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# usual models ---------------------------------
#' @inheritParams print.parameters_model
#' @rdname print.parameters_model
#' @export
format.parameters_model <- function(x,
pretty_names = TRUE,
split_components = TRUE,
select = NULL,
digits = 2,
ci_digits = digits,
p_digits = 3,
ci_width = NULL,
ci_brackets = NULL,
zap_small = FALSE,
format = NULL,
groups = NULL,
include_reference = FALSE,
...) {
# save attributes
coef_name <- attributes(x)$coefficient_name
coef_name2 <- attributes(x)$coefficient_name2
s_value <- attributes(x)$s_value
m_class <- attributes(x)$model_class
htest_type <- attributes(x)$htest_type
mixed_model <- attributes(x)$mixed_model
random_variances <- isTRUE(attributes(x)$ran_pars)
mean_group_values <- attributes(x)$mean_group_values
# process selection of columns
style <- NULL
if (!is.null(select) &&
# glue-like syntax, so we switch to "style" argument here
length(select) == 1 &&
is.character(select) &&
(grepl("{", select, fixed = TRUE) || select %in% .style_shortcuts)) {
style <- select
select <- NULL
}
# is information about grouped parameters stored as attribute?
if (is.null(groups) && !is.null(attributes(x)$coef_groups)) {
groups <- attributes(x)$coef_groups
}
# rename random effect parameters names for stan models
if (isTRUE(random_variances) && any(c("brmsfit", "stanreg", "stanmvreg") %in% m_class)) {
x <- .format_stan_parameters(x)
}
# for the current HTML backend we use (package "gt"), we cannot change
# the column header for subtables, so we need to remove the attributes
# for the "Coefficient" column here, which else allows us to use different
# column labels for subtables by model components
if (identical(format, "html")) {
coef_name <- NULL
coef_name2 <- NULL
attr(x, "coefficient_name") <- NULL
attr(x, "coefficient_name2") <- NULL
attr(x, "zi_coefficient_name") <- NULL
}
# remove method columns for htest and friends - this should be printed as footer
if (!is.null(m_class) &&
any(m_class %in% c(
"BFBayesFactor", "htest", "rma", "t1way", "yuen",
"PMCMR", "osrt", "trendPMCMR", "anova", "afex_aov"
))) {
x$Method <- NULL
x$Alternative <- NULL
}
# remove response for mvord
if (!is.null(m_class) && any(m_class == "mvord")) {
x$Response <- NULL
}
# remove component for nestedLogit
if (!is.null(m_class) && any(m_class == "nestedLogit")) {
x$Component <- NULL
if (insight::n_unique(x$Response) == 1) {
x$Response <- NULL
}
}
# remove type for comparisons()
if (!is.null(m_class) && any(m_class == "comparisons")) {
x$Type <- NULL
}
# rename columns for t-tests
if (!is.null(htest_type) &&
htest_type == "ttest" &&
!is.null(mean_group_values) &&
all(c("Mean_Group1", "Mean_Group2") %in% colnames(x))) {
colnames(x)[which(colnames(x) == "Mean_Group1")] <- paste0(x$Group, " = ", mean_group_values[1])
colnames(x)[which(colnames(x) == "Mean_Group2")] <- paste0(x$Group, " = ", mean_group_values[2])
}
# Special print for mcp from WRS2
if (!is.null(m_class) && any(m_class %in% c("mcp1", "mcp2"))) {
x$Group1 <- paste(x$Group1, x$Group2, sep = " vs. ")
x$Group2 <- NULL
colnames(x)[1] <- "Group"
}
# check if we have mixed models with random variance parameters
# in such cases, we don't need the group-column, but we rather
# merge it with the parameter column
if (isTRUE(random_variances)) {
x <- .format_ranef_parameters(x)
}
# group parameters - this function find those parameters that should be
# grouped, reorders parameters into groups and indents lines that belong
# to one group, adding a header for each group
if (!is.null(groups)) {
x <- .parameter_groups(x, groups)
}
indent_groups <- attributes(x)$indent_groups
indent_rows <- attributes(x)$indent_rows
# prepare output, to have in shape for printing. this function removes
# empty columns, or selects only those columns that should be printed
x <- .prepare_x_for_print(x, select, coef_name, s_value)
# check whether to split table by certain factors/columns (like component, response...)
split_by <- .prepare_splitby_for_print(x)
# add p-stars, if we need this for style-argument
if (!is.null(style) && grepl("{stars}", style, fixed = TRUE)) {
x$p_stars <- insight::format_p(x[["p"]], stars = TRUE, stars_only = TRUE)
