| Prints welcome message on package load | .onAttach |
| The adjusted inverse hyperbolic sine confidence interval for the odds ratio | Adjusted_inv_sinh_CI_OR_2x2 |
| The adjusted inverse hyperbolic sine confidence interval for the ratio of probabilities | Adjusted_inv_sinh_CI_ratio_2x2 |
| The adjusted log confidence interval for the ratio of probabilities | Adjusted_log_CI_2x2 |
| The Agresti-Caffo confidence interval for the difference between probabilities | AgrestiCaffo_CI_2x2 |
| The Agresti-Coull confidence interval for the binomial probability | AgrestiCoull_CI_1x2 |
| Arcsine confidence interval | Arcsine_CI_1x2 |
| The Baptista-Pike exact conditional confidence interval for the odds ratio | BaptistaPike_exact_conditional_CI_2x2 |
| The Baptista-Pike mid-P confidence interval for the odds ratio | BaptistaPike_midP_CI_2x2 |
| Airway hyper-responsiveness before and after stem cell transplantation | bentur_2009 |
| The Bhapkar test for marginal homogeneity | Bhapkar_test_paired_cxc |
| The Blaker exact confidence interval | Blaker_exact_CI_1x2 |
| The Blaker exact test | Blaker_exact_test_1x2 |
| The Blaker mid-P confidence interval for the binomial probability | Blaker_midP_CI_1x2 |
| The Blaker mid-P test | Blaker_midP_test_1x2 |
| The Bonett-Price hybrid Wilson score confidence interval for the ratio of paired probabilities | BonettPrice_hybrid_Wilson_score_CI_CC_paired_2x2 |
| The Bonett-Price hybrid Wilson score confidence interval for the ratio of paired probabilities | BonettPrice_hybrid_Wilson_score_CI_paired_2x2 |
| Bonferroni-type confidence intervals for differences of marginal probabilities | Bonferroni_type_CIs_paired_cxc |
| The Bonferroni-type simultaneous confidence intervals for the differences pi_1|i - pi_1|j | Bonferroni_type_CIs_rxc |
| The Brant test for the proportional odds assumption | Brant_test_2xc |
| The Breslow-Day test of homogeneity of odds ratios over strata | BreslowDay_homogeneity_test_stratified_2x2 |
| Calculate probability | calc_prob |
| Calculate probability | calc_Pvalue_4x2 |
| Calculate probability | calc_Pvalue_5x2 |
| Calculate the lower limit of a confidence interval | calculate_limit_lower |
| Calculate the upper limit of a confidence interval | calculate_limit_upper |
| Complete response before and after consolidation therapy | cavo_2012 |
| The Chacko test for order-restriction | Chacko_test_1xc |
| Chapter 1: Introduction | chap1 |
| Chapter 10: Stratified 2x2 Tables and Meta-Analysis | chap10 |
| Chapter 2: The 1x2 Table and the Binomial Distribution | chap2 |
| Chapter 3: The 1xc Table and the Multinomial Distribution | chap3 |
| Chapter 4: The 2x2 Table | chap4 |
| Chapter 5: The Ordered rx2 Table | chap5 |
| Chapter 6: The Ordered 2xc Table | chap6 |
| Chapter 7: The rxc Table | chap7 |
| Chapter 8: The Paired 2x2 Table | chap8 |
| Chapter 9: The Paired cxc Table | chap9 |
| The Clopper-Pearson exact confidence interval | ClopperPearson_exact_CI_1x2 |
| The Clopper-Pearson exact confidence interval for the binomial probability (beta version) | ClopperPearson_exact_CI_1x2_beta_version |
| The Clopper-Pearson mid-P confidence interval | ClopperPearson_midP_CI_1x2 |
| The Cochran Q test of homogeneity of effects over strata | Cochran_Q_test_stratified_2x2 |
| The Cochran-Armitage confidence interval for trend in the linear model | CochranArmitage_CI_rx2 |
| The Cochran-Armitage exact conditional and mid-P tests | CochranArmitage_exact_cond_midP_tests_rx2 |
| The Cochran-Armitage, modified Cochran-Armitage, and Mantel-Haenszel tests for trend | CochranArmitage_MH_tests_rx2 |
