R: Statistical Analysis of Contingency Tables

# Statistical Analysis of Contingency Tables

## Documentation for package ‘contingencytables’ version 3.1.0

- DESCRIPTION file
- Package NEWS

## Help Pages

A B C D E F G H I J K L M N P Q R S T U V W Z misc

contingencytables-package | Statistical Analysis of Contingency tables

## -- A --

Adjusted_inv_sinh_CI_OR_2x2 | The adjusted inverse hyperbolic sine confidence interval for the odds ratio
Adjusted_inv_sinh_CI_ratio_2x2 | The adjusted inverse hyperbolic sine confidence interval for the ratio of probabilities
Adjusted_log_CI_2x2 | The adjusted log confidence interval for the ratio of probabilities
AgrestiCaffo_CI_2x2 | The Agresti-Caffo confidence interval for the difference between probabilities
AgrestiCoull_CI_1x2 | The Agresti-Coull confidence interval for the binomial probability
Arcsine_CI_1x2 | Arcsine confidence interval

## -- B --

BaptistaPike_exact_conditional_CI_2x2 | The Baptista-Pike exact conditional confidence interval for the odds ratio
BaptistaPike_midP_CI_2x2 | The Baptista-Pike mid-P confidence interval for the odds ratio
bentur_2009 | Airway hyper-responsiveness before and after stem cell transplantation
Bhapkar_test_paired_cxc | The Bhapkar test for marginal homogeneity
Blaker_exact_CI_1x2 | The Blaker exact confidence interval
Blaker_exact_test_1x2 | The Blaker exact test
Blaker_midP_CI_1x2 | The Blaker mid-P confidence interval for the binomial probability
Blaker_midP_test_1x2 | The Blaker mid-P test
bofin_2004 | Breast Tumor
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 | The Bonett-Price hybrid Wilson score confidence interval for the ratio of paired probabilities
Bonferroni_type_CIs_paired_cxc | Bonferroni-type confidence intervals for differences of marginal probabilities
Bonferroni_type_CIs_rxc | The Bonferroni-type simultaneous confidence intervals for the differences pi_1|i - pi_1|j
Brant_test_2xc | The Brant test for the proportional odds assumption
breidablik_2008 | Self-rated health (Table 7.9)
BreslowDay_homogeneity_test_stratified_2x2 | The Breslow-Day test of homogeneity of odds ratios over strata

## -- C --

calculate_limit_lower | Calculate the lower limit of a confidence interval
calculate_limit_upper | Calculate the upper limit of a confidence interval
calc_prob | Calculate probability
calc_Pvalue_4x2 | Calculate probability
calc_Pvalue_5x2 | Calculate probability
cavo_2012 | Complete response before and after consolidation therapy
Chacko_test_1xc | The Chacko test for order-restriction
chap1 | Chapter 1: Introduction
chap10 | Chapter 10: Stratified 2x2 Tables and Meta-Analysis
chap2 | Chapter 2: The 1x2 Table and the Binomial Distribution
chap3 | Chapter 3: The 1xc Table and the Multinomial Distribution
chap4 | Chapter 4: The 2x2 Table
chap5 | Chapter 5: The Ordered rx2 Table
chap6 | Chapter 6: The Ordered 2xc Table
chap7 | Chapter 7: The rxc Table
chap8 | Chapter 8: The Paired 2x2 Table
chap9 | Chapter 9: The Paired cxc Table
ClopperPearson_exact_CI_1x2 | The Clopper-Pearson exact confidence interval
ClopperPearson_exact_CI_1x2_beta_version | The Clopper-Pearson exact confidence interval for the binomial probability (beta version)
ClopperPearson_midP_CI_1x2 | The Clopper-Pearson mid-P confidence interval
CochranArmitage_CI_rx2 | The Cochran-Armitage confidence interval for trend in the linear model
CochranArmitage_exact_cond_midP_tests_rx2 | The Cochran-Armitage exact conditional and mid-P tests
CochranArmitage_MH_tests_rx2 | The Cochran-Armitage, modified Cochran-Armitage, and Mantel-Haenszel tests for trend
CochranMantelHaenszel_test_stratified_2x2 | The Cochran-Mantel-Haenszel test of a common odds ratio
Cochran_Q_test_stratified_2x2 | The Cochran Q test of homogeneity of effects over strata
contingencytables | Statistical Analysis of Contingency tables
contingencytables_result | contingencytables_result class
Cornfield_exact_conditional_CI_2x2 | The Cornfield exact conditional confidence interval for the odds ratio
Cornfield_midP_CI_2x2 | The Cornfield mid-P confidence interval for the odds ratio
Cumulative_models_for_2xc | Cumulative logit and probit models
Cumulative_models_for_rxc | Cumulative logit and probit models