}
# format everything now...
if (split_components && !is.null(split_by) && length(split_by)) {
# this function mainly sets the appropriate column names for each
# "sub table" (i.e. we print a table for each model component, like count,
# zero-inflation, smooth, random, ...) and formats some parameter labels.
# moreover, insight::format_table() is called to do the final formatting
# and .format_model_component_header() is called to set captions for each
# "sub table".
formatted_table <- .format_columns_multiple_components(
x,
pretty_names,
split_column = split_by,
digits = digits,
ci_digits = ci_digits,
p_digits = p_digits,
coef_column = coef_name,
format = format,
ci_width = ci_width,
ci_brackets = ci_brackets,
zap_small = zap_small,
include_reference = include_reference,
...
)
} else {
# for tables that don't have multiple components, formatting is rather
# easy, since we don't need to split the data frame into "sub tables"
formatted_table <- .format_columns_single_component(
x,
pretty_names = pretty_names,
digits = digits,
ci_width = ci_width,
ci_brackets = ci_brackets,
ci_digits = ci_digits,
p_digits = p_digits,
format = format,
coef_name = coef_name,
zap_small = zap_small,
include_reference = include_reference,
...
)
}
# remove unique columns
if (insight::n_unique(formatted_table$Component) == 1) formatted_table$Component <- NULL
if (insight::n_unique(formatted_table$Effects) == 1) formatted_table$Effects <- NULL
if (insight::n_unique(formatted_table$Group) == 1 && isTRUE(mixed_model)) formatted_table$Group <- NULL
# no column with CI-level in output
if (!is.null(formatted_table$CI) && insight::n_unique(formatted_table$CI) == 1) {
formatted_table$CI <- NULL
}
# we also allow style-argument for model parameters. In this case, we need
# some small preparation, namely, we need the p_stars column, and we need
# to "split" the formatted table, because the glue-function needs the columns
# without the parameters-column.
if (!is.null(style)) {
if (is.data.frame(formatted_table)) {
formatted_table <- .style_formatted_table(
formatted_table,
style = style,
format = format
)
} else {
formatted_table[] <- lapply(
formatted_table,
.style_formatted_table,
style = style,
format = format
)
}
}
if (!is.null(indent_rows)) {
attr(formatted_table, "indent_rows") <- indent_rows
attr(formatted_table, "indent_groups") <- NULL
} else if (!is.null(indent_groups)) {
attr(formatted_table, "indent_groups") <- indent_groups
}
# vertical layout possible, if these have just one row
if (identical(list(...)$layout, "vertical")) {
if ("Parameter" %in% colnames(formatted_table)) {
new_colnames <- c("", formatted_table$Parameter)
formatted_table$Parameter <- NULL
} else {
new_colnames <- c("Type", paste0("Value ", seq_len(nrow(formatted_table))))
}
formatted_table <- datawizard::rownames_as_column(as.data.frame(t(formatted_table)), "Type")
colnames(formatted_table) <- new_colnames
}
formatted_table
}
#' @export
format.parameters_simulate <- format.parameters_model
#' @export
format.parameters_brms_meta <- format.parameters_model
#' @export
format.parameters_coef <- function(x, format = NULL, ...) {
insight::format_table(x, format = format, ...)
}
# Compare parameters ----------------------
#' @rdname print.compare_parameters
#' @inheritParams print.parameters_model
#' @export
format.compare_parameters <- function(x,
split_components = TRUE,
select = NULL,
digits = 2,
ci_digits = digits,
p_digits = 3,
ci_width = NULL,
ci_brackets = NULL,
zap_small = FALSE,
format = NULL,
groups = NULL,
engine = NULL,
...) {
m_class <- attributes(x)$model_class
x$Method <- NULL
# remove response for mvord
if (!is.null(m_class) && any(m_class == "mvord")) {
x$Response <- NULL
}
out <- data.frame(
Parameter = x$Parameter,
Effects = x$Effects,
Component = x$Component,
stringsAsFactors = FALSE
)
# remove zi-suffix if we split components anyway
if (isTRUE(split_components)) {
out$Parameter <- insight::trim_ws(gsub(" (zi)", "", out$Parameter, fixed = TRUE))
