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

1 2 3 4 5 6 7 8 9 10 | ```
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 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` |
For odds ratio or risk ratio, a single factor or character vector
that will be combined with For rate ratio, a numeric vector of person-time at risk; if
provided, |

`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':

1 2 3 4 5 6 | ```
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:

1 2 3 4 5 6 |

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`

1 2 3 4 5 6 7 8 9 10 11 | ```
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)
``` |

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