> 
#> -  If all of the following rules are `TRUE`:
#> 
#> -  ≥ 3 cohorts dosed: If 3 or more cohorts have been treated.
#> 
#> 
#> -  P(0.2 ≤ prob(DLE | NBD) ≤ 0.35) ≥ 0.5: If the probability of toxicity at the next best dose is in the range [0.20, 0.35] is at least 0.50.
#> 
#> 
#> 
#> 
#> -  ≥ 20 patients dosed: If 20 or more participants have been treated.

^{Created on 2024-06-25 with reprex v2.1.0}

The rendered output of these rules are all at the same level.

If any of the following rules are TRUE:

• If all of the following rules are TRUE:

• ≥ 3 cohorts dosed: If 3 or more cohorts have been treated.

• P(0.2 ≤ prob(DLE | NBD) ≤ 0.35) ≥ 0.5: If the probability of toxicity at the next best dose is in the range [0.20, 0.35] is at least 0.50.

• ≥ 20 patients dosed: If 20 or more participants have been treated.

What's the problem this feature will solve?

I think some indentation at the beginning of these lists are necessary so the rendered output one can easily see which rules belongs to which list, such as

If any of the following rules are TRUE:

• If ALL of the following rules are TRUE:

  • ≥ 3 cohorts dosed: If 3 or more cohorts have been treated.

  • P(0.2 ≤ prob(DLE | NBD) ≤ 0.35) ≥ 0.5: If the probability of toxicity at the next best dose is in the range [0.20, 0.35] is at least 0.50.

• ≥ 20 patients dosed: If 20 or more participants have been treated.

Currently I'm using a customized knit_print() that pads additional spaces to the begining of the output accordingly to achieve this. But I believe this feature would improve the readability and is worth considering to add into the package. If you like the idea I can submit a PR.

This issue can be related to #803 and #774

[Puzzled-Face]

Thank you for making this suggestion. I agree it's necessary - it's been on my "to do" list for a while. I will review asap.

[Puzzled-Face]

A couple of "nice-to-haves":

• Please ensure consistency of case between "any" (for (StoppingListAny) and "ALL" (for StoppingListAll). I don't mind which.
• Instead of "ALL", regardless of number, could we have "both" if N = 2 and "all" if N >2? Similarly "either" and "any".
• A StoppingList with only one rule in the list is unnecessary, but possible. To allow for that, make the options "this"/"both"/"all" and "this"/"either"/"any".

[fenguoerbian]

Thank you for this quick reply.

• The inconsistency between cases of "any" and "ALL" is due to my typo. I think it's good to keep using small cases which is currently used in the package's code.

• The "this"/"both"/"all" and "this"/"either"/"any" are really nice-to-haves and I like this for better output. Currently knit_print.StoppingAny() and knit_print.StoppingAll() just calls knit_print().StoppingList() and passes the preamble parameter. So for this option, we could leave the preamble parameter in the function definition without any defaults and generate the default preamble string in the function call (maybe another helper function #789 here). When preamble is supplied, we can just use the user supplied version.