Calculate WHO growth standards using the anthro() package.
Source:R/derive_anthro_scores.R
derive_anthro_scores.RdCalculates the Height for Age (HAZ), Weight for Age (WAZ) and Weight for Height (WHZ) z-scores which are used to measure growth against the WHO population standards. This is only for children less than 5 years old.
Arguments
- data
data frame that contains the AGE_YEARS, WEIGHT & HEIGHT variables, typically held in the Demographics (DM) and Vital Signs (VS) domains. Domains should have prepare_domain applied beforehand.
- age_in_years
Boolean. Is the AGE column in years. Default is FALSE, and function will call
convert_age_to_yearsif FALSE, otherwise will not convert age.
Value
data frame with only only 5 year olds included and additional columns for WAZ, HAZ and WHZ scores, along with flags for each.
Details
The function can be applied to a dataset with subjects greater than 5 years old too, but those subjects will be filtered out.
Examples
# Merge the DM (AGE_YEARS, SEX) and VS (WEIGHT, HEIGHT) domains together
data = merge(
prepare_domain(DM_RPTESTB, "dm"),
prepare_domain(VS_RPTESTB, "vs")
)
#> [1] "The timing variable(s) hierarchy being used in prepare_domain() for the VS domain are: VSDY, VISITDY, EPOCH"
#> [1] "Number of rows where values_fn has been used to pick record in the VS domain: 0"
derive_anthro_scores(data)
#> Joining with `by = join_by(STUDYID, USUBJID, DOMAIN, SUBJID, RFSTDTC, DTHDTC,
#> DTHFL, SITEID, INVID, INVNAM, BRTHDTC, AGE_YEARS, AGETXT, SEX, RACE, ETHNIC,
#> ARMCD, ARM, COUNTRY, DMDTC, DMDY, TIME, TIME_SOURCE, `BMI_kg/m2`, HEIGHT_cm,
#> TEMP_C, WEIGHT_kg)`
#> STUDYID USUBJID DOMAIN SUBJID RFSTDTC DTHDTC DTHFL SITEID INVID INVNAM
#> 1 RPTESTB RPTESTB_001 DM 1 2023/01 2023/08 Y OXFORD NA NA
#> 2 RPTESTB RPTESTB_001 DM 1 2023/01 2023/08 Y OXFORD NA NA
#> 3 RPTESTB RPTESTB_001 DM 1 2023/01 2023/08 Y OXFORD NA NA
#> 4 RPTESTB RPTESTB_002 DM 2 2023/01 <NA> <NA> OXFORD NA NA
#> 5 RPTESTB RPTESTB_002 DM 2 2023/01 <NA> <NA> OXFORD NA NA
#> 6 RPTESTB RPTESTB_002 DM 2 2023/01 <NA> <NA> OXFORD NA NA
#> 7 RPTESTB RPTESTB_003 DM 3 2023/02 <NA> <NA> OXFORD NA NA
#> 8 RPTESTB RPTESTB_003 DM 3 2023/02 <NA> <NA> OXFORD NA NA
#> 9 RPTESTB RPTESTB_003 DM 3 2023/02 <NA> <NA> OXFORD NA NA
#> BRTHDTC AGE_YEARS AGETXT SEX RACE ETHNIC ARMCD ARM COUNTRY DMDTC
#> 1 NA 67 NA F White British PBO PLACEBO UK 2023/01
#> 2 NA 67 NA F White British PBO PLACEBO UK 2023/01
#> 3 NA 67 NA F White British PBO PLACEBO UK 2023/01
#> 4 NA 18 NA F White Irish TRT TREATMENT UK 2023/01
#> 5 NA 18 NA F White Irish TRT TREATMENT UK 2023/01
#> 6 NA 18 NA F White Irish TRT TREATMENT UK 2023/01
#> 7 NA 4 NA M White British TRT TREATMENT UK 2023/02
#> 8 NA 4 NA M White British TRT TREATMENT UK 2023/02
#> 9 NA 4 NA M White British TRT TREATMENT UK 2023/02
#> DMDY TIME TIME_SOURCE BMI_kg/m2 HEIGHT_cm TEMP_C WEIGHT_kg HAZ
#> 1 1 1 DY 21.5 167 36.2 60 NA
#> 2 1 3 DY <NA> <NA> 37.4 <NA> NA
#> 3 1 42 DY <NA> <NA> 37.5 <NA> NA
#> 4 1 1 DY 20.5 143 37.5 42 NA
#> 5 1 4 DY <NA> <NA> 37.2 <NA> NA
#> 6 1 40 DY <NA> <NA> 37.9 <NA> NA
#> 7 1 2 DY 0.01 84 37.2 9.6 -4.61
#> 8 1 5 DY <NA> <NA> 37.1 <NA> NA
#> 9 1 FOLLOW UP EPOCH <NA> <NA> 37.7 <NA> NA
#> HAZ_FLAG WAZ WAZ_FLAG WHZ WHZ_FLAG
#> 1 NA NA NA NA NA
#> 2 NA NA NA NA NA
#> 3 NA NA NA NA NA
#> 4 NA NA NA NA NA
#> 5 NA NA NA NA NA
#> 6 NA NA NA NA NA
#> 7 0 -4.11 0 -2.2 0
#> 8 NA NA NA NA NA
#> 9 NA NA NA NA NA