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Add effect size (Cohen's d) to estimate_contrasts #227

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Add effect size (Cohen's d) to estimate_contrasts #227

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31f1596
add effect size (cohen's d) to estimate_contrasts
rempsyc May 8, 2023
d439676
`estimate_contrasts`: now supports optional standardized effect sizes…
rempsyc Jul 1, 2023
eadb798
update docs [skip ci]
rempsyc Jul 2, 2023
7d0c5bc
add method "marginal"
rempsyc Jul 2, 2023
219935d
Buff details of methods [skip ci]
rempsyc Jul 2, 2023
719f546
update docs [skip ci]
rempsyc Aug 5, 2023
0c22e29
rewrite as "difference * (1- R2)/ sigma", rename as "partial_effect_s…
rempsyc Aug 5, 2023
a3aad0d
rewrite output column as "partial_d" when using emmeans [skip ci]
rempsyc Aug 6, 2023
7ebdc3c
Merge branch 'main' into estimate_contrasts_cohens_d
strengejacke Aug 21, 2023
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -68,7 +68,7 @@ VignetteBuilder:
knitr
Encoding: UTF-8
Language: en-US
RoxygenNote: 7.2.3.9000
RoxygenNote: 7.2.3
Config/testthat/edition: 3
Config/testthat/parallel: true
Roxygen: list(markdown = TRUE)
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25 changes: 25 additions & 0 deletions R/estimate_contrasts.R
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Expand Up @@ -135,6 +135,31 @@ estimate_contrasts <- function(model,
contrasts$contrast <- NULL
contrasts <- cbind(level_cols, contrasts)

# Add effect size (Cohen's d)
if (is.null(contrast) && is.null(fixed) && is.null(at)) {
dat <- insight::get_data(model)
resp <- insight::find_response(model)

if (is.numeric(dat[[resp]])) {
dat <- datawizard::data_select(dat, c(resp, info$contrast))

list.dat <- lapply(seq_len(nrow(contrasts)), function(i) {
log.vec <- which(dat[[info$contrast]] == unlist(info$misc$orig.grid)[[i]])
dat.temp <- datawizard::data_filter(dat, log.vec)
})
list.dat <- stats::setNames(list.dat, unique(unlist(level_cols)))

eff <- lapply(seq_len(nrow(contrasts)), function(i) {
effectsize::cohens_d(x = list.dat[[contrasts$Level1[i]]][[resp]],
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y = list.dat[[contrasts$Level2[i]]][[resp]],
verbose = FALSE)
})

eff <- do.call(rbind, eff)
names(eff)[-1] <- paste0("Cohens_d_", names(eff)[-1])
contrasts <- cbind(contrasts, eff)
}
}

# Table formatting
attr(contrasts, "table_title") <- c("Marginal Contrasts Analysis", "blue")
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22 changes: 11 additions & 11 deletions tests/testthat/test-estimate_contrasts.R
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Expand Up @@ -8,7 +8,7 @@ test_that("estimate_contrasts - Frequentist", {
model <- lm(Sepal.Width ~ Species, data = dat)

estim <- suppressMessages(estimate_contrasts(model))
expect_equal(dim(estim), c(3, 9))
expect_equal(dim(estim), c(3, 13))

estim <- suppressMessages(estimate_contrasts(model, at = "Species=c('versicolor', 'virginica')"))
expect_equal(dim(estim), c(1, 9))
Expand All @@ -21,16 +21,16 @@ test_that("estimate_contrasts - Frequentist", {
model <- lm(Sepal.Width ~ Species * fac, data = dat)

estim <- suppressMessages(estimate_contrasts(model))
expect_equal(dim(estim), c(3, 9))
expect_equal(dim(estim), c(3, 13))
estim <- suppressMessages(estimate_contrasts(model, levels = "Species"))
expect_equal(dim(estim), c(3, 9))
expect_equal(dim(estim), c(3, 13))
estim <- suppressMessages(estimate_contrasts(model, fixed = "fac"))
expect_equal(dim(estim), c(3, 10))

# One factor and one continuous
model <- lm(Sepal.Width ~ Species * Petal.Width, data = iris)
estim <- suppressMessages(estimate_contrasts(model))
expect_equal(dim(estim), c(3, 9))
expect_equal(dim(estim), c(3, 13))
estim <- suppressMessages(estimate_contrasts(model, fixed = "Petal.Width"))
expect_equal(dim(estim), c(3, 10))
estim <- suppressMessages(estimate_contrasts(model, at = "Petal.Width", length = 4))
Expand Down Expand Up @@ -84,7 +84,7 @@ test_that("estimate_contrasts - Frequentist", {

model <- lme4::lmer(Sepal.Width ~ Species + (1 | Petal.Length_factor), data = data)
estim <- suppressMessages(estimate_contrasts(model))
expect_equal(dim(estim), c(3, 9))
expect_equal(dim(estim), c(3, 13))


# GLM - binomial
Expand All @@ -107,7 +107,7 @@ test_that("estimate_contrasts - Frequentist", {
model <- glm(counts ~ treatment, data = dat, family = poisson())

estim <- suppressMessages(estimate_contrasts(model, transform = "response"))
expect_equal(dim(estim), c(3, 9))
expect_equal(dim(estim), c(3, 13))
})


Expand Down Expand Up @@ -145,7 +145,7 @@ test_that("estimate_contrasts - Bayesian", {
)
)
estim <- suppressMessages(estimate_contrasts(model))
expect_equal(dim(estim), c(3, 7))
expect_equal(dim(estim), c(3, 11))
estim <- suppressMessages(estimate_contrasts(model, fixed = "Petal.Width"))
expect_equal(dim(estim), c(3, 8))
estim <- suppressMessages(estimate_contrasts(model, at = "Petal.Width", length = 4))
Expand All @@ -161,14 +161,14 @@ test_that("estimate_contrasts - Bayesian", {
))

estim <- suppressMessages(estimate_contrasts(model))
expect_equal(dim(estim), c(3, 7))
expect_equal(dim(estim), c(3, 11))
estim <- suppressMessages(estimate_contrasts(model, transform = "response"))
expect_equal(dim(estim), c(3, 7))
expect_equal(dim(estim), c(3, 11))

estim <- suppressWarnings(suppressMessages(estimate_contrasts(model, test = "bf")))
expect_equal(dim(estim), c(3, 6))
expect_equal(dim(estim), c(3, 10))
estim <- suppressWarnings(suppressMessages(estimate_contrasts(model, transform = "response", test = "bf")))
expect_equal(dim(estim), c(3, 6))
expect_equal(dim(estim), c(3, 10))
})


Expand Down