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Draft plotting simulated residuals (#329)
* Draft plotting simulated residuals * draft plot for check_residuals * fix * docs * include in check_model * version * lintr * fix * add transform argument * use latest performance * fix * fix * fix if qqplotr is missing
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,133 @@ | ||
| #' Plot method for check model for (non-)normality of residuals | ||
| #' | ||
| #' The `plot()` method for the `performance::check_residuals()` resp. | ||
| #' `performance::simulate_residuals()` function. | ||
| #' | ||
| #' @param transform Function to transform the residuals. If `NULL` (default), | ||
| #' no transformation is applied and uniformly distributed residuals are expected. | ||
| #' See argument `quantileFuntion` in `?DHARMa:::residuals.DHARMa` for more details. | ||
| #' | ||
| #' @inheritParams plot.see_check_normality | ||
| #' @inheritParams plot.see_check_model | ||
| #' | ||
| #' @return A ggplot2-object. | ||
| #' | ||
| #' @seealso See also the vignette about [`check_model()`](https://easystats.github.io/performance/articles/check_model.html). | ||
| #' | ||
| #' @examplesIf insight::check_if_installed("performance", "0.10.9.7") && require("glmmTMB") && require("qqplotr") && require("DHARMa") | ||
| #' data(Salamanders, package = "glmmTMB") | ||
| #' model <- glmmTMB::glmmTMB( | ||
| #' count ~ mined + spp + (1 | site), | ||
| #' family = poisson(), | ||
| #' data = Salamanders | ||
| #' ) | ||
| #' simulated_residuals <- performance::simulate_residuals(model) | ||
| #' plot(simulated_residuals) | ||
| #' | ||
| #' # or | ||
| #' simulated_residuals <- performance::simulate_residuals(model) | ||
| #' result <- performance::check_residuals(simulated_residuals) | ||
| #' plot(result) | ||
| #' | ||
| #' @export | ||
| plot.see_performance_simres <- function(x, | ||
| size_line = 0.8, | ||
| size_point = 1, | ||
| alpha = 0.2, | ||
| dot_alpha = 0.8, | ||
| colors = c("#3aaf85", "#1b6ca8"), | ||
| detrend = FALSE, | ||
| transform = NULL, | ||
| style = theme_lucid, | ||
| ...) { | ||
| dp <- list(min = 0, max = 1, lower.tail = TRUE, log.p = FALSE) | ||
|
|
||
| # need DHARMa to be installed | ||
| insight::check_if_installed("DHARMa") | ||
|
|
||
| # extract data, if from check_residuals | ||
| if (inherits(x, "see_check_residuals")) { | ||
| x <- attributes(x)$data | ||
| } | ||
|
|
||
| if (is.null(transform)) { | ||
| res <- stats::residuals(x) | ||
| } else { | ||
| res <- stats::residuals(x, quantileFunction = transform) | ||
| } | ||
|
|
||
| # base plot information | ||
| gg_init <- ggplot2::ggplot( | ||
| data.frame(scaled_residuals = res), | ||
| ggplot2::aes(sample = .data$scaled_residuals) | ||
| ) | ||
|
|
||
| # when we have package qqplotr, we can add confidence bands | ||
| if (requireNamespace("qqplotr", quietly = TRUE)) { | ||
| qq_stuff <- list( | ||
| qqplotr::stat_qq_band( | ||
| distribution = "unif", | ||
| dparams = list(min = 0, max = 1), | ||
| alpha = alpha, | ||
| detrend = detrend | ||
| ), | ||
| qqplotr::stat_qq_line( | ||
| distribution = "unif", | ||
| dparams = dp, | ||
| size = size_line, | ||
| colour = colors[1], | ||
| detrend = detrend | ||
| ), | ||
| qqplotr::stat_qq_point( | ||
| distribution = "unif", | ||
| dparams = dp, | ||
| size = size_point, | ||
| alpha = dot_alpha, | ||
| colour = colors[2], | ||
| detrend = detrend | ||
| ) | ||
| ) | ||
| if (detrend) { | ||
| y_lab <- "Sample Quantile Deviations" | ||
| } else { | ||
| y_lab <- "Sample Quantiles" | ||
| } | ||
| } else { | ||
| insight::format_alert("For confidence bands, please install `qqplotr`.") | ||
| qq_stuff <- list( | ||
| ggplot2::geom_qq( | ||
| shape = 16, | ||
| stroke = 0, | ||
| distribution = stats::qunif, | ||
| dparams = dp, | ||
| size = size_point, | ||
| colour = colors[2] | ||
| ), | ||
| ggplot2::geom_qq_line( | ||
| linewidth = size_line, | ||
| colour = colors[1], | ||
| na.rm = TRUE, | ||
| distribution = stats::qunif, | ||
| dparams = dp | ||
| ) | ||
| ) | ||
| y_lab <- "Sample Quantiles" | ||
| } | ||
|
|
||
| gg_init + | ||
| qq_stuff + | ||
| ggplot2::labs( | ||
| title = "Uniformity of Residuals", | ||
| subtitle = "Dots should fall along the line", | ||
| x = "Standard Uniform Distribution Quantiles", | ||
| y = y_lab | ||
| ) + | ||
| style( | ||
| base_size = 10, | ||
| plot.title.space = 3, | ||
| axis.title.space = 5 | ||
| ) | ||
| } | ||
|
|
||
| #' @export | ||
| plot.see_check_residuals <- plot.see_performance_simres |
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