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

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.

Author
Alexis Gabadinho [aut, cph], Matthias Studer [aut, cph], Nicolas Muller [aut], Reto Buergin [aut], Gilbert Ritschard [aut, cre, cph]
Date of publication
2016-10-06 04:55:38
Maintainer
Gilbert Ritschard <gilbert.ritschard@unige.ch>
License
GPL (>= 2)
Version
1.9-14
URLs

View on R-Forge

Man pages

actcal
Example data set: Activity calendar from the Swiss Household...
actcal.tse
Example data set: Activity calendar from the Swiss Household...
alphabet
Get or set the alphabet of a sequence object
bfspell
Example data set: First 20 biofam sequences in SPELL form
biofam
Example data set: Family life states from the Swiss Household...
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...
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.
seqalign
Computation details about a pairwise alignment
seqcomp
Compare two state sequences
seqconc
Concatenate vectors of states or events into a character...
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...
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.
seqe
Event 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.
seqfcheck
Check if sequences are in the compressed or extended format
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...
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
seqLLCP
Compute the length of the longest common prefix of two...
seqLLCS
Compute the length of the longest common subsequence of two...
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
seqST
Sequences turbulence
seqstatd
Sequence of transversal state distributions and their...
seqstatf
State frequencies in the whole sequence data set
seqstatl
List of distinct states or events (alphabet) in a sequence...
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
str.seqe
String representation of an event sequence object
TraMineR.checkupdates
Check for TraMineR updates
TraMineRInternal
Access to TraMineR internal functions
TraMineR-package
Trajectory Miner: a Toolbox for Exploring and Rendering...

