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#' @name fishers.exact
#' @title Fisher's Exact Test
#' @param targetcolumn Character string, name of response column to be tested.
#' @param alternative Character string(s) specifying the direction of the alternative hypothesis.
#' Must be one or more of "greater", "two.sided", or "less".
#' @param alpha Significance level (numeric) to be used.
#' @param control Level of dose to be used as the control for dichotomous data.
#' @param tot.obs Total number of observations for each dose level for dichotomous data.
#' @param label Output label.
#' @param data Input dataframe.
#' @keywords internal
fishers.exact <- function (targetcolumn, alternative, alpha, control, tot.obs, label, data) {
dose_fac <- data$dose_fac
level_list <- levels(dose_fac)
if (control == "") {control <- min(level_list)}
for (c in 1:length(level_list)) {
if (level_list[c] != control) {
Events <- data[data$dose_fac == level_list[c],]
Sum_events <- sum(Events[get('targetcolumn')])
Sum_noevents <- sum(Events[get('tot.obs')])
Control_events <- data[data$dose_fac == get('control'),]
Control_sum_events <- sum(Control_events[get('targetcolumn')])
Control_sum_noevents <- sum(Control_events[get('tot.obs')])
Matrix <-matrix(c(Sum_events, Control_sum_events, Sum_noevents, Control_sum_noevents),
nrow = 2, dimnames = list(c(paste("Dose", level_list[c], sep = " "), paste("Control", control, sep = " ")),
c(targetcolumn, "Total Obs")))
conf.level <- 1-alpha
Label <- paste("Tested Contrast,", label)
writeLines(Label)
print(Matrix)
print(stats::fisher.test(Matrix, alternative = alternative, conf.level = conf.level))
} else {next}
}
}
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