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Issues with parameters() on marginaleffects objects #901

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Sep 11, 2023
Merged

Issues with parameters() on marginaleffects objects #901

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d59e236
Issues with `parameters()` on `marginaleffects` objects
strengejacke Sep 11, 2023
b696f4a
update RD
strengejacke Sep 11, 2023
36a29cb
update
strengejacke Sep 11, 2023
557bea0
update
strengejacke Sep 11, 2023
a16d49f
fix
strengejacke Sep 11, 2023
698eafa
Merge branch 'main' into strengejacke/issue887
strengejacke Sep 11, 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
@@ -1,7 +1,7 @@
Type: Package
Package: parameters
Title: Processing of Model Parameters
Version: 0.21.1.5
Version: 0.21.1.6
Authors@R:
c(person(given = "Daniel",
family = "Lüdecke",
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8 changes: 8 additions & 0 deletions NEWS.md
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@@ -1,5 +1,13 @@
# parameters 0.21.2

## Changes

* The `ci_digits` argument of the `print()` method for `model_parameters()` now
defaults to the same value of `digits`.

* `model_parameters()` for objects from package *marginaleffects* now also
accepts the `exponentiate` argument.

## Bug fixes

* Fixed issue with wrong calculation of test-statistic and p-values in
Expand Down
6 changes: 3 additions & 3 deletions R/display.R
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Expand Up @@ -81,7 +81,7 @@
footer = NULL,
align = NULL,
digits = 2,
ci_digits = 2,
ci_digits = digits,
p_digits = 3,
footer_digits = 3,
ci_brackets = c("(", ")"),
Expand Down Expand Up @@ -132,7 +132,7 @@
display.compare_parameters <- function(object,
format = "markdown",
digits = 2,
ci_digits = 2,
ci_digits = digits,
p_digits = 3,
select = NULL,
column_labels = NULL,
Expand Down Expand Up @@ -165,7 +165,7 @@
display.parameters_sem <- function(object,
format = "markdown",
digits = 2,
ci_digits = 2,
ci_digits = digits,
p_digits = 3,
ci_brackets = c("(", ")"),
...) {
Expand All @@ -192,7 +192,7 @@
#' @inheritParams model_parameters.principal
#' @rdname display.parameters_model
#' @export
display.parameters_efa <- function(object, format = "markdown", digits = 2, sort = FALSE, threshold = NULL, labels = NULL, ...) {

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file=R/display.R,line=195,col=121,[line_length_linter] Lines should not be more than 120 characters. This line is 129 characters.
print_md(x = object, digits = digits, sort = sort, threshold = threshold, labels = labels, ...)
}

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6 changes: 3 additions & 3 deletions R/equivalence_test.R
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Expand Up @@ -383,7 +383,7 @@
if (all(range == "default")) {
range <- bayestestR::rope_range(x, verbose = verbose)
if (is.list(range)) {
range <- range[[which.max(sapply(range, diff))]]

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file=R/equivalence_test.R,line=386,col=33,[undesirable_function_linter] Function "sapply" is undesirable.
}
} else if (!all(is.numeric(range)) || length(range) != 2) {
insight::format_error(
Expand Down Expand Up @@ -539,7 +539,7 @@


#' @keywords internal
.equivalence_test_numeric <- function(ci_wide, ci_narrow, range_rope, rule, ci = 0.95, verbose) {

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file=R/equivalence_test.R,line=542,col=88,[function_argument_linter] Arguments without defaults should come before arguments with defaults.
final_ci <- NULL

# ==== HDI+ROPE decision rule, by Kruschke ====
Expand Down Expand Up @@ -693,7 +693,7 @@
#' @export
format.equivalence_test_lm <- function(x,
digits = 2,
ci_digits = 2,
ci_digits = digits,
p_digits = 3,
ci_width = NULL,
ci_brackets = NULL,
Expand Down Expand Up @@ -736,7 +736,7 @@
#' @export
print.equivalence_test_lm <- function(x,
digits = 2,
ci_digits = 2,
ci_digits = digits,
p_digits = 3,
ci_brackets = NULL,
zap_small = FALSE,
Expand Down Expand Up @@ -794,7 +794,7 @@
#' #' @export
#' print_md.equivalence_test_lm <- function(x,
#' digits = 2,
#' ci_digits = 2,
#' ci_digits = digits,
#' p_digits = 3,
#' ci_brackets = NULL,
#' zap_small = FALSE,
Expand Down
19 changes: 13 additions & 6 deletions R/format.R
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Expand Up @@ -8,7 +8,7 @@
split_components = TRUE,
select = NULL,
digits = 2,
ci_digits = 2,
ci_digits = digits,
p_digits = 3,
ci_width = NULL,
ci_brackets = NULL,
Expand Down Expand Up @@ -259,7 +259,7 @@
split_components = TRUE,
select = NULL,
digits = 2,
ci_digits = 2,
ci_digits = digits,
p_digits = 3,
ci_width = NULL,
ci_brackets = NULL,
Expand Down Expand Up @@ -468,16 +468,23 @@
#' @export
format.parameters_sem <- function(x,
digits = 2,
ci_digits = 2,
ci_digits = digits,
p_digits = 3,
format = NULL,
ci_width = NULL,
ci_brackets = TRUE,
pretty_names = TRUE,
...) {
if (missing(digits)) digits <- .additional_arguments(x, "digits", 2)
if (missing(ci_digits)) ci_digits <- .additional_arguments(x, "ci_digits", 2)
if (missing(p_digits)) p_digits <- .additional_arguments(x, "p_digits", 3)
if (missing(digits)) {
digits <- .additional_arguments(x, "digits", 2)
}
if (missing(ci_digits)) {
ci_digits <- .additional_arguments(x, "ci_digits", digits)
}
if (missing(p_digits)) {
p_digits <- .additional_arguments(x, "p_digits", 3)
}

