MCL - Markov Cluster Algorithm

Contains the Markov cluster algorithm (MCL) for identifying clusters in networks and graphs. The algorithm simulates random walks on a (n x n) matrix as the adjacency matrix of a graph. It alternates an expansion step and an inflation step until an equilibrium state is reached.

Last updated 10 years ago

4.41 score 2 stars 6 dependents 72 scripts 442 downloads

CVN - Covariate-Varying Networks

Inferring high-dimensional Gaussian graphical networks that change with multiple discrete covariates. Louis Dijkstra, Arne Godt, Ronja Foraita (2024) <arXiv:2407.19978>.

Last updated 7 days ago

graphical-modelshigh-dimensional-statisticsnetwork-analysiscpp

3.70 score 7 scripts

micd - Multiple Imputation in Causal Graph Discovery

Modified functions of the package 'pcalg' and some additional functions to run the PC and the FCI (Fast Causal Inference) algorithm for constraint-based causal discovery in incomplete and multiply imputed datasets. Foraita R, Friemel J, Günther K, Behrens T, Bullerdiek J, Nimzyk R, Ahrens W, Didelez V (2020) <doi:10.1111/rssa.12565>; Andrews RM, Foraita R, Didelez V, Witte J (2021) <arXiv:2108.13395>; Witte J, Foraita R, Didelez V (2022) <doi:10.1002/sim.9535>.

Last updated 2 years ago

causal-discoverygraphical-modelsmultiple-imputation

3.70 score 5 stars 20 scripts 255 downloads

tpc - Tiered PC Algorithm

Constraint-based causal discovery using the PC algorithm while accounting for a partial node ordering, for example a partial temporal ordering when the data were collected in different waves of a cohort study. Andrews RM, Foraita R, Didelez V, Witte J (2021) <arXiv:2108.13395> provide a guide how to use tpc to analyse cohort data.

Last updated 2 years ago

causal-discoverycohort-analysisgraphical-models

3.60 score 5 stars 16 scripts 159 downloads

HMMpa - Analysing Accelerometer Data Using Hidden Markov Models

Analysing time-series accelerometer data to quantify length and intensity of physical activity using hidden Markov models. It also contains the traditional cut-off point method. Witowski V, Foraita R, Pitsiladis Y, Pigeot I, Wirsik N (2014). <doi:10.1371/journal.pone.0114089>.

Last updated 19 days ago

accelerometer-datahidden-markov-modeltime-series

3.18 score 1 dependents 319 downloads