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Matías Castillo Aguilar
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Matías Castillo Aguilar
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Apr 9, 2021
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| export(aov_r) | ||
| export(cent_disp) | ||
| export(contingency) | ||
| export(report) | ||
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| Original file line number | Diff line number | Diff line change |
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| #' Report categorical analyses | ||
| #' | ||
| #' Perform nominal/ordinal analysis on 1 dimensional table for goodnes-of-fit chi-squared, and two dimensional data for Pearson chi-squared, Fisher exact test or (if paired), McNemar test reporting their corresponding stats and effect sizes in APA Style. | ||
| #' @param data Data frame containing the variables `x` and `y`. | ||
| #' @param x Factor variable, quoted or unquoted. | ||
| #' @param y Factor. If `NULL`, a goodness-of-fit is carried, otherwise a two-way analysis is performed. | ||
| #' @param paired Logical. If `TRUE` McNemar's Chi-squared test is carried on. | ||
| #' @param exact Logical. If `TRUE` then Fisher's Exact Test is carried on, but only when `paired = FALSE` (default). If is a 2 x 2 design, Odds Ratio (OR) is returned as effect size, otherwise it will only return the formated p-value. | ||
| #' @param markdown Whether you want the output formated for inline R Markdown or as plain text. | ||
| #' @param ... Currently not used. | ||
| #' @keywords contingency | ||
| #' @return A list of length 3 or 2 with statistical test and `$method` used. | ||
| #' @export | ||
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| contingency <- function(data | ||
| , x | ||
| , y = NULL | ||
| , paired = FALSE | ||
| , exact = FALSE | ||
| , markdown = TRUE | ||
| , ...) { | ||
| .arg <- match.call() | ||
|
|
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| x.var <- data[[.arg$x]] | ||
| if(is.null(.arg$y)) { | ||
| way <- "One" | ||
| } else { | ||
| y.var <- data[[.arg$y]] | ||
| way <- "Two" | ||
| } | ||
|
|
||
| result <- list() | ||
| test <- if(isTRUE(paired)) "Mcnemar" else | ||
| if(isTRUE(exact)) "Exact" else | ||
| "Chi" | ||
|
|
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| if(test == "Chi") { | ||
| tab <- if(way == "One") | ||
| list(table(x.var), | ||
| "gof", | ||
| "Chi-squared test for given probabilities") else | ||
| list(table(x.var, y.var), | ||
| "Pearson", | ||
| "Pearson's Chi-squared test") | ||
| test <- stats::chisq.test( | ||
| x = tab[[1]], | ||
| correct = FALSE) | ||
| es <- effectsize::cramers_v( | ||
| x = tab[[1]], | ||
| adjust = FALSE) | ||
| expr <- if(isTRUE(markdown)) | ||
| list(a = paste0("$\\chi^2_{~", tab[[2]], "}$ ("), | ||
| b = ", $p$ ", | ||
| c = "$V_{~Cramer}$ = ", | ||
| d = ', CI~95%~[') else | ||
| list(a = "X^2 (", | ||
| b = ", p ", | ||
| c = "V = ", | ||
| d = ', CI95% [') | ||
| result[['full']] <- paste0( | ||
| result[['stats']] <- paste0( | ||
| expr$a, | ||
| test$parameter, | ||
| ") = ", | ||
