Package: PST 0.95

Alexis Gabadinho

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.

Authors:Alexis Gabadinho [aut, cre, cph]

PST_0.95.tar.gz
PST_0.95.zip(r-4.5)PST_0.95.zip(r-4.4)PST_0.95.zip(r-4.3)
PST_0.95.tgz(r-4.4-any)PST_0.95.tgz(r-4.3-any)
PST_0.95.tar.gz(r-4.5-noble)PST_0.95.tar.gz(r-4.4-noble)
PST_0.95.tgz(r-4.4-emscripten)PST_0.95.tgz(r-4.3-emscripten)
PST.pdf |PST.html✨
PST/json (API)
NEWS

# Install 'PST' in R:
install.packages('PST', repos = c('https://r-forge.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://r-forge.r-project.org/projects/pst

Datasets:
  • SRH - Longitudinal data on self rated health
  • SRH.seq - Longitudinal data on self rated health
  • s1 - Example sequence data set

On CRAN:

21 exports 4.64 score 12 dependencies 45 mentions 36 scripts 265 downloads

Last updated 4 years agofrom:dfcb482411. Checks:OK: 5 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 31 2024
R-4.5-winNOTEAug 31 2024
R-4.5-linuxNOTEAug 31 2024
R-4.4-winOKAug 31 2024
R-4.4-macOKAug 31 2024
R-4.3-winOKAug 31 2024
R-4.3-macOKAug 31 2024

Exports:cminecplotcprobgenerateimputelogLiknobsnodenamespdistplotpmineppplotpqplotpredictprintprunepstreequerysubtreesummarytune

Dependencies:bootclustercolorspacelatticeMASSMatrixmgcvnlmepermuteRColorBrewerTraMineRvegan

Readme and manuals

Help Manual

Help pageTopics
Mining contextscmine cmine,PSTf-method plot,cprobd.list,ANY-method [,cprobd.list,ANY,ANY,ANY-method [,cprobd.list-method
Plot single nodes of a probabilistic suffix treecplot cplot,PSTf-method
Empirical conditional probability distributions of order 'L'cprob cprob,stslist-method
Generate sequences using a probabilistic suffix treegenerate generate,PSTf-method
Impute missing values using a probabilistic suffix treeimpute impute,PSTf,stslist-method
Log-Likelihood of a variable length Markov chain modellogLik logLik,PSTf-method
Extract the number of observations to which a VLMC model is fittedlnobs nobs,PSTf-method
Retrieve the node labels of a PSTnodenames nodenames,PSTf-method
Compute probabilistic divergence between two PSTpdist pdist,PSTf,PSTf-method
Plot a PSTplot,PSTf,ANY-method plot,PSTr,ANY-method
PST based pattern miningpmine pmine,PSTf,stslist-method
Plotting a branch of a probabilistic suffix treeppplot ppplot,PSTf-method
Prediction quality plotpqplot pqplot,PSTf,stslist-method
Compute the probability of categorical sequences using a probabilistic suffix treepredict predict,PSTf-method
Print method for objects of class 'PSTf' and 'PSTr'print print,PSTf-method print,PSTr-method
Prune a probabilistic suffix treeprune prune,PSTf-method
Flat representation of a probabilistic suffix treePSTf-class
Nested representation of a probabilistic suffix treePSTr-class [[,PSTr-method
Build a probabilistic suffix treepstree pstree,stslist-method
Retrieve counts or next symbol probability distributionquery query,PSTf-method round,cprobd-method
Example sequence data sets1
Longitudinal data on self rated healthSRH SRH.seq
Extract a subtree from a segmented PSTsubtree subtree,PSTf-method
Summary of variable length Markov chain modelsummary,PSTf-method summary,PSTr-method
AIC, AICc or BIC based model selectiontune tune,PSTf-method