R/chapters.R
In ocbe-uio/contingencytables: Statistical Analysis of Contingency Tables
Defines functions
validate_chapter_choice
list_functions
Documented in
list_functions
#' @name chap1
#' @title Chapter 1: Introduction
#' @description There are no functions for Chapter 1 (Introduction), only from
#' Chapters 2 to 10.
#' @references
#' - Fagerland MW, Lydersen S, Laake P (2017) Statistical Analysis of
#' Contingency Tables. Chapman & Hall/CRC, Boca Raton, FL
#' - https://contingencytables.com/
#' - https://www.routledge.com/Statistical-Analysis-of-Contingency-Tables/Fagerland-Lydersen-Laake/p/book/9781466588172
NULL
#' @name chap2
#' @title Chapter 2: The 1x2 Table and the Binomial Distribution
#' @description These are the functions related to chapter 2:
#' \enumerate{
#' \item{AgrestiCoull_CI_1x2}
#' \item{Arcsine_CI_1x2}
#' \item{Wald_CI_1x2}
#' \item{Blaker_exact_CI_1x2}
#' \item{Blaker_exact_test_1x2}
#' \item{Blaker_midP_CI_1x2}
#' \item{Blaker_midP_test_1x2}
#' \item{ClopperPearson_exact_CI_1x2}
#' \item{ClopperPearson_midP_CI_1x2}
#' \item{Exact_binomial_test_1x2}
#' \item{Jeffreys_CI_1x2}
#' \item{LR_CI_1x2}
#' \item{LR_test_1x2}
#' \item{MidP_binomial_test_1x2}
#' \item{Score_test_1x2}
#' \item{Score_test_CC_1x2}
#' \item{Wald_CI_CC_1x2}
#' \item{Wilson_score_CI_1x2}
#' \item{Wilson_score_CI_CC_1x2}
#' \item{the_1x2_table_CIs}
#' \item{Wald_test_1x2}
#' \item{Wald_test_CC_1x2}
#' \item{the_1x2_table_tests}
#' }
#' @note You can also print the list above with \code{list_functions(2)}.
#' @references
#' - Fagerland MW, Lydersen S, Laake P (2017) Statistical Analysis of
#' Contingency Tables. Chapman & Hall/CRC, Boca Raton, FL
#' - https://contingencytables.com/
#' - https://www.routledge.com/Statistical-Analysis-of-Contingency-Tables/Fagerland-Lydersen-Laake/p/book/9781466588172
NULL
#' @name chap3
#' @title Chapter 3: The 1xc Table and the Multinomial Distribution
#' @description These are the functions related to chapter 3:
#' \enumerate{
#' \item{Chacko_test_1xc}
#' \item{Exact_multinomial_test_1xc}
#' \item{Gold_Wald_CIs_1xc}
#' \item{Goodman_Wald_CIs_1xc}
#' \item{Goodman_Wald_CIs_for_diffs_1xc}
#' \item{Goodman_Wilson_score_CIs_1xc}
#' \item{LR_test_1xc}
#' \item{MidP_multinomial_test_1xc}
#' \item{Pearson_chi_squared_test_1xc}
#' \item{QuesenberryHurst_Wilson_score_CIs_1xc}
#' \item{the_1xc_table_CIs}
#' \item{the_1xc_table_tests}
#' }
#' @note You can also print the list above with \code{list_functions(3)}.
#' @references
#' - Fagerland MW, Lydersen S, Laake P (2017) Statistical Analysis of
#' Contingency Tables. Chapman & Hall/CRC, Boca Raton, FL
#' - https://contingencytables.com/
#' - https://www.routledge.com/Statistical-Analysis-of-Contingency-Tables/Fagerland-Lydersen-Laake/p/book/9781466588172
NULL
#' @name chap4
#' @title Chapter 4: The 2x2 Table
#' @description These are the functions related to chapter 4:
#' \enumerate{
#' \item{Adjusted_inv_sinh_CI_OR_2x2}
#' \item{Adjusted_inv_sinh_CI_ratio_2x2}
#' \item{Adjusted_log_CI_2x2}
#' \item{AgrestiCaffo_CI_2x2}
#' \item{Wald_CI_2x2}
#' \item{BaptistaPike_exact_conditional_CI_2x2}
#' \item{BaptistaPike_midP_CI_2x2}
#' \item{Cornfield_exact_conditional_CI_2x2}
#' \item{Cornfield_midP_CI_2x2}
#' \item{Fisher_exact_test_2x2}
#' \item{Exact_unconditional_test_2x2}
#' \item{Fisher_midP_test_2x2}
#' \item{Gart_adjusted_logit_CI_2x2}
#' \item{Independence_smoothed_logit_CI_2x2}
#' \item{Inv_sinh_CI_OR_2x2}
#' \item{Inv_sinh_CI_ratio_2x2}
#' \item{Katz_log_CI_2x2}
#' \item{Koopman_asymptotic_score_CI_2x2}
#' \item{LR_test_2x2}
#' \item{Mee_asymptotic_score_CI_2x2}
#' \item{MiettinenNurminen_asymptotic_score_CI_difference_2x2}
#' \item{MiettinenNurminen_asymptotic_score_CI_OR_2x2}
#' \item{MiettinenNurminen_asymptotic_score_CI_ratio_2x2}
#' \item{MOVER_R_Wilson_CI_OR_2x2}
#' \item{MOVER_R_Wilson_CI_ratio_2x2}
#' \item{Newcombe_hybrid_score_CI_2x2}
#' \item{Pearson_chi_squared_test_2x2}
#' \item{Pearson_chi_squared_test_CC_2x2}
#' \item{PriceBonett_approximate_Bayes_CI_2x2}
#' \item{Wald_CI_CC_2x2}
#' \item{Woolf_logit_CI_2x2}
#' \item{Uncorrected_asymptotic_score_CI_2x2}
#' \item{Z_unpooled_test_2x2}
#' \item{the_2x2_table_CIs_difference}
#' \item{the_2x2_table_CIs_OR}
#' \item{the_2x2_table_CIs_ratio}
#' \item{the_2x2_table_tests}
#' }
#' @note You can also print the list above with \code{list_functions(4)}.
