kml3d (version 2.4.6.1)

clusterLongData3d: ~ Function: clusterLongData3d (or cld3d) ~

Description

clusterLongData3d (or cld3d in short) is the constructor for ClusterLongData3d object.

Usage

clusterLongData3d(traj, idAll, time, timeInData, varNames, maxNA)
cld3d(traj, idAll, time, timeInData, varNames, maxNA)

Value

An object of class ClusterLongData3d.

Arguments

traj

[array(numeric)] or [data.frame]: structure containning the joint-trajectories. Each line (traj[i,,]) is a joint-trajectory of an individual ; columns (traj[,j,]) refer to the time during which measures were made ; the third dimensions (traj[,,l]) are for variables.

idAll

[vector(character)]: single identifier for each trajectory (ie each individual). Note that the identifiers are of type character (that allow to deal identifiers like XUK32-612, identifiers that our favorite epidemiologists are so good at providing). If idAll are numeric, they are converted into characters.

time

[vector(numeric)]: time at which measures were made.

timeInData

[list(vector(numeric))]: precise the column containing the trajectories. The list labels are the names of the variables (like list(A=c(2,3,4),B=c(5,7,9))).

varNames

[character]: name of the variable being measured.

maxNA

[numeric] or [vector(numeric)] : maximum number of NA that are tolerates on a trajectory. If a trajectory has more missing than maxNA, then it is remove from the analysis. Note the maxNA can take diffents values for each variable-trajectories. The default value is length(time)-2.

Details

clusterLongData3d construct a object of class ClusterLongData. Two cases can be distinguised:

traj is an array:

the first dimension (line) are individual. The second dimension (column) are time at which the measurement are made. The third dimension are the differents variable-trajectories. For example, traj[,,2] is the second variable-trajectory.

If idAll is missing, the individuals are labelled i1, i2, i3,...

If timeInData is missing, all the column are used (1:ncol(traj)).

If traj is a data.frame:

lines are individual. Time of measurement and variables should be provide through timeInData. timeInData is a list. The label of the list are the variable-trajectories names. Elements of the list are the column containning the trajectories. For example, if timeInData=list(V=c(2,3,4),W=c(6,8,12)), then the first variable-trajectory is 'V', its mesearment are in column 2,3 and 4. The second variable-trajectory is 'W', its measurment are in column 6,8 and 12.

If idAll is missing, the first column of the data.frame is used.

Examples

###############
### Building an array
tr1n <- array(c(1,2,NA, 1,4,NA, 6,1,8, 10,NA,2, 3,NA,NA,
                4,NA,5,  6,3,4, 3,4,4, 4,NA,NA, 5,5,4),
            dim=c(3,5,2))


###############
### clusterLongData

### With maxNA=3
clusterLongData3d(traj=tr1n,
    idAll=as.character(c(100,102,104)),
    time=c(1,2,4,8,16),
    varNames=c("P","A"),
    maxNA=3
)

### With maxNA=2
### Individual 104 is exclude
clusterLongData3d(traj=tr1n,
    idAll=as.character(c(100,102,104)),
    time=c(1,2,4,8,16),
    varNames=c("P","A"),
    maxNA=2
)