#' Format fisher.test (test of categorical independence).
#'
#' @param statistic wrapped Fisher test
#' @param ... extra arguments (not used)
#' @param format if set the format to return ("html", "latex", "markdown", "ascii", "docx", ...)
#' @param statDigits integer number of digits to show in summaries.
#' @param sigDigits integer number of digits to show in significances.
#' @param pLargeCutoff value to declare non-significance at or above.
#' @param pSmallCutoff smallest value to print
#' @return formatted string and fields
#'
#' @examples
#'
#' d <- data.frame(x=c('b','a','a','a','b','b','b'),
#' y=c('1','1','1','2','2','2','2'))
#' ft <- fisher.test(table(d))
#' wrapFisherTest(ft)
#'
#'
#' @export
render.sigr_fishertest <- function(statistic,
...,
format,
statDigits=4,
sigDigits=4,
pLargeCutoff=0.05,
pSmallCutoff=1.0e-5) {
wrapr::stop_if_dot_args(substitute(list(...)), "sigr::render.sigr_fishertest")
if (missing(format) || is.null(format)) {
format <- getRenderingFormat()
}
if(!isTRUE(format %in% formats)) {
stop(paste("format",format,"not recognized"))
}
fsyms <- syms[format,]
stat_format_str <- paste0('%.',statDigits,'g')
ft <- statistic$ft
pString <- render(wrapSignificance(ft$p.value,
symbol='p'),
format=format,
sigDigits=sigDigits,
pLargeCutoff=pLargeCutoff,
pSmallCutoff=pSmallCutoff)
formatStr <- paste0(fsyms['startB'],ft$method,fsyms['endB'],
': (',fsyms['startI'],'odds.ratio',fsyms['endI'],
'=',sprintf(stat_format_str,ft$estimate),
', ',pString,').')
formatStr
}
#' Wrap fisher.test (test of categorical independence).
#'
#' @param x numeric, data.frame or test.
#' @param ... extra arguments
#'
#' @seealso \code{\link{wrapFisherTest.htest}}, and \code{\link{wrapFisherTest.data.frame}}
#' @export
wrapFisherTest <- function(x,...) {
UseMethod('wrapFisherTest')
}
#' Wrap fisher.test (test of categorical independence).
#'
#' @param x fisher.test result
#' @param ... extra arguments (not used)
#' @return wrapped test.
#'
#' @examples
#'
#' d <- data.frame(x=c('b','a','a','a','b','b','b'),
#' y=c('1','1','1','2','2','2','2'))
#' ft <- fisher.test(table(d))
#' wrapFisherTest(ft)
#'
#'
#' @export
wrapFisherTest.htest <- function(x,
...) {
wrapr::stop_if_dot_args(substitute(list(...)), "sigr::wrapFisherTest.htest")
r <- list(ft=x,
test='fisher.test')
class(r) <- c('sigr_fishertest', 'sigr_statistic')
r
}
#' Wrap fisher.test (test of categorical independence).
#'
#' @param x data.frame
#' @param Column1Name character column 1 name
#' @param Column2Name character column 2 name
#' @param ... extra arguments (not used)
#' @param na.rm logical, if TRUE remove NA values
#' @param workspace passed to \code{\link[stats]{fisher.test}}
#' @param hybrid passed to \code{\link[stats]{fisher.test}}
#' @param control passed to \code{\link[stats]{fisher.test}}
#' @param or passed to \code{\link[stats]{fisher.test}}
#' @param alternative passed to \code{\link[stats]{fisher.test}}
#' @param conf.int passed to \code{\link[stats]{fisher.test}}
#' @param conf.level passed to \code{\link[stats]{fisher.test}}
#' @param simulate.p.value passed to \code{\link[stats]{fisher.test}}
#' @param B passed to \code{\link[stats]{fisher.test}}
#' @return wrapped test.
#'
#' @examples
#'
#' d <- data.frame(x=c('b','a','a','a','b','b','b'),
#' y=c('1','1','1','2','2','2','2'))
#' wrapFisherTest(d, 'x', 'y')
#'
#'
#' @importFrom stats fisher.test
#'
#' @export
wrapFisherTest.data.frame <- function(x,
Column1Name,
Column2Name,
...,
na.rm= FALSE,
workspace = 200000, hybrid = FALSE,
control = list(), or = 1, alternative = "two.sided",
conf.int = TRUE, conf.level = 0.95,
simulate.p.value = FALSE, B = 2000) {
wrapr::stop_if_dot_args(substitute(list(...)), "sigr::wrapFisherTest.data.frame")
c1 <- x[[Column1Name]]
c2 <- x[[Column2Name]]
nNA <- sum(is.na(c1) | is.na(c2))
if(na.rm) {
goodPosns <- (!is.na(c1)) & (!is.na(c2))
c1 <- c1[goodPosns]
c2 <- c2[goodPosns]
}
n <- length(c1)
ft <- stats::fisher.test(x=table(c1,c2),
y=NULL,
workspace = workspace, hybrid = hybrid,
control = control, or = or, alternative = alternative,
conf.int = conf.int, conf.level = conf.level,
simulate.p.value = simulate.p.value, B = B)
r <- list(ft=ft,
test='fisher.test',
Column1Name=Column1Name,
Column2Name=Column2Name,
n=n,
nNA=nNA)
class(r) <- c('sigr_fishertest', 'sigr_statistic')
r
}
#' Wrap fisher.test (test of categorical independence).
#'
#' @param x data.frame
#' @param ... extra arguments (not used)
#' @param workspace passed to \code{\link[stats]{fisher.test}}
#' @param hybrid passed to \code{\link[stats]{fisher.test}}
#' @param control passed to \code{\link[stats]{fisher.test}}
#' @param or passed to \code{\link[stats]{fisher.test}}
#' @param alternative passed to \code{\link[stats]{fisher.test}}
#' @param conf.int passed to \code{\link[stats]{fisher.test}}
#' @param conf.level passed to \code{\link[stats]{fisher.test}}
#' @param simulate.p.value passed to \code{\link[stats]{fisher.test}}
#' @param B passed to \code{\link[stats]{fisher.test}}
#' @return wrapped test.
#'
#' @examples
#'
#' d <- data.frame(x=c('b','a','a','a','b','b','b'),
#' y=c('1','1','1','2','2','2','2'))
#' t <- table(d)
#' wrapFisherTest(t)
#'
#'
#' @importFrom stats fisher.test
#'
#' @export
wrapFisherTest.table <- function(x,
...,
workspace = 200000, hybrid = FALSE,
control = list(), or = 1, alternative = "two.sided",
conf.int = TRUE, conf.level = 0.95,
simulate.p.value = FALSE, B = 2000) {
wrapr::stop_if_dot_args(substitute(list(...)), "sigr::wrapFisherTest.table")
n <- sum(x)
dimnames <- attr(t, 'dimnames')
Column1Name <- names(dimnames)[[1]]
Column2Name <- names(dimnames)[[2]]
ft <- stats::fisher.test(x,
workspace = workspace, hybrid = hybrid,
control = control, or = or, alternative = alternative,
conf.int = conf.int, conf.level = conf.level,
simulate.p.value = simulate.p.value, B = B)
r <- list(ft=ft,
test='fisher.test',
Column1Name=Column1Name,
Column2Name=Column2Name,
n=n,
nNA=0)
class(r) <- c('sigr_fishertest', 'sigr_statistic')
r
}
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