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methods_wrs2.R
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methods_wrs2.R
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#' Parameters from robust statistical objects in `WRS2`
#'
#' @param model Object from `WRS2` package.
#' @param ... Arguments passed to or from other methods.
#' @inheritParams model_parameters.default
#'
#' @examples
#' if (require("WRS2") && packageVersion("WRS2") >= "1.1.3") {
#' model <- t1way(libido ~ dose, data = viagra)
#' model_parameters(model)
#' }
#' @return A data frame of indices related to the model's parameters.
#' @export
# anova ----------------------
model_parameters.t1way <- function(model, keep = NULL, verbose = TRUE, ...) {
parameters <- .extract_wrs2_t1way(model)
parameters <- .add_htest_parameters_attributes(parameters, model, ...)
class(parameters) <- c("parameters_model", "see_parameters_model", class(parameters))
parameters
}
.extract_wrs2_t1way <- function(model) {
fcall <- insight::safe_deparse(model$call)
# effect sizes are by default contained for `t1way` but not `rmanova`
if (grepl("^(t1way|WRS2::t1way)", fcall)) {
data.frame(
`F` = model$test,
df = model$df1,
df_error = model$df2,
p = model$p.value,
Method = "A heteroscedastic one-way ANOVA for trimmed means",
Estimate = model$effsize,
CI = 1 - model$alpha,
CI_low = model$effsize_ci[1],
CI_high = model$effsize_ci[2],
Effectsize = "Explanatory measure of effect size",
stringsAsFactors = FALSE
)
} else if (grepl("^(rmanova|WRS2::rmanova)", fcall)) {
data.frame(
`F` = model$test,
df = model$df1,
df_error = model$df2,
p = model$p.value,
Method = "A heteroscedastic one-way repeated measures ANOVA for trimmed means",
stringsAsFactors = FALSE
)
}
}
#' @export
model_parameters.med1way <- function(model, verbose = TRUE, ...) {
parameters <- .extract_wrs2_med1way(model)
parameters <- .add_htest_parameters_attributes(parameters, model, ...)
class(parameters) <- c("parameters_model", "see_parameters_model", class(parameters))
parameters
}
.extract_wrs2_med1way <- function(model) {
data.frame(
`F` = model$test,
`Critical value` = model$crit.val,
p = model$p.value,
Method = "Heteroscedastic one-way ANOVA for medians",
stringsAsFactors = FALSE
)
}
#' @export
model_parameters.dep.effect <- function(model,
keep = NULL,
verbose = TRUE,
...) {
parameters <- .extract_wrs2_dep.effect(model, keep = keep)
class(parameters) <- c("parameters_model", "see_parameters_model", class(parameters))
parameters
}
.extract_wrs2_dep.effect <- function(model, keep = NULL, ...) {
out <- as.data.frame(model)
out$Parameter <- c(attributes(out)$row.names)
# effectsize descriptions
out$Effectsize <- c(
"Algina-Keselman-Penfield robust standardized difference", # AKP
"Quantile shift based on the median of the distribution of difference scores", # QS (median)
"Quantile shift based on the trimmed mean of the distribution of X-Y", # QStr
"P(X<Y), Probability of first being less than second for a random pair" # SIGN
)
# column names
names(out) <- c(
"Mu", "Estimate", "Small", "Medium", "Large",
"CI_low", "CI_high", "Parameter", "Effectsize"
)
# add CI column
out$CI <- 0.95
# reorder columns
col_order <- c(
"Parameter", "Estimate", "CI", "CI_low", "CI_high", "Effectsize",
"Mu", "Small", "Medium", "Large"
)
out <- out[col_order[col_order %in% names(out)]]
# remove rownames
rownames(out) <- NULL
# select a specific effect size only
if (!is.null(keep)) {
out <- out[out$Parameter == keep, ]
}
out
}
# t-test ----------------------
#' @export
model_parameters.yuen <- function(model, verbose = TRUE, ...) {
parameters <- .extract_wrs2_yuen(model)
parameters <- .add_htest_parameters_attributes(parameters, model, ...)
class(parameters) <- c("parameters_model", "see_parameters_model", class(parameters))
parameters
}
.extract_wrs2_yuen <- function(model) {
fcall <- insight::safe_deparse(model$call)
# the latter regexe covers `rlang::exec` or `do.call` instances
# between-subjects
if (grepl("^(yuen\\(|WRS2::yuen\\()", fcall) ||
grepl("function (formula, data, tr = 0.2, ...)", fcall, fixed = TRUE)) {
out <- data.frame(
t = model$test,
df_error = model$df,
p = model$p.value,
Method = "Yuen's test on trimmed means for independent samples",
Difference = model$diff,
CI = 0.95,
Difference_CI_low = model$conf.int[1],
Difference_CI_high = model$conf.int[2],
Estimate = model$effsize,
Effectsize = "Explanatory measure of effect size",
stringsAsFactors = FALSE
)
} else {
# within-subjects
out <- data.frame(
t = model$test,
df_error = model$df,
p = model$p.value,
Method = "Yuen's test on trimmed means for dependent samples",
Difference = model$diff,
CI = 0.95,
Difference_CI_low = model$conf.int[1],
Difference_CI_high = model$conf.int[2],
Estimate = model$effsize,
Effectsize = "Explanatory measure of effect size",
stringsAsFactors = FALSE
)
}
out
}
# pairwise comparisons ----------------------
#' @export
model_parameters.mcp1 <- function(model, verbose = TRUE, ...) {
parameters <- .extract_wrs2_mcp12(model)
parameters <- .add_htest_parameters_attributes(parameters, model, ...)
