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Closes #2020 chore: rename wt to weight in compute_egfr #2045

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merged 11 commits into from
Aug 10, 2023
Merged

Closes #2020 chore: rename wt to weight in compute_egfr #2045

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4275530
code updated
StefanThoma Aug 3, 2023
ad8394b
Merge branch 'devel' into 2020_wt_to_weight_compute_egfr@devel
StefanThoma Aug 3, 2023
4bf63fd
Chore #2020 go through checklist
StefanThoma Aug 3, 2023
abcaecf
update .lycheeignore
StefanThoma Aug 3, 2023
9c3e9f7
update .lycheeignore
StefanThoma Aug 3, 2023
540883e
Merge branch '2020_wt_to_weight_compute_egfr@devel' of https://github…
StefanThoma Aug 3, 2023
73c1444
adjusted templates
StefanThoma Aug 4, 2023
12f4081
Merge branch 'devel' into 2020_wt_to_weight_compute_egfr@devel
StefanThoma Aug 7, 2023
ce8aa1f
Merge branch 'devel' into 2020_wt_to_weight_compute_egfr@devel
StefanThoma Aug 9, 2023
dd93e3f
chore: removed links from .lycheeignore
StefanThoma Aug 9, 2023
0ed1371
chore: #2020 removing file
bms63 Aug 10, 2023
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1 change: 0 additions & 1 deletion .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,6 @@ vignettes/*.pdf

# website documents
/docs/*
!/docs/pkgdown.yml
doc
Meta
admiral.Rcheck/
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2 changes: 2 additions & 0 deletions NEWS.md
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Expand Up @@ -35,6 +35,8 @@
- The arguments `dataset_adsl` in the function `derive_param_exist_flag()` and
`subject_keys` have been deprecated versions using the next phase of the deprecation process. (#1950)

- The argument `wt` in the function `compute_egfr()` was deprecated in favor of `weight` using the first phase of the deprecation process. (#2020)

- The `filter` argument in `derive_extreme_records()` was deprecated in favor of
the `filter_add` using the next phase of the deprecation process. (#1950)

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32 changes: 21 additions & 11 deletions R/compute_kidney.R
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Expand Up @@ -20,7 +20,7 @@
#'
#' A numeric vector is expected.
#'
#' @param wt Weight (kg)
#' @param weight Weight (kg)
#'
#' A numeric vector is expected if `method = "CRCL"`
#'
Expand All @@ -42,6 +42,8 @@
#'
#' Expected Values: `"CRCL"`, `"CKD-EPI"`, `"MDRD"`
#'
#' @param wt *Deprecated*, please use `weight` instead.
#'
#' @details
#'
#' Calculates an estimate of Glomerular Filtration Rate (eGFR)
Expand Down Expand Up @@ -92,7 +94,7 @@
#'
#' @examples
#' compute_egfr(
#' creat = 90, creatu = "umol/L", age = 53, wt = 85, sex = "M", method = "CRCL"
#' creat = 90, creatu = "umol/L", age = 53, weight = 85, sex = "M", method = "CRCL"
#' )
#'
#' compute_egfr(
Expand Down Expand Up @@ -120,19 +122,27 @@
#' base %>%
#' dplyr::mutate(
#' CRCL_CG = compute_egfr(
#' creat = CREATBL, creatu = CREATBLU, age = AGE, wt = WTBL, sex = SEX,
#' creat = CREATBL, creatu = CREATBLU, age = AGE, weight = WTBL, sex = SEX,
#' method = "CRCL"
#' ),
#' EGFR_EPI = compute_egfr(
#' creat = CREATBL, creatu = CREATBLU, age = AGE, wt = WTBL, sex = SEX,
#' creat = CREATBL, creatu = CREATBLU, age = AGE, weight = WTBL, sex = SEX,
#' method = "CKD-EPI"
#' ),
#' EGFR_MDRD = compute_egfr(
#' creat = CREATBL, creatu = CREATBLU, age = AGE, wt = WTBL, sex = SEX,
#' creat = CREATBL, creatu = CREATBLU, age = AGE, weight = WTBL, sex = SEX,
#' race = RACE, method = "MDRD"
#' ),
#' )
compute_egfr <- function(creat, creatu = "SI", age, wt, sex, race = NULL, method) {
compute_egfr <- function(creat, creatu = "SI", age, weight, sex, race = NULL, method, wt) {
### BEGIN DEPRECATION
if (!missing(wt)) {
deprecate_warn("0.12.0", "compute_egfr(old_param = 'wt')", "compute_egfr(new_param = 'weight')")
# old_param is given using exprs()
weight <- wt
}
### END DEPRECATION

assert_numeric_vector(creat)
assert_character_vector(creatu, values = c(
"SI", "CV", "mg/dL", "umol/L", NA_character_,
Expand Down Expand Up @@ -164,15 +174,15 @@ compute_egfr <- function(creat, creatu = "SI", age, wt, sex, race = NULL, method
sex == "M" ~ 175 * (scr^-1.154) * (age^-0.203)
)
} else if (method == "CRCL") {
assert_numeric_vector(wt)
assert_numeric_vector(weight)

egfr <- case_when(
tolower(creatu) %in% c("cv", "mg/dl") & sex == "F" ~
((140 - age) * wt * 0.85) / (creat * 72),
((140 - age) * weight * 0.85) / (creat * 72),
tolower(creatu) %in% c("cv", "mg/dl") & sex == "M" ~
((140 - age) * wt) / (creat * 72),
sex == "F" ~ ((140 - age) * wt * 1.04) / creat,
sex == "M" ~ ((140 - age) * wt * 1.23) / creat
((140 - age) * weight) / (creat * 72),
sex == "F" ~ ((140 - age) * weight * 1.04) / creat,
sex == "M" ~ ((140 - age) * weight * 1.23) / creat
)
} else if (method == "CKD-EPI") {
kappa <- case_when(
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4 changes: 2 additions & 2 deletions docs/pkgdown.yml
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@cicdguy can this be added to .gitignore?

