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strengejacke committed Jan 2, 2025
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2 changes: 0 additions & 2 deletions R/1_model_parameters.R
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Expand Up @@ -763,8 +763,6 @@ model_parameters.default <- function(model,
}




#################### .glm ----------------------


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6 changes: 0 additions & 6 deletions R/4_standard_error.R
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Expand Up @@ -70,7 +70,6 @@ standard_error <- function(model, ...) {
}



# Default methods ---------------------------------------------------------

#' @rdname standard_error
Expand Down Expand Up @@ -160,8 +159,6 @@ standard_error.default <- function(model,
}




# helper -----------------------------------------------------------------


Expand Down Expand Up @@ -192,15 +189,12 @@ standard_error.default <- function(model,
}



.check_vcov_args <- function(robust, ...) {
dots <- list(...)
isTRUE(isTRUE(robust) || isTRUE(dots$robust) || ("vcov" %in% names(dots) && !is.null(dots[["vcov"]])))
}




# .ranef_se <- function(x) {
# insight::check_if_installed("lme4")
#
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5 changes: 0 additions & 5 deletions R/5_simulate_model.R
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Expand Up @@ -56,7 +56,6 @@ simulate_model <- function(model, iterations = 1000, ...) {
}



# Models with single component only -----------------------------------------

#' @rdname simulate_model
Expand Down Expand Up @@ -224,10 +223,6 @@ simulate_model.brmultinom <- simulate_model.default
simulate_model.bracl <- simulate_model.default






# helper -----------------------------------------


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4 changes: 0 additions & 4 deletions R/bootstrap_model.R
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Expand Up @@ -57,10 +57,6 @@ bootstrap_model <- function(model,
}






#' @rdname bootstrap_model
#' @export
bootstrap_model.default <- function(model,
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1 change: 0 additions & 1 deletion R/ci_kenward.R
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Expand Up @@ -20,7 +20,6 @@ ci_kenward <- function(model, ci = 0.95) {
}



.ci_kenward_dof <- function(model, ci = 0.95, df_kr) {

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file=R/ci_kenward.R,line=23,col=47,[function_argument_linter] Arguments without defaults should come before arguments with defaults.

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file=R/ci_kenward.R,line=23,col=47,[function_argument_linter] Arguments without defaults should come before arguments with defaults.
out <- lapply(ci, function(i) {
.ci_dof(
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3 changes: 0 additions & 3 deletions R/ci_profile_boot.R
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Expand Up @@ -32,7 +32,6 @@
}



# we need this function for models where confint and get_parameters return
# different length (e.g. as for "polr" models)
.ci_profiled2 <- function(model, ci) {
Expand Down Expand Up @@ -98,7 +97,6 @@
}



#' @keywords internal
.ci_uniroot_glmmTMB <- function(x, ci, component, ...) {
# make sure "..." doesn't pass invalid arguments to package TMB
Expand Down Expand Up @@ -157,7 +155,6 @@
}



#' @keywords internal
.ci_boot_merMod <- function(x, ci, iterations = 500, effects = "fixed", ...) {
insight::check_if_installed("lme4")
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3 changes: 0 additions & 3 deletions R/cluster_analysis.R
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Expand Up @@ -197,7 +197,6 @@ cluster_analysis <- function(x,
}



# Apply clustering --------------------------------------------------------


Expand Down Expand Up @@ -286,7 +285,6 @@ cluster_analysis <- function(x,
}



# Clustering Methods --------------------------------------------------------

#' @keywords internal
Expand Down Expand Up @@ -406,7 +404,6 @@ cluster_analysis <- function(x,
}



# Methods ----------------------------------------------------------------

#' @export
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1 change: 0 additions & 1 deletion R/cluster_discrimination.R
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Expand Up @@ -34,7 +34,6 @@ cluster_discrimination.cluster_analysis <- function(x, cluster_groups = NULL, ..
}



#' @export
cluster_discrimination.default <- function(x, cluster_groups = NULL, ...) {
if (is.null(cluster_groups)) {
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4 changes: 0 additions & 4 deletions R/cluster_meta.R
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Expand Up @@ -94,8 +94,6 @@ cluster_meta <- function(list_of_clusters, rownames = NULL, ...) {
}




#' @keywords internal
.cluster_meta_matrix <- function(data) {
# Internal function
Expand Down Expand Up @@ -128,8 +126,6 @@ cluster_meta <- function(list_of_clusters, rownames = NULL, ...) {
}




# Methods ----------------------------------------------------------------

#' @export
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5 changes: 0 additions & 5 deletions R/convert_efa_to_cfa.R
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Expand Up @@ -31,7 +31,6 @@ convert_efa_to_cfa <- function(model, ...) {
}



#' @rdname convert_efa_to_cfa
#' @inheritParams model_parameters.principal
#' @export
Expand All @@ -51,7 +50,6 @@ convert_efa_to_cfa.fa <- function(model,
convert_efa_to_cfa.fa.ci <- convert_efa_to_cfa.fa