out$Effects <- NULL
}
# save model names
models <- attributes(x)$model_names
# save model parameters attributes
parameters_attributes <- attributes(x)$all_attributes
# is information about grouped parameters stored as attribute?
if (is.null(groups) && !is.null(parameters_attributes[[1]]$coef_groups)) {
groups <- parameters_attributes[[1]]$coef_groups
}
# locate random effects rows
ran_pars <- which(x$Effects == "random")
# find all random effect groups
if (is.null(x$Group)) {
ran_groups <- NULL
ran_group_rows <- NULL
} else {
ran_groups <- unique(insight::compact_character(x$Group))
ran_group_rows <- which(nzchar(x$Group, keepNA = TRUE))
}
for (i in models) {
# each column is suffixed with ".model_name", so we extract
# columns for each model separately here
pattern <- paste0("\\.\\Q", i, "\\E$")
cols <- x[grepl(pattern, colnames(x))]
# since we now have the columns for a single model, we clean the
# column names (i.e. remove suffix), so we can use "format_table" function
colnames(cols) <- gsub(pattern, "", colnames(cols))
# find coefficient column, check which rows have non-NA values
# since we merged all models together, and we only have model-specific
# columns for estimates, CI etc. but not for Effects and Component, we
# extract "valid" rows via non-NA values in the coefficient column
coef_column <- which(colnames(cols) %in% c(.all_coefficient_types, "Coefficient"))
valid_rows <- which(!is.na(cols[[coef_column]]))
# check if we have mixed models with random variance parameters
# in such cases, we don't need the group-column, but we rather
# merge it with the parameter column
ran_pars_rows <- NULL
if (length(ran_pars) && length(ran_group_rows) && any(ran_group_rows %in% valid_rows)) {
# ran_pars has row indices for *all* models in this function -
# make sure we have only valid rows for this particular model
ran_pars_rows <- intersect(valid_rows, intersect(ran_pars, ran_group_rows))
}
if (!is.null(ran_pars_rows) && length(ran_pars_rows)) {
# find SD random parameters
stddevs <- startsWith(out$Parameter[ran_pars_rows], "SD (")
# check if we already fixed that name in a previous loop
fixed_name <- unlist(lapply(
ran_groups,
grep,
x = out$Parameter[ran_pars_rows[stddevs]],
fixed = TRUE
))
if (length(fixed_name)) {
stddevs[fixed_name] <- FALSE
}
# collapse parameter name with RE grouping factor
if (length(stddevs)) {
out$Parameter[ran_pars_rows[stddevs]] <- paste0(
gsub("(.*)\\)", "\\1", out$Parameter[ran_pars_rows[stddevs]]),
": ",
x$Group[ran_pars_rows[stddevs]],
")"
)
}
# same for correlations
corrs <- startsWith(out$Parameter[ran_pars_rows], "Cor (")
# check if we already fixed that name in a previous loop
fixed_name <- unlist(lapply(
ran_groups,
grep,
x = out$Parameter[ran_pars_rows[corrs]],
fixed = TRUE
))
if (length(fixed_name)) {
corrs[fixed_name] <- FALSE
}
# collapse parameter name with RE grouping factor
if (length(corrs)) {
out$Parameter[ran_pars_rows[corrs]] <- paste0(
gsub("(.*)\\)", "\\1", out$Parameter[ran_pars_rows[corrs]]),
": ",
x$Group[ran_pars_rows[corrs]],
")"
)
}
out$Parameter[out$Parameter == "SD (Observations: Residual)"] <- "SD (Residual)"
}
# save p-stars in extra column
cols$p_stars <- insight::format_p(cols$p, stars = TRUE, stars_only = TRUE)
cols <- insight::format_table(
cols,
digits = digits,
ci_width = ci_width,
ci_brackets = ci_brackets,
ci_digits = ci_digits,
p_digits = p_digits,
zap_small = zap_small,
...
