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Closes #34 function for growth parameters for height/length #45

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Jun 17, 2024
Merged

Closes #34 function for growth parameters for height/length #45

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rough draft up
zdz2101 May 30, 2024
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Merge branch 'main' into 34_new_func_lengthheight
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Merge branch 'main' into 34_new_func_lengthheight
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28 changes: 14 additions & 14 deletions R/derive_params_growth_height.R
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Original file line number Diff line number Diff line change
@@ -1,7 +1,8 @@
#' Derive Anthropometric indicators (Z-Scores/Percentiles-for-Height) based on Standard Growth Charts
#' Derive Anthropometric indicators (Z-Scores/Percentiles-for-Height/Length)
#' based on Standard Growth Charts
#'
#' Derive Anthropometric indicators (Z-Scores/Percentiles-for-Height) based on Standard Growth Charts
#' for Weight by Height/Length
#' Derive Anthropometric indicators (Z-Scores/Percentiles-for-Height/Lenght)
#' based on Standard Growth Charts for Weight by Height/Length
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#'
#' @param dataset Input dataset
#'
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Missing parameters from the issue:
age,
age_unit,
height_age,
These are all needed as we need to know at which age to assume height instead of body length but they're optional as: If only ever length or height is used then leave this NULL and just feed in only the corresponding by length or height metadata (instead of the combined version which has both)

I agree measure argument in the issue not needed - as we can add the height temp var to the input dataset

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This is so that you use the right metadata from WHO depending on patient age and which way they were likely measuring (height or body length). it'd be good in the examples to use height_age = 730.5 days i.e. 2 years (even as default from what David explained to us?). See https://github.com/pharmaverse/admiralpeds/blob/35_advs_vignette/vignettes/advs.Rmd from line 229 for further explanation.

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@rossfarrugia I think that's why in the example I actually split the dataset into over 2 and under 2 and just ran the function twice, otherwise you would need to create some sort of additional joining variable on both sides, dataset and metadata, which involves additional pre-processing to both datasets, while adding complexity to the function too, the "modularity" of running it twice felt more intuitive to me

I'm open to this adoption with additional arguments, but I wonder what other programmers would think

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@rossfarrugia rossfarrugia Jun 6, 2024 •
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@zdz2101 i'm open to your approach - it does give the user complete control still. we'll just need to well comment this to explain our approach in your roxygen2 function documentation example (e.g. at the end you should add a comment to explain that the 2 resulting dataframes would need to be set back together to get the complete ADVS for this parameter) and also we'll need to explain well in our template comments and our vignette.

@Fanny-Gautier @Lina2689 what do you think? as the template authors i would trust your advice here as you'll have a good read on what makes this least complex for users.

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In the template we selected the records from the metadata where MEASURE ="LENGTH" for patients <730.5 days, and MEASURE="HEIGHT" for patients >=730.5 days. As Zelos mentioned, it will require additional variables to merge the right data depending on the age.
We also added message in the ADVS peds template for the same message("To derive height/length parameters, below function needs to call separately for Height and Length based on the input data and current age of the patient, as it depends on your CRF guidelines.").
I think it is easier to split it because if the user has only HEIGHT then there is only one call, similarly for LENGTH. But if the user has both LENGTH and HEIGHT in the data, it will complexify the merge. I think the user has more flexibility while splitting the derivation.

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makes sense Fanny, sounds like we have a plan then! and thanks for the other comments here too - looks like me and you picked up similar spots.

