epitab: Epidemiologic tabulation for a cohort or case-control study
In epitools: Epidemiology Tools

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

Calculates risks, risk ratio, odds ratio, and confidence intervals for epidemiologic data

epitab(x, y = NULL,
       method = c("oddsratio", "riskratio", "rateratio"),
       conf.level = 0.95,
       rev = c("neither", "rows", "columns", "both"),           
       oddsratio = c("wald", "fisher", "midp", "small"),
       riskratio = c("wald", "boot", "small"),
       rateratio = c("wald", "midp"),
       pvalue = c("fisher.exact", "midp.exact", "chi2"),
       correction = FALSE,
       verbose = FALSE)

`x`	For odds ratio or risk ratio, 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. For rate ratio, input data can be one of the following: r x 2 table where first column contains disease counts and second column contains person time at risk; a single numeric vector of counts followed by person time at risk; a single numeric vector of counts combined with `y` which would be a numeric vector of corresponding person time at risk
`y`	For odds ratio or risk ratio, a single factor or character vector that will be combined with `x` into a table (default is NULL) For rate ratio, a numeric vector of person-time at risk; if provided, `x` must be a numeric vector of disease counts
`method`	select measure of association: "oddsratio" (default), "riskratio", or "rateratio"
`conf.level`	confidence level (default is 0.95)
`rev`	reverse order of "rows", "colums", "both", or "neither" (default)
`oddsratio`	selection estimation method: "wald" (default), "fisher", "midp", "small"
`riskratio`	selection estimation method: "wald" (default), "boot", "small"
`rateratio`	"wald" (default), "midp"
`pvalue`	"fisher.exact" (default), "midp.exact", "chi2" (normal approximation); for rate ratio, "fisher.exact" not calculated
`correction`	set to TRUE for Yate's continuity correction (default is FALSE)
`verbose`	set to TRUE to return more detailed results (default is FALSE)

The epitab calculates odds ratios, risk ratios, or rate ratios for rx2 tables. The odds ratios are estimated using unconditional maximum likelihood (Wald), conditional maximum likelihood (Fisher), median-unbiased method (mid-p), or small-sample adjusted. The confidence intervals are estimated using a normal approximation (Wald), hypergeometric exact (Fisher), mid-p exact, or small sample adjusted method.

The risk ratios are estimated using unconditional maximum likelihood (Wald), or small-sample adjusted. The confidence intervals are estimated using a normal approximation (Wald), or bootstrap estimation.

The rate ratios are estimated using unconditional maximum likelihood estimation (Wald), or median unbiased method (mid-p). The confidence intervals are estimated using normal approximation, or mid-p exact method.

Notice the expected structure of the data to be given to 'epitab':

                 Disease
  Exposure       No (ref)  Yes
   Level 1 (ref)  a         b
   Level 2        c         d
   Level 3        e         f

This function expects the following table struture for rate ratios:

                    counts   person-time
    exposed=0 (ref)   n00        t01
    exposed=1         n10        t11	
    exposed=2         n20        t21
    exposed=3         n30        t31

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 fisher exact, mid-p exact, or normal approximation method.

`tab`	primary table
`measure`	odds ratio, risk ratio, or rate ratio
`conf.level`	confidence level
`pvalue`	p value method
`x`	data input
`data`	data with margin totals
`p.exposed`	proportion exposed
`p.outcome`	proportion outcome
`p.value`	p value
`correction`	TRUE if Yate's continuity correction was used

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

Nicolas P Jewell, Statistics for Epidemiology, 1st Edition, 2004, Chapman & Hall

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

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

riskratio, oddsratio, rateratio

r243 <- matrix(c(12,2,7,9), 2, 2)
dimnames(r243) <- list(Diarrhea = c("Yes", "No"),
                      "Antibody level" = c("Low", "High")
                      )
r243
r243b <- t(r243)
r243b
epitab(r243, rev = "b", verbose = TRUE)
epitab(r243, method="riskratio",rev = "b", verbose = TRUE)
epitab(matrix(c(41, 15, 28010, 19017),2,2)[2:1,],
       method="rateratio", verbose = TRUE)