Files in this package

TraMineR/DESCRIPTION
TraMineR/NAMESPACE
TraMineR/NEWS
TraMineR/R
TraMineR/R/BIOSPELL_to_STS.R
TraMineR/R/DHDdist.R
TraMineR/R/LCPdist.R
TraMineR/R/LCSdist.R
TraMineR/R/Levenshtein.R
TraMineR/R/SPELL_to_STS.R
TraMineR/R/SPS_to_STS.R
TraMineR/R/STS_to_DSS.R
TraMineR/R/STS_to_SPS.R
TraMineR/R/STS_to_SRS.R
TraMineR/R/STS_to_TSE.R
TraMineR/R/TraMineR-checkcost.R
TraMineR/R/TraMineR-group.R
TraMineR/R/TraMineR-legend.R
TraMineR/R/TraMineR-length.R
TraMineR/R/TraMineR-mscore.R
TraMineR/R/TraMineR-permutation.R
TraMineR/R/TraMineR-seqdist.R
TraMineR/R/TraMineR-setlayout.R
TraMineR/R/TraMineR-trunc.R
TraMineR/R/TraMineR.checkupdates.R
TraMineR/R/TraMineRInternal.R
TraMineR/R/alphabet-set.R
TraMineR/R/alphabet.R
TraMineR/R/checktriangleineq.R
TraMineR/R/cpal-set.R
TraMineR/R/cpal.R
TraMineR/R/debuglevel.R
TraMineR/R/diss.rep-methods.R
TraMineR/R/dissassoc.R
TraMineR/R/dissassocweighted.R
TraMineR/R/disscenter.R
TraMineR/R/dissmfac.R
TraMineR/R/dissmfacw.R
TraMineR/R/dissrep.R
TraMineR/R/disstree.dissassoc.R
TraMineR/R/disstree.r
TraMineR/R/disstree2dot.R
TraMineR/R/dissvar.R
TraMineR/R/dist2matrix.R
TraMineR/R/entropy.R
TraMineR/R/implicativestat.R
TraMineR/R/normdist.R
TraMineR/R/plot.seqalign.R
TraMineR/R/plot.stslist.R
TraMineR/R/plot.stslist.freq.R
TraMineR/R/plot.stslist.meant.R
TraMineR/R/plot.stslist.modst.R
TraMineR/R/plot.stslist.rep.R
TraMineR/R/plot.stslist.statd.R
TraMineR/R/print.disstree.R
TraMineR/R/read.tda.mdist.R
TraMineR/R/seqHtplot.R
TraMineR/R/seqLLCP.R
TraMineR/R/seqLLCS.R
TraMineR/R/seqST.R
TraMineR/R/seqalign.R
TraMineR/R/seqasnum.R
TraMineR/R/seqcomp.R
TraMineR/R/seqconc.R
TraMineR/R/seqdecomp.R
TraMineR/R/seqdef.R
TraMineR/R/seqdiff.R
TraMineR/R/seqdim.R
TraMineR/R/seqdist.R
TraMineR/R/seqdistmc.R
TraMineR/R/seqdistold.R
TraMineR/R/seqdplot.R
TraMineR/R/seqdss.R
TraMineR/R/seqdur.R
TraMineR/R/seqe.R
TraMineR/R/seqe2tse.R
TraMineR/R/seqeapplysub.R
TraMineR/R/seqecmpgroup.R
TraMineR/R/seqeconstraint.R
TraMineR/R/seqecontain.R
TraMineR/R/seqecreate.R
TraMineR/R/seqedist.R
TraMineR/R/seqefsub.R
TraMineR/R/seqeid.R
TraMineR/R/seqelength.R
TraMineR/R/seqerules.R
TraMineR/R/seqetm.R
TraMineR/R/seqeweight.R
TraMineR/R/seqfcheck.R
TraMineR/R/seqfind.R
TraMineR/R/seqformat.R
TraMineR/R/seqfplot.R
TraMineR/R/seqfpos.R
TraMineR/R/seqgbar.R
TraMineR/R/seqgen.R
TraMineR/R/seqici.R
TraMineR/R/seqient.R
TraMineR/R/seqientdiff.R
TraMineR/R/seqiplot.R
TraMineR/R/seqistatd.R
TraMineR/R/seqlegend.R
TraMineR/R/seqlength.R
TraMineR/R/seqlogp.R
TraMineR/R/seqmatsaltt.R
TraMineR/R/seqmeant.R
TraMineR/R/seqmodst.R
TraMineR/R/seqmpos.R
TraMineR/R/seqmsplot.R
TraMineR/R/seqmtplot.R
TraMineR/R/seqnum.R
TraMineR/R/seqpcplot.R
TraMineR/R/seqplot.R
TraMineR/R/seqpm.R
TraMineR/R/seqprep.R
TraMineR/R/seqrecode.R
TraMineR/R/seqrep.R
TraMineR/R/seqrplot.R
TraMineR/R/seqsep.R
TraMineR/R/seqshift.R
TraMineR/R/seqstatd.R
TraMineR/R/seqstatf.R
TraMineR/R/seqstatl.R
TraMineR/R/seqsubm.R
TraMineR/R/seqsubsn.R
TraMineR/R/seqtab.R
TraMineR/R/seqtransn.R
TraMineR/R/seqtrate.R
TraMineR/R/seqtree.R
TraMineR/R/seqxtract.R
TraMineR/R/stlab-set.R
TraMineR/R/stlab.R
TraMineR/R/stslist-methods.R
TraMineR/R/stslist.freq-methods.R
TraMineR/R/stslist.meant-methods.R
TraMineR/R/stslist.modst-methods.R
TraMineR/R/stslist.rep-methods.R
TraMineR/R/stslist.statd-methods.R
TraMineR/R/subseqelist.R
TraMineR/R/summary-stslist.R
TraMineR/R/vidx.R
TraMineR/R/zzz.R
TraMineR/build
TraMineR/build/vignette.rds
TraMineR/data
TraMineR/data/actcal.RData
TraMineR/data/actcal.tse.RData
TraMineR/data/bfspell.RData
TraMineR/data/biofam.RData
TraMineR/data/ex1.rda