.format_columns_multiple_components(
x,
pretty_names = TRUE,
Expand Down Expand Up @@ -607,7 +614,7 @@


# footer: generic text
.add_footer_text <- function(footer = NULL, text, type = "text") {

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file=R/format.R,line=617,col=45,[function_argument_linter] Arguments without defaults should come before arguments with defaults.
if (!is.null(text)) {
if (type == "text" || type == "markdown") {
if (is.null(footer)) {
Expand All @@ -625,7 +632,7 @@


# footer: residual standard deviation
.add_footer_sigma <- function(footer = NULL, digits, sigma, residual_df = NULL, type = "text") {

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file=R/format.R,line=635,col=46,[function_argument_linter] Arguments without defaults should come before arguments with defaults.

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file=R/format.R,line=635,col=54,[function_argument_linter] Arguments without defaults should come before arguments with defaults.
if (!is.null(sigma)) {
# format residual df
if (!is.null(residual_df)) {
Expand All @@ -650,7 +657,7 @@


# footer: r-squared
.add_footer_r2 <- function(footer = NULL, digits, r2 = NULL, type = "text") {

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file=R/format.R,line=660,col=43,[function_argument_linter] Arguments without defaults should come before arguments with defaults.
if (!is.null(r2)) {
rsq <- .safe(paste0(unlist(lapply(r2, function(i) {
paste0(attributes(i)$names, ": ", insight::format_value(i, digits = digits))
Expand All @@ -674,7 +681,7 @@


# footer: anova type
.add_footer_anova_type <- function(footer = NULL, aov_type, type = "text") {

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file=R/format.R,line=684,col=51,[function_argument_linter] Arguments without defaults should come before arguments with defaults.
if (!is.null(aov_type)) {
if (type == "text" || type == "markdown") {
if (is.null(footer)) {
Expand All @@ -692,7 +699,7 @@


# footer: marginaleffects::comparisions() prediction_type
.add_footer_prediction_type <- function(footer = NULL, prediction_type, type = "text") {

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file=R/format.R,line=702,col=56,[function_argument_linter] Arguments without defaults should come before arguments with defaults.
if (!is.null(prediction_type)) {
if (type == "text" || type == "markdown") {
if (is.null(footer)) {
Expand All @@ -710,7 +717,7 @@


# footer: anova test
.add_footer_anova_test <- function(footer = NULL, test, type = "text") {

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file=R/format.R,line=720,col=51,[function_argument_linter] Arguments without defaults should come before arguments with defaults.
if (!is.null(test)) {
if (type == "text" || type == "markdown") {
if (is.null(footer)) {
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4 changes: 2 additions & 2 deletions R/methods_htest.R
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Expand Up @@ -695,7 +695,7 @@ model_parameters.svytable <- function(model, verbose = TRUE, ...) {
if ("ci_digits" %in% names(dot.arguments)) {
attr(params, "ci_digits") <- eval(dot.arguments[["ci_digits"]])
} else {
attr(params, "ci_digits") <- 2
attr(params, "ci_digits") <- NULL
}

if ("p_digits" %in% names(dot.arguments)) {
Expand Down Expand Up @@ -747,7 +747,7 @@ model_parameters.svytable <- function(model, verbose = TRUE, ...) {
if ("ci_digits" %in% names(dot.arguments)) {
attr(params, "ci_digits") <- eval(dot.arguments[["ci_digits"]])
} else {
attr(params, "ci_digits") <- 2
attr(params, "ci_digits") <- NULL
}

if ("p_digits" %in% names(dot.arguments)) {
Expand Down
14 changes: 10 additions & 4 deletions R/methods_lavaan.R
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Expand Up @@ -152,11 +152,17 @@ p_value.blavaan <- p_value.BFBayesFactor
# print ---------------------------

