R/derive_params_growth_height.R
derive_params_growth_height.RdDerive Anthropometric indicators (Z-Scores/Percentiles-for-Height/Length) based on Standard Growth Charts for Weight by Height/Length
derive_params_growth_height(
dataset,
sex,
height,
height_unit,
meta_criteria,
parameter,
analysis_var,
who_correction = FALSE,
set_values_to_sds = NULL,
set_values_to_pctl = NULL
)Input dataset
The variables specified in sex, height, height_unit, parameter, analysis_var
are expected to be in the dataset.
Sex
A character vector is expected.
Expected Values: M, F
Current Height/length
A numeric vector is expected. Note that this is the actual height/length at the current visit.
Height/Length Unit A character vector is expected.
Expected values: cm
Metadata dataset
A metadata dataset with the following expected variables:
HEIGHT_LENGTH, HEIGHT_LENGTHU, SEX, L, M, S
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.
Datasets who_wt_for_lgth_boys/who_wt_for_lgth_girls are applicable for
subject age < 730.5 days.
If the height value from dataset falls between two HEIGHT_LENGTH values in
meta_criteria, then the L/M/S values that are chosen/mapped will be the
HEIGHT_LENGTH that has the smaller absolute difference to the value in height.
e.g. If dataset has a current age of 50.49 cm, and the metadata contains records
for 50 and 51 cm, the L/M/S corresponding to the 50 cm record will be used.
HEIGHT_LENGTH - Height/Length
HEIGHT_LENGTHU - Height/Length Unit
SEX - Sex
L - Power in the Box-Cox transformation to normality
M - Median
S - Coefficient of variation
Anthropometric measurement parameter to calculate z-score or percentile
A condition is expected with the input dataset VSTESTCD/PARAMCD
for which we want growth derivations:
e.g. parameter = VSTESTCD == "WEIGHT".
There is WHO metadata available for Weight available in the admiralpeds package.
Weight measures are expected to be in the unit "kg".
Variable containing anthropometric measurement
A numeric vector is expected, e.g. AVAL, VSSTRESN
WHO adjustment for weight-based indicators
A logical scalar, e.g. TRUE/FALSE is expected.
WHO constructed a restricted application of the LMS method for weight-based indicators.
More details on these exact rules applied can be found at the document page 302 of the
WHO Child Growth Standards Guidelines.
If set to TRUE the WHO correction is applied.
Variables to be set for Z-Scores
The specified variables are set to the specified values for the new
observations. For example,
set_values_to_sds(exprs(PARAMCD = "WGTHSDS", PARAM = "Weight-for-height z-score"))
defines the parameter code and parameter.
The formula to calculate the Z-score is as follows:
$$\frac{((\frac{obs}{M})^L - 1)}{L * S}$$
where "obs" is the observed value for the respective anthropometric measure being calculated.
Permitted Values: List of variable-value pairs
If left as default value, NULL, then parameter not derived in output dataset
Variables to be set for Percentile
The specified variables are set to the specified values for the new
observations. For example,
set_values_to_pctl(exprs(PARAMCD = "WGTHPCTL", PARAM = "Weight-for-height percentile"))
defines the parameter code and parameter.
Permitted Values: List of variable-value pair
If left as default value, NULL, then parameter not derived in output dataset
The input dataset additional records with the new parameter added.
