R: Data Structure for Longitudinal Data

longitudinal {longitudinal} | R Documentation

## Data Structure for Longitudinal Data

### Description

The data type `longitudinal` stores multiple time series data. It allows repeated measurements, irregular sampling, and unequal temporal spacing of the time points.

`as.longitudinal` converts a matrix into a `longitudinal` object. The columns of the input matrix are considered as individual variables (time series). The rows contain the measurements in temporal order (for instance, rows 1-10 could contain 10 repeated measurements taken at time point 1, rows 11-20 further 10 measurements taken at time point 2, and so on). The dates for the time points can be specified with the argument `times` and need not be equally spaced. With the argument `repeats` it is possible to specify the number of measurements per time point (this may be different from time point to time point). In the resulting `longitudinal` matrix object the row names will indicate both the time points and the repetition number (e.g., "10-1", "10-2", "10-3", ..., "20-1", "20-2", "20-3", etc.).

`is.longitudinal` checks whether a matrix has the `longitudinal` attributes.

The functions `summary`, `print`, `plot` are the standard generic functions adapted to `longitudinal` objects.

### Usage

    as.longitudinal(x, repeats=1, time)
    is.longitudinal(x)
    ## S3 method for class 'longitudinal'
    summary(object, ...)
    ## S3 method for class 'longitudinal'
    print(x, ...)
    ## S3 method for class 'longitudinal'
    plot(x, series=1, type=c("median", "mean"), autolayout=TRUE, ...)

### Arguments

`x, object` | Time series data, contained in a `longitudinal` object or in matrix form (`as.longitudinal`).
`repeats` | Integer, or a vector of integers, that specifies the number of available measurements per time point. If only one number is given then it is assumed the time series is regularly sampled. If instead a vector is specified, then each time point may have a different number of samples.
`time` | A vector with the dates for the time points. If not specified, equally spaced time points 1, 2, 3, ... are assumed.
`series` | Number, or a vector of numbers, that indicates which time series (=variables and columns of x) are plotted.
`type` | Determines whether the plotted line corresponds to the mean or median value of the samples per time point (default: "median").
`autolayout` | determine the number of columns and rows in the plot automatically in the display of multiple time series (default: TRUE).
`...` | Additional optional parameters

### Value

`as.longitudinal` returns a `longitudinal` object.

`is.longitudinal` returns TRUE or false.

### Author(s)

Korbinian Strimmer (http://strimmerlab.org).

### See Also

`longitudinal.util`, `tcell`, `ts`.

### Examples

    # load "longitudinal" library
    library("longitudinal")

    # load data set
    data(tcell)
    is.longitudinal(tcell.34)
    attributes(tcell.34)
    tcell.34[,1:3]

    # how many samples and how many genes?
    dim(tcell.34)
    summary(tcell.34)

    # plot first nine time series
    plot(tcell.34, 1:9)

    #####

    # an artificial example with repeated measurements, irregular sampling, and unequal spacing
    m <- matrix(rnorm(200), 50, 4)
    z <- as.longitudinal(m, repeats=c(10,5,5,10,20), time=c(2,8,9,15,16))
    plot(z, 1:4)

[Package longitudinal version 1.1.12 Index]