diff --git a/R/003_pvalues_and_permutation_test_tools.R b/R/003_pvalues_and_permutation_test_tools.R index 33e2282..fabb43c 100644 --- a/R/003_pvalues_and_permutation_test_tools.R +++ b/R/003_pvalues_and_permutation_test_tools.R @@ -92,6 +92,7 @@ PermutationTest <- function(control, return(perm_results) } + #' Generates statistical test results for possible hypothesis testings. #' #' This function returns a list that include statistical test results: @@ -239,6 +240,7 @@ pvals_statistics <- function(control, return(pvals_stats) } + #' Generates collated permutaion test results and statistical test results. #' #' This function returns a tibble (list) that includes statistical test results: @@ -266,7 +268,6 @@ Pvalues_statistics <- function(dabest_object, effect_size_type) { permtest_pvals <- tibble::tibble() - # check if effect size function is supplied if (is.null(ef_size_fn)) { stop("No effect size calculation methods are supplied.") } @@ -303,10 +304,8 @@ Pvalues_statistics <- function(dabest_object, tests <- group[2:group_length] for (test_group in tests) { - test_group <- test_group test_tibble <- raw_data %>% dplyr::filter(!!enquo_x == !!test_group) - test_measurement <- test_tibble[[quoname_y]] xlabels <- paste(test_group, group[1], sep = "\nminus\n") @@ -326,6 +325,19 @@ Pvalues_statistics <- function(dabest_object, ) # calculate p values + # If minimeta is TRUE, perform minimeta permutation test + if (isTRUE(minimeta)) { + permutations <- PermutationTest_result$permutations + permutations_var <- PermutationTest_result$permutations_var + permutations_weighted_delta <- calculate_minimeta(permutations, permutations_var) + + threshold <- abs(es) + pvalue_minimeta <- calculate_minimeta_pvalue(permutations_weighted_delta, threshold, perm_count) + + PermutationTest_result$pvalue <- pvalue_minimeta + PermutationTest_result$weighted_delta <- permutations_weighted_delta + } + pvals_and_stats <- pvals_statistics(ctrl_measurement, test_measurement, is_paired = is_paired, @@ -360,7 +372,6 @@ Pvalues_statistics <- function(dabest_object, test_tibble <- raw_data %>% dplyr::filter(!!enquo_x == !!test_group) test_measurement <- test_tibble[[quoname_y]] - xlabels <- paste(test_group, control_group, sep = "\nminus\n") control_test_measurement <- list( @@ -390,7 +401,20 @@ Pvalues_statistics <- function(dabest_object, random_seed = 12345, ef_size_fn = ef_size_fn ) - # calculate p values + + # If minimeta is TRUE, perform minimeta permutation test + if (isTRUE(minimeta)) { + permutations <- PermutationTest_result$permutations + permutations_var <- PermutationTest_result$permutations_var + permutations_weighted_delta <- calculate_minimeta(permutations, permutations_var) + + threshold <- abs(es) + pvalue_minimeta <- calculate_minimeta_pvalue(permutations_weighted_delta, threshold, perm_count) + + PermutationTest_result$pvalue <- pvalue_minimeta + PermutationTest_result$weighted_delta <- permutations_weighted_delta + } + pvals_and_stats <- pvals_statistics(ctrl_measurement, test_measurement, is_paired = is_paired, @@ -398,7 +422,6 @@ Pvalues_statistics <- function(dabest_object, effect_size = effect_size_type ) - pval_row <- list( control_group = control_group, test_group = test_group, @@ -416,3 +439,53 @@ Pvalues_statistics <- function(dabest_object, return(list(permtest_pvals = permtest_pvals)) } + +#' Calculate Weighted Delta for Mini-Meta Analysis +#' +#' This function calculates the weighted delta across multiple groups for a mini-meta analysis. +#' The weights are determined by the inverse of the variance of the permutations for each group. +#' The function returns the weighted average delta for each permutation. +#' +#' @param permutations A matrix where each row represents a group, and each column represents a permutation. +#' @param permutations_var A matrix of the same dimensions as `permutations`, containing the variances of each group for each permutation. +#' +#' @return A numeric vector representing the weighted delta for each permutation. +#' @noRd +calculate_minimeta <- function(permutations, permutations_var) { + #check if the permutations and permutations_var are of the same length + if (length(permutations) != length(permutations_var)) { + stop("The permutations and permutations_var are not of the same length.") + } + + if (length(permutations) == 0) { + stop("The permutations and permutations_var are empty.") + } + all_num <- numeric(length(permutations)) + all_denom <- numeric(length(permutations)) + + # Loop through each permutation + weight <- 1/permutations_var + all_num <- weight * permutations + all_denom <- sum(weight) + # Calculate the weighted delta + output <- all_num / all_denom + return(output) +} + + +#' Calculate P-value for Weighted Delta in Mini-Meta Analysis +#' +#' This function calculates the p-value for the weighted delta in a mini-meta analysis. +#' The p-value is computed based on the number of weighted deltas that exceed a given threshold. +#' +#' @param permutations_weighted_delta A numeric vector of weighted deltas for each permutation. +#' @param threshold A numeric value representing the threshold for significance. +#' @param permutation_count An integer representing the total number of permutations performed. +#' +#' @return A numeric value representing the p-value. +#' @noRd +calculate_minimeta_pvalue <- function(permutations_weighted_delta, threshold, permutation_count) { + count <- sum(abs(permutations_weighted_delta) > threshold) + pvalue <- count / permutation_count + return(pvalue) +} diff --git a/R/005_printing.R b/R/005_printing.R index f635188..5fd6cf9 100644 --- a/R/005_printing.R +++ b/R/005_printing.R @@ -95,8 +95,7 @@ print_each_comparism_effectsize <- function(dabest_object, effectsize) { bca_low <- round(dabest_object$boot_result$bca_ci_low, 3) bca_high <- round(dabest_object$boot_result$bca_ci_high, 3) ci <- dabest_object$boot_result$ci - pvalue <- dabest_object$permtest_pvals$pval_for_tests - + pvalue <- dabest_object$permtest_pvals$pval_permtest if (is.null(paired)) { rm_status <- "" } else if (paired == "sequential") { @@ -147,7 +146,7 @@ print_each_comparism_effectsize <- function(dabest_object, effectsize) { current_bca_low <- bca_low[i] current_bca_high <- bca_high[i] current_ci <- ci[i] - current_pval <- pvalue[i] + current_pval <- as.numeric(pvalue[i]) cat(stringr::str_interp("The ${paired_status} ${es} between ${current_group} and ${previous_group} is ${current_difference} [${current_ci}%CI ${current_bca_low}, ${current_bca_high}].