oddsratio {epitools} R Documentation

## Odds ratio estimation and confidence intervals

### Description

Calculates odds ratio by median-unbiased estimation (mid-p), conditional maximum likelihood estimation (Fisher), unconditional maximum likelihood estimation (Wald), and small sample adjustment (small). Confidence intervals are calculated using exact methods (mid-p and Fisher), normal approximation (Wald), and normal approximation with small sample adjustment (small).

### Usage

oddsratio(x, y = NULL,
method = c("midp", "fisher", "wald", "small"),
conf.level = 0.95,
rev = c("neither", "rows", "columns", "both"),
correction = FALSE,
verbose = FALSE)
oddsratio.midp(x, y = NULL,
conf.level = 0.95,
rev = c("neither", "rows", "columns", "both"),
correction = FALSE,
verbose = FALSE,
interval =  c(0, 1000))
oddsratio.fisher(x, y = NULL,
conf.level = 0.95,
rev = c("neither", "rows", "columns", "both"),
correction = FALSE,
verbose = FALSE)
oddsratio.wald(x, y = NULL,
conf.level = 0.95,
rev = c("neither", "rows", "columns", "both"),
correction = FALSE,
verbose = FALSE)
oddsratio.small(x, y = NULL,
conf.level = 0.95,
rev = c("neither", "rows", "columns", "both"),
correction = FALSE,
verbose = FALSE)


### Arguments

 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) method method for calculating odds ratio and confidence interval conf.level confidence level (default is 0.95) rev reverse order of "rows", "colums", "both", or "neither" (default) correction set to TRUE for Yate's continuity correction (default is FALSE) verbose set to TRUE to return more detailed results (default is FALSE) interval interval for the uniroot that finds the odds ratio median-unbiased estimate and mid-p exact confidence interval for oddsratio.midp

### Details

Calculates odds ratio by median-unbiased estimation (mid-p), conditional maximum likelihood estimation (Fisher), unconditional maximum likelihood estimation (Wald), and small sample adjustment (small). Confidence intervals are calculated using exact methods (mid-p and Fisher), normal approximation (Wald), and normal approximation with small sample adjustment (small).

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 the following table is preferred:

                    disease=0   disease=1
exposed=0 (ref)    n00         n01
exposed=1          n10         n11


however, for odds ratios from 2x2 tables, the following table is equivalent:

                    disease=1   disease=0
exposed=1          n11         n10
exposed=0          n01         n00


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.

### Value

 x table that was used in analysis (verbose = TRUE) data same table as x but with marginal totals p.exposed proportions exposed (verbose = TRUE) p.outcome proportions experienced outcome (verbose = TRUE) measure risk ratio and confidence interval conf.level confidence level used (verbose = TRUE) p.value p value for test of independence replicates number of replicates used in Monte Carlo simulation p value (verbose = TRUE) correction logical specifying if continuity correction was used

### Author(s)

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

### References

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

tab2by2.test, riskratio, rateratio, ormidp.test, epitab

### Examples


##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)
oddsratio(dat, rev="c")
oddsratio.midp(dat, rev="c")
oddsratio.fisher(dat, rev="c")
oddsratio.wald(dat, rev="c")
oddsratio.small(dat, rev="c")



[Package epitools version 0.5-10.1 Index]