#' @references
#' - Fagerland MW, Lydersen S, Laake P (2017) Statistical Analysis of
#' Contingency Tables. Chapman & Hall/CRC, Boca Raton, FL
#' - https://contingencytables.com/
#' - https://www.routledge.com/Statistical-Analysis-of-Contingency-Tables/Fagerland-Lydersen-Laake/p/book/9781466588172
NULL
#' @name chap5
#' @title Chapter 5: The Ordered rx2 Table
#' @description These are the functions related to chapter 5:
#' \enumerate{
#' \item{CochranArmitage_CI_rx2}
#' \item{CochranArmitage_exact_cond_midP_tests_rx2}
#' \item{CochranArmitage_MH_tests_rx2}
#' \item{Exact_cond_midP_unspecific_ordering_rx2}
#' \item{Pearson_LR_tests_unspecific_ordering_rx2}
#' \item{the_rx2_table}
#' \item{Trend_estimate_CI_tests_rx2}
#' }
#' @note You can also print the list above with \code{list_functions(5)}.
#' @references
#' - Fagerland MW, Lydersen S, Laake P (2017) Statistical Analysis of
#' Contingency Tables. Chapman & Hall/CRC, Boca Raton, FL
#' - https://contingencytables.com/
#' - https://www.routledge.com/Statistical-Analysis-of-Contingency-Tables/Fagerland-Lydersen-Laake/p/book/9781466588172
NULL
#' @name chap6
#' @title Chapter 6: The Ordered 2xc Table
#' @description These are the functions related to chapter 6:
#' \enumerate{
#' \item{Brant_test_2xc}
#' \item{Cumulative_models_for_2xc}
#' \item{Exact_cond_midP_linear_rank_tests_2xc}
#' \item{ClopperPearson_exact_CI_1x2_beta_version}
#' \item{Exact_cond_midP_unspecific_ordering_rx2}
#' \item{MantelHaenszel_test_2xc}
#' \item{Pearson_LR_tests_cum_OR_2xc}
#' \item{Score_test_for_effect_in_the_probit_model_2xc}
#' \item{the_2xc_table}
#' }
#' @note You can also print the list above with \code{list_functions(6)}.
#' @references
#' - Fagerland MW, Lydersen S, Laake P (2017) Statistical Analysis of
#' Contingency Tables. Chapman & Hall/CRC, Boca Raton, FL
#' - https://contingencytables.com/
#' - https://www.routledge.com/Statistical-Analysis-of-Contingency-Tables/Fagerland-Lydersen-Laake/p/book/9781466588172
NULL
#' @name chap7
#' @title Chapter 7: The rxc Table
#' @description These are the functions related to chapter 7:
#' \enumerate{
#' \item{Bonferroni_type_CIs_rxc}
#' \item{Cumulative_models_for_rxc}
#' \item{Exact_cond_midP_tests_rxc}
#' \item{FisherFreemanHalton_asymptotic_test_rxc}
#' \item{gamma_coefficient_rxc_bca}
#' \item{gamma_coefficient_rxc}
#' \item{JonckheereTerpstra_test_rxc}
#' \item{Kendalls_tau_b_rxc}
#' \item{Kendalls_tau_b_rxc_bca}
#' \item{KruskalWallis_asymptotic_test_rxc}
#' \item{linear_by_linear_test_rxc}
#' \item{Pearson_correlation_coefficient_rxc}
#' \item{Pearson_correlation_coefficient_rxc_bca}
#' \item{Pearson_LR_tests_rxc}
#' \item{Pearson_residuals_rxc}
#' \item{Scheffe_type_CIs_rxc}
#' \item{Spearman_correlation_coefficient_rxc}
#' \item{Spearman_correlation_coefficient_rxc_bca}
#' \item{the_rxc_table}
#' }
#' @note You can also print the list above with \code{list_functions(7)}.
#' @references
#' - Fagerland MW, Lydersen S, Laake P (2017) Statistical Analysis of
#' Contingency Tables. Chapman & Hall/CRC, Boca Raton, FL
#' - https://contingencytables.com/
#' - https://www.routledge.com/Statistical-Analysis-of-Contingency-Tables/Fagerland-Lydersen-Laake/p/book/9781466588172
NULL
#' @name chap8
#' @title Chapter 8: The Paired 2x2 Table
#' @description These are the functions related to chapter 8:
#' \enumerate{
#' \item{BonettPrice_hybrid_Wilson_score_CI_CC_paired_2x2}
#' \item{BonettPrice_hybrid_Wilson_score_CI_paired_2x2}
#' \item{ClopperPearson_exact_CI_1x2_beta_version}
#' \item{McNemar_asymptotic_test_CC_paired_2x2}
#' \item{McNemar_asymptotic_test_paired_2x2}
#' \item{McNemar_exact_cond_test_paired_2x2}
#' \item{McNemar_exact_unconditional_test_paired_2x2}
#' \item{McNemar_midP_test_paired_2x2}
#' \item{Tang_asymptotic_score_CI_paired_2x2}
#' \item{Tango_asymptotic_score_CI_paired_2x2}
#' \item{MOVER_Wilson_score_CI_paired_2x2}
#' \item{Newcombe_square_and_add_CI_paired_2x2}
#' \item{Transformed_Blaker_exact_CI_paired_2x2}
#' \item{Transformed_Clopper_Pearson_exact_CI_paired_2x2}
#' \item{Transformed_Clopper_Pearson_midP_CI_paired_2x2}
#' \item{Transformed_Wilson_score_CI_paired_2x2}
#' \item{Wald_CI_diff_paired_2x2}
#' \item{Wald_CI_diff_CC_paired_2x2}
#' \item{Wald_CI_AgrestiMin_paired_2x2}
#' \item{Wald_CI_BonettPrice_paired_2x2}
#' \item{Wald_CI_OR_Laplace_paired_2x2}
#' \item{Wald_CI_OR_paired_2x2}
#' \item{Wald_CI_ratio_paired_2x2}
#' \item{the_paired_2x2_table_CIs_difference}
#' \item{the_paired_2x2_table_CIs_OR}
#' \item{the_paired_2x2_table_CIs_ratio}
#' \item{the_paired_2x2_table_tests}
#' }
#' @note You can also print the list above with \code{list_functions(8)}.