class(parameters) <- c("parameters_model", "see_parameters_model", class(parameters))
parameters
}
#' @export
model_parameters.mcp2 <- model_parameters.mcp1
.extract_wrs2_mcp12 <- function(model) {
# component of the object containing results from multiple comparisons
out <- as.data.frame(model$comp)
# rename to `eaystats` conventions
names(out)[1:6] <- c("Group1", "Group2", "Psihat", "CI_low", "CI_high", "p")
# convert names to character
out$Group1 <- model$fnames[model$comp[, 1]]
out$Group2 <- model$fnames[model$comp[, 2]]
# CI column
out$CI <- 1 - model$alpha
# reorder
col_order <- c("Group1", "Group2", "Psihat", "CI", "CI_low", "CI_high", "p", "p.crit")
out <- out[col_order[col_order %in% names(out)]]
out
}
# comparison of discrete distributions ----------------------
#' @export
model_parameters.robtab <- function(model, verbose = TRUE, ...) {
parameters <- .extract_wrs2_robtab(model)
parameters <- .add_htest_parameters_attributes(parameters, model, ...)
class(parameters) <- c("parameters_model", "see_parameters_model", class(parameters))
parameters
}
.extract_wrs2_robtab <- function(model) {
fcall <- insight::safe_deparse(model$call)
# dataframe
out <- as.data.frame(model$partable)
# rename to `eaystats` conventions
if (grepl("^(discmcp\\(|WRS2::discmcp\\()", fcall)) {
names(out)[1:3] <- c("Group1", "Group2", "p")
}
if (grepl("^(discstep\\(|WRS2::discstep\\()", fcall)) {
names(out)[1:2] <- c("Groups", "p")
}
if (grepl("^(binband\\(|WRS2::binband\\()", fcall)) {
names(out)[1:4] <- c("Value", "Probability1", "Probability2", "Difference")
if ("p.value" %in% names(out)) {
out$p <- out$p.value
out$p.value <- NULL
}
}
out
}
# one-sample percentile bootstrap ----------------------
#' @export
model_parameters.onesampb <- function(model, verbose = TRUE, ...) {
parameters <- .extract_wrs2_onesampb(model)
parameters <- .add_htest_parameters_attributes(parameters, model, ...)
class(parameters) <- c("parameters_model", "see_parameters_model", class(parameters))
parameters
}
.extract_wrs2_onesampb <- function(model) {
data.frame(
Estimate = model$estimate,
CI = 1 - model$alpha,
CI_low = model$ci[1],
CI_high = model$ci[2],
p = model$p.value,
n_Obs = model$n,
Effectsize = "Robust location measure",
Method = "One-sample percentile bootstrap",
stringsAsFactors = FALSE
)
}
#' @export
model_parameters.trimcibt <- function(model, verbose = TRUE, ...) {
parameters <- .extract_wrs2_trimcibt(model)
parameters <- .add_htest_parameters_attributes(parameters, model, ...)
class(parameters) <- c("parameters_model", "see_parameters_model", class(parameters))
parameters
}
.extract_wrs2_trimcibt <- function(model) {
data.frame(
t = model$test.stat,
p = model$p.value,
n_Obs = model$n,
Method = "Bootstrap-t method for one-sample test",
Estimate = model$estimate[[1]],
CI = 1 - model$alpha,
CI_low = model$ci[1],
CI_high = model$ci[2],
Effectsize = "Trimmed mean",
stringsAsFactors = FALSE
)
}
# AKP effect sizes ----------------------
#' @export
model_parameters.AKP <- function(model, verbose = TRUE, ...) {
parameters <- .extract_wrs2_AKP(model)
parameters <- .add_htest_parameters_attributes(parameters, model, ...)
class(parameters) <- c("parameters_model", "see_parameters_model", class(parameters))
parameters
}
.extract_wrs2_AKP <- function(model) {
data.frame(
Estimate = model$AKPeffect,
CI = 1 - model$alpha,
CI_low = model$AKPci[1],
CI_high = model$AKPci[2],
Effectsize = "Algina-Keselman-Penfield robust standardized difference",
stringsAsFactors = FALSE
)
}
#' @export
model_parameters.wmcpAKP <- function(model, verbose = TRUE, ...) {
parameters <- .extract_wrs2_wmcpAKP(model)
class(parameters) <- c("parameters_model", "see_parameters_model", class(parameters))
parameters
}
.extract_wrs2_wmcpAKP <- function(model) {
data.frame(
Estimate = model[[1]],
CI = 0.95,
CI_low = model[[2]],
CI_high = model[[3]],
Effectsize = "Algina-Keselman-Penfield robust standardized difference average",
stringsAsFactors = FALSE
)
}