R/pairchi2.b.R

In sbalci/ClinicoPathJamoviModule: Analysis for Clinicopathological Research

#' Title
#'
# @importFrom stats chisq.test
# @importFrom stats fisher.test
# @importFrom stats p.adjust
# @importFrom stats p.adjust.methods
# @importFrom stats pairwise.table


pairchi2Class <- if (requireNamespace('jmvcore'))
    R6::R6Class("pairchi2Class",
                inherit = pairchi2Base,
                private = list(
                    .run = function(){}
)
)

# pairchi2Class <- if (requireNamespace('jmvcore'))
#     R6::R6Class("pairchi2Class",
#                 inherit = pairchi2Base,
#                 private = list(
#                     .run = function() {
#                         # prepare data ----
#
#                         data <- self$data
#
#                         row <- self$options$row
#                         col <- self$options$col
#
#                         row <- jmvcore::composeTerm(components = row)
#                         col <- jmvcore::composeTerm(components = col)
#
#
#                         data <- jmvcore::select(df = data,
#                                                 columnNames = c(row, col))
#
#
#                         # conftable ----
#
#                         conftable <- table(data[[row]], data[[col]],
#                                             dnn = list(row, col))
#
#
#                         self$results$conftable$setContent(conftable)
#
#
#                         # chisq.test ----
#
#
#                         chi2test <- try(chisq.test(conftable, correct = FALSE))
#
#                         # chi2test
#                         # chi2test[["statistic"]]
#                         # chi2test[["statistic"]][["X-squared"]]
#                         # chi2test[["parameter"]]
#                         # chi2test[["parameter"]][["df"]]
#                         # chi2test[["p.value"]]
#                         # chi2test[["method"]]
#                         # chi2test[["data.name"]]
#                         # chi2test[["observed"]]
#                         # chi2test[["expected"]]
#                         # chi2test[["residuals"]]
#                         # chi2test[["stdres"]]
#
#
#                         self$results$chi2test$setContent(chi2test)
#
#
#
#                         # pairwise function ------
#
#                         # RVAideMemoire::chisq.multcomp()
#                         # RVAideMemoire::fisher.multcomp()
#
#                         # rmngb::pairwise.chisq.test(x, ...)
#                         # rmngb::pairwise.fisher.test(x, ...)
#
#
#                         # pairwise function 1 ------
#
#
#                         pairwiseRVAideMemoire <- RVAideMemoire::chisq.multcomp(conftable
#                                                                                # , p.method = "fdr"
#                                                                                )
#
#                         p_pairwiseRVAideMemoire <- pairwiseRVAideMemoire[["p.value"]]
#
#                         # tab_pairwiseRVAideMemoire <-
#                         #     as.data.frame(pairwiseRVAideMemoire) %>%
#                         #     tibble::rownames_to_column()
#
#                         # tab_pairwiseRVAideMemoire <-
#                         #     tab_pairwiseRVAideMemoire %>%
#                         #     tidyr::pivot_longer(cols = -rowname) %>%
#                         #     dplyr::filter(complete.cases(.))
#
#                         pairwise1 <- list(
#                             "RVAideMemoire" = pairwiseRVAideMemoire,
#                             "p-value" = p_pairwiseRVAideMemoire
#                             # ,
#                             # "table" = tab_pairwiseRVAideMemoire
#                         )
#
#
#                         self$results$pairwise1$setContent(pairwise1)
#
#
#                         # pairwise function 2 ------
#
#
#                         pairwisermngb <- rmngb::pairwise.chisq.test.table(conftable)
#
#                         p_pairwisermngb <- pairwisermngb[["p.value"]]
#
#
#
#                         # tab_pairwisermngb <-
#                         #     as.data.frame(pairwisermngb) %>%
#                         #     tibble::rownames_to_column()
#
#
#                         # tab_pairwisermngb <-
#                         #     tab_pairwisermngb %>%
#                         #     tidyr::pivot_longer(cols = -rowname) %>%
#                         #     dplyr::filter(complete.cases(.))
#
#                         pairwise2 <- list("rmngb" = pairwisermngb,
#                                           "p-value" = p_pairwisermngb
#                                           # ,
#                                           # "table" = tab_pairwisermngb
#                                           )
#
#                         self$results$pairwise2$setContent(pairwise2)
#
#
#                         # pairwise function 3 ------
#
#                         pairwise3 <- chisq.posthoc.test::chisq.posthoc.test(conftable)
#
#                         self$results$pairwise3$setContent(pairwise3)
#
#
#                     }
#
#                 ))