Package: antedep 0.1.0

Chenyang Li

antedep: Antedependence Models for Longitudinal Data

Fitting, simulation, and inference for antedependence models for longitudinal data, as described in Zimmerman and Nunez-Anton (2009, ISBN:9781420011074). Supports integer-valued antedependence (INAD) models for count data with thinning operators (binomial, Poisson, negative binomial) and flexible innovation distributions (Poisson, Bell, negative binomial), categorical antedependence models for discrete-state longitudinal outcomes, and Gaussian antedependence (AD) models for continuous data. Implements maximum likelihood estimation via time-separable optimization and block coordinate descent, with confidence intervals based on Louis' identity and profile likelihood.

Authors:Chenyang Li [aut, cre], Dale Zimmerman [aut, ctb]

antedep_0.1.0.tar.gz
antedep_0.1.0.zip(r-4.7-any)antedep_0.1.0.zip(r-4.6-any)antedep_0.1.0.zip(r-4.5-any)
antedep_0.1.0.tgz(r-4.6-any)antedep_0.1.0.tgz(r-4.5-any)
antedep_0.1.0.tar.gz(r-4.7-any)antedep_0.1.0.tar.gz(r-4.6-any)
antedep_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
antedep/json (API)

# Install 'antedep' in R:

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

Bug tracker:https://github.com/tanchyking/antedep/issues

Pkgdown/docs site:https://tanchyking.github.io

Datasets:

bolus_inad - Morphine bolus analgesia counts
cattle_growth - Cattle growth data
cochlear_implant - Cochlear implant speech recognition data
labor_force_cat - Labor force longitudinal categorical data
race_100km - 100km race split-time data

On CRAN:

4.60 score 350 downloads 50 exports 19 dependencies

Last updated from:355a34576c. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel	OK	191
source / vignettes	OK	251
linux-release	OK	156
macos-release	OK	180
macos-oldrel	OK	226
windows-devel	OK	128
windows-release	OK	150
windows-oldrel	OK	119
wasm-release	OK	100

Exports:aic_cat aic_gau aic_inad bic_cat bic_gau bic_inad bic_order_cat bic_order_gau bic_order_inad ci_cat ci_gau ci_inad dbell em_cat em_gau em_inad fit_cat fit_gau fit_inad logL_cat logL_gau logL_inad logL_inad_i partial_corr pbell plot_prism plot_profile qbell rbell run_homogeneity_tests_inad run_order_tests_cat run_stationarity_tests_cat run_stationarity_tests_gau run_stationarity_tests_inad simulate_cat simulate_gau simulate_inad test_contrast_gau test_homogeneity_cat test_homogeneity_gau test_homogeneity_inad test_one_sample_gau test_order_cat test_order_gau test_order_inad test_stationarity_cat test_stationarity_gau test_stationarity_inad test_timeinvariance_cat test_two_sample_gau

Dependencies:cli cpp11 farver ggplot2 glue gtable isoband labeling lifecycle MASS nloptr R6 RColorBrewer rlang S7 scales vctrs viridisLite withr