#' @export
print.parameters_sem <- function(x, digits = 2, ci_digits = 2, p_digits = 3, ...) {
print.parameters_sem <- function(x, digits = 2, ci_digits = digits, p_digits = 3, ...) {
# check if user supplied digits attributes
if (missing(digits)) digits <- .additional_arguments(x, "digits", 2)
if (missing(ci_digits)) ci_digits <- .additional_arguments(x, "ci_digits", 2)
if (missing(p_digits)) p_digits <- .additional_arguments(x, "p_digits", 3)
if (missing(digits)) {
digits <- .additional_arguments(x, "digits", 2)
}
if (missing(ci_digits)) {
ci_digits <- .additional_arguments(x, "ci_digits", digits)
}
if (missing(p_digits)) {
p_digits <- .additional_arguments(x, "p_digits", 3)
}

verbose <- .additional_arguments(x, "verbose", TRUE)

Expand Down
14 changes: 9 additions & 5 deletions R/methods_marginaleffects.R
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Expand Up @@ -7,6 +7,7 @@
#' @export
model_parameters.marginaleffects <- function(model,
ci = 0.95,
exponentiate = FALSE,
...) {
insight::check_if_installed("marginaleffects")
out <- insight::standardize_names(
Expand All @@ -18,10 +19,7 @@ model_parameters.marginaleffects <- function(model,
colnames(out)[colnames(out) == "contrast"] <- "Comparison"
colnames(out) <- gsub("^contrast_", "Comparison: ", colnames(out))

out <- tryCatch(
.add_model_parameters_attributes(out, model, ci, ...),
error = function(e) out
)
out <- .safe(.add_model_parameters_attributes(out, model, ci, exponentiate = exponentiate, ...), out)

attr(out, "object_name") <- insight::safe_deparse_symbol(substitute(model))

Expand All @@ -41,6 +39,8 @@ model_parameters.marginaleffects <- function(model,
attr(out, "coefficient_name") <- "Estimate"
}

# exponentiate coefficients and SE/CI, if requested
out <- .exponentiate_parameters(out, model = NULL, exponentiate)

class(out) <- c("parameters_model", "see_parameters_model", class(out))
out
Expand Down Expand Up @@ -70,6 +70,7 @@ model_parameters.slopes <- model_parameters.marginaleffects
#' @export
model_parameters.predictions <- function(model,
ci = 0.95,
exponentiate = TRUE,
...) {
insight::check_if_installed("marginaleffects")

Expand All @@ -89,12 +90,15 @@ model_parameters.predictions <- function(model,
out[[resp]] <- NULL
}

out <- .safe(.add_model_parameters_attributes(out, model, ci, ...), out)
out <- .safe(.add_model_parameters_attributes(out, model, ci, exponentiate = exponentiate, ...), out)

attr(out, "object_name") <- insight::safe_deparse_symbol(substitute(model))
attr(out, "coefficient_name") <- "Predicted"
attr(out, "no_caption") <- TRUE

# exponentiate coefficients and SE/CI, if requested
out <- .exponentiate_parameters(out, model = NULL, exponentiate)

class(out) <- c("parameters_model", "see_parameters_model", class(out))
out
}
4 changes: 2 additions & 2 deletions R/print.compare_parameters.R
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Expand Up @@ -5,7 +5,7 @@ print.compare_parameters <- function(x,
subtitle = NULL,
footer = NULL,
digits = 2,
ci_digits = 2,
ci_digits = digits,
p_digits = 3,
zap_small = FALSE,
groups = NULL,
Expand All @@ -21,7 +21,7 @@ print.compare_parameters <- function(x,
digits <- .additional_arguments(x, "digits", digits)
}
if (missing(ci_digits)) {
ci_digits <- .additional_arguments(x, "ci_digits", ci_digits)
ci_digits <- .additional_arguments(x, "ci_digits", digits)
}
if (missing(p_digits)) {
p_digits <- .additional_arguments(x, "p_digits", p_digits)
Expand Down
6 changes: 3 additions & 3 deletions R/print.parameters_model.R
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Expand Up @@ -224,7 +224,7 @@ print.parameters_model <- function(x,
caption = NULL,
footer = NULL,
digits = 2,
ci_digits = 2,
ci_digits = digits,
p_digits = 3,
footer_digits = 3,
show_sigma = FALSE,
Expand Down Expand Up @@ -256,7 +256,7 @@ print.parameters_model <- function(x,
digits <- .additional_arguments(x, "digits", digits)
}
if (missing(ci_digits)) {
ci_digits <- .additional_arguments(x, "ci_digits", ci_digits)
ci_digits <- .additional_arguments(x, "ci_digits", digits)
}
if (missing(p_digits)) {
p_digits <- .additional_arguments(x, "p_digits", p_digits)
Expand Down Expand Up @@ -371,7 +371,7 @@ print.parameters_random <- function(x, digits = 2, ...) {
split_components = TRUE,
select = NULL,
digits = 2,
ci_digits = 2,
ci_digits = digits,
p_digits = 3,
zap_small = FALSE,
ci_width = "auto",
Expand Down
8 changes: 4 additions & 4 deletions R/print_html.R
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Expand Up @@ -11,7 +11,7 @@ print_html.parameters_model <- function(x,
footer = NULL,
align = NULL,
digits = 2,
ci_digits = 2,
ci_digits = digits,
p_digits = 3,
footer_digits = 3,
ci_brackets = c("(", ")"),
Expand All @@ -30,7 +30,7 @@ print_html.parameters_model <- function(x,
}