#' @references
#' - Fagerland MW, Lydersen S, Laake P (2017) Statistical Analysis of
#' Contingency Tables. Chapman & Hall/CRC, Boca Raton, FL
#' - https://contingencytables.com/
#' - https://www.routledge.com/Statistical-Analysis-of-Contingency-Tables/Fagerland-Lydersen-Laake/p/book/9781466588172
NULL
#' @name chap9
#' @title Chapter 9: The Paired cxc Table
#' @description These are the functions related to chapter 9:
#' \enumerate{
#' \item{Bhapkar_test_paired_cxc}
#' \item{Bonferroni_type_CIs_paired_cxc}
#' \item{FleissEveritt_test_paired_cxc}
#' \item{FleissLevinPaik_test_paired_cxc}
#' \item{McNemarBowker_test_paired_cxc}
#' \item{Scheffe_type_CIs_paired_cxc}
#' \item{Score_test_and_CI_marginal_mean_scores_paired_cxc}
#' \item{Stuart_test_paired_cxc}
#' \item{Wald_test_and_CI_marginal_mean_ranks_paired_cxc}
#' \item{Wald_test_and_CI_marginal_mean_scores_paired_cxc}
#' \item{the_paired_cxc_table_nominal}
#' \item{the_paired_cxc_table_ordinal}
#' }
#' @note You can also print the list above with \code{list_functions(9)}.
#' @references
#' - Fagerland MW, Lydersen S, Laake P (2017) Statistical Analysis of
#' Contingency Tables. Chapman & Hall/CRC, Boca Raton, FL
#' - https://contingencytables.com/
#' - https://www.routledge.com/Statistical-Analysis-of-Contingency-Tables/Fagerland-Lydersen-Laake/p/book/9781466588172
NULL
#' @name chap10
#' @title Chapter 10: Stratified 2x2 Tables and Meta-Analysis
#' @description These are the functions related to chapter 10:
#' \enumerate{
#' \item{BreslowDay_homogeneity_test_stratified_2x2}
#' \item{CochranMantelHaenszel_test_stratified_2x2}
#' \item{Cochran_Q_test_stratified_2x2}
#' \item{InverseVariance_estimate_stratified_2x2}
#' \item{ML_estimates_and_CIs_stratified_2x2}
#' \item{MantelHaenszel_estimate_stratified_2x2}
#' \item{Pearson_LR_homogeneity_test_stratified_2x2}
#' \item{Pearson_LR_test_common_effect_stratified_2x2}
#' \item{Peto_homogeneity_test_stratified_2x2}
#' \item{Peto_OR_estimate_stratified_2x2}
#' \item{RBG_test_and_CI_stratified_2x2}
#' \item{Wald_test_and_CI_common_diff_stratified_2x2}
#' \item{Wald_test_and_CI_common_ratio_stratified_2x2}
#' \item{Woolf_test_and_CI_stratified_2x2}
#' \item{stratified_2x2_tables}
#' }
#' @note You can also print the list above with \code{list_functions(10)}.
#' @references
#' - Fagerland MW, Lydersen S, Laake P (2017) Statistical Analysis of
#' Contingency Tables. Chapman & Hall/CRC, Boca Raton, FL
#' - https://contingencytables.com/
#' - https://www.routledge.com/Statistical-Analysis-of-Contingency-Tables/Fagerland-Lydersen-Laake/p/book/9781466588172
NULL
#' @title List functions from a chapter
#' @description Complements the \code{?chapX} command by printing a list of
#' functions related to a particular chapter `X` on the R console.
#' @param chap_num Number of book chapter (from 2 to 10)
#' @return List of functions from that chapter
#' @author Waldir Leoncio
#' @export
list_functions <- function(chap_num) {
validate_chapter_choice(chap_num)
message("Chapter ", chap_num, " functions:")
cat(paste0(full_list_chapter_functions[[chap_num - 1]], "()"), sep = "\n")
message(
"Learn more about an individual function with ?<function_name> and ",
"example(<function_name>)."
)
}
# ============================================================================ #
# Internal functions and objects used in this file #
# ============================================================================ #
validate_chapter_choice <- function(chap_num) {
# Makes sure the user chooses a proper chapter number
if (missing(chap_num)) stop("Please choose a chapter between 2 and 10.")
if (chap_num < 2 | chap_num > 10) {
stop("Please choose a chapter between 2 and 10.")
}
}
full_list_chapter_functions <- list(
# Lists of functions pertaining to a certain chapter
ch2 = c(
"AgrestiCoull_CI_1x2",
"Arcsine_CI_1x2",
"Wald_CI_1x2",
"Blaker_exact_CI_1x2",
"Blaker_exact_test_1x2",
"Blaker_midP_CI_1x2",
"Blaker_midP_test_1x2",
"ClopperPearson_exact_CI_1x2",
"ClopperPearson_midP_CI_1x2",
"Exact_binomial_test_1x2",
"Jeffreys_CI_1x2",
"LR_CI_1x2",
"LR_test_1x2",
"MidP_binomial_test_1x2",
"Score_test_1x2",
"Score_test_CC_1x2",
"Wald_CI_CC_1x2",
"Wilson_score_CI_1x2",
"Wilson_score_CI_CC_1x2",
"the_1x2_table_CIs",
"Wald_test_1x2",
"Wald_test_CC_1x2",
"the_1x2_table_tests"
),
ch3 = c(
"Chacko_test_1xc",
"Exact_multinomial_test_1xc",
"Gold_Wald_CIs_1xc",
"Goodman_Wald_CIs_1xc",
"Goodman_Wald_CIs_for_diffs_1xc",
"Goodman_Wilson_score_CIs_1xc",
"LR_test_1xc",
"MidP_multinomial_test_1xc",
"Pearson_chi_squared_test_1xc",
"QuesenberryHurst_Wilson_score_CIs_1xc",
"the_1xc_table_CIs",
"the_1xc_table_tests"
),
ch4 = c(
