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exact2x2 - Exact Tests and Confidence Intervals for 2x2 Tables

Calculates conditional exact tests (Fisher's exact test, Blaker's exact test, or exact McNemar's test) and unconditional exact tests (including score-based tests on differences in proportions, ratios of proportions, and odds ratios, and Boshcloo's test) with appropriate matching confidence intervals, and provides power and sample size calculations. Gives melded confidence intervals for the binomial case (Fay, et al, 2015, <DOI:10.1111/biom.12231>). Gives boundary-optimized rejection region test (Gabriel, et al, 2018, <DOI:10.1002/sim.7579>), an unconditional exact test for the situation where the controls are all expected to fail. Gives confidence intervals compatible with exact McNemar's or sign tests (Fay and Lumbard, 2021, <DOI:10.1002/sim.8829>). For review of these kinds of exact tests see Fay and Hunsberger (2021, <DOI:10.1214/21-SS131>).

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7.38 score 3 stars 4 dependents 339 scripts 3.9k downloads

exactci - Exact P-Values and Matching Confidence Intervals for Simple Discrete Parametric Cases

Calculates exact tests and confidence intervals for one-sample binomial and one- or two-sample Poisson cases (see Fay (2010) <doi:10.32614/rj-2010-008>).

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5.84 score 8 dependents 41 scripts 4.4k downloads

interval - Weighted Logrank Tests and NPMLE for Interval Censored Data

Functions to fit nonparametric survival curves, plot them, and perform logrank or Wilcoxon type tests [see Fay and Shaw <doi:10.18637/jss.v036.i02>].

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5.02 score 4 dependents 52 scripts 5.6k downloads

perm - Exact or Asymptotic Permutation Tests

Perform Exact or Asymptotic permutation tests [see Fay and Shaw <doi:10.18637/jss.v036.i02>].

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4.35 score 10 dependents 145 scripts 5.1k downloads

bpcp - Beta Product Confidence Procedure for Right Censored Data

Calculates nonparametric pointwise confidence intervals for the survival distribution for right censored data, and for medians [Fay and Brittain <DOI:10.1002/sim.6905>]. Has two-sample tests for dissimilarity (e.g., difference, ratio or odds ratio) in survival at a fixed time, and differences in medians [Fay, Proschan, and Brittain <DOI:10.1111/biom.12231>]. Basically, the package gives exact inference methods for one- and two-sample exact inferences for Kaplan-Meier curves (e.g., generalizing Fisher's exact test to allow for right censoring), which are especially important for latter parts of the survival curve, small sample sizes or heavily censored data. Includes mid-p options.

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3.94 score 3 dependents 36 scripts 2.7k downloads

ssanv - Sample Size Adjusted for Nonadherence or Variability of Input Parameters

A set of functions to calculate sample size for two-sample difference in means tests. Does adjustments for either nonadherence or variability that comes from using data to estimate parameters.

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3.24 score 11 dependents 13 scripts 4.1k downloads

asht - Applied Statistical Hypothesis Tests

Gives some hypothesis test functions (sign test, median and other quantile tests, Wilcoxon signed rank test, coefficient of variation test, test of normal variance, test on weighted sums of Poisson [see Fay and Kim <doi:10.1002/bimj.201600111>], sample size for t-tests with different variances and non-equal n per arm, Behrens-Fisher test, nonparametric ABC intervals, Wilcoxon-Mann-Whitney test [with effect estimates and confidence intervals, see Fay and Malinovsky <doi:10.1002/sim.7890>], two-sample melding tests [see Fay, Proschan, and Brittain <doi:10.1111/biom.12231>], one-way ANOVA allowing var.equal=FALSE [see Brown and Forsythe, 1974, Biometrics]), prevalence confidence intervals that adjust for sensitivity and specificity [see Lang and Reiczigel, 2014 <doi:10.1016/j.prevetmed.2013.09.015>] or Bayer, Fay, and Graubard, 2023 <doi:10.48550/arXiv.2205.13494>). The focus is on hypothesis tests that have compatible confidence intervals, but some functions only have confidence intervals (e.g., prevSeSp).

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3.16 score 1 dependents 61 scripts 2.6k downloads

rateratio.test - Exact Rate Ratio Test

Performs exact rate ratio tests.

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2.38 score 24 scripts 468 downloads

hbim - Hill/Bliss Independence Model for Combination Vaccines

Calculate expected relative risk and proportion protected assuming normally distributed log10 transformed antibody dose for a several component vaccine. Uses Hill models for each component which are combined under Bliss independence. See Saul and Fay, 2007 <DOI:10.1371/journal.pone.0000850>.

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2.30 score 8 scripts 234 downloads

binseqtest - Exact Binary Sequential Designs and Analysis

For a series of binary responses, create stopping boundary with exact results after stopping, allowing updating for missing assessments.

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2.04 score 11 scripts 258 downloads

choplump - Permutation Test for Some Positive and Many Zero Responses

Calculates permutation tests that can be powerful for comparing two groups with some positive but many zero responses (see Follmann, Fay, and Proschan <DOI:10.1111/j.1541-0420.2008.01131.x>).

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2.00 score 6 scripts 245 downloads

oceCens - Ordered Composite Endpoints with Censoring

Estimates win ratio or Mann-Whitney parameter for two group comparisons using ordered composite endpoints with right censoring as described in Follmann, Fay, Hamasaki, and Evans (2020)<doi:10.1002/sim.7890>.

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2.00 score 3 scripts 126 downloads

csci - Current Status Confidence Intervals

Calculates pointwise confidence intervals for the cumulative distribution function of the event time for current status data, data where each individual is assessed at one time to see if they had the event or not by the assessment time.

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1.34 score 22 scripts 248 downloads

saws - Small-Sample Adjustments for Wald Tests Using Sandwich Estimators

Tests coefficients with sandwich estimator of variance and with small samples. Regression types supported are gee, linear regression, and conditional logistic regression.

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1.11 score 13 scripts 309 downloads

nivm - Noninferiority Tests with Variable Margins

Noninferiority tests for difference in failure rates at a prespecified control rate or prespecified time. For details, see Fay and Follmann, 2016 <DOI:10.1177/1740774516654861>.

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1.00 score 6 scripts 197 downloads

MChtest - Monte Carlo Hypothesis Tests with Sequential Stopping

Performs Monte Carlo hypothesis tests, allowing a couple of different sequential stopping boundaries. For example, a truncated sequential probability ratio test boundary (Fay, Kim and Hachey, 2007 <DOI:10.1198/106186007X257025>) and a boundary proposed by Besag and Clifford, 1991 <DOI:10.1093/biomet/78.2.301>. Gives valid p-values and confidence intervals on p-values.

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1.00 score 146 downloads