)
out <- cbind(out, .format_output_style(cols, style = select, format, i))
}
# remove group column
out$Group <- NULL
x$Group <- NULL
# sort by effects and component
if (isFALSE(split_components)) {
out <- datawizard::data_arrange(out, c("Effects", "Component"))
}
# group parameters - this function find those parameters that should be
# grouped, reorders parameters into groups and indents lines that belong
# to one group, adding a header for each group
if (!is.null(groups) && !identical(engine, "tt")) {
out <- .parameter_groups(out, groups)
}
indent_groups <- attributes(x)$indent_groups
indent_rows <- attributes(x)$indent_rows
# check whether to split table by certain factors/columns (like component, response...)
split_by <- split_column <- .prepare_splitby_for_print(x)
if (length(split_by) > 0L && isTRUE(split_components)) {
# set up split-factor
if (length(split_column) > 1L) {
split_by <- lapply(split_column, function(i) x[[i]])
} else {
split_by <- list(x[[split_column]])
}
names(split_by) <- split_column
# make sure we have correct sorting here...
formatted_table <- split(out, f = split_by)
formatted_table <- lapply(names(formatted_table), function(tab) {
i <- formatted_table[[tab]]
# check if data frame is empty - this may happen if not all combinations
# of split_by factors are present in the data (e.g., zero-inflated mixed
# models, that have random effects for the count, but not for the zero-
# inflation component)
if (nrow(i) == 0L) {
return(NULL)
}
# remove unique columns
if (insight::n_unique(i$Component) == 1L) i$Component <- NULL
if (insight::n_unique(i$Effects) == 1L) i$Effects <- NULL
# format table captions for sub tables
table_caption <- .format_model_component_header(
x,
type = tab, split_column = tab, is_zero_inflated = FALSE,
is_ordinal_model = FALSE, is_multivariate = FALSE, ran_pars = FALSE,
formatted_table = i
)
# add as attribute, so table captions are printed
if (identical(format, "html")) {
i$Component <- table_caption$name
} else if (identical(format, "md") || identical(format, "markdown")) {
attr(i, "table_caption") <- table_caption$name
} else {
attr(i, "table_caption") <- c(paste("#", table_caption$name), "blue")
}
i
})
# remove empty tables
formatted_table <- insight::compact_list(formatted_table)
# for HTML, bind data frames
if (identical(format, "html")) {
# fix non-equal length of columns and bind data frames
formatted_table <- do.call(rbind, .fix_nonmatching_columns(formatted_table))
}
} else {
formatted_table <- out
# remove unique columns
if (insight::n_unique(formatted_table$Component) == 1L) formatted_table$Component <- NULL
if (insight::n_unique(formatted_table$Effects) == 1L) formatted_table$Effects <- NULL
# add line with info about observations
formatted_table <- .add_obs_row(formatted_table, parameters_attributes, style = select)
}
formatted_table
}
# sem-models ---------------------------------
#' @export
format.parameters_sem <- function(x,
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", digits)
}
if (missing(p_digits)) {
p_digits <- .additional_arguments(x, "p_digits", 3)
}
.format_columns_multiple_components(
x,
pretty_names = TRUE,
split_column = "Component",
digits = digits,
ci_digits = ci_digits,
p_digits = p_digits,
format = format,
ci_width = ci_width,
ci_brackets = ci_brackets,
...
)
}
# helper ---------------------
.style_formatted_table <- function(formtab, style, format) {
additional_columns <- intersect(c("Effects", "Group", "Component"), colnames(formtab))
if (length(additional_columns)) {
additional_columns <- formtab[additional_columns]