"Adjusted_inv_sinh_CI_OR_2x2",
"Adjusted_inv_sinh_CI_ratio_2x2",
"Adjusted_log_CI_2x2",
"AgrestiCaffo_CI_2x2",
"Wald_CI_2x2",
"BaptistaPike_exact_conditional_CI_2x2",
"BaptistaPike_midP_CI_2x2",
"Cornfield_exact_conditional_CI_2x2",
"Cornfield_midP_CI_2x2",
"Fisher_exact_test_2x2",
"Exact_unconditional_test_2x2",
"Fisher_midP_test_2x2",
"Gart_adjusted_logit_CI_2x2",
"Independence_smoothed_logit_CI_2x2",
"Inv_sinh_CI_OR_2x2",
"Inv_sinh_CI_ratio_2x2",
"Katz_log_CI_2x2",
"Koopman_asymptotic_score_CI_2x2",
"LR_test_2x2",
"Mee_asymptotic_score_CI_2x2",
"MiettinenNurminen_asymptotic_score_CI_difference_2x2",
"MiettinenNurminen_asymptotic_score_CI_OR_2x2",
"MiettinenNurminen_asymptotic_score_CI_ratio_2x2",
"MOVER_R_Wilson_CI_OR_2x2",
"MOVER_R_Wilson_CI_ratio_2x2",
"Newcombe_hybrid_score_CI_2x2",
"Pearson_chi_squared_test_2x2",
"Pearson_chi_squared_test_CC_2x2",
"PriceBonett_approximate_Bayes_CI_2x2",
"Wald_CI_CC_2x2",
"Woolf_logit_CI_2x2",
"Uncorrected_asymptotic_score_CI_2x2",
"Z_unpooled_test_2x2",
"the_2x2_table_CIs_difference",
"the_2x2_table_CIs_OR",
"the_2x2_table_CIs_ratio",
"the_2x2_table_tests"
),
ch5 = c(
"CochranArmitage_CI_rx2",
"CochranArmitage_exact_cond_midP_tests_rx2",
"CochranArmitage_MH_tests_rx2",
"Exact_cond_midP_unspecific_ordering_rx2",
"Pearson_LR_tests_unspecific_ordering_rx2",
"the_rx2_table",
"Trend_estimate_CI_tests_rx2"
),
ch6 = c(
"Brant_test_2xc",
"Cumulative_models_for_2xc",
"Exact_cond_midP_linear_rank_tests_2xc",
"ClopperPearson_exact_CI_1x2_beta_version",
"Exact_cond_midP_unspecific_ordering_rx2",
"MantelHaenszel_test_2xc",
"Pearson_LR_tests_cum_OR_2xc",
"Score_test_for_effect_in_the_probit_model_2xc",
"the_2xc_table"
),
ch7 = c(
"Bonferroni_type_CIs_rxc",
"Cumulative_models_for_rxc",
"Exact_cond_midP_tests_rxc",
"FisherFreemanHalton_asymptotic_test_rxc",
"gamma_coefficient_rxc_bca",
"gamma_coefficient_rxc",
"JonckheereTerpstra_test_rxc",
"Kendalls_tau_b_rxc",
"Kendalls_tau_b_rxc_bca",
"KruskalWallis_asymptotic_test_rxc",
"linear_by_linear_test_rxc",
"Pearson_correlation_coefficient_rxc",
"Pearson_correlation_coefficient_rxc_bca",
"Pearson_LR_tests_rxc",
"Pearson_residuals_rxc",
"Scheffe_type_CIs_rxc",
"Spearman_correlation_coefficient_rxc",
"Spearman_correlation_coefficient_rxc_bca",
"the_rxc_table"
),
ch8 = c(
"BonettPrice_hybrid_Wilson_score_CI_CC_paired_2x2",
"BonettPrice_hybrid_Wilson_score_CI_paired_2x2",
"ClopperPearson_exact_CI_1x2_beta_version",
"McNemar_asymptotic_test_CC_paired_2x2",
"McNemar_asymptotic_test_paired_2x2",
"McNemar_exact_cond_test_paired_2x2",
"McNemar_exact_unconditional_test_paired_2x2",
"McNemar_midP_test_paired_2x2",
"Tang_asymptotic_score_CI_paired_2x2",
"Tango_asymptotic_score_CI_paired_2x2",
"MOVER_Wilson_score_CI_paired_2x2",
"Newcombe_square_and_add_CI_paired_2x2",
"Transformed_Blaker_exact_CI_paired_2x2",
"Transformed_Clopper_Pearson_exact_CI_paired_2x2",
"Transformed_Clopper_Pearson_midP_CI_paired_2x2",
"Transformed_Wilson_score_CI_paired_2x2",
"Wald_CI_diff_paired_2x2",
"Wald_CI_diff_CC_paired_2x2",
"Wald_CI_AgrestiMin_paired_2x2",
"Wald_CI_BonettPrice_paired_2x2",
"Wald_CI_OR_Laplace_paired_2x2",
"Wald_CI_OR_paired_2x2",
"Wald_CI_ratio_paired_2x2",
"the_paired_2x2_table_CIs_difference",
"the_paired_2x2_table_CIs_OR",
"the_paired_2x2_table_CIs_ratio",
"the_paired_2x2_table_tests"
),
ch9 = c(
"Bhapkar_test_paired_cxc",
"Bonferroni_type_CIs_paired_cxc",
"FleissEveritt_test_paired_cxc",
"FleissLevinPaik_test_paired_cxc",
"McNemarBowker_test_paired_cxc",
"Scheffe_type_CIs_paired_cxc",
"Score_test_and_CI_marginal_mean_scores_paired_cxc",
"Stuart_test_paired_cxc",
"Wald_test_and_CI_marginal_mean_ranks_paired_cxc",
"Wald_test_and_CI_marginal_mean_scores_paired_cxc",
"the_paired_cxc_table_nominal",
"the_paired_cxc_table_ordinal"
),
ch10 = c(
"BreslowDay_homogeneity_test_stratified_2x2",
"CochranMantelHaenszel_test_stratified_2x2",
"Cochran_Q_test_stratified_2x2",
"InverseVariance_estimate_stratified_2x2",
"ML_estimates_and_CIs_stratified_2x2",
"MantelHaenszel_estimate_stratified_2x2",
"Pearson_LR_homogeneity_test_stratified_2x2",
"Pearson_LR_test_common_effect_stratified_2x2",
"Peto_homogeneity_test_stratified_2x2",
"Peto_OR_estimate_stratified_2x2",
"RBG_test_and_CI_stratified_2x2",
"Wald_test_and_CI_common_diff_stratified_2x2",
"Wald_test_and_CI_common_ratio_stratified_2x2",
"Woolf_test_and_CI_stratified_2x2",
"stratified_2x2_tables"
)
)
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Defines functions validate_chapter_choice list_functions
Documented in list_functions
#' @name chap1
#' @title Chapter 1: Introduction
#' @description There are no functions for Chapter 1 (Introduction), only from
#' Chapters 2 to 10.
