tab2by2.test: Comparative tests of independence in rx2 contigency tables
In epitools: Epidemiology Tools

Description Usage Arguments Details Value Author(s) References See Also Examples

Tests for independence where each row of the rx2 table is compared to the exposure reference level and test of independence two-sided p values are calculated using mid-p exact, Fisher's Exact, and the chi-square test.

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tab2by2.test(x, y = NULL,
             correction = FALSE,
             rev = c("neither", "rows", "columns", "both"))

`x`	input data can be one of the following: r x 2 table, vector of numbers from a contigency table (will be transformed into r x 2 table in row-wise order), or single factor or character vector that will be combined with `y` into a table.
`y`	single factor or character vector that will be combined with `x` into a table (default is NULL)
`correction`	set to TRUE for Yate's continuity correction (default is FALSE)
`rev`	reverse order of "rows", "colums", "both", or "neither" (default)

This function expects the following table struture:

                    disease=0   disease=1
    exposed=0 (ref)    n00         n01
    exposed=1          n10         n11	
    exposed=2          n20         n21
    exposed=3          n30         n31

The reason for this is because each level of exposure is compared to the reference level.

If you are providing a 2x2 table order does not matter:

If the table you want to provide to this function is not in the preferred form, just use the rev option to "reverse" the rows, columns, or both. If you are providing categorical variables (factors or character vectors), the first level of the "exposure" variable is treated as the reference. However, you can set the reference of a factor using the relevel function.

Likewise, each row of the rx2 table is compared to the exposure reference level and test of independence two-sided p values are calculated using mid-p exact, Fisher's Exact, Monte Carlo simulation, and the chi-square test.

`x`	table that was used in analysis
`p.value`	p value for test of independence
`correction`	logical specifying if continuity correction was used

Tomas Aragon, aragon@berkeley.edu, http://www.phdata.science

Kenneth J. Rothman and Sander Greenland (1998), Modern Epidemiology, Lippincott-Raven Publishers

Kenneth J. Rothman (2002), Epidemiology: An Introduction, Oxford University Press

Nicolas P. Jewell (2004), Statistics for Epidemiology, 1st Edition, 2004, Chapman & Hall, pp. 73-81

oddsratio, riskratio

##Case-control study assessing whether exposure to tap water
##is associated with cryptosporidiosis among AIDS patients

tapw <- c("Lowest", "Intermediate", "Highest")
outc <- c("Case", "Control")	
dat <- matrix(c(2, 29, 35, 64, 12, 6),3,2,byrow=TRUE)
dimnames(dat) <- list("Tap water exposure" = tapw, "Outcome" = outc)
tab2by2.test(dat, rev="c")