michaelfay-niaid.r-universe.dev

[michaelfay-niaid] bpcp 1.5.1

mfay@niaid.nih.gov (Michael P. Fay) — Thu, 19 Feb 2026 06:10:39 GMT

Calculates nonparametric pointwise confidence intervals for the survival distribution for right censored data, and for medians [Fay and Brittain ]. 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 ]. 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.

[michaelfay-niaid] asht 1.0.3

mfay@niaid.nih.gov (Michael P. Fay) — Wed, 20 Aug 2025 22:34:57 GMT

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 ], 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 ], two-sample melding tests [see Fay, Proschan, and Brittain ], 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 ] or Bayer, Fay, and Graubard, 2023 ). The focus is on hypothesis tests that have compatible confidence intervals, but some functions only have confidence intervals (e.g., prevSeSp).

[michaelfay-niaid] exactci 1.4-5

mfay@niaid.nih.gov (Michael P. Fay) — Wed, 20 Aug 2025 21:10:01 GMT

Calculates exact tests and confidence intervals for one-sample binomial and one- or two-sample Poisson cases (see Fay (2010) ).

[michaelfay-niaid] exact2x2 1.7.0

mfay@niaid.nih.gov (Michael P. Fay) — Wed, 20 Aug 2025 19:40:13 GMT

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, ). Gives boundary-optimized rejection region test (Gabriel, et al, 2018, ), 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, ). For review of these kinds of exact tests see Fay and Hunsberger (2021, ).

[michaelfay-niaid] nivm 0.6

mfay@niaid.nih.gov (Michael P. Fay) — Wed, 20 Aug 2025 19:00:03 GMT

Noninferiority tests for difference in failure rates at a prespecified control rate or prespecified time. For details, see Fay and Follmann, 2016 .

[michaelfay-niaid] choplump 1.1.2

mfay@niaid.nih.gov (Michael P. Fay) — Fri, 26 Jan 2024 02:39:02 GMT

Calculates permutation tests that can be powerful for comparing two groups with some positive but many zero responses (see Follmann, Fay, and Proschan ).

[michaelfay-niaid] perm 1.0-0.4

mfay@niaid.nih.gov (Michael P. Fay) — Thu, 24 Aug 2023 23:30:45 GMT

Perform Exact or Asymptotic permutation tests [see Fay and Shaw ].

[michaelfay-niaid] interval 1.1-1.0

mfay@niaid.nih.gov (Michael P. Fay) — Thu, 24 Aug 2023 23:30:40 GMT

Functions to fit nonparametric survival curves, plot them, and perform logrank or Wilcoxon type tests [see Fay and Shaw ].

[michaelfay-niaid] oceCens 0.1.2

mfay@niaid.nih.gov (Michael P. Fay) — Thu, 24 Aug 2023 16:35:20 GMT

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).

[michaelfay-niaid] hbim 1.1.2

mfay@niaid.nih.gov (Michael P. Fay) — Thu, 24 Aug 2023 16:35:17 GMT

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 .

[michaelfay-niaid] binseqtest 1.0.4

mfay@niaid.nih.gov (Michael P. Fay) — Thu, 24 Aug 2023 16:35:12 GMT

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

[michaelfay-niaid] saws 0.9-7.0

mfay@niaid.nih.gov (Michael P. Fay) — Thu, 23 Jun 2022 17:00:02 GMT

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

[michaelfay-niaid] rateratio.test 1.1

mfay@niaid.nih.gov (Michael Fay) — Mon, 09 May 2022 13:50:02 GMT

Performs exact rate ratio tests.

[michaelfay-niaid] csci 0.9.3

mfay@niaid.nih.gov (Michael P. Fay) — Mon, 07 Dec 2020 08:40:05 GMT

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.

[michaelfay-niaid] MChtest 1.0-3

mfay@niaid.nih.gov (Michael P. Fay) — Thu, 16 May 2019 12:10:03 GMT

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 ) and a boundary proposed by Besag and Clifford, 1991 . Gives valid p-values and confidence intervals on p-values.

[michaelfay-niaid] ssanv 1.1

mfay@niaid.nih.gov (Michael P. Fay) — Mon, 22 Jun 2015 00:00:00 GMT

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.