## -- D --

doll_hill_1950 | Smoking and lung cancer

## -- E --

Exact_binomial_test_1x2 | The exact binomial test for the binomial probability (pi)
Exact_cond_midP_linear_rank_tests_2xc | Exact conditional and mid-P linear rank tests
Exact_cond_midP_tests_rxc | Exact conditional and mid-P tests for the rxc table
Exact_cond_midP_unspecific_ordering_rx2 | The exact conditional and mid-P tests for unspecific ordering
Exact_multinomial_test_1xc | The exact multinomial test for multinomial probabilities
Exact_unconditional_test_2x2 | Exact unconditional test for association in 2x2 tables
ezra_2010 | Floppy eyelid syndrome vs obstructive sleep apnea

## -- F --

fischer_1999 | A comparison between serial and retrospective measurements
FisherFreemanHalton_asymptotic_test_rxc | The Fisher-Freeman-Halton asymptotic test for unordered rxc tables
Fisher_exact_test_2x2 | The Fisher exact test for association in 2x2 tables
Fisher_midP_test_2x2 | The Fisher mid-P test for association in 2x2 tables
FleissEveritt_test_paired_cxc | The Fleiss-Everitt version of the Stuart test for marginal homogeneity
FleissLevinPaik_test_paired_cxc | The Fleiss-Levin-Paik test for three-level ordinal outcomes
fleiss_2003 | Table 13.6, page 382, of Fleiss et al. (2003)
fontanella_2008 | The Adolescent Placement Study

## -- G --

gamma_coefficient_rxc | The gamma coefficient
gamma_coefficient_rxc_bca | The gamma coefficient with the bias-corrected and accelerated boostrap confidence interval
Gart_adjusted_logit_CI_2x2 | The Gart adjusted logit confidence interval for the odds ratio
Gold_Wald_CIs_1xc | The Gold Wald simultaneous intervals for the multinomial probabilities
Goodman_Wald_CIs_1xc | The Goodman Wald simultaneous intervals for the multinomial probabilities
Goodman_Wald_CIs_for_diffs_1xc | The Goodman Wald simultaneous intervals for the differences between the
Goodman_Wilson_score_CIs_1xc | The Goodman Wilson score simultaneous intervals for the multinomial probabilities

## -- H --

hine_1989 | Prophylactice use of Lidocaine in myocardial infarction
hypothetical | Hypothetical experiment

## -- I --

Independence_smoothed_logit_CI_2x2 | The Independence-smoothed logit confidence interval for the odds ratio
indredavik_2008 | Elevated troponin T levels in stroke patients
InverseVariance_estimate_stratified_2x2 | The inverse variance estimate of the overall effect across strata
Inv_sinh_CI_OR_2x2 | The inverse hyperbolic sine confidence interval for the odds ratio
Inv_sinh_CI_ratio_2x2 | The inverse hyperbolic sine confidence interval for the ratio of probabilities

## -- J --

Jeffreys_CI_1x2 | Jeffreys confidence interval for the binomial probability
JonckheereTerpstra_test_rxc | The Jonckheere-Terpstra test for association
jullumstroe_2009 | Colorectal cancer (Table 7.7)

## -- K --

Katz_log_CI_2x2 | The Katz log confidence interval for the ratio of probabilities
Kendalls_tau_b_rxc | Kendall's tau-b with confidence interval based on the Fieller standard deviation
Kendalls_tau_b_rxc_bca | Kendall's tau-b with the bias-corrected and accelerated boostrap confidence interval
Koopman_asymptotic_score_CI_2x2 | The Koopman asymptotic score confidence interval for the ratio of probabilities
KruskalWallis_asymptotic_test_rxc | The Kruskal-Wallis asymptotic test for singly ordered rxc tables

## -- L --

lampasona_2013 | A case-control study of GADA exposure on IPEX syndrome
ligarden_2010 | Ligarden et al., 2010
linear_by_linear_test_rxc | The linear-by-linear test for association
list_functions | List functions from a chapter
LR_CI_1x2 | The likelihood ratio confidence interval for the binomial probability
LR_test_1x2 | The likelihood ratio test for the binomial probability (pi)
LR_test_1xc | The likelihood ratio test for multinomial probabilities
LR_test_2x2 | The likelihood ratio test for association in 2x2 tables
lund_2012 | Low Birth Weight vs psychiatric morbitidy with control as reference category
lydersen_2012a | Postoperative nausea

