R/set_refcodes.R
set_refcodes.RdDetermines the reference name for each measurement based on age, sex, outcome and gestational age.
set_refcodes(data)Data frame in the long form, where each measurement has its
own row. Required variables are xname, yname, x and sex.
Optional variables are age and ga.
A character vector of nrow(data) elements.
The present implementation uses three Dutch references: a term reference,
a pre-term reference for children born ga <= 36 aged 0 - 4 years, and
a reference for the D-score. For head circumference, pre-term references up to
1.5 years are used, and term references thereafter. Together, this
specification defines the analysis metric in JAMES.
The pre-term references govern gestational ages between 25 and 36 weeks. The function scores pre-term born infants with gestational ages between 21 and 24 weeks relative to the 25-week references.
If the variable ga is not present in data, the function assumes
term births for all children and prints a message.
References for the Development Score (D-score) for pre-term were created by shifting the term reference by 40 - ga weeks to the right, so the references start at a later calender age. Because pre-terms are older their Z-score initially score higher than those of terms. The effect disappears after four months.
The yname field currently supports the following measurements:
hgt (length/height in cm), wgt (body weight in kg),
hdc (head circumference in cm), bmi (body mass index in kg/m**2),
wfh (weight for height in kg) and dsc (D-score).
The xname field currently supports the following measurements:
age (child age, decimal years) and hgt (height in cm, only for wfh).
df <- data.frame(
xname = c("age", "age", "age", "age", "hgt", "age", "age"),
yname = c("hgt", "hgt", "hdc", "hdc", "wfh", "dsc", "wgt"),
x = c(0.1, NA, 0.1, 1.6, 60, 1.0, 1.0),
sex = c(rep(c("male", "female"), 3), "male"),
ga = c(39, 27, 27, 27, 39, 40, 40))
refcodes <- set_refcodes(df)
# show the preterm 27 weeks hgt reference
centile::load_reference(refcodes[2], pkg = "nlreferences")
#> # A tibble: 69 × 4
#> x L M S
#> <dbl> <dbl> <dbl> <dbl>
#> 1 0 1 50.9 0.0376
#> 2 0.0192 1 51.6 0.0375
#> 3 0.0383 1 52.3 0.0375
#> 4 0.0575 1 52.9 0.0374
#> 5 0.0767 1 53.6 0.0373
#> 6 0.0958 1 54.3 0.037
#> 7 0.115 1 55.0 0.0369
#> 8 0.134 1 55.7 0.0368
#> 9 0.153 1 56.4 0.0368
#> 10 0.172 1 57.0 0.0367
#> # ℹ 59 more rows