\n")) cat(stringr::str_interp("The p-value of the two-sided permutation t-test is ${sprintf(current_pval, fmt = '%#.4f')}, calculated for legacy purposes only.")) diff --git a/R/999_plot_palettes.R b/R/999_plot_palettes.R index 5d17c4a..d335d56 100644 --- a/R/999_plot_palettes.R +++ b/R/999_plot_palettes.R @@ -20,7 +20,7 @@ apply_palette <- function(ggplot_object, palette_name) { "ucscgb" = ggplot_object + ggsci::scale_color_ucscgb() + ggsci::scale_fill_ucscgb(), "d3" = - ggplot_object + ggsci::scale_color_d3() + ggsci::scale_fill_d3(), + ggplot_object + ggsci::scale_color_d3(palette = "category20") + ggsci::scale_fill_d3(palette = "category20"), "locuszoom" = ggplot_object + ggsci::scale_color_locuszoom() + ggsci::scale_fill_locuszoom(), "igv" = diff --git a/_pkgdown.yml b/_pkgdown.yml index 5f2e7ed..b0e78a3 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -53,7 +53,7 @@ authors: Kah Seng Lian: href: https://github.com/sunroofgod Zhuoyu Wang: - href: ~ + href: https://github.com/Lucas1213WZY Jun Yang Liao: href: https://github.com/junyangliao ACCLAB: diff --git a/tests/testthat/_snaps/001_plotter/deltadelta-mean-diff.svg b/tests/testthat/_snaps/001_plotter/deltadelta-mean-diff.svg index 7ed51d6..d772cdb 100644 --- a/tests/testthat/_snaps/001_plotter/deltadelta-mean-diff.svg +++ b/tests/testthat/_snaps/001_plotter/deltadelta-mean-diff.svg @@ -34,152 +34,152 @@ - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -2 -3 -4 -5 - - - - -W Placebo -N = 10 -M Placebo -N = 10 -W Drug -N = 10 -M Drug -N = 10 -value + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +2 +3 +4 +5 + + + + +W Placebo +N = 10 +M Placebo +N = 10 +W Drug +N = 10 +M Drug +N = 10 +value - + - + - - + + - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + - --2 --1 -0 -1 - - - - - - - - - --2 --1 -0 -1 -M Placebo -minus -W Placebo -M Drug -minus -W Drug -delta-delta -Mean difference -delta-delta + +-2 +-1 +0 +1 + + + + + + + + + +-2 +-1 +0 +1 +M Placebo +minus +W Placebo +M Drug +minus +W Drug +delta-delta +Mean difference +delta-delta @@ -189,10 +189,12 @@ - - - -M -W + + + + + +M +W diff --git a/tests/testthat/_snaps/001_plotter/minimeta-mean-diff.svg b/tests/testthat/_snaps/001_plotter/minimeta-mean-diff.svg index 4e916f2..17cbc01 100644 --- a/tests/testthat/_snaps/001_plotter/minimeta-mean-diff.svg +++ b/tests/testthat/_snaps/001_plotter/minimeta-mean-diff.svg @@ -28,241 +28,241 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -2 -3 -4 -5 - - - - -Control 1 -N = 20 -Test 1 -N = 20 -Control 2 -N = 20 -Test 2 -N = 20 -Control 3 -N = 20 -Test 3 -N = 20 -value + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +2 +3 +4 +5 + + + + +Control 1 +N = 20 +Test 1 +N = 20 +Control 2 +N = 20 +Test 2 +N = 20 +Control 3 +N = 20 +Test 3 +N = 20 +value - + - + - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - --2 --1 -0 -1 - - - - -Test 1 -minus -Control 1 -Test 2 -minus -Control 2 -Test 3 -minus -Control 3 -Weighted -Delta -Mean difference + +-2 +-1 +0 +1 + + + + +Test 1 +minus +Control 1 +Test 2 +minus +Control 2 +Test 3 +minus +Control 3 +Weighted +Delta +Mean difference diff --git a/tests/testthat/_snaps/001_plotter/multigroup-baseline-colour-mean-diff.svg b/tests/testthat/_snaps/001_plotter/multigroup-baseline-colour-mean-diff.svg index a9a534e..60770a4 100644 --- a/tests/testthat/_snaps/001_plotter/multigroup-baseline-colour-mean-diff.svg +++ b/tests/testthat/_snaps/001_plotter/multigroup-baseline-colour-mean-diff.svg @@ -37,74 +37,74 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -2 -3 -4 -5 - - - - -Control 1 -N = 20 -Test 1 -N = 20 -Control 2 -N = 20 -Test 2 -N = 20 -Test 3 -N = 20 -value + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +2 +3 +4 +5 + + + + +Control 1 +N = 20 +Test 1 +N = 20 +Control 2 +N = 20 +Test 2 +N = 20 +Test 3 +N = 20 +value @@ -112,60 +112,60 @@ - + - - + + - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - --2 --1 -0 -1 - - - - -Test 1 -minus -Control 1 -Test 2 -minus -Control 2 -Test 3 -minus -Control 2 -Paired -mean difference + +-2 +-1 +0 +1 + + + + +Test 1 +minus +Control 1 +Test 2 +minus +Control 2 +Test 3 +minus +Control 2 +Paired +mean difference @@ -175,12 +175,14 @@ - - - - - -Female -Male + + + + + + + +Female +Male diff --git a/tests/testthat/_snaps/001_plotter/multigroup-baseline-mean-diff.svg b/tests/testthat/_snaps/001_plotter/multigroup-baseline-mean-diff.svg index f54057e..06f44ea 100644 --- a/tests/testthat/_snaps/001_plotter/multigroup-baseline-mean-diff.svg +++ b/tests/testthat/_snaps/001_plotter/multigroup-baseline-mean-diff.svg @@ -28,74 +28,74 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -2 -3 -4 -5 - - - - -Control 1 -N = 20 -Test 1 -N = 20 -Control 2 -N = 20 -Test 2 -N = 20 -Test 3 -N = 20 -value + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +2 +3 +4 +5 + + + + +Control 1 +N = 20 +Test 1 +N = 20 +Control 2 +N = 20 +Test 2 +N = 20 +Test 3 +N = 20 +value @@ -103,59 +103,59 @@ - + - - + + - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - --2 --1 -0 -1 - - - - -Test 1 -minus -Control 1 -Test 2 -minus -Control 2 -Test 3 -minus -Control 2 -Paired -mean difference + +-2 +-1 +0 +1 + + + + +Test 1 +minus +Control 1 +Test 2 +minus +Control 2 +Test 3 +minus +Control 2 +Paired +mean difference diff --git a/tests/testthat/_snaps/001_plotter/multigroup-sequential-mean-diff.svg b/tests/testthat/_snaps/001_plotter/multigroup-sequential-mean-diff.svg index 8cc9f90..24078cb 100644 --- a/tests/testthat/_snaps/001_plotter/multigroup-sequential-mean-diff.svg +++ b/tests/testthat/_snaps/001_plotter/multigroup-sequential-mean-diff.svg @@ -28,74 +28,74 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -2 -3 -4 -5 - - - - -Control 1 -N = 20 -Test 1 -N = 20 -Control 2 -N = 20 -Test 2 -N = 20 -Test 3 -N = 20 -value + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +2 +3 +4 +5 + + + + +Control 1 +N = 20 +Test 1 +N = 20 +Control 2 +N = 20 +Test 2 +N = 20 +Test 3 +N = 20 +value @@ -103,59 +103,59 @@ - + - - + + - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - --2 --1 -0 -1 - - - - -Test 1 -minus -Control 1 -Test 2 -minus -Control 2 -Test 3 -minus -Test 2 -Paired -mean difference + +-2 +-1 +0 +1 + + + + +Test 1 +minus +Control 1 +Test 2 +minus +Control 2 +Test 3 +minus +Test 2 +Paired +mean difference diff --git a/tests/testthat/_snaps/001_plotter/multigroup-unpaired-mean-diff-colour.svg b/tests/testthat/_snaps/001_plotter/multigroup-unpaired-mean-diff-colour.svg index ab315b9..56e57b8 100644 --- a/tests/testthat/_snaps/001_plotter/multigroup-unpaired-mean-diff-colour.svg +++ b/tests/testthat/_snaps/001_plotter/multigroup-unpaired-mean-diff-colour.svg @@ -37,204 +37,204 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -2 -3 -4 -5 - - - - -Control 1 -N = 20 -Test 1 -N = 20 -Control 2 -N = 20 -Test 2 -N = 20 -Test 3 -N = 20 -value + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +2 +3 +4 +5 + + + + +Control 1 +N = 20 +Test 1 +N = 20 +Control 2 +N = 20 +Test 2 +N = 20 +Test 3 +N = 20 +value - + - + - - + + - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - --2 --1 -0 -1 - - - - -Test 1 -minus -Control 1 -Test 2 -minus -Control 2 -Test 3 -minus -Control 2 -Mean difference + +-2 +-1 +0 +1 + + + + +Test 1 +minus +Control 1 +Test 2 +minus +Control 2 +Test 3 +minus +Control 2 +Mean difference @@ -244,10 +244,12 @@ - - - -Female -Male + + + + + +Female +Male diff --git a/tests/testthat/_snaps/001_plotter/multigroup-unpaired-mean-diff.svg b/tests/testthat/_snaps/001_plotter/multigroup-unpaired-mean-diff.svg index 0cefd5e..561ac65 100644 --- a/tests/testthat/_snaps/001_plotter/multigroup-unpaired-mean-diff.svg +++ b/tests/testthat/_snaps/001_plotter/multigroup-unpaired-mean-diff.svg @@ -28,203 +28,203 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -2 -3 -4 -5 - - - - -Control 1 -N = 20 -Test 1 -N = 20 -Control 2 -N = 20 -Test 2 -N = 20 -Test 3 -N = 20 -value + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +2 +3 +4 +5 + + + + +Control 1 +N = 20 +Test 1 +N = 20 +Control 2 +N = 20 +Test 2 +N = 20 +Test 3 +N = 20 +value - + - + - - + + - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - --2 --1 -0 -1 - - - - -Test 1 -minus -Control 1 -Test 2 -minus -Control 2 -Test 3 -minus -Control 2 -Mean difference + +-2 +-1 +0 +1 + + + + +Test 1 +minus +Control 1 +Test 2 +minus +Control 2 +Test 3 +minus +Control 2 +Mean difference diff --git a/tests/testthat/_snaps/001_plotter/proportion-baseline-flow-false-mean-diff.svg b/tests/testthat/_snaps/001_plotter/proportion-baseline-flow-false-mean-diff.svg index 2c68bff..ad07ce3 100644 --- a/tests/testthat/_snaps/001_plotter/proportion-baseline-flow-false-mean-diff.svg +++ b/tests/testthat/_snaps/001_plotter/proportion-baseline-flow-false-mean-diff.svg @@ -21,96 +21,96 @@ - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -0.00 -0.25 -0.50 -0.75 -1.00 - - - - - -Control 1 -v.s. - Test 1 -N= 40 -Test 1 -v.s. - Test 2 -N= 40 -Test 2 -v.s. - Test 3 -N= 40 -Control 2 -v.s. - Test 4 -N= 40 -proportion of success + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +0.00 +0.25 +0.50 +0.75 +1.00 + + + + + +Control 1 +v.s. + Test 1 +N= 40 +Test 1 +v.s. + Test 2 +N= 40 +Test 2 +v.s. + Test 3 +N= 40 +Control 2 +v.s. + Test 4 +N= 40 +proportion of success @@ -118,62 +118,62 @@ - + - - + + - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + - --0.25 -0.00 -0.25 -0.50 -0.75 - - - - - -Test 1 -minus -Control 1 -Test 2 -minus -Control 1 -Test 3 -minus -Control 1 -Test 4 -minus -Control 2 -Paired -mean difference + +-0.25 +0.00 +0.25 +0.50 +0.75 + + + + + +Test 1 +minus +Control 1 +Test 2 +minus +Control 1 +Test 3 +minus +Control 1 +Test 4 +minus +Control 2 +Paired +mean difference diff --git a/tests/testthat/_snaps/001_plotter/proportion-baseline-mean-diff.svg b/tests/testthat/_snaps/001_plotter/proportion-baseline-mean-diff.svg index e6cee39..a9f6dd5 100644 --- a/tests/testthat/_snaps/001_plotter/proportion-baseline-mean-diff.svg +++ b/tests/testthat/_snaps/001_plotter/proportion-baseline-mean-diff.svg @@ -21,86 +21,86 @@ - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -0.00 -0.25 -0.50 -0.75 -1.00 - - - - - -Control 1 -N = 40 -Test 1 -N = 40 -Test 2 -N = 40 -Test 3 -N = 40 -Control 2 -N = 40 -Test 4 -N = 40 -proportion of success + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +0.00 +0.25 +0.50 +0.75 +1.00 + + + + + +Control 1 +N = 40 +Test 1 +N = 40 +Test 2 +N = 40 +Test 3 +N = 40 +Control 2 +N = 40 +Test 4 +N = 40 +proportion of success @@ -108,68 +108,68 @@ - + - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + - --0.25 -0.00 -0.25 -0.50 -0.75 - - - - - -Test 1 -minus -Control 1 -Test 2 -minus -Control 1 -Test 3 -minus -Control 1 -Test 4 -minus -Control 2 -Paired -mean difference + +-0.25 +0.00 +0.25 +0.50 +0.75 + + + + + +Test 1 +minus +Control 1 +Test 2 +minus +Control 1 +Test 3 +minus +Control 1 +Test 4 +minus +Control 2 +Paired +mean difference diff --git a/tests/testthat/_snaps/001_plotter/proportion-paired-mean-diff-float-false.svg b/tests/testthat/_snaps/001_plotter/proportion-paired-mean-diff-float-false.svg index 400e3c9..a63ee43 100644 --- a/tests/testthat/_snaps/001_plotter/proportion-paired-mean-diff-float-false.svg +++ b/tests/testthat/_snaps/001_plotter/proportion-paired-mean-diff-float-false.svg @@ -21,45 +21,45 @@ - + - + - - - - - - - - - - - - - - - - - -0.00 -0.25 -0.50 -0.75 -1.00 - - - - - -Control 1 -N = 40 -Test 1 -N = 40 -proportion of success + + + + + + + + + + + + + + + + + +0.00 +0.25 +0.50 +0.75 +1.00 + + + + + +Control 1 +N = 40 +Test 1 +N = 40 +proportion of success @@ -72,36 +72,36 @@ - - + + - - - - - - - - - - - + + + + + + + + + + + - -0.0 -0.2 -0.4 -0.6 - - - - -Test 1 -minus -Control 1 -Paired -mean difference + +0.0 +0.2 +0.4 +0.6 + + + + +Test 1 +minus +Control 1 +Paired +mean difference diff --git a/tests/testthat/_snaps/001_plotter/proportion-paired-mean-diff-float-true.svg b/tests/testthat/_snaps/001_plotter/proportion-paired-mean-diff-float-true.svg index 82cf533..3522a10 100644 --- a/tests/testthat/_snaps/001_plotter/proportion-paired-mean-diff-float-true.svg +++ b/tests/testthat/_snaps/001_plotter/proportion-paired-mean-diff-float-true.svg @@ -21,43 +21,43 @@ - + - + - - - - - - - - - - - - - - - -0.00 -0.25 -0.50 -0.75 -1.00 - - - - - -Control 1 -N = 40 -Test 1 -N = 40 -proportion of success + + + + + + + + + + + + + + + +0.00 +0.25 +0.50 +0.75 +1.00 + + + + + +Control 1 +N = 40 +Test 1 +N = 40 +proportion of success @@ -70,39 +70,39 @@ - - + + - - - - - - - - - - + + + + + + + + + + - - - - - - - --0.2 -0.0 -0.2 -0.4 -0.6 -0.8 -Test 1 -minus -Control 1 -Paired -mean difference + + + + + + + +-0.2 +0.0 +0.2 +0.4 +0.6 +0.8 +Test 1 +minus +Control 1 +Paired +mean difference diff --git a/tests/testthat/_snaps/001_plotter/proportion-sequential-mean-diff.svg b/tests/testthat/_snaps/001_plotter/proportion-sequential-mean-diff.svg index 0afd7af..220958a 100644 --- a/tests/testthat/_snaps/001_plotter/proportion-sequential-mean-diff.svg +++ b/tests/testthat/_snaps/001_plotter/proportion-sequential-mean-diff.svg @@ -28,79 +28,79 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -0.00 -0.25 -0.50 -0.75 -1.00 - - - - - -Control 1 -N = 40 -Test 1 -N = 40 -Test 2 -N = 40 -Test 3 -N = 40 -Control 2 -N = 40 -Test 4 -N = 40 -proportion of success + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +0.00 +0.25 +0.50 +0.75 +1.00 + + + + + +Control 1 +N = 40 +Test 1 +N = 40 +Test 2 +N = 40 +Test 3 +N = 40 +Control 2 +N = 40 +Test 4 +N = 40 +proportion of success @@ -108,64 +108,64 @@ - + - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + - --0.4 -0.0 -0.4 - - - -Test 1 -minus -Control 1 -Test 2 -minus -Test 1 -Test 3 -minus -Test 2 -Test 4 -minus -Control 2 -Paired -mean difference + +-0.4 +0.0 +0.4 + + + +Test 1 +minus +Control 1 +Test 2 +minus +Test 1 +Test 3 +minus +Test 2 +Test 4 +minus +Control 2 +Paired +mean difference diff --git a/tests/testthat/_snaps/001_plotter/proportion-unpaired-mean-diff-float-false.svg b/tests/testthat/_snaps/001_plotter/proportion-unpaired-mean-diff-float-false.svg index 789ac62..45a1abf 100644 --- a/tests/testthat/_snaps/001_plotter/proportion-unpaired-mean-diff-float-false.svg +++ b/tests/testthat/_snaps/001_plotter/proportion-unpaired-mean-diff-float-false.svg @@ -21,41 +21,41 @@ - + - + - - - - - - - - - - - - - -0.00 -0.25 -0.50 -0.75 -1.00 - - - - - -Control 1 -N = 40 -Test 1 -N = 40 -proportion of success + + + + + + + + + + + + + +0.00 +0.25 +0.50 +0.75 +1.00 + + + + + +Control 1 +N = 40 +Test 1 +N = 40 +proportion of success @@ -68,35 +68,35 @@ - - + + - - - - - - - - - - - + + + + + + + + + + + - -0.0 -0.2 -0.4 -0.6 - - - - -Test 1 -minus -Control 1 -Mean difference + +0.0 +0.2 +0.4 +0.6 + + + + +Test 1 +minus +Control 1 +Mean difference diff --git a/tests/testthat/_snaps/001_plotter/proportion-unpaired-mean-diff-float-true.svg b/tests/testthat/_snaps/001_plotter/proportion-unpaired-mean-diff-float-true.svg index 850e1e5..5cb901d 100644 --- a/tests/testthat/_snaps/001_plotter/proportion-unpaired-mean-diff-float-true.svg +++ b/tests/testthat/_snaps/001_plotter/proportion-unpaired-mean-diff-float-true.svg @@ -21,41 +21,41 @@ - + - + - - - - - - - - - - - - - -0.00 -0.25 -0.50 -0.75 -1.00 - - - - - -Control 1 -N = 40 -Test 1 -N = 40 -proportion of success + + + + + + + + + + + + + +0.00 +0.25 +0.50 +0.75 +1.00 + + + + + +Control 1 +N = 40 +Test 1 +N = 40 +proportion of success @@ -68,38 +68,38 @@ - - + + - - - - - - - - - - + + + + + + + + + + - - - - - - - --0.2 -0.0 -0.2 -0.4 -0.6 -0.8 -Test 1 -minus -Control 1 -Mean difference + + + + + + + +-0.2 +0.0 +0.2 +0.4 +0.6 +0.8 +Test 1 +minus +Control 1 +Mean difference diff --git a/tests/testthat/_snaps/001_plotter/proportion-unpaired-multigroup-mean-diff.svg b/tests/testthat/_snaps/001_plotter/proportion-unpaired-multigroup-mean-diff.svg index 31b5a0e..2055ab6 100644 --- a/tests/testthat/_snaps/001_plotter/proportion-unpaired-multigroup-mean-diff.svg +++ b/tests/testthat/_snaps/001_plotter/proportion-unpaired-multigroup-mean-diff.svg @@ -28,41 +28,41 @@ - - - - - - - - - - - - - - - - - - -0.00 -0.25 -0.50 -0.75 -1.00 - - - - - -Control 1 -N = 40 -Test 1 -N = 40 -Test 2 -N = 40 -proportion of success + + + + + + + + + + + + + + + + + + +0.00 +0.25 +0.50 +0.75 +1.00 + + + + + +Control 1 +N = 40 +Test 1 +N = 40 +Test 2 +N = 40 +proportion of success @@ -75,42 +75,42 @@ - - + + - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + - --0.25 -0.00 -0.25 -0.50 - - - - -Test 1 -minus -Control 1 -Test 2 -minus -Control 1 -Mean difference + +-0.25 +0.00 +0.25 +0.50 + + + + +Test 1 +minus +Control 1 +Test 2 +minus +Control 1 +Mean difference diff --git