| Package | Function | Use |
| cta | mph.fit | Fits nonlinear constraints to contingency tables. |
| DescTools | BinomDiffCI | Calculates confidence intervals for differences in binomial proportions. |
| DescTools | BreslowDayTest | Tests the null hypothesis of homogeneity of odds ratios in stratified contingency tables. |
| elrm | elrm | Calculate test results for exact logistic regression via Monte Carlo. |
| gmodels | estimable | Fits linear constraints to generalized linear models. |
| Hmisc | binconf | Gives Wilson and standard binomial confidence intervals. |
| MASS | polr | Fits ordinal categorical regression models. |
| nleqslv | nleqslv | Solves a nonlinear set of equations. |
| nnet | multinom | Fits the multinomial regression model. |
| PHInfiniteEstimates | network and inference | Calculate test results for exact logistic regression. |
| poLCA | poLCA | Perform latent class analysis. |
| polycor | polychor | Calculates polychoric correlation. |
| PropCIs | orci.bayes | Performs Bayesian inference on the odds ratio. |
| psych | alpha | Calculate Cronbach's alpha to measure reliability. |
| psych | cohen.kappa | Calculates Cohen's kappa to measure agreement. |
| pwr | pwr.chisq.test | Calculates approximate power for tests of proportions. |
| rstanarm | stan_glm | Fits the generalized linear model with a prior. |
| TheorStat | bivariatebincover | Plots countour plots of coverage of confidence intervals for the difference between two binomial proportions as a function of the two marginal probabilities. |
| TheorStat | ccplot | Graphically presents correction for continuity. |
| TheorStat | ctsci | Graphially represents continuous confidence interval construction. |
| TheorStat | fun.allcover | Calculates and plots relationship between nominal and exact coverage for binomial confidence intervals. |
| TheorStat | fun.coverageplot | Plots coverage of binomial confidence intervals. |
| TheorStat | fun.stratsize | Simulates operating characteristic of nested tests in stratified tables. |
| TheorStat | fun.testncp | Presents graphically the quality of the non-central chi-square approximation to the alternative distribution for contingency table testing. |
| TheorStat | wilsonpicture | Graphically represents Wilson confidence interval construction. |
| vcdExtra | CMHtest | Performs Cochran Mantel Haenszel test for the null hypothesis of no association vs. the alternative of a common non-unit odds ratio. |
| VGAM | vglm | Fits an ordinal baseline logit model and some variants. |