}
# define column names in case the glue-pattern has multiple columns.
if (grepl("|", style, fixed = TRUE)) {
cn <- NULL
} else {
cn <- .style_pattern_to_name(style)
}
formtab <- cbind(
formtab[1],
.format_output_style(
formtab[2:ncol(formtab)],
style = style,
format = format,
modelname = cn
)
)
if (!insight::is_empty_object(additional_columns)) {
formtab <- cbind(formtab, additional_columns)
}
formtab
}
# footer functions ------------------
.format_footer <- function(x,
digits = 3,
verbose = TRUE,
show_sigma = FALSE,
show_formula = FALSE,
show_r2 = FALSE,
show_rmse = FALSE,
format = "text") {
# prepare footer
footer <- NULL
type <- tolower(format)
sigma_value <- attributes(x)$sigma
r2 <- attributes(x)$r2
rmse <- attributes(x)$rmse
residual_df <- attributes(x)$residual_df
p_adjust <- attributes(x)$p_adjust
model_formula <- attributes(x)$model_formula
anova_test <- attributes(x)$anova_test
anova_type <- attributes(x)$anova_type
prediction_type <- attributes(x)$prediction_type
footer_text <- attributes(x)$footer_text
text_alternative <- attributes(x)$text_alternative
n_obs <- attributes(x)$n_obs
is_ggeffects <- isTRUE(attributes(x)$is_ggeffects)
# footer: model formula
if (isTRUE(show_formula)) {
footer <- .add_footer_formula(footer, model_formula, n_obs, type)
}
# footer: residual standard deviation
if (isTRUE(show_sigma)) {
footer <- .add_footer_sigma(footer, digits, sigma_value, residual_df, type)
}
# footer: r-squared
if (isTRUE(show_rmse)) {
footer <- .add_footer_values(footer, digits, value = rmse, text = "RMSE ", type)
}
# footer: r-squared
if (isTRUE(show_r2)) {
footer <- .add_footer_r2(footer, digits, r2, type)
}
# footer: p-adjustment
if ("p" %in% colnames(x) && isTRUE(verbose) && !is.null(p_adjust) && p_adjust != "none") {
footer <- .add_footer_text(footer, text = paste("p-value adjustment method:", format_p_adjust(p_adjust)))
}
# footer: anova test
if (!is.null(anova_test)) {
footer <- .add_footer_text(footer, text = sprintf("%s test statistic", anova_test))
}
# footer: anova type
if (!is.null(anova_type)) {
footer <- .add_footer_text(footer, text = sprintf("Anova Table (Type %s tests)", anova_type))
}
# footer: marginaleffects::comparisons()
if (!is.null(prediction_type)) {
footer <- .add_footer_text(footer, text = sprintf("Prediction type: %s", prediction_type))
}
# footer: htest alternative
if (!is.null(text_alternative)) {
footer <- .add_footer_text(footer, text = text_alternative)
}
# footer: generic text
if (!is.null(footer_text)) {
footer <- .add_footer_text(footer, footer_text, type, is_ggeffects)
}
# if we have two trailing newlines, remove one
if (identical(type, "text") && !is.null(footer) && endsWith(footer[1], "\n\n")) {
footer[1] <- substr(footer[1], 0, nchar(x) - 1)
}
# finally, for ggeffects and HTML, remove *
if (is_ggeffects && type == "html") {
footer <- gsub("*", "", footer, fixed = TRUE)
footer <- gsub(":;", ":", footer, fixed = TRUE)
}
footer
}
# footer: generic text
.add_footer_text <- function(footer = NULL, text = NULL, type = "text", is_ggeffects = FALSE) {
if (!is.null(text) && length(text)) {
if (type == "text" || type == "markdown") {
if (is.null(footer)) {
fill <- "\n"
} else {
fill <- ""
}
footer <- paste0(footer, sprintf("%s%s\n", fill, text))
} else if (type == "html") {
replacement <- ifelse(is_ggeffects, ";", "")
footer <- c(footer, gsub("\n", replacement, text, fixed = TRUE))
}
}
footer
}
# footer: generic values
.add_footer_values <- function(footer = NULL,
digits = 3,
value = NULL,
text = NULL,
type = "text") {
if (!is.null(value) && !is.null(text)) {
string <- sprintf("%s: %s", text, insight::format_value(value, digits = digits))
if (type == "text" || type == "markdown") {
if (is.null(footer)) {
fill <- "\n"
} else {
fill <- ""
}
footer <- paste0(footer, fill, string, "\n")
} else if (type == "html") {
footer <- c(footer, string)
}
}
footer
}
# footer: residual standard deviation
.add_footer_sigma <- function(footer = NULL, digits = 3, sigma = NULL, residual_df = NULL, type = "text") {
if (!is.null(sigma)) {
# format residual df
if (is.null(residual_df)) {
res_df <- ""
} else {