Vital Signs Functions for adding Parameters/Records
derive_params_growth_age()
library(dplyr, warn.conflicts = FALSE)
library(lubridate, warn.conflicts = FALSE)
library(rlang, warn.conflicts = FALSE)
library(admiral, warn.conflicts = FALSE)
library(pharmaversesdtm, warn.conflicts = FALSE)
# derive weight for height/length only for those under 2 years old using WHO
# weight for length reference file
advs <- pharmaversesdtm::dm_peds %>%
select(USUBJID, BRTHDTC, SEX) %>%
right_join(., pharmaversesdtm::vs_peds, by = "USUBJID") %>%
mutate(
VSDT = ymd(VSDTC),
BRTHDT = ymd(BRTHDTC)
) %>%
derive_vars_duration(
new_var = AAGECUR,
new_var_unit = AAGECURU,
start_date = BRTHDT,
end_date = VSDT,
out_unit = "days"
)
heights <- pharmaversesdtm::vs_peds %>%
filter(VSTESTCD == "HEIGHT") %>%
select(USUBJID, VSSTRESN, VSSTRESU, VSDTC) %>%
rename(
HGTTMP = VSSTRESN,
HGTTMPU = VSSTRESU
)
advs <- advs %>%
right_join(., heights, by = c("USUBJID", "VSDTC"))
advs_under2 <- advs %>%
filter(AAGECUR < 730.5)
who_under2 <- bind_rows(
(admiralpeds::who_wt_for_lgth_boys %>%
mutate(
SEX = "M",
height_unit = "cm"
)
),
(admiralpeds::who_wt_for_lgth_girls %>%
mutate(
SEX = "F",
height_unit = "cm"
)
)
) %>%
rename(
HEIGHT_LENGTH = Length,
HEIGHT_LENGTHU = height_unit
)
derive_params_growth_height(
advs_under2,
sex = SEX,
height = HGTTMP,
height_unit = HGTTMPU,
meta_criteria = who_under2,
parameter = VSTESTCD == "WEIGHT",
analysis_var = VSSTRESN,
who_correction = TRUE,
set_values_to_sds = exprs(
PARAMCD = "WGTHSDS",
PARAM = "Weight-for-height/length z-score"
),
set_values_to_pctl = exprs(
PARAMCD = "WGTHPCTL",
PARAM = "Weight-for-height/length percentile"
)
)
#> # A tibble: 162 × 37
#> USUBJID BRTHDTC SEX STUDYID DOMAIN VSSEQ VSTESTCD VSTEST VSPOS VSORRES
#> <chr> <chr> <chr> <chr> <chr> <int> <chr> <chr> <chr> <chr>
#> 1 01-701-1015 2013-01… F CDISCP… VS 1 BMI BMI NA 16.577…
#> 2 01-701-1015 2013-01… F CDISCP… VS 5 BMI BMI NA 16.615…
#> 3 01-701-1015 2013-01… F CDISCP… VS 9 BMI BMI NA 16.697…
#> 4 01-701-1015 2013-01… F CDISCP… VS 13 BMI BMI NA 16.816…
#> 5 01-701-1015 2013-01… F CDISCP… VS 17 BMI BMI NA 16.824…
#> 6 01-701-1015 2013-01… F CDISCP… VS 21 BMI BMI NA 16.915…
#> 7 01-701-1015 2013-01… F CDISCP… VS 25 BMI BMI NA 17.051…
#> 8 01-701-1015 2013-01… F CDISCP… VS 29 BMI BMI NA 17.162…
#> 9 01-701-1015 2013-01… F CDISCP… VS 33 BMI BMI NA 17.248…
#> 10 01-701-1015 2013-01… F CDISCP… VS 37 BMI BMI NA 17.433…
#> # ℹ 152 more rows
#> # ℹ 27 more variables: VSORRESU <chr>, VSSTRESC <chr>, VSSTRESN <dbl>,
#> # VSSTRESU <chr>, VSSTAT <chr>, VSLOC <chr>, VSBLFL <chr>, VISITNUM <dbl>,
#> # VISIT <chr>, VISITDY <int>, VSDTC <chr>, VSDY <int>, VSTPT <chr>,
#> # VSTPTNUM <dbl>, VSELTM <chr>, VSTPTREF <chr>, VSEVAL <chr>, EPOCH <chr>,
#> # VSDT <date>, BRTHDT <date>, AAGECUR <dbl>, AAGECURU <chr>, HGTTMP <dbl>,
#> # HGTTMPU <chr>, AVAL <dbl>, PARAMCD <chr>, PARAM <chr>