| The Cochran-Mantel-Haenszel test of a common odds ratio | CochranMantelHaenszel_test_stratified_2x2 |
| Statistical Analysis of Contingency tables | contingencytables-package contingencytables |
| contingencytables_result class | contingencytables_result |
| The Cornfield exact conditional confidence interval for the odds ratio | Cornfield_exact_conditional_CI_2x2 |
| The Cornfield mid-P confidence interval for the odds ratio | Cornfield_midP_CI_2x2 |
| Cumulative logit and probit models | Cumulative_models_for_2xc |
| Cumulative logit and probit models | Cumulative_models_for_rxc |
| Smoking and lung cancer | doll_hill_1950 |
| The exact binomial test for the binomial probability (pi) | Exact_binomial_test_1x2 |
| Exact conditional and mid-P linear rank tests | Exact_cond_midP_linear_rank_tests_2xc |
| Exact conditional and mid-P tests for the rxc table | Exact_cond_midP_tests_rxc |
| The exact conditional and mid-P tests for unspecific ordering | Exact_cond_midP_unspecific_ordering_rx2 |
| The exact multinomial test for multinomial probabilities | Exact_multinomial_test_1xc |
| Exact unconditional test for association in 2x2 tables | Exact_unconditional_test_2x2 |
| Floppy eyelid syndrome vs obstructive sleep apnea | ezra_2010 |
| A comparison between serial and retrospective measurements | fischer_1999 |
| The Fisher exact test for association in 2x2 tables | Fisher_exact_test_2x2 |
| The Fisher mid-P test for association in 2x2 tables | Fisher_midP_test_2x2 |
| The Fisher-Freeman-Halton asymptotic test for unordered rxc tables | FisherFreemanHalton_asymptotic_test_rxc |
| Table 13.6, page 382, of Fleiss et al. (2003) | fleiss_2003 |
| The Fleiss-Everitt version of the Stuart test for marginal homogeneity | FleissEveritt_test_paired_cxc |
| The Fleiss-Levin-Paik test for three-level ordinal outcomes | FleissLevinPaik_test_paired_cxc |
| The Adolescent Placement Study | fontanella_2008 |
| The gamma coefficient | gamma_coefficient_rxc |
| The gamma coefficient with the bias-corrected and accelerated boostrap confidence interval | gamma_coefficient_rxc_bca |
| The Gart adjusted logit confidence interval for the odds ratio | Gart_adjusted_logit_CI_2x2 |
| The Gold Wald simultaneous intervals for the multinomial probabilities | Gold_Wald_CIs_1xc |
| The Goodman Wald simultaneous intervals for the multinomial probabilities | Goodman_Wald_CIs_1xc |
| The Goodman Wald simultaneous intervals for the differences between the | Goodman_Wald_CIs_for_diffs_1xc |
| The Goodman Wilson score simultaneous intervals for the multinomial probabilities | Goodman_Wilson_score_CIs_1xc |
| Prophylactice use of Lidocaine in myocardial infarction | hine_1989 |
| Hypothetical experiment | hypothetical |
| The Independence-smoothed logit confidence interval for the odds ratio | Independence_smoothed_logit_CI_2x2 |
| Elevated troponin T levels in stroke patients | indredavik_2008 |
| The inverse hyperbolic sine confidence interval for the odds ratio | Inv_sinh_CI_OR_2x2 |
| The inverse hyperbolic sine confidence interval for the ratio of probabilities | Inv_sinh_CI_ratio_2x2 |
| The inverse variance estimate of the overall effect across strata | InverseVariance_estimate_stratified_2x2 |
| Jeffreys confidence interval for the binomial probability | Jeffreys_CI_1x2 |
| The Jonckheere-Terpstra test for association | JonckheereTerpstra_test_rxc |
| The Katz log confidence interval for the ratio of probabilities | Katz_log_CI_2x2 |
| Kendall's tau-b with confidence interval based on the Fieller standard deviation | Kendalls_tau_b_rxc |
