two_samp_bin_test: Binary (Response) Variable Compared to Binary (Group)...

In FredHutch/VISCfunctions: VISC STP/SRA functions

Binary (Response) Variable Compared to Binary (Group) Variable Test (VISC)

Description

Either Barnard, Fisher's, or Chi-sq test performed for unpaired data and McNemar's test for paired data

Usage

two_samp_bin_test(
  x,
  y,
  method = c("barnard", "fisher", "chi.sq", "mcnemar"),
  barnard_method = c("z-pooled", "z-unpooled", "boschloo", "santner and snell", "csm",
    "csm approximate", "csm modified"),
  alternative = c("two.sided", "less", "greater"),
  verbose = FALSE,
  ...
)

Arguments

x	vector with only 2 levels (can include NA values).
y	vector with only 2 levels (can include NA values unless method = 'mcnemar').
method	what test to run, "barnard" (default), "fisher" , "chi.sq" , or "mcnemar")
barnard_method	indicates the Barnard method for finding tables as or more extreme than the observed table: must be either "z-pooled", "z-unpooled", "santner and snell", "boschloo", "csm", "csm approximate", or "csm modified". Only used when method = 'barnard'
alternative	a character string specifying the alternative hypothesis, must be one of "two.sided" (default), "greater" or "less". You can specify just the initial letter. Only "two.sided" available for method = 'chi.sq' or 'mcnemar'
verbose	a logical variable indicating if warnings and messages should be displayed.
...	other parameters to pass to Exact::exact.test when running Barnard test

Details

For one sided tests if y is a factor variable the level order is respected, otherwise the levels will set to alphabetical order (i.e. if alternative = less then testing a < b ).

If method = 'mcnemar' assumes the first observations of the first group matches the first observation of the second group, and so on. Also if method = 'mcnemar' then y must have the same number of samples for each level.

If only one value of x than p=1 is returned, however if only one value of y than p=NA is returned. This is to match expactations since normally y is a group variable and x is the outcome (i.e. if both group response rates are 0\ returned)

Value

p-value for comparing x at the different levels of y.

Examples

set.seed(5432322)
outcome <- c(sample(0:1,10,replace = TRUE, prob = c(.75,.25)),
             sample(0:1,10,replace = TRUE, prob = c(.25,.75)))
grp <- c(rep('a', 10), rep('b', 10))
two_samp_bin_test(outcome, grp, method = 'barnard')
two_samp_bin_test(outcome, grp, 'fisher')
two_samp_bin_test(outcome, grp, 'chi.sq')
two_samp_bin_test(outcome, grp, 'mcnemar')

FredHutch/VISCfunctions documentation built on Oct. 14, 2024, 11:33 p.m.