FunChisq: Model-Free Functional Chi-Squared and Exact Tests

Statistical hypothesis testing methods for inferring model-free functional dependency using asymptotic chi-squared or exact distributions. Functional test statistics are asymmetric and functionally optimal, unique from other related statistics. Tests in this package reveal evidence for causality based on the causality-by- functionality principle. They include asymptotic functional chi-squared tests (Zhang & Song 2013) <doi:10.48550/arXiv.1311.2707>, an adapted functional chi-squared test (Kumar & Song 2022) <doi:10.1093/bioinformatics/btac206>, and an exact functional test (Zhong & Song 2019) <doi:10.1109/TCBB.2018.2809743> (Nguyen et al. 2020) <doi:10.24963/ijcai.2020/372>. The normalized functional chi-squared test was used by Best Performer 'NMSUSongLab' in HPN-DREAM (DREAM8) Breast Cancer Network Inference Challenges (Hill et al. 2016) <doi:10.1038/nmeth.3773>. A function index (Zhong & Song 2019) <doi:10.1186/s12920-019-0565-9> (Kumar et al. 2018) <doi:10.1109/BIBM.2018.8621502> derived from the functional test statistic offers a new effect size measure for the strength of functional dependency, a better alternative to conditional entropy in many aspects. For continuous data, these tests offer an advantage over regression analysis when a parametric functional form cannot be assumed; for categorical data, they provide a novel means to assess directional dependency not possible with symmetrical Pearson's chi-squared or Fisher's exact tests.

Version:	2.5.4
Depends:	R (≥ 3.0.0)
Imports:	Rcpp, Rdpack (≥ 0.6-1), stats, dqrng
LinkingTo:	BH, Rcpp
Suggests:	Ckmeans.1d.dp, DescTools, DiffXTables, GridOnClusters, infotheo, knitr, rmarkdown, testthat (≥ 3.0.0)
Published:	2024-05-10
Author:	Yang Zhang [aut], Hua Zhong [aut], Hien Nguyen [aut], Ruby Sharma [aut], Sajal Kumar [aut], Yiyi Li [aut], Joe Song [aut, cre]
Maintainer:	Joe Song <joemsong at cs.nmsu.edu>
License:	LGPL (≥ 3)
URL:	https://www.cs.nmsu.edu/~joemsong/publications/
NeedsCompilation:	yes
Citation:	FunChisq citation info
Materials:	README NEWS
CRAN checks:	FunChisq results

Documentation:

Reference manual:	FunChisq.pdf
Vignettes:	Adapted versus original functional chi-squared tests and conditional entropy Using the exact functional test Measuring functional dependency model-free Examples of discrete patterns

Downloads:

Package source:	FunChisq_2.5.4.tar.gz
Windows binaries:	r-devel: FunChisq_2.5.4.zip, r-release: FunChisq_2.5.4.zip, r-oldrel: FunChisq_2.5.4.zip
macOS binaries:	r-release (arm64): FunChisq_2.5.4.tgz, r-oldrel (arm64): FunChisq_2.5.4.tgz, r-release (x86_64): FunChisq_2.5.4.tgz, r-oldrel (x86_64): FunChisq_2.5.4.tgz
Old sources:	FunChisq archive

Reverse dependencies:

Reverse suggests:

DiffXTables, GridOnClusters

Linking:

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