TraMineR (version 1.8-9)

TraMineR-package: Trajectory Miner: a Toolbox for Exploring and Rendering Sequences

Description

This is a toolbox for the manipulation, description and rendering of sequences, and more generally the mining of sequence data in the field of social sciences. Although the toolbox is primarily intended for analyzing state or event sequences that describe life courses such as family formation histories or professional careers, its features also apply to many other kinds of categorical sequence data. It accepts many different sequence representations as input and provides tools for converting sequences from one format to another. It offers several functions for describing and rendering sequences, for computing distances between sequences with different metrics (among which optimal matching), original dissimilarity-based analysis tools, and simple functions for extracting the most frequent subsequences and identifying the most discriminating ones among them. A user's guide can be found on the TraMineR web page. TraMineR provides tools for both state sequences and event sequences. The first step when using the package is to define a state sequence object (with seqdef) if you want to explore state sequences, and an event sequence object (with seqecreate) if you are interested in event sequencing. State sequences are defined from a series of variables giving the states at the successive positions, while event sequences are defined from (vertical) time stamped event data. The package, however, can handle many other different data organizations and provides tools to help converting state sequences into event sequences and vice versa.

Details

ll{ Package: TraMineR Version: 1.8-9 Date: 2015-01-27 Authors@R: c( person("Alexis", "Gabadinho", role = c("aut", "cph")), person("Matthias", "Studer", role = c("aut", "cph")), person("Nicolas", "Muller", role = "aut"), person("Reto", "Buergin", role = "aut"), person("Gilbert", "Ritschard", role = c("aut", "cre", "cph"), email = "[e-mail]")) Depends: R (>= 2.8.1), Imports: utils, RColorBrewer, boot Suggests: cluster, xtable License: GPL (>= 2) URL: http://mephisto.unige.ch/traminer Encoding: latin1 } Index: TraMineR-package Trajectory miner: a toolbox for exploring and rendering sequence data TraMineR.checkupdates Check for TraMineR updates TraMineRInternalLayout Access to TraMineR internal functions actcal Example data set: Activity calendar from the Swiss Household Panel actcal.tse Example data set: Activity calendar from the Swiss Household Panel (time stamped event format) alphabet Get or set the alphabet of a sequence object biofam Example data set: Family life states from the Swiss Household Panel biographical survey cpal Get or set the color palette of a sequence object dissassoc Analysis of discrepancy from dissimilarity measures disscenter Compute distances to the center of a group dissmfac Multi-factor ANOVA from a dissimilarity matrix dissrep Extracting sets of representative objects using a dissimilarity matrix disstree Dissimilarity Tree disstree2dot Graphical representation of a dissimilarity tree disstreeleaf Terminal node membership dissvar Dissimilarity based discrepancy ex1 Example data set with missing values and weights ex2 Example data sets with weighted and unweighted sequence data famform Example data set: sequences of family formation mvad Example data set: Transition from school to work plot.seqdiff Plotting a seqdiff object. plot.stslist Plot method for state sequence objects plot.stslist.freq Plot method for sequence frequency tables plot.stslist.meant Plot method for objects produced by the seqmeant function plot.stslist.modst Plot method for modal state sequences plot.stslist.rep Plot method for representative sequence sets plot.stslist.statd Plot method for objects produced by the seqstatd function plot.subseqelist Plot frequencies of subsequences plot.subseqelistchisq Plot discriminant subsequences read.tda.mdist Read a distance matrix produced by TDA. seqLLCP Compute the length of the longest common prefix of two sequences seqLLCS Compute the length of the longest common subsequence of two sequences seqST Sequences turbulence seqalign Computation details about a pairwise alignment seqcomp Compare two state sequences seqconc Concatenate vectors of states or events into a character string seqdecomp Convert a character string into a vector of states or events seqdef Create a state sequence object seqdiff Position-wise discrepancy analysis between groups of sequences seqdim Dimension of a set of sequences seqdist Distances (dissimilarities) between sequences seqdistmc Multichannel distances between sequences seqdss Extract distinct states sequence from a sequence object seqdur Extract state durations from a sequence object. seqeapplysub Checking for the presence of given event subsequences seqecmpgroup Identifying discriminating subsequences seqeconstraint Setting time constraints and the counting method seqecontain Check if sequence contains events seqecreate Create event sequence objects. seqefsub Searching for frequent subsequences seqeid Retrieve unique ids from an event sequence object. seqelength Lengths of event sequences seqetm Create a transition-definition matrix seqeweight Setting or retrieving weights of an event sequence object. seqfind Indexes of state sequence(s) x in state sequence object y seqformat Conversion between sequence formats seqfpos Search for the first occurrence of a given element in a sequence seqgen Random sequences generation seqici Complexity index of individual sequences seqient Within sequence entropies seqistatd State frequencies in each individual sequence seqlegend Plot a legend for the states in a sequence object seqlength Sequence length seqlogp Logarithm of the probabilities of state sequences seqmeant Mean durations in each state seqmodst Sequence of modal states seqmpos Number of matching positions between two sequences. seqnum Transform into a sequence object with numerical alphabet. seqpcplot Parallel coordinate plot for sequence data seqplot Plot state sequence objects seqpm Find substring patterns in sequences seqrecode Recoding state sequence objects and factors seqrep Extracting sets of representative sequences seqsep Adds separators to sequences stored as character string seqstatd Sequence of transversal state distributions and their entropies seqstatf State frequencies in the whole sequence data set seqstatl List of distinct states or events (alphabet) in a sequence data set. seqsubm Create a substitution-cost matrix seqsubsn Number of distinct subsequences in a sequence. seqtab Frequency table of the sequences seqtransn Number of transitions in a sequence seqtrate Compute transition rates between states seqtree Tree structured analysis of a state sequence object. seqtreedisplay Graphical rendering of a sequence regression tree stlab Get or set the state labels of a sequence object

References

Gabadinho, A., G. Ritschard, N. S. M�ller and M. Studer (2011). Analyzing and Visualizing State Sequences in R with TraMineR. Journal of Statistical Software 40(4), 1-37. Gabadinho, A., G. Ritschard, M. Studer and N. S. M�ller (2009). Mining Sequence Data in R with the TraMineR package: A user's guide. Department of Econometrics and Laboratory of Demography, University of Geneva

Examples

## load the mvad data
library(TraMineR)
data(mvad)

## create a state sequence object from columns 17 to 86
mvad.seq <- seqdef(mvad[,17:86])

## distribution plot by sex (male)
seqdplot(mvad.seq, group=mvad$male, border=NA)

## compute the LCS pairwise distance matrix
## among the first 10 sequences
mvad.lcs <- seqdist(mvad.seq[1:10,], method="LCS")