if (missing(ci_digits)) {
ci_digits <- .additional_arguments(x, "ci_digits", ci_digits)
ci_digits <- .additional_arguments(x, "ci_digits", digits)
}

if (missing(p_digits)) {
Expand Down Expand Up @@ -139,7 +139,7 @@ print_html.compare_parameters <- function(x,
subtitle = NULL,
footer = NULL,
digits = 2,
ci_digits = 2,
ci_digits = digits,
p_digits = 3,
zap_small = FALSE,
groups = NULL,
Expand All @@ -155,7 +155,7 @@ print_html.compare_parameters <- function(x,
}

if (missing(ci_digits)) {
ci_digits <- .additional_arguments(x, "ci_digits", ci_digits)
ci_digits <- .additional_arguments(x, "ci_digits", digits)
}

if (missing(p_digits)) {
Expand Down
12 changes: 6 additions & 6 deletions R/print_md.R
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Expand Up @@ -11,7 +11,7 @@ print_md.parameters_model <- function(x,
footer = NULL,
align = NULL,
digits = 2,
ci_digits = 2,
ci_digits = digits,
p_digits = 3,
footer_digits = 3,
ci_brackets = c("(", ")"),
Expand All @@ -26,7 +26,7 @@ print_md.parameters_model <- function(x,
digits <- .additional_arguments(x, "digits", digits)
}
if (missing(ci_digits)) {
ci_digits <- .additional_arguments(x, "ci_digits", ci_digits)
ci_digits <- .additional_arguments(x, "ci_digits", digits)
}
if (missing(p_digits)) {
p_digits <- .additional_arguments(x, "p_digits", p_digits)
Expand Down Expand Up @@ -124,7 +124,7 @@ print_md.parameters_simulate <- print_md.parameters_model
#' @export
print_md.compare_parameters <- function(x,
digits = 2,
ci_digits = 2,
ci_digits = digits,
p_digits = 3,
caption = NULL,
subtitle = NULL,
Expand All @@ -137,7 +137,7 @@ print_md.compare_parameters <- function(x,
digits <- .additional_arguments(x, "digits", digits)
}
if (missing(ci_digits)) {
ci_digits <- .additional_arguments(x, "ci_digits", ci_digits)
ci_digits <- .additional_arguments(x, "ci_digits", digits)
}
if (missing(p_digits)) {
p_digits <- .additional_arguments(x, "p_digits", p_digits)
Expand Down Expand Up @@ -178,7 +178,7 @@ print_md.compare_parameters <- function(x,
#' @export
print_md.parameters_sem <- function(x,
digits = 2,
ci_digits = 2,
ci_digits = digits,
p_digits = 3,
ci_brackets = c("(", ")"),
...) {
Expand All @@ -188,7 +188,7 @@ print_md.parameters_sem <- function(x,
digits <- .additional_arguments(x, "digits", digits)
}
if (missing(ci_digits)) {
ci_digits <- .additional_arguments(x, "ci_digits", ci_digits)
ci_digits <- .additional_arguments(x, "ci_digits", digits)
}
if (missing(p_digits)) {
p_digits <- .additional_arguments(x, "p_digits", p_digits)
Expand Down
4 changes: 2 additions & 2 deletions R/utils_format.R
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Expand Up @@ -273,7 +273,7 @@
.format_columns_single_component <- function(x,
pretty_names,
digits = 2,
ci_digits = 2,
ci_digits = digits,
p_digits = 3,
ci_width = "auto",
ci_brackets = TRUE,
Expand Down Expand Up @@ -758,7 +758,7 @@
pretty_names,
split_column = "Component",
digits = 2,
ci_digits = 2,
ci_digits = digits,
p_digits = 3,
coef_column = NULL,
format = NULL,
Expand Down
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