seqdef {TraMineR}R Documentation

Create a state sequence object

Description

Create a state sequence object with attributes such as alphabet, color palette and state labels. Most TraMineR functions for state sequences require such a state sequence object as input argument. There are specific methods for plotting, summarizing and printing state sequence objects.

Usage

seqdef(data, var=NULL, informat="STS", stsep=NULL,
        alphabet=NULL, states=NULL, id=NULL, weights=NULL, start=1,
        left=NA, right="DEL", gaps=NA, missing=NA, void="%", nr="*",
        cnames=NULL, cpal=NULL, missing.color="darkgrey", 
        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 user's manual (Gabadinho et al., 2008) 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. If NULL (default value), the seqfcheck function is called for detecting automatically a separator among "-" and ":". Other separators must be specified explicitely.
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 you want to reorder the states. The specified vector MUST contain AT LEAST all the states appearing in the data. It may possibly contain additional states not appearing in the data. If NULL, the alphabet is set to the distinct states appearing in the data as returned by the seqstatl function.
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 ordered accordingly with the values returned by the seqstatl function.
id optional argument for setting the rownames of the sequence object. If NULL (default), the rownames are taken from the input data. If set to "auto", sequences are number 1 to number of sequences. A vector containing the rownames of length equal to number of sequences may be specified as well.
weights optional numerical vector containing weights, which may be used by some functions to compute weighted statistics. EXPERIMENTAL.
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.
left the behavior for missing values appearing before the first (leftmost) valid state in each sequence. See Gabadinho et al. (2008) for more details on the options for handling missing values when defining sequence objects. By default, left missing values are treated as 'real' missing values and converted to the internal missing value code defined by the nr option. Other options are "DEL" to delete the positions containing missing values or a state code (belonging to the alphabet or not) to replace the missing values.
right the behavior for missing values appearing after the last (rightmost) valid state in each sequence. Same options as for the left argument.
gaps the behavior for missing values appearing inside the sequences, i.e. after the first (leftmost) valid state and before the last (rightmost) valid state of each sequence. Same options as for the left argument.
missing the code used for missing values in the input data. When 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.
void the internal code used by TraMineR for representing void elements in the sequences. Default is "%".
nr the internal code used by TraMineR for representing real missing elements in the sequences. Default is "*".
cnames optional names for the columns composing the sequence data. Those names will be used by default in the graphics as axis labels. If NULL (default), names are taken from the original column names in the data.
cpal an optional color palette for representing the states in the graphics. If NULL (default), a color palette is created by calling the brewer.pal function of the RColorBrewer package. If number of states is less or equal than 8, the "Accent" palette is used. If number of states is between 8 and 12, the "Set3" palette is used. If the number of states in the data is greater than 12, you have to specify your own palette. The list of available colors is displayed by the colors function. You can also use alternatively some other palettes from the RColorBrewer package.
missing.color alternative color for representing missing values inside the sequences. Defaults to "darkgrey".
labels optional state labels used for the color legend of TraMineR's graphics. If NULL (default), the state names in the alphabet are used as state labels as well.
... options passed to the seqformat function for handling input data that is not in STS format.

Details

Applying subscripts to sequence objects (eg. seq[,1:5] or seq[1:10,]) returns a state sequence object with some attributes preserved (alphabet, missing) and some others (start, column names) adapted to the selected column or row subset. If only one column is specified, a factor is returned.

Value

An object of class stslist. There are print, plot and summary methods for such objects. State sequence objects are required as argument to other functions such as plotting functions (seqdplot, seqiplot or seqfplot), functions to compute distances (seqdist), etc...

References

Gabadinho, A., G. Ritschard, M. Studer and N. S. Müller (2008). Mining Sequence Data in R with TraMineR: A user's guide. Department of Econometrics and Laboratory of Demography, University of Geneva.

See Also

plot.stslist to plot state sequence objects, seqplot for high level plots of state sequence objects, seqecreate to create an event sequence object, seqformat for options to handle several longitudinal data formats.

Examples

## 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")

## Plotting the first 10 sequences
plot(actcal.seq)

## 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,]

## ============================
## Example with missings values
## ============================
data(ex1)

## With right="DEL" default value
seqdef(ex1,1:13)

## Eliminating 'left' missing values
seqdef(ex1,1:13, left="DEL")

## Eliminating 'left' missing values and gaps
seqdef(ex1,1:13, left="DEL", gaps="DEL")

## ====================
## Example with weights
## ====================
ex1.seq <- seqdef(ex1, 1:13, weights=ex1$weights)

## weighted sequence frequencies
seqtab(ex1.seq)

[Package TraMineR version 1.4-1 Index]