y2z: Converts measurements to standard deviation scores (SDS)

In stefvanbuuren/AGD: Analysis of Growth Data

Description

Converts measurements into age- and sex-conditional standard deviation score (SDS) using an external reference.

Usage

y2z(
  y = c(75, 80, 85),
  x = 1,
  sex = "M",
  sub = "N",
  ref = get("nl4.hgt"),
  dist = "LMS",
  dec = 3,
  sex.fallback = NA,
  sub.fallback = NA,
  tail.adjust = FALSE
)

Arguments

y	A numerical vector containing the outcome measurements. The length length(y) determines the size of the output vector.
x	A vector containing the values of the numerical covariate (typically decimal age or height) at which conversion is desired. Values are replicated to match length(y).
sex	A character vector indicating whether the male ("M") of female ("F")reference should be used. Values are replicated to match length(y).
sub	A character vector indicating the level of the sub field of the reference standard defined in ref
ref	A data frame containing a factor sex, a numerical variable age containing the tabulated decimal point ages, and two or more numerical variables with reference values. See details.
dist	A string identifying the type of distribution. Values values are: "NO", "BCCG", "LMS", "BCPE" and "BCT". The default is "LMS".
dec	A scalar value indicating the number of decimals used to round the value.
sex.fallback	The level of the sex field used when no match is found. The default sex.fallback=NA specifies that unmatched entries should receive a NA value.
sub.fallback	The level of the sub field used when no match is found. The default sub.fallback=NA specifies that unmatched entries should receive a NA value.
tail.adjust	Logical. If TRUE then the WHO method for tail adjustment is applied. The default is FALSE.

Details

Functions z2y() and y2z() are the inverse of each other.

The argument dist determines the statistical distribution. The possibilities are as follows:

list("\"NO\"")

ref should contain columns mean and sd, containing the mean and the standard deviation in the external reference population.

list("\"LMS\"")

ref should contain columns L, S and M containing the LMS parameters.

list("\"BCCG\"")

ref should contain columns mu, sigma and nu containing the Box-Cox Cole-Green parameters.

list("\"BCPE\"")

ref should contain columns mu, sigma, nu and tau containing the Box-Cox Power Exponential parameters.

list("\"BCT\"")

ref should contain columns mu, sigma, nu and tau containing the Box-Cox T distribution parameters.

Value

For y2z(): A vector with length(y) elements containing the standard deviation score. For z2y(): A vector with length(z) elements containing quantiles.

Author(s)

Stef van Buuren, 2010

See Also

z2y

Examples

boys <- boys7482

# SDS of height 115 cm at age 5 years, 
# relative to Dutch boys reference
y2z(y=115, x=5)

# same relative to Dutch girls
y2z(y=115, x=5, sex="F")

# SDS of IOTF BMI cut-off value for overweight (boys 2-18) 
# relative to Dutch boys reference
cutoff <- c(
18.41, 18.15, 17.89, 17.72, 17.55, 17.49, 17.42, 17.49, 17.55, 17.74,
17.92, 18.18, 18.44, 18.77, 19.10, 19.47, 19.84, 20.20, 20.55, 20.89, 
21.22, 21.57, 21.91, 22.27, 22.62, 22.96, 23.29, 23.60, 23.90, 24.18, 
24.46, 24.73, 25.00)
age <- seq(2, 18, by=0.5)
(z <- y2z(y=cutoff, x=age, sex="M", ref=nl4.bmi))

# apply inverse transformation to check calculations
round(z2y(z, age, ref=nl4.bmi), 2)
cutoff

# calculate percentiles of weight 12 kg at 2 years (boys, girls)
100*round(pnorm(y2z(y=c(12,12), x=2, sex=c("M","F"), ref=nl4.wgt)),2)

# # percentage of children lighter than 15kg at ages 2-5
e <- expand.grid(age=2:5, sex=c("M","F"))
z <- y2z(y=rep(15,nrow(e)), x=e$age, sex=e$sex, ref=nl4.wgt)
w <- matrix(100*round(pnorm(z),2), nrow=2, byrow=TRUE)
dimnames(w) <- list(c("boys","girls"),2:5)
w

# analysis in Z scale
hgt.z <- y2z(y=boys$hgt, x=boys$age, sex="M", ref=nl4.hgt)
wgt.z <- y2z(y=boys$wgt, x=boys$age, sex="M", ref=nl4.wgt)
plot(hgt.z, wgt.z, col="blue")


# z2y

# quantile at SD=0 of age 2 years, 
# height Dutch boys
z2y(z=0, x=2)

# same for Dutch girls
z2y(z=0, x=2, sex="F")

# quantile at SD=c(-1,0,1) of age 2 years, BMI Dutch boys
z2y(z=c(-1,0,+1), x=2, ref=nl4.bmi)

# 0SD line (P50) in kg of weight for age in 5-10 year, Dutch boys
z2y(z=rep(0,6), x=5:10, ref=nl4.wgt)

# 95th percentile (P95), age 10 years, wfa, Dutch boys
z2y(z=qnorm(0.95), x=10, ref=nl4.wgt)

# table of P3, P10, P50, P90, P97 of weight for 5-10 year old dutch boys
# age per year
age <- 5:10
p <- c(0.03,0.1,0.5,0.9,0.97)
z <- rep(qnorm(p), length(age))
x <- rep(age, each=length(p))
w <- matrix(z2y(z, x=x, sex="M", ref=nl4.wgt), ncol=length(p),
 byrow=TRUE)
dimnames(w) <- list(age, p)
round(w,1)

# standard set of Z-scores of weight for all tabulated ages, boys & girls
# and three etnicities
sds <- c(-2.5, -2, -1, 0, 1, 2, 2.5)
age <- nl4.wgt$x
z <- rep(sds, times=length(age))
x <- rep(age, each=length(sds))
sex <- rep(c("M","F"), each=length(z)/2)
w <- z2y(z=z, x=x, sex=sex, ref=nl4.wgt)
w <- matrix(w, ncol=length(sds), byrow=TRUE)
dimnames(w) <- list(age, sds)
data.frame(sub=nl4.wgt$sub,sex=nl4.wgt$sex,round(w,2), row.names=NULL)

# P85 of BMI in 5-8 year old Dutch boys and girls
e <- expand.grid(age=5:8, sex=c("M","F"))
w <- z2y(z=rep(qnorm(0.85),nrow(e)), x=e$age, sex=e$sex, ref=nl4.bmi)
w <- matrix(w, nrow=2, byrow=TRUE)
dimnames(w) <- list(c("boys","girls"),5:8)
w

# data transformation of height z-scores to cm-scale
z <- c(-1.83, 0.09, 2.33, 0.81, -1.20)
x <- c(8.33,  0.23, 19.2, 24.3, 10)
sex <- c("M", "M", "F", "M", "F")
round(z2y(z=z, x=x, sex=sex, ref=nl4.hgt), 1)

# interpolate published height standard 
# to daily values, days 0-31, boys
# on centiles -2SD, 0SD and +2SD 
days <- 0:31
sds  <- c(-2, 0, +2)
z    <- rep(sds, length(days))
x    <- rep(round(days/365.25,4), each=length(sds))
w    <- z2y(z, x, sex="M", ref=nl4.hgt)
w    <- matrix(w, ncol=length(sds), byrow=TRUE)
dimnames(w) <- list(days, sds)
w

stefvanbuuren/AGD documentation built on June 3, 2021, 8:59 a.m.