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Add method for Fischer's exact test (#395)
* add fisher * linter, simplify tests * bump effectsize version to get fei effect size output and update snapshots * Trigger lintr tests * update snapshots * Add all packages to Remotes in DESCRIPTION * add commas * change order of Remotes, header, remove tab
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,111 @@ | ||
| # report_table ----------------- | ||
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| .report_table_fisher <- function(table_full, effsize) { | ||
| table_full <- cbind(table_full, attributes(effsize)$table) | ||
| list(table = NULL, table_full = table_full) | ||
| } | ||
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| # report_effectsize --------------------- | ||
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| .report_effectsize_fisher <- function(x, table, dot_args, rules = "funder2019") { | ||
| args <- c(list(x), dot_args) | ||
| table <- do.call(effectsize::effectsize, args) | ||
| ci <- attributes(table)$ci | ||
| estimate <- names(table)[1] | ||
| rules <- ifelse(is.null(dot_args$rules), rules, dot_args$rules) | ||
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| args <- list(table, rules = rules, dot_args) | ||
| interpretation <- do.call(effectsize::interpret, args)$Interpretation | ||
| rules <- .text_effectsize(attr(attr(interpretation, "rules"), "rule_name")) | ||
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| if (estimate == "Cramers_v_adjusted") { | ||
| main <- paste0("Adjusted Cramer's v = ", insight::format_value(table[[estimate]])) | ||
| } else if (estimate == "Tschuprows_t") { | ||
| main <- paste0("Tschuprow's t = ", insight::format_value(table[[estimate]])) | ||
| } else if (estimate == "Tschuprows_t_adjusted") { | ||
| main <- paste0("Adjusted Tschuprow's t = ", insight::format_value(table[[estimate]])) | ||
| } else if (estimate == "Pearsons_c") { | ||
| main <- paste0("Pearson's c = ", insight::format_value(table[[estimate]])) | ||
| } else if (estimate == "phi_adjusted") { | ||
| main <- paste0("Adjusted Phi = ", insight::format_value(table[[estimate]])) | ||
| } else if (estimate == "Cohens_h") { | ||
| main <- paste0("Cohen's h = ", insight::format_value(table[[estimate]])) | ||
| } else if (estimate == "Odds_ratio") { | ||
| main <- paste0("Odds ratio = ", insight::format_value(table[[estimate]])) | ||
| } else if (estimate == "Ris_kratio") { | ||
| main <- paste0("Risk ratio = ", insight::format_value(table[[estimate]])) | ||
| } else if (estimate == "cohens_h") { | ||
| main <- paste0("Cohen's w = ", insight::format_value(table[[estimate]])) | ||
| } else { | ||
| main <- paste0(estimate, " = ", insight::format_value(table[[estimate]])) | ||
| } | ||
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| statistics <- paste0( | ||
| main, | ||
| ", ", | ||
| insight::format_ci(table$CI_low, table$CI_high, ci) | ||
| ) | ||
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| table <- datawizard::data_rename( | ||
| as.data.frame(table), | ||
| c("CI_low", "CI_high"), | ||
| paste0(estimate, c("_CI_low", "_CI_high")) | ||
| ) | ||
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| table <- table[c(estimate, paste0(estimate, c("_CI_low", "_CI_high")))] | ||
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| list( | ||
| table = table, statistics = statistics, interpretation = interpretation, | ||
| rules = rules, ci = ci, main = main | ||
| ) | ||
| } | ||
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| # report_model ---------------------------- | ||
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| .report_model_fisher <- function(x, table) { | ||
| vars_full <- paste0(names(attributes(x$observed)$dimnames), collapse = " and ") | ||
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| text <- paste0( | ||
| trimws(x$method), | ||
| " testing the association between the variables of the ", | ||
| x$data.name, " dataset " | ||
| ) | ||
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| text | ||
| } | ||
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| chi2_type <- function(x) { | ||
| if (grepl("probabilities", x$method, fixed = TRUE)) { | ||
| out <- "probabilities" | ||
| } else if (grepl("Pearson", x$method, fixed = TRUE)) { | ||
| out <- "pearson" | ||
| } else if (grepl("Fisher", x$method, fixed = TRUE)) { | ||
| out <- "fisher" | ||
| } | ||
| out | ||
| } | ||
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| .report_parameters_fisher <- function(table, stats, effsize, ...) { | ||
| text_full <- paste0( | ||
| "statistically ", | ||
| effectsize::interpret_p(table$p, rules = "default"), | ||
| ", and ", | ||
| attributes(effsize)$interpretation, | ||
| " (", | ||
| stats, | ||
| ")" | ||
| ) | ||
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| text_short <- paste0( | ||
| "statistically ", | ||
| effectsize::interpret_p(table$p, rules = "default"), | ||
| ", and ", | ||
| attributes(effsize)$interpretation, | ||
| " (", | ||
| summary(stats), | ||
| ")" | ||
| ) | ||
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| list(text_short = text_short, text_full = text_full) | ||
| } |
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