xyz-class: An S4 class for anthropometric data

In stefvanbuuren/minihealth: Mini Dossier for Individual Health Data

Description

The xyz class stores three variables useful for growth curves: x (usually age), y (height, weight, etc) and z (Z-score, or standard deviation score (SDS) corresponding to y given x). The class calculates z (when y is specified), or y (when z is specified).

Slots

x:

Numeric vector of decimal ages (in years) at which measurements y and Z-scores z are made. The length of x determines how many measurements (including NA's) are stored.

y:

Numeric vector of measurement of length length(x).

z:

Numeric vector of Z-score of length length(x).

xname:

A character scalar with the name of the x variable,usually something like "age".

yname:

A character scalar with the name of the measurement. Currently restricted to one of c("hgt", "wgt", "hdc", "wfh", "bmi", "dsc") for height (in cm), weight (in kg), head circumference (in cm), weight-for-height (kg/m), body mass index (kg/m^2) and D-score, respectively.

zname:

A character scalar with the name of the z variable. By default, is it equal to paste0(yname, "_z").

call:

An object of class call that specifies the appropriate reference table from the clopus package. Use the function create.reference.call to set call manually. Alternatively, specify one or more of libname, prefix, sex, yname and sub arguments, which are passed down to create.reference.call(). DEPRECATED.

refcode:

Since minihealth 0.90.0, Name of the reference. See make_refcode.

pkg:

Since minihealth 0.90.0, Name of the package containing the reference. See make_refcode. The default is nlreferences.

found:

Internal logical flag indicating whether the reference specified by call was actually found.

usetransform:

Logical indicating whether conversion to and from should be done using nlreferences::transform2z() and nlreferences::transform2y().

transform:

Name of the nlreferences transform function.

sex:

Sex specified by user argument.

ga:

Gestational age specified by user argument.

age:

Decimal age specified by user argument.

digits:

Number of digits for round() function. Default is 3.

Author(s)

Stef van Buuren

Examples

# specify length (in cm) for boy at ages 0, 0.2 and 0.5 years
d1 <- new("xyz", x = c(0, 0.2, 0.5), y = c(51.0, 54.1, 63.4))
d1

# Z-scores of weight (in kg) at same ages
d2 <- new("xyz", x = c(0, 0.2, 0.5), y = c(3.2, 5.2, 7.0), yname = "wgt",
  sex = "female")
d2

# As as data.frame
data.frame(d2)

# Head circumference of girl, relative to WHO standard
d3 <- new("xyz", x = c(0, 0.2, 0.5), y = c(35, 38, 41), pkg = "centile",
refcode = "who_2007_hdc_female_")
d3
data.frame(d3)

# Standard weight centiles at age 0.5 year of Dutch girls
d5 <- new("xyz", x = rep(0.5, 5), z = -2:2, sex = "female", yname = "wgt")
d5

# calculate centiles at 1 year using the female WHO head circumference reference
d6 <- new("xyz", yname = "hdc", x = rep(1, 5), z = -2:2, pkg = "centile",
refcode = "who_2007_hdc_female_")
d6

# calculate P50 for preterms, female and born a GA week 32
d7 <- new("xyz", yname = "hgt", x = seq(0, 1, 1/12), z = rep(0, 13),
 refcode = "nl_2012_hgt_female_32")
d7

# use nlreferences::transform2y() as an alternative
d8 <- new("xyz", yname = "hgt", x = seq(0, 1, 1/12), z = rep(0, 13),
  usetransform = TRUE, ga = 32, sex = "female")
d8

# use nlreferences::transform2z function
d9 <- new("xyz", yname = "hgt", x = seq(0, 0.25, 1/12), y = c(43, 46, 48, 50),
  usetransform = TRUE, ga = 32, sex = "female", digits = 10)
d9

stefvanbuuren/minihealth documentation built on March 11, 2021, 7:10 p.m.