res_df <- paste0(" (df = ", residual_df, ")")
}
if (type == "text" || type == "markdown") {
if (is.null(footer)) {
fill <- "\n"
} else {
fill <- ""
}
footer <- paste0(footer, sprintf("%sSigma: %.*f%s\n", fill, digits, sigma, res_df))
} else if (type == "html") {
footer <- c(footer, insight::trim_ws(sprintf("Sigma: %.*f%s", digits, sigma, res_df)))
}
}
footer
}
# footer: r-squared
.add_footer_r2 <- function(footer = NULL, digits = 3, r2 = NULL, type = "text") {
if (!is.null(r2)) {
rsq <- .safe(paste(unlist(lapply(r2, function(i) {
paste0(attributes(i)$names, ": ", insight::format_value(i, digits = digits))
})), collapse = "; "))
if (!is.null(rsq)) {
if (type == "text" || type == "markdown") {
if (is.null(footer)) {
fill <- "\n"
} else {
fill <- ""
}
footer <- paste0(footer, fill, rsq, "\n")
} else if (type == "html") {
footer <- c(footer, rsq)
}
}
}
footer
}
# footer: model formula
.add_footer_formula <- function(footer = NULL, model_formula = NULL, n_obs = NULL, type = "text") {
if (!is.null(model_formula)) {
# format n of observations
if (is.null(n_obs)) {
n <- ""
} else {
n <- paste0(" (", n_obs, " Observations)")
}
if (type == "text" || type == "markdown") {
if (is.null(footer)) {
fill <- "\n"
} else {
fill <- ""
}
footer <- paste0(footer, fill, "Model: ", model_formula, n, "\n")
} else if (type == "html") {
footer <- c(footer, insight::trim_ws(paste0("Model: ", model_formula, n)))
}
}
footer
}
# footer: type of uncertainty interval
.print_footer_cimethod <- function(x) {
if (isTRUE(getOption("parameters_cimethod", TRUE))) {
# get attributes
ci_method <- .additional_arguments(x, "ci_method", NULL)
test_statistic <- .additional_arguments(x, "test_statistic", NULL)
bootstrap <- .additional_arguments(x, "bootstrap", FALSE)
is_bayesian <- .additional_arguments(x, "is_bayesian", FALSE)
simulated <- .additional_arguments(x, "simulated", FALSE)
residual_df <- .additional_arguments(x, "residual_df", NULL)
random_variances <- .additional_arguments(x, "ran_pars", FALSE)
model_class <- .additional_arguments(x, "model_class", NULL)
# prepare strings
if (!is.null(ci_method)) {
# only random effects? no message for fixed effects ci-approximation
if (!is.null(x$Effects) && all(x$Effects == "random")) {
msg <- "\n"
string_method <- ""
# here we have fixed effects only, or fixed and random effects
} else {
# since `.format_ci_method_name()` changes the CI method names to have a
# mix of cases, standardize them by converting to lower case
ci_method <- tolower(ci_method)
# in case of glm's that have df.residual(), and where residual df where requested
is_test_statistic_t <- ci_method == "residual" &&
test_statistic == "z-statistic" &&
!is.null(residual_df) &&
!is.infinite(residual_df) && !is.na(residual_df)
if (is_test_statistic_t) {
test_statistic <- "t-statistic"
}
string_tailed <- switch(ci_method,
hdi = "highest-density",
uniroot = ,
profile = "profile-likelihood",
"equal-tailed"
)
# sampling method
if (isTRUE(bootstrap)) {
sampling_method <- ifelse(isTRUE(.unicode_symbols()), "na\u0131ve bootstrap", "naive bootstrap")
} else if (isTRUE(simulated)) {
sampling_method <- "simulated multivariate normal"
} else {
sampling_method <- "MCMC"
}
string_method <- switch(ci_method,
bci = ,
bcai = "bias-corrected accelerated bootstrap",
si = ,
ci = ,
quantile = ,
eti = ,
hdi = sampling_method,
normal = "Wald normal",
boot = "parametric bootstrap",
"Wald"
)
if (toupper(ci_method) %in% c("KENWARD", "KR", "KENWARD-ROGER", "KENWARD-ROGERS", "SATTERTHWAITE")) {
string_approx <- paste0("with ", format_df_adjust(ci_method, approx_string = "", dof_string = ""), " ")
} else {
string_approx <- ""
}
if (!is.null(test_statistic) && ci_method != "normal" && !isTRUE(bootstrap)) {
string_statistic <- switch(tolower(test_statistic),
`t-statistic` = "t",
`chi-squared statistic` = ,
`z-statistic` = "z",
""
)
string_method <- paste0(string_method, " ", string_statistic, "-")
} else {
string_method <- paste0(string_method, " ")
}
# bootstrapped intervals
if (isTRUE(bootstrap)) {
msg <- paste0("\nUncertainty intervals (", string_tailed, ") are ", string_method, "intervals.")
