# PST: Probabilistic Suffix Trees and Variable Length Markov Chains

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.

- Author
- Alexis Gabadinho [aut, cre, cph]
- Date of publication
- 2016-08-10 02:40:28
- Maintainer
- Alexis Gabadinho <alexis.gabadinho@unige.ch>
- License
- GPL (>= 2)
- Version
- 0.90
- URLs

## Man pages

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

## Files in this package

PST |

PST/inst |

PST/inst/CITATION |

PST/NAMESPACE |

PST/NEWS |

PST/data |

PST/data/SRH.RData |

PST/data/s1.rda |

PST/R |

PST/R/gain.R |

PST/R/plotNode.R |

PST/R/PST-setlayout.R |

PST/R/plotNodeProb.R |

PST/R/subtree.R |

PST/R/logLik.R |

PST/R/seqgbar.R |

PST/R/plot.PSTr.R |

PST/R/plotEdge.R |

PST/R/impute.R |

PST/R/AllClass.R |

PST/R/PST-flist.R |

PST/R/predict.R |

PST/R/cprobd-methods.R |

PST/R/PST-legend.R |

PST/R/plotTree.R |

PST/R/as.pstree.R |

PST/R/plotNodeLimit.R |

PST/R/PSTf-methods.R |

PST/R/print-PSTr.R |

PST/R/query.R |

PST/R/nobs.R |

PST/R/pdist.R |

PST/R/longest-suffix.R |

PST/R/gain-G2.R |

PST/R/PSTr-functions.R |

PST/R/PSTr-methods.R |

PST/R/cmine.R |

PST/R/generate.R |

PST/R/pstree.R |

PST/R/PSTf-functions.R |

PST/R/pmine.R |

PST/R/AllGeneric.R |

PST/R/gain-G1.R |

PST/R/ppplot.R |

PST/R/prune.R |

PST/R/pqplot.R |

PST/R/plotProb.R |

PST/R/tune.R |

PST/R/zzz.R |

PST/R/context.R |

PST/R/cprob.R |

PST/R/cplot.R |

PST/MD5 |

PST/DESCRIPTION |

PST/man |

PST/man/ppplot.Rd |

PST/man/pqplot.Rd |

PST/man/tune.Rd |

PST/man/subtree.Rd |

PST/man/cprob.Rd |

PST/man/logLik.Rd |

PST/man/nobs.Rd |

PST/man/s1-data.Rd |

PST/man/predict.Rd |

PST/man/cmine.Rd |

PST/man/pmine.Rd |

PST/man/prune.Rd |

PST/man/PSTr-class.Rd |

PST/man/PSTf-class.Rd |

PST/man/generate.Rd |

PST/man/nodenames.Rd |

PST/man/impute.Rd |

PST/man/query.Rd |

PST/man/print.Rd |

PST/man/pstree.Rd |

PST/man/SRH-data.Rd |

PST/man/pdist.Rd |

PST/man/cplot.Rd |

PST/man/summary.Rd |

PST/man/plot-PSTr.Rd |