sbalci/ClinicoPathJamoviModule

# # functions from: https://raw.githubusercontent.com/cran/rmngb/master/R/pairwise.R
#
#
# pairwise.chisq.test <- function(x, ...)
#     UseMethod("pairwise.chisq.test")
#
# pairwise.chisq.test.table <- function(x, p.adj = p.adjust.methods,
#                                       DNAME = NULL, ...) {
#     if (is.null(DNAME))
#         DNAME <- deparse(substitute(tab))
#     p.adj <- match.arg(p.adj)
#
#     k <- dim(x)[1]
#     p.value <- rep(NA, k ^ 2)
#     for (row1 in 1:(k - 1)) {
#         for (row2 in (row1 + 1):k) {
#             xi <- rmngb::asInteger(k * (row1 - 1) + row2)
#             p.value[xi] <- chisq.test(x[c(row1, row2), ])$p.value
#         }
#     }
#
#     p.value <- p.adjust(p.value, method = p.adj)
#     dn <- list(dimnames(x)[[1]],
#                dimnames(x)[[1]])
#     p.value <- matrix(p.value, nrow = k, dimnames = dn)
#
#     structure(list(method = "Pearson's Chi-squared tests",
#                    data.name = DNAME,
#                    p.value = p.value,
#                    p.adjust.method = p.adj),
#               class = "pairwise.htest")
# }
#
# pairwise.chisq.test.default <- function(x, g, p.adj = p.adjust.methods, ...) {
#     DNAME <- paste(deparse(substitute(x)), "and", deparse(substitute(g)))
#     p.adj <- match.arg(p.adj)
#     tab <- table(g, x)
#
#     pairwise.chisq.test(tab, p.adj = p.adj, DNAME = DNAME)
# }
#
# pairwise.fisher.test <- function(x, ...)
#     UseMethod("pairwise.fisher.test")
#
# pairwise.fisher.test.table <- function(x, p.adj = p.adjust.methods,
#                                        DNAME = NULL, ...) {
#     if (is.null(DNAME))
#         DNAME <- deparse(substitute(tab))
#     p.adj <- match.arg(p.adj)
#
#     k <- dim(x)[1]
#     p.value <- rep(NA, k ^ 2)
#     for (row1 in 1:(k - 1)) {
#         for (row2 in (row1 + 1):k) {
#             xi <- rmngb::asInteger(k * (row1 - 1) + row2)
#             p.value[xi] <- fisher.test(x[c(row1, row2), ])$p.value
#         }
#     }
#
#     p.value <- p.adjust(p.value, method = p.adj)
#     dn <- list(dimnames(x)[[1]],
#                dimnames(x)[[1]])
#     p.value <- matrix(p.value, nrow = k, dimnames = dn)
#
#     structure(list(method = "Fisher's Exact Tests for Count Data",
#                    data.name = DNAME,
#                    p.value = p.value,
#                    p.adjust.method = p.adj),
#               class = "pairwise.htest")
# }
#
# pairwise.fisher.test.default <- function(x, g, p.adj = p.adjust.methods, ...) {
#     DNAME <- paste(deparse(substitute(x)), "and", deparse(substitute(g)))
#     p.adj <- match.arg(p.adj)
#     tab <- table(g, x)
#
#     pairwise.fisher.test(tab, p.adj = p.adj, DNAME = DNAME)
# }