Introduction to antedep

Rendered fromantedep-intro.Rmdusingknitr::rmarkdown

Last update: 2026-04-21
Started: 2026-02-08

Help page	Topics
Akaike information criterion for fitted categorical AD models	aic_cat
Akaike information criterion for fitted Gaussian AD models	aic_gau
Akaike information criterion for fitted INAD models	aic_inad
The Bell distribution	Bell dbell pbell qbell rbell
Bayesian information criterion for fitted categorical AD models	bic_cat
Bayesian information criterion for fitted Gaussian AD models	bic_gau
Bayesian information criterion for fitted INAD models	bic_inad
BIC-based order selection for categorical AD models	bic_order_cat
BIC-based order selection for Gaussian AD models	bic_order_gau
BIC-based order selection for INAD models	bic_order_inad
Morphine bolus analgesia counts	bolus_inad
Cattle growth data (Treatments A and B)	cattle_growth
Confidence intervals for fitted categorical AD models	ci_cat
Confidence intervals for fitted Gaussian AD models	ci_gau
Confidence intervals for fitted INAD models	ci_inad
Cochlear implant speech recognition data	cochlear_implant
EM algorithm for categorical AD model estimation	em_cat
EM algorithm for Gaussian AD model estimation	em_gau
EM algorithm for INAD model estimation	em_inad
Fit categorical antedependence model by maximum likelihood	fit_cat
Fit Gaussian antedependence model by maximum likelihood	fit_gau
Fit INAD antedependence model by maximum likelihood	fit_inad
Labor force longitudinal categorical data (Table 1)	labor_force_cat
Log-likelihood for categorical AD models (with missing data support)	logL_cat
Log-likelihood for Gaussian AD models (with missing data support)	logL_gau
Log-likelihood for INAD models (with missing data support)	logL_inad
INAD log likelihood contribution at time i (no fixed effect)	logL_inad_i
Compute intervenor-adjusted partial correlation matrix	partial_corr
PRISM plot (Partial Residual Intervenor Scatterplot Matrix)	plot_prism
Profile plot (spaghetti plot) for longitudinal data	plot_profile
Print method for cat_ci objects	print.cat_ci
Print method for cat_fit objects	print.cat_fit
Print method for cat_lrt objects	print.cat_lrt
Print method for BIC order selection	print.gau_bic_order
Print method for AD confidence intervals	print.gau_ci
Print method for AD contrast test	print.gau_contrast_test
Print method for gau_fit objects	print.gau_fit
Print method for AD homogeneity test	print.gau_homogeneity_test
Print method for AD mean test	print.gau_mean_test
Print method for AD order test	print.gau_order_test
Print method for homogeneity_tests_inad	print.homogeneity_tests_inad
Print method for INAD confidence intervals	print.inad_ci
Print method for INAD model fits	print.inad_fit
Print method for test_homogeneity_inad	print.test_homogeneity_inad
100km race split-time data	race_100km
Run all homogeneity tests for INAD	run_homogeneity_tests_inad
Run all pairwise order tests	run_order_tests_cat
Run all stationarity-related tests for categorical AD	run_stationarity_tests_cat
Run all stationarity-related tests for Gaussian AD	run_stationarity_tests_gau
Run all stationarity-related tests for INAD	run_stationarity_tests_inad
Simulate categorical antedependence series	simulate_cat
Simulate Gaussian antedependence series	simulate_gau
Simulate INAD antedependence series	simulate_inad
Summary method for cat_ci objects	summary.cat_ci
Summary method for gau_ci objects	summary.gau_ci
Summary method for inad_ci objects	summary.inad_ci
Test linear hypotheses on the mean under antedependence	test_contrast_gau
Likelihood ratio test for homogeneity across groups (categorical AD data)	test_homogeneity_cat
Likelihood ratio test for homogeneity across groups (Gaussian AD data)	test_homogeneity_gau
Likelihood ratio test for homogeneity across groups (INAD data)	test_homogeneity_inad
One-sample test for mean structure under antedependence	test_one_sample_gau
Likelihood ratio test for antedependence order (categorical AD data)	test_order_cat
Likelihood ratio test for antedependence order (Gaussian AD data)	test_order_gau
Likelihood ratio test for antedependence order (INAD data)	test_order_inad
Likelihood ratio test for stationarity (categorical AD data)	test_stationarity_cat
Likelihood ratio test for stationarity (Gaussian AD data)	test_stationarity_gau
Likelihood ratio test for stationarity (INAD data)	test_stationarity_inad
Likelihood ratio test for time-invariance (categorical data)	test_timeinvariance_cat
Two-sample test for equality of mean profiles under antedependence	test_two_sample_gau

Package: antedep 0.1.0

antedep: Antedependence Models for Longitudinal Data

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