Package: tpc 1.0

Ronja Foraita

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.

Authors:Janine Witte [aut], Ronja Foraita [cre, ctb], DFG [fnd]

tpc_1.0.tar.gz
tpc_1.0.zip(r-4.7)tpc_1.0.zip(r-4.6)tpc_1.0.zip(r-4.5)
tpc_1.0.tgz(r-4.6-any)tpc_1.0.tgz(r-4.5-any)
tpc_1.0.tar.gz(r-4.7-any)tpc_1.0.tar.gz(r-4.6-any)
tpc_1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
tpc/json (API)

# Install 'tpc' in R:

install.packages('tpc', repos = c('https://bips-hb.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bips-hb/tpc/issues

Datasets:

dat_cohort - Simulated Cohort Data
dat_cohort_dis - Simulated Cohort Data - discretized
dat_cohort_mis - Simulated Cohort Data - with missing values
dat_sim - Simulated Data with a Partial Ordering
true_cohort - Cohort Data Structure
true_sim - A DAG with a Partial Ordering

On CRAN:

causal-discovery cohort-analysis graphical-models

3.90 score 8 stars 20 scripts 205 downloads 4 exports 35 dependencies

Last updated from:137e18be73. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	170
source / vignettes	OK	226
linux-release-x86_64	OK	205
macos-release-arm64	OK	111
macos-oldrel-arm64	OK	122
windows-devel	OK	157
windows-release	OK	111
windows-oldrel	OK	105
wasm-release	OK	176

Exports:MeekRules tpc tpc.cons.intern tskeleton

Dependencies:abind bdsmatrix BH BiocGenerics BiocManager cli clue cluster colorspace corpcor cpp11 DEoptimR fastICA generics ggm glue graph igraph lattice lifecycle lmtest magrittr MASS Matrix pcalg pkgconfig RBGL Rcpp RcppArmadillo rlang robustbase sfsmisc vcd vctrs zoo

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Simulated Cohort Data	dat_cohort
Simulated Cohort Data - discretized	dat_cohort_dis
Simulated Cohort Data - with missing values	dat_cohort_mis
Simulated Data with a Partial Ordering	dat_sim
Last Step of tPC Algorithm: Apply Meek's rules	MeekRules
PC Algorithm Accounting for a Partial Node Ordering	tpc
Utility for Conservative and Majority Rule in tpc	tpc.cons.intern
Cohort Data Structure	true_cohort
A DAG with a Partial Ordering	true_sim
Estimate the Skeleton of a DAG while Accounting for a Partial Ordering	tskeleton