| Kendall's tau-b with the bias-corrected and accelerated boostrap confidence interval | Kendalls_tau_b_rxc_bca |
| The Koopman asymptotic score confidence interval for the ratio of probabilities | Koopman_asymptotic_score_CI_2x2 |
| The Kruskal-Wallis asymptotic test for singly ordered rxc tables | KruskalWallis_asymptotic_test_rxc |
| A case-control study of GADA exposure on IPEX syndrome | lampasona_2013 |
| Ligarden et al., 2010 | ligarden_2010 |
| The linear-by-linear test for association | linear_by_linear_test_rxc |
| List functions from a chapter | list_functions |
| The likelihood ratio confidence interval for the binomial probability | LR_CI_1x2 |
| The likelihood ratio test for the binomial probability (pi) | LR_test_1x2 |
| The likelihood ratio test for multinomial probabilities | LR_test_1xc |
| The likelihood ratio test for association in 2x2 tables | LR_test_2x2 |
| Postoperative nausea | lydersen_2012a |
| The Mantel-Haenszel estimate of the overall effect across strata | MantelHaenszel_estimate_stratified_2x2 |
| The Mantel-Haenszel test of association with column scores | MantelHaenszel_test_2xc |
| The McNemar asymptotic test with continuity correction | McNemar_asymptotic_test_CC_paired_2x2 |
| The McNemar asymptotic test | McNemar_asymptotic_test_paired_2x2 |
| The McNemar exact conditional test | McNemar_exact_cond_test_paired_2x2 |
| The McNemar exact unconditional test | McNemar_exact_unconditional_test_paired_2x2 |
| The McNemar mid-P test | McNemar_midP_test_paired_2x2 |
| The McNemar-Bowker test for marginal symmetry | McNemarBowker_test_paired_cxc |
| The Mee asymptotic score confidence interval for the difference between probabilities | Mee_asymptotic_score_CI_2x2 |
| The mid-P binomial test for the binomial probability (pi) | MidP_binomial_test_1x2 |
| The mid-P multinomial test for multinomial probabilities | MidP_multinomial_test_1xc |
| The Miettinen-Nurminen asymptotic score confidence interval for the | MiettinenNurminen_asymptotic_score_CI_difference_2x2 |
| The Miettinen-Nurminen asymptotic score CI for the odds ratio | MiettinenNurminen_asymptotic_score_CI_OR_2x2 |
| The Miettinen-Nurminen asymptotic score confidence interval for the ratio of probabilities | MiettinenNurminen_asymptotic_score_CI_ratio_2x2 |
| Alcohol consumption and malformations | mills_graubard_1987 |
| Calculate ML estimates | ML_estimates |
| Maximum likelihood estimates with CIs of the grouping and strata effects | ML_estimates_and_CIs_stratified_2x2 |
| The MOVER-R Wilson confidence interval for the odds ratio | MOVER_R_Wilson_CI_OR_2x2 |
| The MOVER-R Wilson confidence interval for the ratio of probabilities | MOVER_R_Wilson_CI_ratio_2x2 |
| The MOVER Wilson score confidence interval for the ratio of paired probabilities | MOVER_Wilson_score_CI_paired_2x2 |
| The Newcombe hybrid score confidence interval for the difference between probabilities | Newcombe_hybrid_score_CI_2x2 |
| The Newcombe square-and-add confidence interval for the difference | Newcombe_square_and_add_CI_paired_2x2 |
| The Pearson chi-squared test for multinomial probabilities | Pearson_chi_squared_test_1xc |
| The Pearson chi-squared test for association in 2x2 tables | Pearson_chi_squared_test_2x2 |
| The Pearson chi-squared test for association in 2x2 tables | Pearson_chi_squared_test_CC_2x2 |
| The Pearson correlation coefficient | Pearson_correlation_coefficient_rxc |
| The Pearson correlation coefficient with the bias-corrected and accelerated | Pearson_correlation_coefficient_rxc_bca |
| The Pearson chi-squared and likelihood ratio tests for homogeneity over strata | Pearson_LR_homogeneity_test_stratified_2x2 |
