ext_bmiz Calculates the sigma (scale parameter for the half-normal
distribution), extended BMI percentile, extended BMIz, and the CDC LMS
Z-scores for weight, height, and BMI for children between 2 and 19.9 years
of age. Note that for BMIs <= 95th percentile of the CDC growth charts, the
extended values for BMI are equal to the LMS values. The extended values
differ only for children who have a BMI > 95th percentile.
Usage
ext_bmiz(
data,
age = "agem",
wt = "wt",
ht = "ht",
bmi = "bmi",
adjust.integer.age = TRUE,
ref.data.path = ""
)Arguments
- data
Input data frame or data table
- age
Name of input column containing subject age in months in quotes, default "agem"
- wt
Name of input column containing weight (kg) value in quotes, default "wt"
- ht
Name of input column containing height (cm) value in quotes, default "ht"
- bmi
Name of input column containing calculated BMI in quotes, default "bmi"
- adjust.integer.age
If age inputs are all integer, add 0.5 if TRUE; default TRUE
- ref.data.path
Path to directory containing reference data
Value
A data.table: a copy of data (same rows, row order, column
names, and values) with these columns added: bmiz, bmip,
waz, wp, haz, hp, p95, p97,
bmip95, mod_bmiz, mod_waz, mod_haz,
sigma, original_bmip, original_bmiz,
sev_obese, obese.
Details
This function produces output equivalent to CDC software and the cdcanthro R package.
The extended BMIz is the inverse cumulative distribution function (CDF) of
the extended BMI percentile. If the extended percentile is very close to
100, the qnorm function in R produces an infinite value. This occurs
only if the extended BMI percentile is > 99.99999999999999. This occurs
infrequently, such as a 48-month-old with a BMI > 39, and it is likely that
these BMIs represent data entry errors. For these cases, extended BMIz is
set to 8.21, a value that is slightly greater than the largest value that
can be calculated.
The output columns are listed under Value below.
data must have columns for at least age, sex, weight, height, and bmi.
age should be coded in months, using the most precise values available.
To convert to months from age in years, multiply by 12. To convert to months
from age in days, divide by 30.4375 (365.25 / 12).
sex: we recommend M and F, which is what longwide() returns.
Male can be coded as boy, Boy, b, B, male, Male, m, or M, and female can be
coded as girl, Girl, g, G, female, Female, f, or F. Numeric sex is accepted
only if sex has both 1s and 2s and no other values, read as 1 = male,
2 = female; otherwise ext_bmiz() stops. This is because 0/1 is the
numeric coding in cleangrowth(), and a column of only 1s could be either
coding. The 1/2 coding matches the CDC reference data, CDC software, and the
cdcanthro package. Other text values, and logical values, are not recognized:
their z-scores are NA, with a warning.
wt should be in kilograms.
ht should be in centimeters.
Specify the input data column names for age, wt,
ht, bmi using quotation marks. See example below.
ext_bmiz() does not change data. It returns a copy of
data with the new columns added; your column names and values are
kept as they are (the 0.5 added by adjust.integer.age is used only in
the calculation). If data already has a column with the name of one of
the columns ext_bmiz() adds (bmiz, bmip, waz,
wp, haz, hp, p95, p97, bmip95,
mod_bmiz, mod_waz, mod_haz, sigma,
original_bmip, original_bmiz, sev_obese,
obese), for example from an earlier run, it warns and the returned
data has the newly calculated values in that column; rename the column first
to keep both.
Values are calculated for ages 24 through 240 months, as in the cdcanthro
package. Age 730 days is 23.98 months (730 / 30.4375), which is below 24
months, so a row at 730 days has NA values even though a child at that
age may be exactly 2 years old; values begin at 731 days. A warning gives the
number of rows at about 729-730 days.
If the argument adjust.integer.age is TRUE (the default),
0.5 will be added to all age values for the calculation if all input values are integers. Set to
FALSE to disable.
By default, the reference data file CDCref_d.csv, made available at
https://www.cdc.gov/growth-chart-training/hcp/computer-programs/index.html, is included
in this package for convenience. If you are developing this package, use
ref.data.path to adjust the path to this file from your working
directory if necessary.
References
Wei R, Ogden CL, Parsons VL, Freedman DS, Hales CM. A method for calculating BMI z-scores and percentiles above the 95th percentile of the CDC growth charts. Ann Hum Biol. 2020 Sep;47(6):514-521. doi:10.1080/03014460.2020.1808065 .
Examples
# \donttest{
# Run on a small subset of given data
df <- as.data.frame(syngrowth)
df <- df[df$subjid %in% unique(df[, "subjid"])[1:5], ]
# cleangrowth() returns the data with an 'exclude' column
clean_df <- cleangrowth(df)
#> [15:39:57] growthcleanr: cleaning in progress — 5 subjects, 93 measurements, 1 batch of up to 5,000 subjects
#> ************************************************************
#> growthcleanr cleaning summary (93 measurements)
#> Weight : 45 included (80.4%), 11 excluded (19.6%)
#> Height : 32 included (86.5%), 5 excluded (13.5%)
#> Set aside : 0 (0.0%)
#> ************************************************************
df_wide <- longwide(clean_df) # convert to wide format for ext_bmiz
df_wide_bmi <- simple_bmi(df_wide) # compute simple BMI
# Calling the function with default column names
df_bmiz <- ext_bmiz(df_wide_bmi)
# Specifying different column names; note that quotes are used
dfc <- simple_bmi(df_wide)
colnames(dfc)[colnames(dfc) %in% c("agem", "wt", "ht")] <-
c("agemos", "weightkg", "heightcm")
df_bmiz <- ext_bmiz(dfc, age="agemos", wt="weightkg", ht="heightcm")
# Disabling conversion of all-integer age in months to (age + 0.5)
dfc <- simple_bmi(df_wide)
df_bmiz <- ext_bmiz(dfc, adjust.integer.age=FALSE)
# }