#' @references
#' - Fagerland MW, Lydersen S, Laake P (2017) Statistical Analysis of
#' Contingency Tables. Chapman & Hall/CRC, Boca Raton, FL
#' - https://contingencytables.com/
#' - https://www.routledge.com/Statistical-Analysis-of-Contingency-Tables/Fagerland-Lydersen-Laake/p/book/9781466588172
NULL
#' @name chap2
#' @title Chapter 2: The 1x2 Table and the Binomial Distribution
#' @description These are the functions related to chapter 2:
#' \enumerate{
#' \item{AgrestiCoull_CI_1x2}
#' \item{Arcsine_CI_1x2}
#' \item{Wald_CI_1x2}
#' \item{Blaker_exact_CI_1x2}
#' \item{Blaker_exact_test_1x2}
#' \item{Blaker_midP_CI_1x2}
#' \item{Blaker_midP_test_1x2}
#' \item{ClopperPearson_exact_CI_1x2}
#' \item{ClopperPearson_midP_CI_1x2}
#' \item{Exact_binomial_test_1x2}
#' \item{Jeffreys_CI_1x2}
#' \item{LR_CI_1x2}
#' \item{LR_test_1x2}
#' \item{MidP_binomial_test_1x2}
#' \item{Score_test_1x2}
#' \item{Score_test_CC_1x2}
#' \item{Wald_CI_CC_1x2}
#' \item{Wilson_score_CI_1x2}
#' \item{Wilson_score_CI_CC_1x2}
#' \item{the_1x2_table_CIs}
#' \item{Wald_test_1x2}
#' \item{Wald_test_CC_1x2}
#' \item{the_1x2_table_tests}
#' }
#' @note You can also print the list above with \code{list_functions(2)}.
#' @references
#' - Fagerland MW, Lydersen S, Laake P (2017) Statistical Analysis of
#' Contingency Tables. Chapman & Hall/CRC, Boca Raton, FL
#' - https://contingencytables.com/
#' - https://www.routledge.com/Statistical-Analysis-of-Contingency-Tables/Fagerland-Lydersen-Laake/p/book/9781466588172
NULL
#' @name chap3
#' @title Chapter 3: The 1xc Table and the Multinomial Distribution
#' @description These are the functions related to chapter 3:
#' \enumerate{
#' \item{Chacko_test_1xc}
#' \item{Exact_multinomial_test_1xc}
#' \item{Gold_Wald_CIs_1xc}
#' \item{Goodman_Wald_CIs_1xc}
#' \item{Goodman_Wald_CIs_for_diffs_1xc}
#' \item{Goodman_Wilson_score_CIs_1xc}
#' \item{LR_test_1xc}
#' \item{MidP_multinomial_test_1xc}
#' \item{Pearson_chi_squared_test_1xc}
#' \item{QuesenberryHurst_Wilson_score_CIs_1xc}
#' \item{the_1xc_table_CIs}
#' \item{the_1xc_table_tests}
#' }
#' @note You can also print the list above with \code{list_functions(3)}.
#' @references
#' - Fagerland MW, Lydersen S, Laake P (2017) Statistical Analysis of
#' Contingency Tables. Chapman & Hall/CRC, Boca Raton, FL
#' - https://contingencytables.com/
#' - https://www.routledge.com/Statistical-Analysis-of-Contingency-Tables/Fagerland-Lydersen-Laake/p/book/9781466588172
NULL
#' @name chap4
#' @title Chapter 4: The 2x2 Table
#' @description These are the functions related to chapter 4:
#' \enumerate{
#' \item{Adjusted_inv_sinh_CI_OR_2x2}
#' \item{Adjusted_inv_sinh_CI_ratio_2x2}
#' \item{Adjusted_log_CI_2x2}
#' \item{AgrestiCaffo_CI_2x2}
#' \item{Wald_CI_2x2}
#' \item{BaptistaPike_exact_conditional_CI_2x2}
#' \item{BaptistaPike_midP_CI_2x2}
#' \item{Cornfield_exact_conditional_CI_2x2}
#' \item{Cornfield_midP_CI_2x2}
#' \item{Fisher_exact_test_2x2}
#' \item{Exact_unconditional_test_2x2}
#' \item{Fisher_midP_test_2x2}
#' \item{Gart_adjusted_logit_CI_2x2}
#' \item{Independence_smoothed_logit_CI_2x2}
#' \item{Inv_sinh_CI_OR_2x2}
#' \item{Inv_sinh_CI_ratio_2x2}
#' \item{Katz_log_CI_2x2}
#' \item{Koopman_asymptotic_score_CI_2x2}
#' \item{LR_test_2x2}
#' \item{Mee_asymptotic_score_CI_2x2}
#' \item{MiettinenNurminen_asymptotic_score_CI_difference_2x2}
#' \item{MiettinenNurminen_asymptotic_score_CI_OR_2x2}
#' \item{MiettinenNurminen_asymptotic_score_CI_ratio_2x2}
#' \item{MOVER_R_Wilson_CI_OR_2x2}
#' \item{MOVER_R_Wilson_CI_ratio_2x2}
#' \item{Newcombe_hybrid_score_CI_2x2}
#' \item{Pearson_chi_squared_test_2x2}
#' \item{Pearson_chi_squared_test_CC_2x2}
#' \item{PriceBonett_approximate_Bayes_CI_2x2}
#' \item{Wald_CI_CC_2x2}
#' \item{Woolf_logit_CI_2x2}
#' \item{Uncorrected_asymptotic_score_CI_2x2}
#' \item{Z_unpooled_test_2x2}
#' \item{the_2x2_table_CIs_difference}
#' \item{the_2x2_table_CIs_OR}
#' \item{the_2x2_table_CIs_ratio}
#' \item{the_2x2_table_tests}
#' }
#' @note You can also print the list above with \code{list_functions(4)}.