| The Pearson chi-squared and likelihood ratio tests of a common difference | Pearson_LR_test_common_effect_stratified_2x2 |
| The Pearson chi-squared and likelihood ratio tests for cumulative ORs in 2xc tables | Pearson_LR_tests_cum_OR_2xc |
| The Pearson chi-squared and likelihood ratio tests for association in rxc tables | Pearson_LR_tests_rxc |
| The Pearson chi-squared and likelihood ratio tests for unspecific ordering in rx2 tables | Pearson_LR_tests_unspecific_ordering_rx2 |
| The Pearson residuals and the standardized Pearson residuals | Pearson_residuals_rxc |
| An RCT of high vs standard dose of epinephrine | perondi_2004 |
| Pretherapy susceptability of pathogens | peterson_2007 |
| The Peto test for homogeneity of odds ratios over strata | Peto_homogeneity_test_stratified_2x2 |
| The Peto estimate of the common odds ratio across strata | Peto_OR_estimate_stratified_2x2 |
| The Price-Bonett approximate Bayes confidence interval for the ratio of probabilities | PriceBonett_approximate_Bayes_CI_2x2 |
| Output from a contingency tables method | print.contingencytables_result |
| The Quesenberry-Hurst Wilson score simultaneous intervals for the multinomial probabilities | QuesenberryHurst_Wilson_score_CIs_1xc |
| The RBG test and CI for a common odds ratio | RBG_test_and_CI_stratified_2x2 |
| The association between CHRNA4 genotype and XFS | ritland_2007 |
| Scheffe-type confidence intervals for differences of marginal probabilities | Scheffe_type_CIs_paired_cxc |
| The Scheffe-type simultaneous confidence intervals for the differences pi_1|i - pi_1|j | Scheffe_type_CIs_rxc |
| The score test for the binomial probability (pi) | Score_test_1x2 |
| Score test and CI marginal mean scores paired CxC | Score_test_and_CI_marginal_mean_scores_paired_cxc |
| The score test with continuity correction for the | Score_test_CC_1x2 |
| Score test for effect in the cumulative probit model | Score_test_for_effect_in_the_probit_model_2xc |
| Calculate ML estimates | score_test_statistic |
| The number of n-th order male births | singh_2010 singh_2010_1 |
| Genotype counts for SNP rs 6498169 in RA patients | snp6498169 |
| The Spearman correlation coefficient | Spearman_correlation_coefficient_rxc |
| The Spearman correlation coefficient with the bias-corrected and accelerated | Spearman_correlation_coefficient_rxc_bca |
| Stratified 2x2 tables | stratified_2x2_tables |
| The Stuart test for marginal homogeneity | Stuart_test_paired_cxc |
| Treatment for ear infection | table_7.3 vanbalen_2003 |
| Psychiatric Diagnoses and Physical Activity | mangerud_2014_PA table_7.4 |
| Psychiatric diag. vs BMI with hyperkinetic disorders as reference category | mangerud_2014_BMI table_7.5 |
| Low Birth Weight vs psychiatric morbitidy with control as reference category | lund_2012 table_7.6 |
| Colorectal cancer (Table 7.7) | jullumstroe_2009 table_7.7 |
| Breast Tumor | bofin_2004 table_7.8 |
| Self-rated health (Table 7.9) | breidablik_2008 table_7.9 |
| The Tang asymptotic score confidence interval for the ratio of paired probabilities | Tang_asymptotic_score_CI_paired_2x2 |
| The Tango asymptotic score confidence interval for the difference between paired probabilities | Tango_asymptotic_score_CI_paired_2x2 |
| A lady tasting a cup of tea | tea |
| The 1x2 Table CIs | the_1x2_table_CIs |
| The 1x2 Table tests | the_1x2_table_tests |
| The 1xc table CIs | the_1xc_table_CIs |
| The 1xc table tests | the_1xc_table_tests |
| The 2x2 table CIs difference | the_2x2_table_CIs_difference |
