# R/oddsRatio.R In ProjectMOSAIC/mosaic: Project MOSAIC Statistics and Mathematics Teaching Utilities

#### Documented in oddsRatioorrrprint.oddsRatioprint.relriskrelrisksummary.oddsRatiosummary.relrisk

```# Function to calculate odds ratios and confidence intervals
# on odds ratios.

# Written by Kevin Middleton; largely redone by R. Pruim

# Successes in Column 1
# Treatment of interest in Row 2

#' Odds Ratio and Relative Risk for 2 x 2 Contingency Tables
#'
#' This function calculates the odds ratio and relative risk for a 2 x 2
#' contingency table and a
#' confidence interval (default `conf.level` is 95 percent) for the
#' each estimate. `x` should be a matrix, data frame or table. "Successes"
#' should be located in column 1 of `x`, and the treatment of interest
#' should be located in row 2. The odds ratio is calculated as (Odds row 2) /
#' (Odds row 1). The confidence interval is calculated from the log(OR) and
#' backtransformed.
#'
#'
#' @rdname oddsRatio
#' @param x a 2 x 2 matrix, data frame, or table of counts
#' @param object an R object to print or summarise.  Here an object of class
#' `"oddsRatio"` or `"relrisk"`.
#' @param conf.level the confidence interval level
#' @param verbose a logical indicating whether verbose output should be displayed
#' @param quiet a logical indicating whether verbose output should be suppressed
#' @param relrisk a logical indicating whether the relative risk should be returned
#' instead of the odds ratio
#' @param digits number of digits to display

#' @param ... additional arguments
#' @return an odds ratio or relative risk.  If `verpose` is true,
#' more details and the confidence intervals are displayed.
#' @author Kevin Middleton (\email{[email protected]@csusb.edu}); modified by
#' R Pruim.
#' @seealso [chisq.test()], [fisher.test()]
#' @keywords stats
#' @examples
#' M1 <- matrix(c(14, 38, 51, 11), nrow = 2)
#' M1
#' oddsRatio(M1)
#'
#' M2 <- matrix(c(18515, 18496, 1427, 1438), nrow = 2)
#' rownames(M2) <- c("Placebo", "Aspirin")
#' colnames(M2) <- c("No", "Yes")
#' M2
#' oddsRatio(M2)
#' oddsRatio(M2, verbose = TRUE)
#' relrisk(M2, verbose = TRUE)
#' if (require(mosaicData)) {
#' relrisk(tally(~ homeless + sex, data = HELPrct) )
#' do(3) * relrisk( tally( ~ homeless + shuffle(sex), data = HELPrct) )
#' }
#' @export

orrr <- function(x, conf.level = 0.95, verbose = !quiet, quiet = TRUE, digits = 3,
relrisk = FALSE){
if (any(dim(x) != c(2,2))) {
stop("expecting something 2 x 2")
}
x <- as.matrix(x)
names(x) <- NULL
row.names(x) <- NULL
colnames(x) <- NULL
rowsums <- rowSums(x)
p1 <- x[1, 1] / rowsums[1]
p2 <- x[2, 1] / rowsums[2]
o1 <- p1 / (1 - p1)
o2 <- p2 / (1 - p2)
RR <- p2 / p1
OR <- o2 / o1
crit <- qnorm((1 - conf.level)/2, lower.tail = FALSE)

names(RR) <- "RR"
log.RR <- log(RR)
SE.log.RR <- sqrt( sum( x[,2]/x[,1]/rowsums) )
log.lower.RR <- log.RR - crit * SE.log.RR
log.upper.RR <- log.RR + crit * SE.log.RR
lower.RR <- exp(log.lower.RR)
upper.RR <- exp(log.upper.RR)

names(OR) <- "OR"
log.OR <- log(OR)
SE.log.OR <- sqrt(sum(1/x))
log.lower.OR <- log.OR - crit * SE.log.OR
log.upper.OR <- log.OR + crit * SE.log.OR
lower.OR <- exp(log.lower.OR)
upper.OR <- exp(log.upper.OR)

res <- if (relrisk) {
structure(RR,
p1 = p1,
p2 = p2,
o1 = o1,
o2 = o2,
OR = OR,
lower.OR = lower.OR,
upper.OR = upper.OR,
RR = RR,
lower.RR = lower.RR,
upper.RR = upper.RR,
conf.level = conf.level,
class=c("relrisk", "numeric"))
} else {
structure(OR,
p1 = p1,
p2 = p2,
o1 = o1,
o2 = o2,
OR = OR,
lower.OR = lower.OR,
upper.OR = upper.OR,
RR = RR,
lower.RR = lower.RR,
upper.RR = upper.RR,
conf.level = conf.level,
class=c("oddsRatio", "numeric"))
}
if (verbose) print(summary(res))
res
}

#' @rdname oddsRatio
#' @export
oddsRatio <- function(x, conf.level = 0.95, verbose = !quiet, quiet = TRUE, digits = 3) {
orrr(x, conf.level = conf.level, verbose = verbose, digits = digits, relrisk = FALSE)
}

#' @rdname oddsRatio
#' @export
relrisk <- function(x, conf.level = 0.95, verbose = !quiet, quiet = TRUE, digits = 3) {
orrr(x, conf.level = conf.level, verbose = verbose, digits = digits, relrisk = TRUE)
}

#' @rdname oddsRatio
#' @export
print.oddsRatio <- function(x, digits = 4, ...) {
print(as.numeric(x))
}

#' @rdname oddsRatio
#' @export
print.relrisk <- function(x, digits = 4, ...) {
print(as.numeric(x))
}

#' @rdname oddsRatio
#' @export
summary.oddsRatio <-
function(object, digits = 4, ...){
summary_relrisk_oddsratio(object, digits = digits, ...)
}

#' @rdname oddsRatio
#' @export
summary.relrisk <-
function(object, digits = 4, ...){
summary_relrisk_oddsratio(object, digits = digits, ...)
}

summary_relrisk_oddsratio <- function(x, digits = 4, ...){
cat("\n")
cat("Odds Ratio\n")
cat("\n")
cat("Proportions\n")
cat("\t   Prop. 1:\t", format(attr(x,"p1"), digits = digits), "\n")
cat("\t   Prop. 2:\t", format(attr(x,"p2"), digits = digits), "\n")
cat("\t Rel. Risk:\t", format(attr(x,"RR"), digits = digits), "\n\n")
cat("Odds\n")
cat("\t    Odds 1:\t", format(attr(x,"o1"), digits = digits), "\n")
cat("\t    Odds 2:\t", format(attr(x,"o2"), digits = digits), "\n")
cat("\tOdds Ratio:\t", format(attr(x,"OR"), digits = digits), "\n\n")
cat(format(100 * attr(x,"conf.level")), "percent confidence interval:\n")
cat("\t", format(attr(x,"lower.RR"), digits = digits), "< RR <",
format(attr(x,"upper.RR"), digits = digits), "\n")
cat("\t", format(attr(x,"lower.OR"), digits = digits), "< OR <",
format(attr(x,"upper.OR"), digits = digits), "\n")
}
```
ProjectMOSAIC/mosaic documentation built on Aug. 19, 2018, 9:14 a.m.