| round(test$statistic,2), | ||
| expr$b, | ||
| ifelse( | ||
| test$p.value < 0.001, | ||
| '< 0.001', | ||
| paste( | ||
| '=', | ||
| round(test$p.value, 3) | ||
| ) | ||
| ) | ||
| ), ', ', | ||
| result[['es']] <- paste0( | ||
| expr$c, | ||
| round(es$Cramers_v,2), | ||
| expr$d, | ||
| round(es$CI_low,2), | ||
| ', ', | ||
| round(es$CI_high,2), | ||
| ']') | ||
| ) | ||
| result[['method']] <- tab[[3]] | ||
| return(result) | ||
|
|
||
| } else { | ||
| if(test == "Exact") { | ||
| tab <- table(x.var, y.var) | ||
| test <- stats::fisher.test( | ||
| x = tab) | ||
| error <- class( | ||
| try( | ||
| expr = { | ||
| (es <- effectsize::oddsratio( | ||
| x = x.var, | ||
| y = y.var) ) | ||
| }, | ||
| silent = TRUE) | ||
| ) == "try-error" | ||
| if(isTRUE(error)) { | ||
| expr <- if(isTRUE(markdown)) | ||
| list(a = "$p_{~FET}$ ") else | ||
| list(a = "FET, p ") | ||
| result[['full']] <- paste0( | ||
| result[['stats']] <- paste0( | ||
| expr$a, | ||
| ifelse( | ||
| test = test$p.value < 0.001, | ||
| yes = '< 0.001', | ||
| no = paste( | ||
| '=', | ||
| round(test$p.value, 3) | ||
| ) | ||
| ) | ||
| ) | ||
| ) | ||
| result[['es']] <- "Not available" | ||
| result[['method']] <- "Fisher's Exact Test for Count Data" | ||
| return(result) | ||
| } else { | ||
| expr <- if(isTRUE(markdown)) | ||
| list(a = "$p_{~FET}$ ", | ||
| b = "$OR$ = ", | ||
| c = ', CI~95%~[') else | ||
| list(a = "FET: p ", | ||
| b = "OR = ", | ||
| c = ', CI95% [') | ||
| result[['full']] <- paste0( | ||
| result[['stats']] <- paste0( | ||
| expr$a, | ||
| ifelse( | ||
| test = test$p.value < 0.001, | ||
| yes = '< 0.001', | ||
| no = paste( | ||
| '=', | ||
| round(test$p.value, 3) | ||
| ) | ||
| ) | ||
| ) | ||
| , ', ', | ||
| result[['es']] <- paste0( | ||
| expr$b, | ||
| round(es$Odds_ratio,2), | ||
| expr$c, | ||
| round(es$CI_low,2), | ||
| ', ', | ||
| round(es$CI_high,2), | ||
| ']') | ||
| ) | ||
| result[['method']] <- "Fisher's Exact Test for Count Data" | ||
| return(result) | ||
| } | ||
| } else { | ||
| tab <- table(x.var,y.var) | ||
| test <- stats::mcnemar.test( | ||
| x = tab, | ||
| correct = FALSE) | ||
| es <- effectsize::cohens_g( | ||
| x = tab) | ||
| expr <- if(isTRUE(markdown)) | ||
| list(a = paste0("$\\chi^2_{~McNemar}$ ("), | ||
| b = ", $p$ ", | ||
| c = "$g_{~Cohen}$ = ", | ||
| d = ', CI~95%~[') else | ||
| list(a = "X^2 (", | ||
| b = ", p ", | ||
| c = "g = ", | ||
| d = ', CI95% [') | ||
| result[['full']] <- paste0( | ||
| result[['stats']] <- paste0( | ||
| expr$a, | ||
| test$parameter, | ||
| ") = ", | ||
| round(test$statistic,2), | ||
| expr$b, | ||
| ifelse( | ||
| test = test$p.value < 0.001, | ||
| yes = '< 0.001', | ||
| no = paste( | ||
| '=', | ||
| round(test$p.value, 3) | ||
| ) | ||
| ) | ||
| ), | ||
| ', ', | ||
| result[['es']] <- paste0( | ||
| expr$c, | ||
| round(es$Cohens_g,2), | ||
| expr$d, | ||
| round(es$CI_low,2), | ||
| ', ', | ||
| round(es$CI_high,2), | ||
| ']') | ||
| ) | ||
| result[['method']] <- "McNemar's Chi-squared test" | ||
| return(result) | ||
| } | ||
| } | ||
| } | ||
|
|
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