| The 2x2 table CIs odds ratio | the_2x2_table_CIs_OR |
| The 2x2 table CIs ratio | the_2x2_table_CIs_ratio |
| The 2x2 table tests | the_2x2_table_tests |
| The 2xc table | the_2xc_table |
| The Paired 2x2 table CIs difference | the_paired_2x2_table_CIs_difference |
| The Paired 2x2 table CIs OR | the_paired_2x2_table_CIs_OR |
| The Paired 2x2 table CIs ratio | the_paired_2x2_table_CIs_ratio |
| The Paired 2x2 table tests | the_paired_2x2_table_tests |
| The Paired CxC table - nominal | the_paired_cxc_table_nominal |
| The Paired CxC table - ordinal | the_paired_cxc_table_ordinal |
| The rx2 table | the_rx2_table |
| The rxc table | the_rxc_table |
| The Transformed Blaker exact confidence interval for the conditional odds ratio | Transformed_Blaker_exact_CI_paired_2x2 |
| The Transformed Clopper-Pearson exact confidence interval for the conditional odds ratio | Transformed_Clopper_Pearson_exact_CI_paired_2x2 |
| The Transformed Clopper-Pearson mid-P confidence interval for the conditional odds ratio | Transformed_Clopper_Pearson_midP_CI_paired_2x2 |
| The Transformed Wilson score confidence interval for the conditional odds ratio | Transformed_Wilson_score_CI_paired_2x2 |
| Trend estimate for linear and logit models | Trend_estimate_CI_tests_rx2 |
| The uncorrected asymptotic score confidence interval for the odds ratio | Uncorrected_asymptotic_score_CI_2x2 |
| Validate arguments of a function | validateArguments |
| The Wald confidence interval for the binomial probability | Wald_CI_1x2 |
| The Wald confidence interval for the difference between probabilities | Wald_CI_2x2 |
| The Wald confidence interval for the difference between paired probabilities | Wald_CI_AgrestiMin_paired_2x2 |
| The Wald confidence interval for the difference between paired probabilities | Wald_CI_BonettPrice_paired_2x2 |
| The Wald CI with CC for the binomial probability | Wald_CI_CC_1x2 |
| The Wald confidence interval for the difference between probabilities | Wald_CI_CC_2x2 |
| The Wald confidence interval for the difference between paired probabilities | Wald_CI_diff_CC_paired_2x2 |
| The Wald confidence interval for the difference between paired probabilities | Wald_CI_diff_paired_2x2 |
| The Wald confidence interval for the conditional odds ratio with Laplace adjustment | Wald_CI_OR_Laplace_paired_2x2 |
| The Wald confidence interval for the conditional odds ratio | Wald_CI_OR_paired_2x2 |
| The Wald confidence interval for the ratio of paired probabilities | Wald_CI_ratio_paired_2x2 |
| The Wald test for the binomial probability (pi) | Wald_test_1x2 |
| The Wald test and CI for a common difference between probabilities | Wald_test_and_CI_common_diff_stratified_2x2 |
| The Wald test and CI for a common ratio of probabilities | Wald_test_and_CI_common_ratio_stratified_2x2 |
| The Wald test and confidence interval for the difference between marginal mean ranks / ridits | Wald_test_and_CI_marginal_mean_ranks_paired_cxc |
| The Wald test and confidence interval for the difference between marginal mean scores | Wald_test_and_CI_marginal_mean_scores_paired_cxc |
| The Wald test with continuity correction for the binomial probability | Wald_test_CC_1x2 |
| The Wilson score confidence interval | Wilson_score_CI_1x2 |
| The Wilson score confidence interval with continuity correction for the binomial probability | Wilson_score_CI_CC_1x2 |
| The Woolf logit confidence interval for the odds ratio | Woolf_logit_CI_2x2 |
| The Woolf test and CI for a common odds ratio | Woolf_test_and_CI_stratified_2x2 |
| The Z-unpooled test for association in 2x2 tables | Z_unpooled_test_2x2 |