a/tests/testthat/_snaps/001_plotter/two-groups-unpaired-mean-diff-colour-float-false.svg b/tests/testthat/_snaps/001_plotter/two-groups-unpaired-mean-diff-colour-float-false.svg index 22afb07..34cf4f3 100644 --- a/tests/testthat/_snaps/001_plotter/two-groups-unpaired-mean-diff-colour-float-false.svg +++ b/tests/testthat/_snaps/001_plotter/two-groups-unpaired-mean-diff-colour-float-false.svg @@ -34,67 +34,67 @@ - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -3 -4 - - -Control 1 -N = 20 -Test 1 -N = 20 -value + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +3 +4 + + +Control 1 +N = 20 +Test 1 +N = 20 +value @@ -107,36 +107,36 @@ - - + + - - - - - - - - - - - + + + + + + + + + + + - -0.0 -0.3 -0.6 -0.9 - - - - -Test 1 -minus -Control 1 -Mean difference + +0.0 +0.3 +0.6 +0.9 + + + + +Test 1 +minus +Control 1 +Mean difference @@ -146,10 +146,12 @@ - - - -Female -Male + + + + + +Female +Male diff --git a/tests/testthat/_snaps/001_plotter/two-groups-unpaired-mean-diff-colour-float-true.svg b/tests/testthat/_snaps/001_plotter/two-groups-unpaired-mean-diff-colour-float-true.svg index 69d104b..7952a2e 100644 --- a/tests/testthat/_snaps/001_plotter/two-groups-unpaired-mean-diff-colour-float-true.svg +++ b/tests/testthat/_snaps/001_plotter/two-groups-unpaired-mean-diff-colour-float-true.svg @@ -37,64 +37,64 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -3 -4 - - -Control 1 -N = 20 -Test 1 -N = 20 -value + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +3 +4 + + +Control 1 +N = 20 +Test 1 +N = 20 +value @@ -107,35 +107,30 @@ - - + + - - - - - - - - - - + + + + + + + + + + - - - -0 -1 -Test 1 -minus -Control 1 -Mean difference - - - -Female -Male + + + +0 +1 +Test 1 +minus +Control 1 +Mean difference diff --git a/tests/testthat/_snaps/001_plotter/two-groups-unpaired-mean-diff-float-false.svg b/tests/testthat/_snaps/001_plotter/two-groups-unpaired-mean-diff-float-false.svg index 0b7401d..e49f2cc 100644 --- a/tests/testthat/_snaps/001_plotter/two-groups-unpaired-mean-diff-float-false.svg +++ b/tests/testthat/_snaps/001_plotter/two-groups-unpaired-mean-diff-float-false.svg @@ -25,67 +25,67 @@ - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -3 -4 - - -Control 1 -N = 20 -Test 1 -N = 20 -value + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +3 +4 + + +Control 1 +N = 20 +Test 1 +N = 20 +value @@ -98,35 +98,35 @@ - - + + - - - - - - - - - - - + + + + + + + + + + + - -0.0 -0.3 -0.6 -0.9 - - - - -Test 1 -minus -Control 1 -Mean difference + +0.0 +0.3 +0.6 +0.9 + + + + +Test 1 +minus +Control 1 +Mean difference diff --git a/tests/testthat/_snaps/001_plotter/two-groups-unpaired-mean-diff-float-true.svg b/tests/testthat/_snaps/001_plotter/two-groups-unpaired-mean-diff-float-true.svg index fa9ae42..c03a26b 100644 --- a/tests/testthat/_snaps/001_plotter/two-groups-unpaired-mean-diff-float-true.svg +++ b/tests/testthat/_snaps/001_plotter/two-groups-unpaired-mean-diff-float-true.svg @@ -28,64 +28,64 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -3 -4 - - -Control 1 -N = 20 -Test 1 -N = 20 -value + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +3 +4 + + +Control 1 +N = 20 +Test 1 +N = 20 +value @@ -98,30 +98,30 @@ - - + + - - - - - - - - - - + + + + + + + + + + - - - -0 -1 -Test 1 -minus -Control 1 -Mean difference + + + +0 +1 +Test 1 +minus +Control 1 +Mean difference