Expand All @@ -18,7 +19,7 @@
#'
#' A numeric vector is expected. Note that this is the actual height at the current visit.
#'
#' @param height_unit Lenght/Height Unit
#' @param height_unit Height/Length Unit
#
#' A character vector is expected.
#'
Expand All @@ -29,11 +30,11 @@
#' A metadata dataset with the following expected variables:
#' `HEIGHT_LENGTH`, `HEIGHT_LENGTHU`, `SEX`, `L`, `M`, `S`
#'
#' The dataset can be derived from CDC/WHO or user-defined datasets.
#' The CDC/WHO growth chart metadata datasets are available in the package and will
#' The dataset can be derived from WHO or user-defined datasets.
#' The WHO growth chart metadata datasets are available in the package and will
#' require small modifications.
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@Minlei0201 Minlei0201 Jun 11, 2024 •
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Shall we list out the names of the metadata and clarify that "who_wt_for_lgth_boys" and "who_wt_for_lgth_girls" are for subjects with age <730.5 days, and "who_wt_for_ht_boys" and "who_wt_for_ht_girls" are for those with age>=730.5 days? By doing this, the user knows the metadata he/she can use, and also knows to apply different metadata based on subjects' age.

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This is a good idea, but I think we'll need to draw up a bigger vignette/article for metadata creation/preprocessing anyway

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hopefully the template and vignette can cover this more so user gets the full context

#' * `HEIGHT_LENGTH` - Height/Length
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The original WHO metadata table has height/length increment of 0.5, but the metadata in the admiralpeds packages has increment of 0.1. How was it extrapolated? Do we have any documentation on that?

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https://www.who.int/tools/child-growth-standards/standards/weight-for-length-height

scroll to the bottom on the expanded tables section you will find the increments were by 0.1

#' * `HEIGHT_LENGTHU` - Height Unit
#' * `HEIGHT_LENGTHU` - Height/Length Unit
#' * `SEX` - Sex
#' * `L` - Power in the Box-Cox transformation to normality
#' * `M` - Median
Expand Down Expand Up @@ -67,7 +68,7 @@
#'
#' The specified variables are set to the specified values for the new
#' observations. For example,
#' `set_values_to_pctl(exprs(PARAMCD = “WTAPCTL”, PARAM = “Weight-for-height percentile”))`
#' `set_values_to_pctl(exprs(PARAMCD = “WTHPCTL”, PARAM = “Weight-for-height percentile”))`
#' defines the parameter code and parameter.
#'
#' *Permitted Values*: List of variable-value pair
Expand Down Expand Up @@ -101,8 +102,7 @@
#' new_var_unit = AAGECURU,
#' start_date = BRTHDT,
#' end_date = VSDT,
#' out_unit = "months",
#' trunc_out = FALSE
#' out_unit = "months"
#' )
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In the ad_advs.R template (PR #32 ), the unit of age is days (with 730.5 days as cutoff). Shall we be consistent in the example here?

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Yes I will fix this

#'
#' heights <- vs_peds %>%
Expand Down Expand Up @@ -170,11 +170,11 @@
#' parameter = VSTESTCD == "WEIGHT",
#' analysis_var = VSSTRESN,
#' set_values_to_sds = exprs(
#' PARAMCD = "WTASDS",
#' PARAMCD = "WTHSDS",
#' PARAM = "Weight-for-height z-score"
#' ),
#' set_values_to_pctl = exprs(
#' PARAMCD = "WTAPCTL",
#' PARAMCD = "WTHPCTL",
#' PARAM = "Weight-for-height percentile"
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@zdz2101 please modify the PARAMCD to WGTHSDS/WGTHPCTL to be consistent with the ADVS template. Same changes are required for derive_params_by_age() function as well.
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#' )
#' )
Expand All @@ -188,11 +188,11 @@
#' parameter = VSTESTCD == "WEIGHT",
#' analysis_var = VSSTRESN,
#' set_values_to_sds = exprs(
#' PARAMCD = "WTASDS",
#' PARAMCD = "WTHSDS",
#' PARAM = "Weight-for-height z-score"
#' ),
#' set_values_to_pctl = exprs(
#' PARAMCD = "WTAPCTL",
#' PARAMCD = "WTHPCTL",
#' PARAM = "Weight-for-height percentile"
#' )
#' )
Expand Down
28 changes: 14 additions & 14 deletions man/derive_params_growth_height.Rd
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