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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
DOI: 10.32614/CRAN.package.FunChisq
Author: Yang Zhang [aut], Hua Zhong ORCID iD [aut], Hien Nguyen ORCID iD [aut], Ruby Sharma ORCID iD [aut], Sajal Kumar ORCID iD [aut], Yiyi Li ORCID iD [aut], Joe Song ORCID iD [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:

Please use the canonical form https://CRAN.R-project.org/package=FunChisq to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.