# Trajectory Miner: a Sequence Analysis Toolkit

## Documentation for package ‘TraMineR’ version 2.2-9

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.
- Package NEWS.

## Help Pages

A B C D E F G H I M P R S T

TraMineR-package | Trajectory Miner: Sequence Analysis Toolkit

## -- A --

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 state or event sequence object
alphabet<- | Get or set the alphabet of a state or event sequence object

## -- B --

bfpdata20 | Example data set: First 20 biofam sequences in SPELL form
bfspell | Example data set: First 20 biofam sequences in SPELL form
bfspell20 | Example data set: First 20 biofam sequences in SPELL form
biofam | Example data set: Family life states from the Swiss Household Panel biographical survey

## -- C --

cpal | Get or set the color palette of a sequence object
cpal<- | Get or set the color palette of a sequence object

## -- D --

dissassoc | Analysis of discrepancy from dissimilarity measures
disscenter | Compute distances to the center of a group
dissdomassoc | Domain association measures
dissmfacw | Multi-factor ANOVA from a dissimilarity matrix
dissrep | Extracting sets of representative objects using a dissimilarity matrix
dissrf | Relative Frequency Groups.
disstree | Dissimilarity Tree
disstree.assign | Assign rules to profiles provided
disstree.get.rules | Tree classification rules
disstree2dot | Graphical representation of a dissimilarity tree
disstree2dotp | Graphical representation of a dissimilarity tree
disstreedisplay | Graphical rendering of a sequence regression tree
disstreeleaf | Terminal node membership
dissvar | Dissimilarity based discrepancy

## -- E --

ex1 | Example data set with missing values and weights
ex2 | Example data sets with weighted and unweighted sequence data
ex2.unweighted | Example data sets with weighted and unweighted sequence data
ex2.weighted | Example data sets with weighted and unweighted sequence data

## -- F --

famform | Example data set: sequences of family formation

## -- G --

gower_matrix | Multi-factor ANOVA from a dissimilarity matrix

## -- H --

hist.dissassoc | Analysis of discrepancy from dissimilarity measures

## -- I --

is.stslist | Test if is a proper state sequence (stslist) object
is.subseqelist | Searching for frequent subsequences

## -- M --

mvad | Example data set: Transition from school to work

## -- P --

plot.eseq | Parallel coordinate plot for sequence data
plot.seqalign | Computation details about a pairwise alignment
plot.seqdiff | Plotting a seqdiff object.
plot.seqelist | Parallel coordinate plot for sequence data
plot.seqrf | Plot method for seqrf objects of relative frequency groups of sequences.
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
print.dissassoc | Analysis of discrepancy from dissimilarity measures
print.dissmultifactor | Multi-factor ANOVA from a dissimilarity matrix
print.dissrf | Relative Frequency Groups.
print.disstree | Dissimilarity Tree
print.sdomassoc | Measures of association between domains of sequence data
print.seqalign | Computation details about a pairwise alignment
print.seqdiff | Position-wise discrepancy analysis between groups of sequences
print.seqeconstraint | Setting time constraints and the counting method
print.seqidegrad | Degradation, Precarity, and Insecurity indexes
print.seqivardur | Variance of spell durations in individual sequences
print.seqprec | Degradation, Precarity, and Insecurity indexes
print.seqrf | Relative Frequency Groups.
print.stslist | Print method for state sequence objects
print.stslist.freq | Frequency table of the sequences
print.subseqelist | Searching for frequent subsequences

## -- R --

rbind.stslist | Create a state sequence object
read.tda.mdist | Read a distance matrix produced by TDA.
recodef | Recoding state sequence objects and factors