} else if (isTRUE(is_bayesian)) {
msg <- paste0("\nUncertainty intervals (", string_tailed, ") computed using a ", string_method, "distribution ", string_approx, "approximation.") # nolint
} else {
msg <- paste0("\nUncertainty intervals (", string_tailed, ") and p-values (two-tailed) computed using a ", string_method, "distribution ", string_approx, "approximation.") # nolint
}
}
# do we have random effect variances from lme4/glmmTMB?
# must be glmmTMB
show_re_msg <- (identical(model_class, "glmmTMB") &&
# and not Wald-/normalCIs
(!string_method %in% c("Wald z-", "Wald normal") || !ci_method %in% c("wald", "normal"))) ||
# OR must be merMod
((identical(model_class, "lmerMod") || identical(model_class, "glmerMod")) &&
# and not Wald CIs
!ci_method %in% c("wald", "normal", "profile", "boot"))
if (show_re_msg && isTRUE(random_variances) && !is.null(x$Effects) && "random" %in% x$Effects) {
msg <- paste(msg, "Uncertainty intervals for random effect variances computed using a Wald z-distribution approximation.") # nolint
}
insight::format_alert(insight::color_text(msg, "yellow"))
}
}
}
.print_footer_exp <- function(x) {
# we need this to check whether we have extremely large cofficients
if (isTRUE(getOption("parameters_exponentiate", TRUE))) {
msg <- NULL
# try to find out the name of the coefficient column
coef_column <- intersect(colnames(x), .all_coefficient_names)
if (length(coef_column) && "Parameter" %in% colnames(x)) {
spurious_coefficients <- abs(x[[coef_column[1]]][!.in_intercepts(x$Parameter)])
} else {
spurious_coefficients <- NULL
}
exponentiate <- .additional_arguments(x, "exponentiate", FALSE)
if (!.is_valid_exponentiate_argument(exponentiate)) {
if (isTRUE(.additional_arguments(x, "log_link", FALSE))) {
msg <- "The model has a log- or logit-link. Consider using `exponentiate = TRUE` to interpret coefficients as ratios." # nolint
# we only check for exp(coef), so exp() here since coefficients are on logit-scale
if (!is.null(spurious_coefficients)) {
spurious_coefficients <- exp(spurious_coefficients)
}
} else if (isTRUE(.additional_arguments(x, "log_response", FALSE))) {
msg <- "The model has a log-transformed response variable. Consider using `exponentiate = TRUE` to interpret coefficients as ratios." # nolint
# don't show warning about complete separation
spurious_coefficients <- NULL
}
} else if (.is_valid_exponentiate_argument(exponentiate) && isTRUE(.additional_arguments(x, "log_response", FALSE))) { # nolint
# don't show warning about complete separation
spurious_coefficients <- NULL
}
# following check only for models with logit-link
logit_model <- isTRUE(.additional_arguments(x, "logit_link", FALSE)) ||
isTRUE(attributes(x)$coefficient_name %in% c("Log-Odds", "Odds Ratio"))
# remove NA and infinite values from spurios coefficients
if (!is.null(spurious_coefficients)) {
spurious_coefficients <- spurious_coefficients[!is.na(spurious_coefficients) & !is.infinite(spurious_coefficients)] # nolint
}
# check for complete separation coefficients or possible issues with
# too few data points
if (!is.null(spurious_coefficients) && length(spurious_coefficients) && logit_model) {
if (any(spurious_coefficients > 50)) {
msg <- c(msg, "Some coefficients are very large, which may indicate issues with complete separation.") # nolint
} else if (any(spurious_coefficients > 15)) {
msg <- c(msg, "Some coefficients seem to be rather large, which may indicate issues with (quasi) complete separation. Consider using bias-corrected or penalized regression models.") # nolint
}
}
if (!is.null(msg) && isTRUE(getOption("parameters_warning_exponentiate", TRUE))) {
insight::format_alert(paste0("\n", msg))
# set flag, so message only displayed once per session
options(parameters_warning_exponentiate = FALSE)
}
}
}
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