#' @references
#' - Fagerland MW, Lydersen S, Laake P (2017) Statistical Analysis of
#' Contingency Tables. Chapman & Hall/CRC, Boca Raton, FL
#' - https://contingencytables.com/
#' - https://www.routledge.com/Statistical-Analysis-of-Contingency-Tables/Fagerland-Lydersen-Laake/p/book/9781466588172
NULL
#' @name chap5
#' @title Chapter 5: The Ordered rx2 Table
#' @description These are the functions related to chapter 5:
#' \enumerate{
#' \item{CochranArmitage_CI_rx2}
#' \item{CochranArmitage_exact_cond_midP_tests_rx2}
#' \item{CochranArmitage_MH_tests_rx2}
#' \item{Exact_cond_midP_unspecific_ordering_rx2}
#' \item{Pearson_LR_tests_unspecific_ordering_rx2}
#' \item{the_rx2_table}
#' \item{Trend_estimate_CI_tests_rx2}
#' }
#' @note You can also print the list above with \code{list_functions(5)}.
#' @references
#' - Fagerland MW, Lydersen S, Laake P (2017) Statistical Analysis of
#' Contingency Tables. Chapman & Hall/CRC, Boca Raton, FL
#' - https://contingencytables.com/
#' - https://www.routledge.com/Statistical-Analysis-of-Contingency-Tables/Fagerland-Lydersen-Laake/p/book/9781466588172
NULL
#' @name chap6
#' @title Chapter 6: The Ordered 2xc Table
#' @description These are the functions related to chapter 6:
#' \enumerate{
#' \item{Brant_test_2xc}
#' \item{Cumulative_models_for_2xc}
#' \item{Exact_cond_midP_linear_rank_tests_2xc}
#' \item{ClopperPearson_exact_CI_1x2_beta_version}
#' \item{Exact_cond_midP_unspecific_ordering_rx2}
#' \item{MantelHaenszel_test_2xc}
#' \item{Pearson_LR_tests_cum_OR_2xc}
#' \item{Score_test_for_effect_in_the_probit_model_2xc}
#' \item{the_2xc_table}
#' }
#' @note You can also print the list above with \code{list_functions(6)}.
#' @references
#' - Fagerland MW, Lydersen S, Laake P (2017) Statistical Analysis of
#' Contingency Tables. Chapman & Hall/CRC, Boca Raton, FL
#' - https://contingencytables.com/
#' - https://www.routledge.com/Statistical-Analysis-of-Contingency-Tables/Fagerland-Lydersen-Laake/p/book/9781466588172
NULL
#' @name chap7
#' @title Chapter 7: The rxc Table
#' @description These are the functions related to chapter 7:
#' \enumerate{
#' \item{Bonferroni_type_CIs_rxc}
#' \item{Cumulative_models_for_rxc}
#' \item{Exact_cond_midP_tests_rxc}
#' \item{FisherFreemanHalton_asymptotic_test_rxc}
#' \item{gamma_coefficient_rxc_bca}
#' \item{gamma_coefficient_rxc}
#' \item{JonckheereTerpstra_test_rxc}
#' \item{Kendalls_tau_b_rxc}
#' \item{Kendalls_tau_b_rxc_bca}
#' \item{KruskalWallis_asymptotic_test_rxc}
#' \item{linear_by_linear_test_rxc}
#' \item{Pearson_correlation_coefficient_rxc}
#' \item{Pearson_correlation_coefficient_rxc_bca}
#' \item{Pearson_LR_tests_rxc}
#' \item{Pearson_residuals_rxc}
#' \item{Scheffe_type_CIs_rxc}
#' \item{Spearman_correlation_coefficient_rxc}
#' \item{Spearman_correlation_coefficient_rxc_bca}
#' \item{the_rxc_table}
#' }
#' @note You can also print the list above with \code{list_functions(7)}.
#' @references
#' - Fagerland MW, Lydersen S, Laake P (2017) Statistical Analysis of
#' Contingency Tables. Chapman & Hall/CRC, Boca Raton, FL
#' - https://contingencytables.com/
#' - https://www.routledge.com/Statistical-Analysis-of-Contingency-Tables/Fagerland-Lydersen-Laake/p/book/9781466588172
NULL
#' @name chap8
#' @title Chapter 8: The Paired 2x2 Table
#' @description These are the functions related to chapter 8:
#' \enumerate{
#' \item{BonettPrice_hybrid_Wilson_score_CI_CC_paired_2x2}
#' \item{BonettPrice_hybrid_Wilson_score_CI_paired_2x2}
#' \item{ClopperPearson_exact_CI_1x2_beta_version}
#' \item{McNemar_asymptotic_test_CC_paired_2x2}
#' \item{McNemar_asymptotic_test_paired_2x2}
#' \item{McNemar_exact_cond_test_paired_2x2}
#' \item{McNemar_exact_unconditional_test_paired_2x2}
#' \item{McNemar_midP_test_paired_2x2}
#' \item{Tang_asymptotic_score_CI_paired_2x2}
#' \item{Tango_asymptotic_score_CI_paired_2x2}
#' \item{MOVER_Wilson_score_CI_paired_2x2}
#' \item{Newcombe_square_and_add_CI_paired_2x2}
#' \item{Transformed_Blaker_exact_CI_paired_2x2}
#' \item{Transformed_Clopper_Pearson_exact_CI_paired_2x2}
#' \item{Transformed_Clopper_Pearson_midP_CI_paired_2x2}
#' \item{Transformed_Wilson_score_CI_paired_2x2}
#' \item{Wald_CI_diff_paired_2x2}
#' \item{Wald_CI_diff_CC_paired_2x2}
#' \item{Wald_CI_AgrestiMin_paired_2x2}
#' \item{Wald_CI_BonettPrice_paired_2x2}
#' \item{Wald_CI_OR_Laplace_paired_2x2}
#' \item{Wald_CI_OR_paired_2x2}
#' \item{Wald_CI_ratio_paired_2x2}
#' \item{the_paired_2x2_table_CIs_difference}
#' \item{the_paired_2x2_table_CIs_OR}
#' \item{the_paired_2x2_table_CIs_ratio}
#' \item{the_paired_2x2_table_tests}
#' }
#' @note You can also print the list above with \code{list_functions(8)}.