## -- M --

mangerud_2014_BMI | Psychiatric diag. vs BMI with hyperkinetic disorders as reference category
mangerud_2014_PA | Psychiatric Diagnoses and Physical Activity
MantelHaenszel_estimate_stratified_2x2 | The Mantel-Haenszel estimate of the overall effect across strata
MantelHaenszel_test_2xc | The Mantel-Haenszel test of association with column scores
McNemarBowker_test_paired_cxc | The McNemar-Bowker test for marginal symmetry
McNemar_asymptotic_test_CC_paired_2x2 | The McNemar asymptotic test with continuity correction
McNemar_asymptotic_test_paired_2x2 | The McNemar asymptotic test
McNemar_exact_cond_test_paired_2x2 | The McNemar exact conditional test
McNemar_exact_unconditional_test_paired_2x2 | The McNemar exact unconditional test
McNemar_midP_test_paired_2x2 | The McNemar mid-P test
Mee_asymptotic_score_CI_2x2 | The Mee asymptotic score confidence interval for the difference between probabilities
MidP_binomial_test_1x2 | The mid-P binomial test for the binomial probability (pi)
MidP_multinomial_test_1xc | The mid-P multinomial test for multinomial probabilities
MiettinenNurminen_asymptotic_score_CI_difference_2x2 | The Miettinen-Nurminen asymptotic score confidence interval for the
MiettinenNurminen_asymptotic_score_CI_OR_2x2 | The Miettinen-Nurminen asymptotic score CI for the odds ratio
MiettinenNurminen_asymptotic_score_CI_ratio_2x2 | The Miettinen-Nurminen asymptotic score confidence interval for the ratio of probabilities
mills_graubard_1987 | Alcohol consumption and malformations
ML_estimates | Calculate ML estimates
ML_estimates_and_CIs_stratified_2x2 | Maximum likelihood estimates with CIs of the grouping and strata effects
MOVER_R_Wilson_CI_OR_2x2 | The MOVER-R Wilson confidence interval for the odds ratio
MOVER_R_Wilson_CI_ratio_2x2 | The MOVER-R Wilson confidence interval for the ratio of probabilities
MOVER_Wilson_score_CI_paired_2x2 | The MOVER Wilson score confidence interval for the ratio of paired probabilities

## -- N --

Newcombe_hybrid_score_CI_2x2 | The Newcombe hybrid score confidence interval for the difference between probabilities
Newcombe_square_and_add_CI_paired_2x2 | The Newcombe square-and-add confidence interval for the difference

## -- P --

Pearson_chi_squared_test_1xc | The Pearson chi-squared test for multinomial probabilities
Pearson_chi_squared_test_2x2 | The Pearson chi-squared test for association in 2x2 tables
Pearson_chi_squared_test_CC_2x2 | The Pearson chi-squared test for association in 2x2 tables
Pearson_correlation_coefficient_rxc | The Pearson correlation coefficient
Pearson_correlation_coefficient_rxc_bca | The Pearson correlation coefficient with the bias-corrected and accelerated
Pearson_LR_homogeneity_test_stratified_2x2 | The Pearson chi-squared and likelihood ratio tests for homogeneity over strata
Pearson_LR_tests_cum_OR_2xc | The Pearson chi-squared and likelihood ratio tests for cumulative ORs in 2xc tables
Pearson_LR_tests_rxc | The Pearson chi-squared and likelihood ratio tests for association in rxc tables
Pearson_LR_tests_unspecific_ordering_rx2 | The Pearson chi-squared and likelihood ratio tests for unspecific ordering in rx2 tables
Pearson_LR_test_common_effect_stratified_2x2 | The Pearson chi-squared and likelihood ratio tests of a common difference
Pearson_residuals_rxc | The Pearson residuals and the standardized Pearson residuals
perondi_2004 | An RCT of high vs standard dose of epinephrine
peterson_2007 | Pretherapy susceptability of pathogens
Peto_homogeneity_test_stratified_2x2 | The Peto test for homogeneity of odds ratios over strata
Peto_OR_estimate_stratified_2x2 | The Peto estimate of the common odds ratio across strata
PriceBonett_approximate_Bayes_CI_2x2 | The Price-Bonett approximate Bayes confidence interval for the ratio of probabilities
print.contingencytables_result | Output from a contingency tables method

## -- Q --

QuesenberryHurst_Wilson_score_CIs_1xc | The Quesenberry-Hurst Wilson score simultaneous intervals for the multinomial probabilities

## -- R --

RBG_test_and_CI_stratified_2x2 | The RBG test and CI for a common odds ratio
ritland_2007 | The association between CHRNA4 genotype and XFS

