seqdef: Create a sequence object

Description

Create a sequence object to be passed to other functions provided by the TraMineR package. There are specific method for plotting and printing sequences objects.

Usage

seqdef(data, var=NULL, informat='STS', stsep="-", 
	  alphabet=NULL, states=NULL, 
       start=1, missing=NA, cnames=NULL,
	  cpal=NULL, labels=NULL)

Arguments

data

a data frame or matrix containing sequence data.

var

the list of columns containing the sequences. Defaut to NULL, ie all the columns. Whether the sequences are in the compressed (successive states in a character string) or extended format is automatically detected.

informat

format of the original data. Default is 'STS'. Avalaible formats are: STS, SPS, SPELL. See TraMineR manual for a description of the formats.

stsep

the character used as separator in the original data if input format is successive states in a character string. By default, "-".

alphabet

optional vector containing the alphabet (the list of all possible states). Use this option if some states in the alphabet don't appear in the data or if yopu want to reorder the states in the alphabet. The specified vector MUST contain AT LEAST all the st

states

an optional vector containing the labels for the states. Must have a length equal to the number of states in the data, and the labels must be sorted according to the output of the seqstatl function.

start

starting time. For instance, if your sequences begin at age 15, you can specify 15. At this stage, used only for labelling column names.

missing

the code for the missing values appearing in the data. If specified, all cells containing this value will be replaced by NA's, the internal R code for missing values. If 'missing' is not specified, cells containing NA's are considered to be missing values

cnames

optional names for the columns composing the sequence data. Those names will be used by default in the graphics as axis labels. If not specified, names are taken from the original columns names in the data.

cpal

an optional color palette for representing the states in the graphics. If not specified, colors palette is created with the RColorBrewer package, using the "accent" palette. Note that the maximum number of colors in this palette is 8. If the number of sta

labels

labels for the states, to appear in the graphics' legend.

Value

a sequence object that can be passed as argument to other functions such as plotting functions (seqdplot, seqiplot or seqfplot), functions to compute distances (seqdist), etc...

Details

Subscripts applied to sequence objects (eg. seq[,1:5] or seq[1:10,]) returns a sequence object with preserved (alphabet, missing) and adapted attributes (start, column names), unless only one column is selected, in which case a factor is returned.

Examples

Run this code

## Creating a sequence object with the columns 13 to 24 
## in the 'actcal' example data set
data(actcal)
actcal.seq <- seqdef(actcal,13:24,
	labels=c("> 37 hours", "19-36 hours", "1-18 hours", "no work"))

## Displaying the first 10 rows of the sequence object
actcal.seq[1:10,]

## Displaying the first 10 rows of the sequence object
## in SPS format
print(actcal.seq[1:10,], format="SPS")

## Frequency plot for the monthes June to September
seqfplot(actcal.seq[,6:9])

## Re-ordering the alphabet
actcal.seq <- seqdef(actcal,13:24,alphabet=c("B","A","D","C"))
alphabet(actcal.seq)

## Adding a state not appearing in the data to the
## alphabet
actcal.seq <- seqdef(actcal,13:24,alphabet=c("A","B","C","D","E"))
alphabet(actcal.seq)

## Adding a state not appearing in the data to the
## alphabet and changing the states labels
actcal.seq <- seqdef(actcal,13:24,
  alphabet=c("A","B","C","D","E"),
  states=c("FT","PT","LT","NO","TR"))
alphabet(actcal.seq)
actcal.seq[1:10,]