#' @references
#' - Fagerland MW, Lydersen S, Laake P (2017) Statistical Analysis of
#' Contingency Tables. Chapman & Hall/CRC, Boca Raton, FL
#' - https://contingencytables.com/
#' - https://www.routledge.com/Statistical-Analysis-of-Contingency-Tables/Fagerland-Lydersen-Laake/p/book/9781466588172
NULL
#' @name chap9
#' @title Chapter 9: The Paired cxc Table
#' @description These are the functions related to chapter 9:
#' \enumerate{
#' \item{Bhapkar_test_paired_cxc}
#' \item{Bonferroni_type_CIs_paired_cxc}
#' \item{FleissEveritt_test_paired_cxc}
#' \item{FleissLevinPaik_test_paired_cxc}
#' \item{McNemarBowker_test_paired_cxc}
#' \item{Scheffe_type_CIs_paired_cxc}
#' \item{Score_test_and_CI_marginal_mean_scores_paired_cxc}
#' \item{Stuart_test_paired_cxc}
#' \item{Wald_test_and_CI_marginal_mean_ranks_paired_cxc}
#' \item{Wald_test_and_CI_marginal_mean_scores_paired_cxc}
#' \item{the_paired_cxc_table_nominal}
#' \item{the_paired_cxc_table_ordinal}
#' }
#' @note You can also print the list above with \code{list_functions(9)}.
#' @references
#' - Fagerland MW, Lydersen S, Laake P (2017) Statistical Analysis of
#' Contingency Tables. Chapman & Hall/CRC, Boca Raton, FL
#' - https://contingencytables.com/
#' - https://www.routledge.com/Statistical-Analysis-of-Contingency-Tables/Fagerland-Lydersen-Laake/p/book/9781466588172
NULL
#' @name chap10
#' @title Chapter 10: Stratified 2x2 Tables and Meta-Analysis
#' @description These are the functions related to chapter 10:
#' \enumerate{
#' \item{BreslowDay_homogeneity_test_stratified_2x2}
#' \item{CochranMantelHaenszel_test_stratified_2x2}
#' \item{Cochran_Q_test_stratified_2x2}
#' \item{InverseVariance_estimate_stratified_2x2}
#' \item{ML_estimates_and_CIs_stratified_2x2}
#' \item{MantelHaenszel_estimate_stratified_2x2}
#' \item{Pearson_LR_homogeneity_test_stratified_2x2}
#' \item{Pearson_LR_test_common_effect_stratified_2x2}
#' \item{Peto_homogeneity_test_stratified_2x2}
#' \item{Peto_OR_estimate_stratified_2x2}
#' \item{RBG_test_and_CI_stratified_2x2}
#' \item{Wald_test_and_CI_common_diff_stratified_2x2}
#' \item{Wald_test_and_CI_common_ratio_stratified_2x2}
#' \item{Woolf_test_and_CI_stratified_2x2}
#' \item{stratified_2x2_tables}
#' }
#' @note You can also print the list above with \code{list_functions(10)}.
#' @references
#' - Fagerland MW, Lydersen S, Laake P (2017) Statistical Analysis of
#' Contingency Tables. Chapman & Hall/CRC, Boca Raton, FL
#' - https://contingencytables.com/
#' - https://www.routledge.com/Statistical-Analysis-of-Contingency-Tables/Fagerland-Lydersen-Laake/p/book/9781466588172
NULL
#' @title List functions from a chapter
#' @description Complements the \code{?chapX} command by printing a list of
#' functions related to a particular chapter `X` on the R console.
#' @param chap_num Number of book chapter (from 2 to 10)
#' @return List of functions from that chapter
#' @author Waldir Leoncio
#' @export
list_functions <- function(chap_num) {
validate_chapter_choice(chap_num)
message("Chapter ", chap_num, " functions:")
cat(paste0(full_list_chapter_functions[[chap_num - 1]], "()"), sep = "\n")
message(
"Learn more about an individual function with ?<function_name> and ",
"example(<function_name>)."
)
}
# ============================================================================ #
# Internal functions and objects used in this file #
# ============================================================================ #
validate_chapter_choice <- function(chap_num) {
# Makes sure the user chooses a proper chapter number
if (missing(chap_num)) stop("Please choose a chapter between 2 and 10.")
if (chap_num < 2 | chap_num > 10) {
stop("Please choose a chapter between 2 and 10.")
}
}
full_list_chapter_functions <- list(
# Lists of functions pertaining to a certain chapter
ch2 = c(
"AgrestiCoull_CI_1x2",
"Arcsine_CI_1x2",
"Wald_CI_1x2",
"Blaker_exact_CI_1x2",
"Blaker_exact_test_1x2",
"Blaker_midP_CI_1x2",
"Blaker_midP_test_1x2",
"ClopperPearson_exact_CI_1x2",
"ClopperPearson_midP_CI_1x2",
"Exact_binomial_test_1x2",
"Jeffreys_CI_1x2",
"LR_CI_1x2",
"LR_test_1x2",
"MidP_binomial_test_1x2",
"Score_test_1x2",
"Score_test_CC_1x2",
"Wald_CI_CC_1x2",
"Wilson_score_CI_1x2",
"Wilson_score_CI_CC_1x2",
"the_1x2_table_CIs",
"Wald_test_1x2",
"Wald_test_CC_1x2",
"the_1x2_table_tests"
),
ch3 = c(
"Chacko_test_1xc",
"Exact_multinomial_test_1xc",
"Gold_Wald_CIs_1xc",
"Goodman_Wald_CIs_1xc",
"Goodman_Wald_CIs_for_diffs_1xc",
"Goodman_Wilson_score_CIs_1xc",
"LR_test_1xc",
"MidP_multinomial_test_1xc",
"Pearson_chi_squared_test_1xc",