## -- S --

Scheffe_type_CIs_paired_cxc | Scheffe-type confidence intervals for differences of marginal probabilities
Scheffe_type_CIs_rxc | The Scheffe-type simultaneous confidence intervals for the differences pi_1|i - pi_1|j
Score_test_1x2 | The score test for the binomial probability (pi)
Score_test_and_CI_marginal_mean_scores_paired_cxc | Score test and CI marginal mean scores paired CxC
Score_test_CC_1x2 | The score test with continuity correction for the
Score_test_for_effect_in_the_probit_model_2xc | Score test for effect in the cumulative probit model
score_test_statistic | Calculate ML estimates
singh_2010 | The number of n-th order male births
singh_2010_1 | The number of n-th order male births
snp6498169 | Genotype counts for SNP rs 6498169 in RA patients
Spearman_correlation_coefficient_rxc | The Spearman correlation coefficient
Spearman_correlation_coefficient_rxc_bca | The Spearman correlation coefficient with the bias-corrected and accelerated
stratified_2x2_tables | Stratified 2x2 tables
Stuart_test_paired_cxc | The Stuart test for marginal homogeneity

## -- T --

table_7.3 | Treatment for ear infection
table_7.4 | Psychiatric Diagnoses and Physical Activity
table_7.5 | Psychiatric diag. vs BMI with hyperkinetic disorders as reference category
table_7.6 | Low Birth Weight vs psychiatric morbitidy with control as reference category
table_7.7 | Colorectal cancer (Table 7.7)
table_7.8 | Breast Tumor
table_7.9 | Self-rated health (Table 7.9)
Tango_asymptotic_score_CI_paired_2x2 | The Tango asymptotic score confidence interval for the difference between paired probabilities
Tang_asymptotic_score_CI_paired_2x2 | The Tang asymptotic score confidence interval for the ratio of paired probabilities
tea | A lady tasting a cup of 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_OR | The 2x2 table CIs odds ratio
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
Transformed_Blaker_exact_CI_paired_2x2 | The Transformed Blaker exact confidence interval for the conditional odds ratio
Transformed_Clopper_Pearson_exact_CI_paired_2x2 | The Transformed Clopper-Pearson exact confidence interval for the conditional odds ratio
Transformed_Clopper_Pearson_midP_CI_paired_2x2 | The Transformed Clopper-Pearson mid-P confidence interval for the conditional odds ratio
Transformed_Wilson_score_CI_paired_2x2 | The Transformed Wilson score confidence interval for the conditional odds ratio
Trend_estimate_CI_tests_rx2 | Trend estimate for linear and logit models

## -- U --

Uncorrected_asymptotic_score_CI_2x2 | The uncorrected asymptotic score confidence interval for the odds ratio

## -- V --

validateArguments | Validate arguments of a function
vanbalen_2003 | Treatment for ear infection

## -- W --

Wald_CI_1x2 | The Wald confidence interval for the binomial probability
Wald_CI_2x2 | The Wald confidence interval for the difference between probabilities
Wald_CI_AgrestiMin_paired_2x2 | The Wald confidence interval for the difference between paired probabilities
Wald_CI_BonettPrice_paired_2x2 | The Wald confidence interval for the difference between paired probabilities
Wald_CI_CC_1x2 | The Wald CI with CC for the binomial probability
Wald_CI_CC_2x2 | The Wald confidence interval for the difference between 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 difference between paired probabilities
Wald_CI_OR_Laplace_paired_2x2 | The Wald confidence interval for the conditional odds ratio with Laplace adjustment
Wald_CI_OR_paired_2x2 | The Wald confidence interval for the conditional odds ratio
Wald_CI_ratio_paired_2x2 | The Wald confidence interval for the ratio of paired probabilities
Wald_test_1x2 | The Wald test for the binomial probability (pi)
Wald_test_and_CI_common_diff_stratified_2x2 | The Wald test and CI for a common difference between probabilities
Wald_test_and_CI_common_ratio_stratified_2x2 | The Wald test and CI for a common ratio of probabilities
Wald_test_and_CI_marginal_mean_ranks_paired_cxc | The Wald test and confidence interval for the difference between marginal mean ranks / ridits
Wald_test_and_CI_marginal_mean_scores_paired_cxc | The Wald test and confidence interval for the difference between marginal mean scores
Wald_test_CC_1x2 | The Wald test with continuity correction for the binomial probability
Wilson_score_CI_1x2 | The Wilson score confidence interval
Wilson_score_CI_CC_1x2 | The Wilson score confidence interval with continuity correction for the binomial probability
Woolf_logit_CI_2x2 | The Woolf logit confidence interval for the odds ratio
Woolf_test_and_CI_stratified_2x2 | The Woolf test and CI for a common odds ratio

## -- Z --

Z_unpooled_test_2x2 | The Z-unpooled test for association in 2x2 tables

## -- misc --

.onAttach | Prints welcome message on package load