## -- S --

seqalign | Computation details about a pairwise alignment
seqcomp | Compare two state sequences
seqconc | Concatenate vectors of states or events into a character string
seqcost | Generate substitution and indel costs
seqdecomp | Convert a character string into a vector of states or events
seqdef | Create a state sequence object
seqdHplot | Plot state sequence objects
seqdiff | Position-wise discrepancy analysis between groups of sequences
seqdim | Dimension of a set of sequences
seqdist | Distances (dissimilarities) between sequences
seqdistmc | Multidomain sequences
seqdomassoc | Measures of association between domains of sequence data
seqdplot | Plot state sequence objects
seqdss | Extract sequences of distinct successive states
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
seqelength<- | Lengths of event sequences
seqetm | Create a transition-definition matrix
seqeweight | Setting or retrieving weights of an event sequence object.
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
seqfplot | Plot state sequence objects
seqfpos | Search for the first occurrence of a given element in a sequence
seqfposend | End of first spell in given state
seqgen | Random sequences generation
seqHtplot | Plot state sequence objects
seqibad | Badness index
seqici | Complexity index of individual sequences
seqidegrad | Degradation, Precarity, and Insecurity indexes
seqient | Within sequence entropies
seqindic | Sequence indicators
seqinsecurity | Degradation, Precarity, and Insecurity indexes
seqintegr | Integrative potential
seqintegration | Integrative potential
seqIplot | Plot state sequence objects
seqiplot | Plot state sequence objects
seqipos | Indicators for binary sequences of positive and negative states.
seqistatd | State frequencies in each individual sequence
seqivardur | Variance of spell durations in individual sequences
seqivolatility | Volatility of individual state sequences
seqlegend | Plot a legend for the states in a sequence object
seqlength | Sequence length
seqlength.align | Align sequence length across domains
seqLLCP | Compute the length of the longest common prefix of two sequences
seqLLCS | Compute the length of the longest common subsequence of two sequences
seqlogp | Logarithm of the probabilities of state sequences
seqmaintokens | Indexes of most frequent tokens
seqMD | Multidomain sequences
seqmeant | Mean durations in each state
seqmodst | Sequence of modal states
seqmpos | Number of matching positions between two sequences.
seqmsplot | Plot state sequence objects
seqmtplot | Plot state sequence objects
seqnum | Transform into a sequence object with numerical alphabet.
seqpcfilter | Parallel coordinate plot for sequence data
seqpcplot | Parallel coordinate plot for sequence data
seqplot | Plot state sequence objects
seqplotMD | Plot multidomain state sequences
seqpm | Find substring patterns in sequences
seqprecarity | Degradation, Precarity, and Insecurity indexes
seqprecorr | Degradation, Precarity, and Insecurity indexes
seqprecstart | State precarity
seqrecode | Recoding state sequence objects and factors
seqrep | Extracting sets of representative sequences
seqrf | Relative Frequency Groups.
seqrfplot | Plot state sequence objects
seqrplot | Plot state sequence objects
seqsep | Adds separators to sequences stored as character string
seqST | Sequences turbulence
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 | Generate substitution and indel costs
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.
seqtree2dot | Graphical representation of a dissimilarity tree
seqtreedisplay | Graphical rendering of a sequence regression tree
stlab | Get or set the state labels of a sequence object
stlab<- | Get or set the state labels of a sequence object
summary.ddomassoc | Domain association measures
summary.dissrf | Relative Frequency Groups.
summary.seqrf | Relative Frequency Groups.
summary.stslist | Create a state sequence object

## -- T --

TraMineR | Trajectory Miner: Sequence Analysis Toolkit
TraMineR.check.depr.args | Checking and managing deprecated arguments
TraMineRInternalLayout | Access to TraMineR internal functions
TraMineRInternalLegend | Access to TraMineR internal functions
TraMineRInternalNodeInit | Access to TraMineR internal functions
TraMineRInternalSeqeage | Access to TraMineR internal functions
TraMineRInternalSeqgbar | Access to TraMineR internal functions
TraMineRInternalSplitInit | Access to TraMineR internal functions
TraMineRInternalWeightedInertiaDist | Access to TraMineR internal functions