"QuesenberryHurst_Wilson_score_CIs_1xc",
"the_1xc_table_CIs",
"the_1xc_table_tests"
),
ch4 = c(
"Adjusted_inv_sinh_CI_OR_2x2",
"Adjusted_inv_sinh_CI_ratio_2x2",
"Adjusted_log_CI_2x2",
"AgrestiCaffo_CI_2x2",
"Wald_CI_2x2",
"BaptistaPike_exact_conditional_CI_2x2",
"BaptistaPike_midP_CI_2x2",
"Cornfield_exact_conditional_CI_2x2",
"Cornfield_midP_CI_2x2",
"Fisher_exact_test_2x2",
"Exact_unconditional_test_2x2",
"Fisher_midP_test_2x2",
"Gart_adjusted_logit_CI_2x2",
"Independence_smoothed_logit_CI_2x2",
"Inv_sinh_CI_OR_2x2",
"Inv_sinh_CI_ratio_2x2",
"Katz_log_CI_2x2",
"Koopman_asymptotic_score_CI_2x2",
"LR_test_2x2",
"Mee_asymptotic_score_CI_2x2",
"MiettinenNurminen_asymptotic_score_CI_difference_2x2",
"MiettinenNurminen_asymptotic_score_CI_OR_2x2",
"MiettinenNurminen_asymptotic_score_CI_ratio_2x2",
"MOVER_R_Wilson_CI_OR_2x2",
"MOVER_R_Wilson_CI_ratio_2x2",
"Newcombe_hybrid_score_CI_2x2",
"Pearson_chi_squared_test_2x2",
"Pearson_chi_squared_test_CC_2x2",
"PriceBonett_approximate_Bayes_CI_2x2",
"Wald_CI_CC_2x2",
"Woolf_logit_CI_2x2",
"Uncorrected_asymptotic_score_CI_2x2",
"Z_unpooled_test_2x2",
"the_2x2_table_CIs_difference",
"the_2x2_table_CIs_OR",
"the_2x2_table_CIs_ratio",
"the_2x2_table_tests"
),
ch5 = c(
"CochranArmitage_CI_rx2",
"CochranArmitage_exact_cond_midP_tests_rx2",
"CochranArmitage_MH_tests_rx2",
"Exact_cond_midP_unspecific_ordering_rx2",
"Pearson_LR_tests_unspecific_ordering_rx2",
"the_rx2_table",
"Trend_estimate_CI_tests_rx2"
),
ch6 = c(
"Brant_test_2xc",
"Cumulative_models_for_2xc",
"Exact_cond_midP_linear_rank_tests_2xc",
"ClopperPearson_exact_CI_1x2_beta_version",
"Exact_cond_midP_unspecific_ordering_rx2",
"MantelHaenszel_test_2xc",
"Pearson_LR_tests_cum_OR_2xc",
"Score_test_for_effect_in_the_probit_model_2xc",
"the_2xc_table"
),
ch7 = c(
"Bonferroni_type_CIs_rxc",
"Cumulative_models_for_rxc",
"Exact_cond_midP_tests_rxc",
"FisherFreemanHalton_asymptotic_test_rxc",
"gamma_coefficient_rxc_bca",
"gamma_coefficient_rxc",
"JonckheereTerpstra_test_rxc",
"Kendalls_tau_b_rxc",
"Kendalls_tau_b_rxc_bca",
"KruskalWallis_asymptotic_test_rxc",
"linear_by_linear_test_rxc",
"Pearson_correlation_coefficient_rxc",
"Pearson_correlation_coefficient_rxc_bca",
"Pearson_LR_tests_rxc",
"Pearson_residuals_rxc",
"Scheffe_type_CIs_rxc",
"Spearman_correlation_coefficient_rxc",
"Spearman_correlation_coefficient_rxc_bca",
"the_rxc_table"
),
ch8 = c(
"BonettPrice_hybrid_Wilson_score_CI_CC_paired_2x2",
"BonettPrice_hybrid_Wilson_score_CI_paired_2x2",
"ClopperPearson_exact_CI_1x2_beta_version",
"McNemar_asymptotic_test_CC_paired_2x2",
"McNemar_asymptotic_test_paired_2x2",
"McNemar_exact_cond_test_paired_2x2",
"McNemar_exact_unconditional_test_paired_2x2",
"McNemar_midP_test_paired_2x2",
"Tang_asymptotic_score_CI_paired_2x2",
"Tango_asymptotic_score_CI_paired_2x2",
"MOVER_Wilson_score_CI_paired_2x2",
"Newcombe_square_and_add_CI_paired_2x2",
"Transformed_Blaker_exact_CI_paired_2x2",
"Transformed_Clopper_Pearson_exact_CI_paired_2x2",
"Transformed_Clopper_Pearson_midP_CI_paired_2x2",
"Transformed_Wilson_score_CI_paired_2x2",
"Wald_CI_diff_paired_2x2",
"Wald_CI_diff_CC_paired_2x2",
"Wald_CI_AgrestiMin_paired_2x2",
"Wald_CI_BonettPrice_paired_2x2",
"Wald_CI_OR_Laplace_paired_2x2",
"Wald_CI_OR_paired_2x2",
"Wald_CI_ratio_paired_2x2",
"the_paired_2x2_table_CIs_difference",
"the_paired_2x2_table_CIs_OR",
"the_paired_2x2_table_CIs_ratio",
"the_paired_2x2_table_tests"
),
ch9 = c(
"Bhapkar_test_paired_cxc",
"Bonferroni_type_CIs_paired_cxc",
"FleissEveritt_test_paired_cxc",
"FleissLevinPaik_test_paired_cxc",
"McNemarBowker_test_paired_cxc",
"Scheffe_type_CIs_paired_cxc",
"Score_test_and_CI_marginal_mean_scores_paired_cxc",
"Stuart_test_paired_cxc",
"Wald_test_and_CI_marginal_mean_ranks_paired_cxc",
"Wald_test_and_CI_marginal_mean_scores_paired_cxc",
"the_paired_cxc_table_nominal",
"the_paired_cxc_table_ordinal"
),
ch10 = c(
"BreslowDay_homogeneity_test_stratified_2x2",
"CochranMantelHaenszel_test_stratified_2x2",
"Cochran_Q_test_stratified_2x2",
"InverseVariance_estimate_stratified_2x2",
"ML_estimates_and_CIs_stratified_2x2",
"MantelHaenszel_estimate_stratified_2x2",
"Pearson_LR_homogeneity_test_stratified_2x2",
"Pearson_LR_test_common_effect_stratified_2x2",
"Peto_homogeneity_test_stratified_2x2",
"Peto_OR_estimate_stratified_2x2",
"RBG_test_and_CI_stratified_2x2",
"Wald_test_and_CI_common_diff_stratified_2x2",
"Wald_test_and_CI_common_ratio_stratified_2x2",
"Woolf_test_and_CI_stratified_2x2",
"stratified_2x2_tables"
)
)
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