Fixed an error where the p-value was sometimes incorrect for imbalanced designs. Only occurred when the p-value would be large, but exact test gave a much higher p-value. Thanks to Andrea Smith for pointing out the issue
Added more stored tables for CSM test comparing two independent proportions. Tables with (n1+1)x(n2+1) <= 15,000 and group ratio between 1:1 and 2:1 were added to the existing stored tables. Stored CSM ordering matrix is around 85MB, so is loaded from the ExactData R package from GitHub using the drat R package
Improved computation time for multinomial tests
Added tsmethod parameter to unconditional paired tests
Added "UCM" test and changed names of method options for unconditional paired tests
Fixed issue with unconditional paired tests where confidence bounds are not possible based on extreme delta
Fixed error message for two independent sample tests when confidence bounds are either 0 or 1. Thanks to Ping Mahling for pointing out this issue
Added unconditional exact tests to compare two paired proportions! Three functions are added: paired.exact.test, paired.reject.region, and power.paired.test
Fixed issues with CSM test and greatly improved computation time. Added the parameter "useStoredCSM", which uses a stored pre-computed CSM ordering matrix for sample sizes with max(n1,n2) <= 100 for two independent proportions and sample size <= 200 for two paired proportions. Stored CSM ordering matrix is around 25MB, so is loaded from the ExactData R package from GitHub using the drat R package
For two independent proportions, removed method option "csm approximate", changed method option "chisq" to "pearson chisq", and removed ref.pvalue option in exact.reject.region() and power.exact.test() functions. Added more checks to make it more user-friendly
Fixed non-inferiority (equivalence) tests and confidence interval calculations. Code can now perform these tests and CIs for all methods
Added tsmethod parameter. This allows user to perform a two-sided test by either squaring the statistic (default; previous versions), or by performing one-sided test and doubling the p-value
Removed precision parameter and use rootSolve R package to determine confidence interval
Added exact.reject.region function
Added input parameters in exact.test. Input parameters include calculating confidence intervals and non-zero null hypothesis for the difference in proportion (only "z-pooled" and "csm" methods)
Added "Chisq" and "Yates chisq" method to power.exact.test
Removed "CSM Modified" method (determined not to be level-alpha)
Changed input parameters in exact.test. Parameter interval changed to np.interval and alpha changed to reject.alpha
Converted power.exact.test output to be "power.htest" object
Greatly improved computation time, especially for Boschloo's test, large sample sizes, and power calculations
Converted exact.test output to be "htest" object
Added "Fisher" method to power.exact.test
Greatly improved computation time
Fixed a floating point issue where two tables were equally extreme but had different test statistic. Thanks to Long Qu for pointing out this issue
Resolved an error message that occurred when two proportions were nearly identical
Added "CSM", "CSM Modified", and "CSM Approximate" methods
Added to.plot and ref.pvalue input parameters to the exact.test function
Added "Santner and Snell" method
Greatly improved computation time
Changed npNumbers from an increment to a number representing the number of nuisance parameters considered
Added cond.row representing whether the rows or margins are fixed for "binomial" model
First CRAN release.
Can perform Z-pooled, Z-unpooled, and Boschloo's test. Can perform "binomial" and "multinomial" models with or without interval approach recommended by Berger and Boos (1994)