epitools (version 0.5-2)

epitab: 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 combine

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 nume

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)

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

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.

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

See Also

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)