TraMineR/data/ex1.txt.gz
TraMineR/data/ex2.rda
TraMineR/data/famform.rda
TraMineR/data/mvad.RData
TraMineR/demo
TraMineR/demo/00Index
TraMineR/demo/Events.R
TraMineR/demo/Rendering.R
TraMineR/demo/Seqdist.R
TraMineR/inst
TraMineR/inst/CITATION
TraMineR/inst/doc
TraMineR/inst/doc/TraMineR-state-sequence.R
TraMineR/inst/doc/TraMineR-state-sequence.Rnw
TraMineR/inst/doc/TraMineR-state-sequence.pdf
TraMineR/man
TraMineR/man/TraMineR-package.Rd
TraMineR/man/TraMineR.checkupdates.Rd
TraMineR/man/TraMineRInternal.Rd
TraMineR/man/actcal.Rd
TraMineR/man/actcal.tse.Rd
TraMineR/man/alphabet.Rd
TraMineR/man/bfspell.Rd
TraMineR/man/biofam.Rd
TraMineR/man/cpal.Rd
TraMineR/man/dissassoc.Rd
TraMineR/man/disscenter.Rd
TraMineR/man/dissmfac.Rd
TraMineR/man/dissrep.Rd
TraMineR/man/disstree.Rd
TraMineR/man/disstree2dot.Rd
TraMineR/man/disstreeleaf.Rd
TraMineR/man/dissvar.Rd
TraMineR/man/ex1.Rd
TraMineR/man/ex2.Rd
TraMineR/man/famform.Rd
TraMineR/man/mvad.Rd
TraMineR/man/plot.seqdiff.Rd
TraMineR/man/plot.stslist.Rd
TraMineR/man/plot.stslist.freq.Rd
TraMineR/man/plot.stslist.meant.Rd
TraMineR/man/plot.stslist.modst.Rd
TraMineR/man/plot.stslist.rep.Rd
TraMineR/man/plot.stslist.statd.Rd
TraMineR/man/plot.subseqelist.Rd
TraMineR/man/plot.subseqelistchisq.Rd
TraMineR/man/read.tda.mdist.Rd
TraMineR/man/seqLLCP.Rd
TraMineR/man/seqLLCS.Rd
TraMineR/man/seqST.Rd
TraMineR/man/seqalign.Rd
TraMineR/man/seqcomp.Rd
TraMineR/man/seqconc.Rd
TraMineR/man/seqdecomp.Rd
TraMineR/man/seqdef.Rd
TraMineR/man/seqdiff.Rd
TraMineR/man/seqdim.Rd
TraMineR/man/seqdist.Rd
TraMineR/man/seqdistmc.Rd
TraMineR/man/seqdss.Rd
TraMineR/man/seqdur.Rd
TraMineR/man/seqe.Rd
TraMineR/man/seqeapplysub.Rd
TraMineR/man/seqecmpgroup.Rd
TraMineR/man/seqeconstraint.Rd
TraMineR/man/seqecontain.Rd
TraMineR/man/seqecreate.Rd
TraMineR/man/seqefsub.Rd
TraMineR/man/seqeid.Rd
TraMineR/man/seqelength.Rd
TraMineR/man/seqetm.Rd
TraMineR/man/seqeweight.Rd
TraMineR/man/seqfcheck.Rd
TraMineR/man/seqfind.Rd
TraMineR/man/seqformat.Rd
TraMineR/man/seqfpos.Rd
TraMineR/man/seqgen.Rd
TraMineR/man/seqici.Rd
TraMineR/man/seqient.Rd
TraMineR/man/seqistatd.Rd
TraMineR/man/seqlegend.Rd
TraMineR/man/seqlength.Rd
TraMineR/man/seqlogp.Rd
TraMineR/man/seqmeant.Rd
TraMineR/man/seqmodst.Rd
TraMineR/man/seqmpos.Rd
TraMineR/man/seqnum.Rd
TraMineR/man/seqpcplot.Rd
TraMineR/man/seqplot.Rd
TraMineR/man/seqpm.Rd
TraMineR/man/seqrecode.Rd
TraMineR/man/seqrep.Rd
TraMineR/man/seqsep.Rd
TraMineR/man/seqstatd.Rd
TraMineR/man/seqstatf.Rd
TraMineR/man/seqstatl.Rd
TraMineR/man/seqsubm.Rd
TraMineR/man/seqsubsn.Rd
TraMineR/man/seqtab.Rd
TraMineR/man/seqtransn.Rd
TraMineR/man/seqtrate.Rd
TraMineR/man/seqtree.Rd
TraMineR/man/seqtreedisplay.Rd
TraMineR/man/stlab.Rd
TraMineR/man/str.seqe.Rd
TraMineR/src
TraMineR/src/TraMineR.h
TraMineR/src/alignement.cpp
TraMineR/src/alignement.h
TraMineR/src/checktriangleineq.c
TraMineR/src/constraint.cpp
TraMineR/src/constraint.h
TraMineR/src/dist2matrix.c
TraMineR/src/distancefunctions.cpp
TraMineR/src/eventdictionary.cpp
TraMineR/src/eventdictionary.h
TraMineR/src/eventseq.cpp
TraMineR/src/eventseq.h
TraMineR/src/ffunctions.c
TraMineR/src/inertiafunctions.c
TraMineR/src/prefixtree.cpp
TraMineR/src/prefixtree.h
TraMineR/src/saltt.cpp
TraMineR/src/salttseq.cpp
TraMineR/src/salttseq.h
TraMineR/src/seqedist.cpp
TraMineR/src/tmrformat.cpp
TraMineR/src/tmrformat.h
TraMineR/src/tmrsequence.cpp
TraMineR/src/traminerdebug.cpp
TraMineR/src/treeeventmap.cpp
TraMineR/src/treeeventmap.h
TraMineR/src/treeeventnode.cpp
TraMineR/src/treeeventnode.h
TraMineR/src/weightedinertia.cpp
TraMineR/vignettes
TraMineR/vignettes/TraMineR-state-sequence.Rnw