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glmmTMB shouldn't use qqhalfnormal #322

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Feb 5, 2024
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Merged

glmmTMB shouldn't use qqhalfnormal #322

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4 changes: 3 additions & 1 deletion R/plot.check_model.R
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Original file line number Diff line number Diff line change
Expand Up @@ -9,14 +9,14 @@
#'
#' @return A ggplot2-object.
#'
#' @seealso See also the vignette about [`check_model()`](https://easystats.github.io/performance/articles/check_model.html).

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file=R/plot.check_model.R,line=12,col=121,[line_length_linter] Lines should not be more than 120 characters. This line is 125 characters.

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file=R/plot.check_model.R,line=12,col=121,[line_length_linter] Lines should not be more than 120 characters. This line is 125 characters.
#'
#' @examplesIf require("performance") && require("patchwork")
#' model <- lm(qsec ~ drat + wt, data = mtcars)
#' plot(check_model(model))
#'
#' @export
plot.see_check_model <- function(x,

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file=R/plot.check_model.R,line=19,col=1,[cyclocomp_linter] Reduce the cyclomatic complexity of this function from 78 to at most 40.

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file=R/plot.check_model.R,line=19,col=1,[cyclocomp_linter] Reduce the cyclomatic complexity of this function from 78 to at most 40.
style = theme_lucid,
colors = NULL,
type = c("density", "discrete_dots", "discrete_interval", "discrete_both"),
Expand All @@ -39,8 +39,9 @@
model_info <- attr(x, "model_info")
overdisp_type <- attr(x, "overdisp_type")
plot_type <- attr(x, "type")
model_class <- attr(x, "model_class")

if (missing(type) && !is.null(plot_type) && plot_type %in% c("density", "discrete_dots", "discrete_interval", "discrete_both")) {

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file=R/plot.check_model.R,line=44,col=121,[line_length_linter] Lines should not be more than 120 characters. This line is 131 characters.

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file=R/plot.check_model.R,line=44,col=121,[line_length_linter] Lines should not be more than 120 characters. This line is 131 characters.
type <- plot_type
} else {
type <- match.arg(type)
Expand Down Expand Up @@ -174,7 +175,8 @@
colors = colors,
dot_alpha_level = dot_alpha_level,
show_dots = TRUE, # qq-plots w/o dots makes no sense
model_info = model_info
model_info = model_info,
model_class = model_class
)
}

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13 changes: 9 additions & 4 deletions R/plot.check_normality.R
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Expand Up @@ -24,7 +24,7 @@
#'
#' @return A ggplot2-object.
#'
#' @seealso See also the vignette about [`check_model()`](https://easystats.github.io/performance/articles/check_model.html).

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file=R/plot.check_normality.R,line=27,col=121,[line_length_linter] Lines should not be more than 120 characters. This line is 125 characters.

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file=R/plot.check_normality.R,line=27,col=121,[line_length_linter] Lines should not be more than 120 characters. This line is 125 characters.
#'
#' @examplesIf require("performance")
#' m <<- lm(mpg ~ wt + cyl + gear + disp, data = mtcars)
Expand Down Expand Up @@ -70,9 +70,12 @@
} else {
if (type == "qq") { # nolint
model_info <- attributes(x)$model_info
if (inherits(model, c("lme", "lmerMod", "merMod", "glmmTMB", "afex_aov", "BFBayesFactor"))) {
if (inherits(model, c("lme", "lmerMod", "merMod", "afex_aov", "BFBayesFactor"))) {
res_ <- suppressMessages(sort(stats::residuals(model), na.last = NA))
dat <- stats::na.omit(data.frame(y = res_))
} else if (inherits(model, "glmmTMB")) {
res_ <- abs(stats::residuals(model, type = "deviance"))
dat <- stats::na.omit(data.frame(y = res_))
} else if (inherits(model, "glm")) {
res_ <- abs(stats::rstandard(model, type = "deviance"))
fitted_ <- stats::qnorm((stats::ppoints(length(res_)) + 1) / 2)[order(order(res_))]
Expand All @@ -90,7 +93,8 @@
detrend = detrend,
dot_alpha_level = dot_alpha,
model_info = model_info,
method = method
method = method,
model_class = class(model)[1]
)
} else if (type == "density") {
r <- suppressMessages(stats::residuals(model))
Expand Down Expand Up @@ -166,10 +170,11 @@
colors = unname(social_colors(c("green", "blue", "red"))),
dot_alpha_level = 0.8,
show_dots = TRUE,
model_info = NULL) {
model_info = NULL,
model_class = NULL) {
qhalfnorm <- function(p) stats::qnorm((p + 1) / 2)
# qq-halfnorm for GLM
if (isTRUE(model_info$is_binomial) || isTRUE(model_info$is_count)) {
if (!identical(model_class, "glmmTMB") && (isTRUE(model_info$is_binomial) || isTRUE(model_info$is_count))) {
gg_init <- ggplot2::ggplot(x, ggplot2::aes(x = .data$x, y = .data$y))
qq_stuff <- list(
ggplot2::geom_point(
Expand Down Expand Up @@ -235,7 +240,7 @@
)
},
ggplot2::geom_qq(
mapping = if (detrend) ggplot2::aes(y = ggplot2::after_stat(.data$sample) - ggplot2::after_stat(.data$theoretical)),

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file=R/plot.check_normality.R,line=243,col=121,[line_length_linter] Lines should not be more than 120 characters. This line is 124 characters.

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file=R/plot.check_normality.R,line=243,col=121,[line_length_linter] Lines should not be more than 120 characters. This line is 124 characters.
shape = 16,
na.rm = TRUE,
stroke = 0,
Expand Down
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