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Closes #2510 enhance derive param computed #2544

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@bundfussr bundfussr commented Oct 29, 2024 •
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@bundfussr bundfussr linked an issue Oct 29, 2024 that may be closed by this pull request
Bug: derive_param_computed() does nothing #2510
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github-actions bot commented Oct 29, 2024 •
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Code Coverage

Package Line Rate Health
admiral 97% ✔
Summary 97% (4965 / 5127) ✔

bms63
bms63 reviewed Oct 29, 2024
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R/derive_param_computed.R
@@ -117,13 +117,18 @@
#' @param keep_nas Keep observations with `NA`s
#'
#' If the argument is set to `TRUE`, observations are added even if some of
#' the values contributing to the computed value are `NA`.
#' the values contributing to the computed value are `NA` (see Example 1b).
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Be so cool if we could hyperlink to this example

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Yes, linking to examples would be really cool.

Unfortunately, I'm not aware of an easy way to do this. We discussed creating a roclet for such improvements in #1590 but it was never implemented and I don't think we have resources for this.

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One day we shall be great again!!

bms63
bms63 reviewed Oct 29, 2024
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R/derive_param_computed.R
#' the values contributing to the computed value are `NA`.
#' the values contributing to the computed value are `NA` (see Example 1b).
#'
#' If the argument is set to a list of variables, observations are added even
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So keep_nas can be TRUE, FALSE or a list of variables? I like not adding another argument but do we do this in other functions - is this common in other packages?

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We have something similar for the parameters argument in derive_param_computed(). I'm not sure if we do this in other functions.

I don't know how common this is in other packages but there are definitely examples in other packages. Consider for example dplyr::select(). It accepts both symbols and strings.

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Cool Cool! That is good example.

All good for me then.

bms63
bms63 reviewed Oct 29, 2024
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_pkgdown.yml
@@ -1,6 +1,7 @@
url: https://pharmaverse.github.io/admiral

template:
math-rendering: mathjax
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is this intentional? Just checking!?! :)

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Yes, I rendered the documentation with pkgdown 2.1.1 and noticed that formulas are no longer rendered correctly. Adding this line fixes the issues.

bms63
bms63 reviewed Oct 29, 2024
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tests/testthat/test-derive_param_computed.R
ADT = ADT.SYSBP,
ADTF = ADTF.SYSBP
),
keep_nas = exprs(ADTF)
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what happens if I do exprs(TRUE) ?

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+     keep_nas = exprs(TRUE)
+ )
Error in `derive_param_computed()`:
! Each element of the list in argument `keep_nas` must be class/type <symbol>.
ℹ But, element 1 is `TRUE`

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Okay - was just a sanity check for me.

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bms63 commented Oct 29, 2024

@yurovska does this meet your needs for this function?

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yurovska commented Oct 29, 2024 •
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@yurovska does this meet your needs for this function?

@bms63 @bundfussr Yes, sort of... It indeed gives a possibility to do what I wanted to do as described in the issue. However, users might still be falling into a trap if keep_nas is omitted in the call (which is exactly what you'd do in the first place) and the function will simply return the input dataset with no new parameters added if one of the variables used in set_values_to is populated with NA.

advs <- tribble(
  ~USUBJID,      ~PARAMCD, ~PARAM,        ~AVAL, ~AVALU, ~VISIT,      ~TESTVAR,
  "01-701-1015", "HEIGHT", "Height (cm)", 147.0, "cm",   "SCREENING", NA_character_,
  "01-701-1015", "WEIGHT", "Weight (kg)",  54.0, "kg",   "SCREENING", NA_character_,
  "01-701-1015", "WEIGHT", "Weight (kg)",  54.4, "kg",   "BASELINE",  NA_character_,
  "01-701-1015", "WEIGHT", "Weight (kg)",  53.1, "kg",   "WEEK 2",    NA_character_,
  "01-701-1028", "HEIGHT", "Height (cm)", 163.0, "cm",   "SCREENING", NA_character_,
  "01-701-1028", "WEIGHT", "Weight (kg)",  78.5, "kg",   "SCREENING", NA_character_,
  "01-701-1028", "WEIGHT", "Weight (kg)",  80.3, "kg",   "BASELINE",  NA_character_,
  "01-701-1028", "WEIGHT", "Weight (kg)",  80.7, "kg",   "WEEK 2",    NA_character_
)

derive_param_computed(
  dataset = advs,
  by_vars = exprs(USUBJID, VISIT),
  parameters = "WEIGHT",
  set_values_to = exprs(
    AVAL = AVAL.WEIGHT / (AVAL.HEIGHT / 100)^2,
    AVALU = "kg/m^2",
    PARAMCD = "BMI",
    PARAM = "Body Mass Index (kg/m^2)",
    TESTVAR = TESTVAR.WEIGHT
  ),
  constant_parameters = c("HEIGHT"),
  constant_by_vars = exprs(USUBJID)
)
# A tibble: 8 × 7
  USUBJID     PARAMCD PARAM        AVAL AVALU VISIT     TESTVAR
  <chr>       <chr>   <chr>       <dbl> <chr> <chr>     <chr>  
1 01-701-1015 HEIGHT  Height (cm) 147   cm    SCREENING NA     
2 01-701-1015 WEIGHT  Weight (kg)  54   kg    SCREENING NA     
3 01-701-1015 WEIGHT  Weight (kg)  54.4 kg    BASELINE  NA     
4 01-701-1015 WEIGHT  Weight (kg)  53.1 kg    WEEK 2    NA     
5 01-701-1028 HEIGHT  Height (cm) 163   cm    SCREENING NA     
6 01-701-1028 WEIGHT  Weight (kg)  78.5 kg    SCREENING NA     
7 01-701-1028 WEIGHT  Weight (kg)  80.3 kg    BASELINE  NA     
8 01-701-1028 WEIGHT  Weight (kg)  80.7 kg    WEEK 2    NA

Shall derive_param_computed at least check if it derived anything before returning the result and, if not, throw a sort of cli_alert_info of something like that?

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Shall derive_param_computed at least check if it derived anything before returning the result and, if not, throw a sort of cli_alert_info of something like that?

Yes, good idea.
I've added a cli_inform() if no records were added due to NAs in contributing values.

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Shall derive_param_computed at least check if it derived anything before returning the result and, if not, throw a sort of cli_alert_info of something like that?

Yes, good idea. I've added a cli_inform() if no records were added due to NAs in contributing values.

Awesome. It is much more clear for the user now. Thanks a lot!

No more comments from my side. Good job @bundfussr!

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Bug: derive_param_computed() does nothing
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@bundfussr @bms63 @yurovska