#' @export
convert_efa_to_cfa.parameters_efa <- function(model,
threshold = NULL,
Expand All @@ -69,14 +67,11 @@ convert_efa_to_cfa.parameters_efa <- function(model,
convert_efa_to_cfa.parameters_pca <- convert_efa_to_cfa.parameters_efa



#' @rdname convert_efa_to_cfa
#' @export
efa_to_cfa <- convert_efa_to_cfa




#' @keywords internal
.efa_to_cfa <- function(loadings, names = NULL, max_per_dimension = NULL, ...) {
loadings <- attributes(loadings)$loadings_long
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14 changes: 0 additions & 14 deletions R/display.R
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Expand Up @@ -135,9 +135,6 @@ display.parameters_simulate <- display.parameters_model
display.parameters_brms_meta <- display.parameters_model





# Compare Parameters ------------------------


Expand Down Expand Up @@ -167,9 +164,6 @@ display.compare_parameters <- function(object,
}





# SEM models ------------------------


Expand All @@ -186,9 +180,6 @@ display.parameters_sem <- function(object,
}





# PCA /EFA models ------------------------


Expand All @@ -213,9 +204,6 @@ display.parameters_efa <- function(object, format = "markdown", digits = 2, sort
display.parameters_pca <- display.parameters_efa





# Equivalence tests ------------------------


Expand All @@ -226,8 +214,6 @@ display.equivalence_test_lm <- function(object, format = "markdown", digits = 2,
}




# Other functions ------------------------


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2 changes: 0 additions & 2 deletions R/dof_kenward.R
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Expand Up @@ -13,7 +13,6 @@ dof_kenward <- function(model) {
}



# The following code was taken from the "pbkrtest" package and slightly modified
#' @author Søren Højsgaard, \email{sorenh@@math.aau.dk}
.kenward_adjusted_ddf <- function(model, linear_coef, adjusted_vcov) {
Expand Down Expand Up @@ -90,7 +89,6 @@ dof_kenward <- function(model) {
}



.get_SigmaG <- function(model) {
insight::check_if_installed("lme4")
insight::check_if_installed("Matrix")
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4 changes: 0 additions & 4 deletions R/dof_ml1.R
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Expand Up @@ -38,8 +38,6 @@ dof_ml1 <- function(model) {
}




.get_df_ml1_approx <- function(x, g) {
if (!is.factor(g)) {
g <- as.factor(g)
Expand All @@ -62,8 +60,6 @@ dof_ml1 <- function(model) {
}




.find_term_assignment <- function(model_data, predictors, parameters) {
parms <- unlist(lapply(seq_along(predictors), function(i) {
p <- predictors[i]
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2 changes: 0 additions & 2 deletions R/dominance_analysis.R
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Expand Up @@ -596,8 +596,6 @@ dominance_analysis <- function(model, sets = NULL, all = NULL,
}




# methods ------------------------------


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18 changes: 0 additions & 18 deletions R/equivalence_test.R
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Expand Up @@ -3,7 +3,6 @@
bayestestR::equivalence_test



#' @title Equivalence test
#'
#' @description Compute the (conditional) equivalence test for frequentist models.
Expand Down Expand Up @@ -268,7 +267,6 @@ equivalence_test.lm <- function(x,
}



# standard models, only fixed effects ----------------------

#' @export
Expand Down Expand Up @@ -305,9 +303,6 @@ equivalence_test.zeroinfl <- equivalence_test.lm
equivalence_test.rma <- equivalence_test.lm





# mixed models, also random effects ----------------------

#' @export
Expand Down Expand Up @@ -363,7 +358,6 @@ equivalence_test.glmmTMB <- equivalence_test.merMod
equivalence_test.MixMod <- equivalence_test.merMod



# Special classes -------------------------

#' @export
Expand Down Expand Up @@ -490,7 +484,6 @@ equivalence_test.ggeffects <- function(x,
}



# helper -------------------


Expand Down Expand Up @@ -590,7 +583,6 @@ equivalence_test.ggeffects <- function(x,
}



#' @keywords internal
.equivalence_test_frequentist_random <- function(x,
range = "default",
Expand Down Expand Up @@ -667,8 +659,6 @@ equivalence_test.ggeffects <- function(x,
}




#' @keywords internal
.equivalence_test_numeric <- function(ci = 0.95,
ci_wide,
Expand Down Expand Up @@ -736,8 +726,6 @@ equivalence_test.ggeffects <- function(x,
}




# helper ---------------------

# this function simply takes the length of the range and calculates the proportion
Expand Down Expand Up @@ -849,14 +837,9 @@ equivalence_test.ggeffects <- function(x,
}






# methods ----------------



#' @export
format.equivalence_test_lm <- function(x,
digits = 2,
Expand Down Expand Up @@ -899,7 +882,6 @@ format.equivalence_test_lm <- function(x,
}



#' @export
print.equivalence_test_lm <- function(x,
digits = 2,
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