epitab {epitools} R Documentation

## Epidemiologic tabulation for a cohort or case-control study

### Description

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

### Usage

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)


### Arguments

 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)

### Details

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.

### Value

 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

### Author(s)

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

### References

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

### Examples

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)



[Package epitools version 0.5-10.1 Index]