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Yeah that's be nice. I personally see no benefit in storing docs/ in version control.

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@StefanThoma can you put this in .gitignore please.

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It looks like this was added in a long time ago - can just remove this line
image

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@StefanThoma , @bms63 , @cicdguy , docs/pkgdown.yml was added to create links across packages, e.g., if an example in admiralonco uses an admiral function it is linked automatically to the documentation of the admiral function. It has stopped working when we introduced multiversions docs. Maybe we do not need it anymore if we find a different solution (see pharmaverse/admiralci#131).

However, if we remove the file from .gitignore we should also remove the file itself.

Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
pandoc: 2.11.4
pandoc: 3.1.1
pkgdown: 2.0.7
pkgdown_sha: ~
articles:
Expand All @@ -19,7 +19,7 @@ articles:
queries_dataset: queries_dataset.html
questionnaires: questionnaires.html
visits_periods: visits_periods.html
last_built: 2023-07-19T10:42Z
last_built: 2023-08-07T09:14Z
urls:
reference: https://pharmaverse.github.io/admiral/cran-release/reference/
article: https://pharmaverse.github.io/admiral/cran-release/articles/
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4 changes: 2 additions & 2 deletions inst/templates/ad_adppk.R
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Expand Up @@ -448,11 +448,11 @@ covar_vslb <- covar %>%
method = "Mosteller"
),
CRCLBL = compute_egfr(
creat = CREATBL, creatu = "SI", age = AGE, wt = WTBL, sex = SEX,
creat = CREATBL, creatu = "SI", age = AGE, weight = WTBL, sex = SEX,
method = "CRCL"
),
EGFRBL = compute_egfr(
creat = CREATBL, creatu = "SI", age = AGE, wt = WTBL, sex = SEX,
creat = CREATBL, creatu = "SI", age = AGE, weight = WTBL, sex = SEX,
method = "CKD-EPI"
)
) %>%
Expand Down
14 changes: 8 additions & 6 deletions man/compute_egfr.Rd
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18 changes: 14 additions & 4 deletions tests/testthat/test-compute_kidney.R
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Expand Up @@ -27,7 +27,7 @@ test_that("compute_egfr Test 3: CRCL calculation", {
# CRCL Cockcroft and Gault (1973) calculator at
# https://www.kidney.org/professionals/kdoqi/gfr_calculatorCoc
expect_equal(round(compute_egfr(
creat = 1.09, creatu = "mg/dL", age = 55, sex = "M", wt = 90, method = "CRCL"
creat = 1.09, creatu = "mg/dL", age = 55, sex = "M", weight = 90, method = "CRCL"
), 0L), 97)
})

Expand All @@ -38,7 +38,7 @@ test_that("compute_egfr Test 4: CRCL calculation", {
# CRCL Cockcroft and Gault (1973) calculator at
# https://www.kidney.org/professionals/kdoqi/gfr_calculatorCoc
expect_equal(round(compute_egfr(
creat = 85, creatu = "umol/L", age = 65, sex = "F", wt = 60, method = "CRCL"
creat = 85, creatu = "umol/L", age = 65, sex = "F", weight = 60, method = "CRCL"
), 0L), 55)
})

Expand All @@ -49,7 +49,7 @@ test_that("compute_egfr Test 5: EGFR MDRD calculation", {
# MDRD GFR calculator at
# https://www.mdcalc.com/calc/76/mdrd-gfr-equation
expect_equal(round(compute_egfr(
creat = 1.09, creatu = "mg/dL", age = 55, sex = "M", wt = 90, race = "WHITE",
creat = 1.09, creatu = "mg/dL", age = 55, sex = "M", weight = 90, race = "WHITE",
method = "MDRD"
), 1L), 70.2)
})
Expand Down Expand Up @@ -87,7 +87,7 @@ test_that("compute_egfr Test 7: CKD-EPI calculated on input data", {
egfr <- input %>%
dplyr::mutate(
EGFR = compute_egfr(
creat = CREATBL, creatu = CREATBLU, age = AGE, wt = WTBL, sex = SEX,
creat = CREATBL, creatu = CREATBLU, age = AGE, weight = WTBL, sex = SEX,
method = "CKD-EPI"
),
EGFR = round(EGFR, 4L)
Expand All @@ -99,3 +99,13 @@ test_that("compute_egfr Test 7: CKD-EPI calculated on input data", {
keys = c("USUBJID")
)
})

## Test 8: Deprecate wt ----
test_that("compute_egfr Test 8: 'wt' argument deprecation warning", {
# expect deprecation warning
expect_warning(
compute_egfr(
creat = 1.09, creatu = "mg/dL", age = 55, sex = "M", wt = 90, method = "CRCL"
)
)
})
4 changes: 2 additions & 2 deletions vignettes/pk_adnca.Rmd
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Expand Up @@ -1377,11 +1377,11 @@ covar_vslb <- covar %>%
),
# Derive CRCLBL and EGFRBL using new function
CRCLBL = compute_egfr(
creat = CREATBL, creatu = "SI", age = AGE, wt = WTBL, sex = SEX,
creat = CREATBL, creatu = "SI", age = AGE, weight = WTBL, sex = SEX,
method = "CRCL"
),
EGFRBL = compute_egfr(
creat = CREATBL, creatu = "SI", age = AGE, wt = WTBL, sex = SEX,
creat = CREATBL, creatu = "SI", age = AGE, weight = WTBL, sex = SEX,
method = "CKD-EPI"
)
) %>%
Expand Down
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