PST: Probabilistic Suffix Trees and Variable Length Markov Chains
Version 0.94

Provides a framework for analysing state sequences with probabilistic suffix trees (PST), the construction that stores variable length Markov chains (VLMC). Besides functions for learning and optimizing VLMC models, the PST library includes many additional tools to analyse sequence data with these models: visualization tools, functions for sequence prediction and artificial sequences generation, as well as for context and pattern mining. The package is specifically adapted to the field of social sciences by allowing to learn VLMC models from sets of individual sequences possibly containing missing values, and by accounting for case weights. The library also allows to compute probabilistic divergence between two models, and to fit segmented VLMC, where sub-models fitted to distinct strata of the learning sample are stored in a single PST. This software results from research work executed within the framework of the Swiss National Centre of Competence in Research LIVES, which is financed by the Swiss National Science Foundation. The authors are grateful to the Swiss National Science Foundation for its financial support.

AuthorAlexis Gabadinho [aut, cre, cph]
Date of publication2017-02-03 00:26:10
MaintainerAlexis Gabadinho <alexis.gabadinho@wanadoo.fr>
LicenseGPL (>= 2)
Version0.94
URL http://r-forge.r-project.org/projects/pst
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("PST")

Popular man pages

cmine: Mining contexts
cplot: Plot single nodes of a probabilistic suffix tree
impute: Impute missing values using a probabilistic suffix tree
logLik: Log-Likelihood of a variable length Markov chain model
nobs: Extract the number of observations to which a VLMC model is...
pdist: Compute probabilistic divergence between two PST
ppplot: Plotting a branch of a probabilistic suffix tree
See all...

All man pages Function index File listing

Man pages

cmine: Mining contexts
cplot: Plot single nodes of a probabilistic suffix tree
cprob: Empirical conditional probability distributions of order 'L'
generate: Generate sequences using a probabilistic suffix tree
impute: Impute missing values using a probabilistic suffix tree
logLik: Log-Likelihood of a variable length Markov chain model
nobs: Extract the number of observations to which a VLMC model is...
nodenames: Retrieve the node labels of a PST
pdist: Compute probabilistic divergence between two PST
plot-PSTr: Plot a PST
pmine: PST based pattern mining
ppplot: Plotting a branch of a probabilistic suffix tree
pqplot: Prediction quality plot
predict: Compute the probability of categorical sequences using a...
print: Print method for objects of class 'PSTf' and 'PSTr'
prune: Prune a probabilistic suffix tree
PSTf-class: Flat representation of a probabilistic suffix tree
PSTr-class: Nested representation of a probabilistic suffix tree
pstree: Build a probabilistic suffix tree
query: Retrieve counts or next symbol probability distribution
s1-data: Example sequence data set
SRH-data: Longitudinal data on self rated health
subtree: Extract a subtree from a segmented PST
summary: Summary of variable length Markov chain model
tune: AIC, AICc or BIC based model selection

Functions

G1 Source code
G2 Source code
PST.legend Source code
PST.setlayout Source code
PSTf-class Man page
PSTf.stats Source code
PSTr-class Man page
PSTr.stats Source code
SRH Man page
SRH.seq Man page
Xtract Source code
[,cprobd.list,ANY,ANY,ANY-method Man page
[,cprobd.list-method Man page
[[,PSTr-method Man page
as.pstree Source code
asTxt Source code
cmine Man page
cmine,PSTf-method Man page Man page
context Source code
cplot Man page
cplot,PSTf-method Man page Man page
cprob Man page
cprob,stslist-method Man page
cprob-methods Man page
delete.pruned Source code
flist Source code
generate Man page
generate,PSTf-method Man page Man page
has.cdata Source code
impute Man page
impute,PSTf,stslist-method Man page Man page
is.leaf Source code
is.pruned Source code
is.stationary Source code
leaves Source code
leaves.count Source code
leaves.list Source code
likelihood Source code
lnobs Man page
logLik Man page
logLik,PSTf-method Man page Man page
lsuffix Source code
merge.cprob Source code
nobs,PSTf-method Man page Man page
node.gain Source code
node.keep Source code
node.leaf Source code
node.list Source code
node.merge Source code
node.mine Source code
node.nmin Source code
node.parent Source code
node.prune Source code
nodenames Man page
nodenames,PSTf-method Man page Man page
nodenames-methods Man page
nodes.count Source code
onAttach Source code
pdist Man page
pdist,PSTf,PSTf-method Man page Man page
plot,PSTf,ANY-method Man page Man page
plot,PSTr,ANY-method Man page Man page
plot,cprobd.list,ANY-method Man page
plotEdge Source code
plotNode Source code
plotNodeLimit Source code
plotNodeProb Source code
plotProb Source code
plotTree Source code
pmine Man page
pmine,PSTf,stslist-method Man page Man page
pmine-methods Man page
ppplot Man page
ppplot,PSTf-method Man page Man page
pqplot Man page
pqplot,PSTf,stslist-method Man page Man page
predict Man page
predict,PSTf-method Man page Man page
print Man page
print,PSTf-method Man page Man page
print,PSTr-method Man page Man page
print-methods Man page
prune Man page
prune,PSTf-method Man page Man page
prune-methods Man page
pruned.nodes Source code
pstree Man page
pstree,stslist-method Man page
pstree-methods Man page
query Man page
query,PSTf-method Man page Man page
query-methods Man page
round,cprobd-method Man page
rowProds Source code
s1 Man page
select.segment Source code
seqgbar Source code
set.leaves Source code
subtree Man page
subtree,PSTf-method Man page Man page
summary,PSTf-method Man page Man page
summary,PSTr-method Man page Man page
tune Man page
tune,PSTf-method Man page Man page
which.child Source code Source code

Files

inst
inst/CITATION
NAMESPACE
NEWS
data
data/SRH.RData
data/s1.rda
R
R/gain.R
R/plotNode.R
R/PST-setlayout.R
R/plotNodeProb.R
R/subtree.R
R/logLik.R
R/seqgbar.R
R/plot.PSTr.R
R/plotEdge.R
R/impute.R
R/AllClass.R
R/PST-flist.R
R/predict.R
R/cprobd-methods.R
R/PST-legend.R
R/plotTree.R
R/as.pstree.R
R/plotNodeLimit.R
R/PSTf-methods.R
R/print-PSTr.R
R/query.R
R/nobs.R
R/pdist.R
R/longest-suffix.R
R/gain-G2.R
R/PSTr-functions.R
R/PSTr-methods.R
R/cmine.R
R/generate.R
R/pstree.R
R/PSTf-functions.R
R/pmine.R
R/AllGeneric.R
R/gain-G1.R
R/ppplot.R
R/prune.R
R/pqplot.R
R/plotProb.R
R/tune.R
R/zzz.R
R/context.R
R/cprob.R
R/cplot.R
MD5
DESCRIPTION
man
man/ppplot.Rd
man/pqplot.Rd
man/tune.Rd
man/subtree.Rd
man/cprob.Rd
man/logLik.Rd
man/nobs.Rd
man/s1-data.Rd
man/predict.Rd
man/cmine.Rd
man/pmine.Rd
man/prune.Rd
man/PSTr-class.Rd
man/PSTf-class.Rd
man/generate.Rd
man/nodenames.Rd
man/impute.Rd
man/query.Rd
man/print.Rd
man/pstree.Rd
man/SRH-data.Rd
man/pdist.Rd
man/cplot.Rd
man/summary.Rd
man/plot-PSTr.Rd
PST documentation built on May 19, 2017, 2:36 p.m.

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