collect in single file

Author: teunbrand

DESCRIPTION

@@ -127,9 +127,8 @@ Collate:
     'facet-grid-.R'
     'facet-null.R'
     'facet-wrap.R'
-    'fortify-lm.R'
     'fortify-map.R'
-    'fortify-multcomp.R'
+    'fortify-models.R'
     'fortify-spatial.R'
     'fortify.R'
     'stat-.R'

R/fortify-lm.R

@@ -1,3 +1,58 @@
+#' Supplement the data fitted to a linear model with model fit statistics.
+#'
+#' @description
+#' `r lifecycle::badge("deprecated")`
+#'
+#' This method is deprecated because using `broom::augment()` is a better
+#' solution to supplement data from a linear model.
+#' If you have missing values in your model data, you may need to refit
+#' the model with `na.action = na.exclude`.
+#'
+#' @return The original data with extra columns:
+#'   \item{.hat}{Diagonal of the hat matrix}
+#'   \item{.sigma}{Estimate of residual standard deviation when
+#'     corresponding observation is dropped from model}
+#'   \item{.cooksd}{Cooks distance, [cooks.distance()]}
+#'   \item{.fitted}{Fitted values of model}
+#'   \item{.resid}{Residuals}
+#'   \item{.stdresid}{Standardised residuals}
+#' @param model linear model
+#' @param data data set, defaults to data used to fit model
+#' @param ... not used by this method
+#' @keywords internal
+#' @export
+#' @examplesIf require("broom")
+#' mod <- lm(mpg ~ wt, data = mtcars)
+#'
+#' # Show augmented model
+#' head(augment(mod))
+#' head(fortify(mod))
+#'
+#' # Using augment to convert model to ready-to-plot data
+#' ggplot(augment(mod), aes(.fitted, .resid)) +
+#'   geom_point() +
+#'   geom_hline(yintercept = 0) +
+#'   geom_smooth(se = FALSE)
+#'
+#' # Colouring by original data not included in the model
+#' ggplot(augment(mod, mtcars), aes(.fitted, .std.resid, colour = factor(cyl))) +
+#'   geom_point()
+fortify.lm <- function(model, data = model$model, ...) {
+  lifecycle::deprecate_warn(
+    "3.6.0", I("`fortify(<lm>)`"), I("`broom::augment(<lm>)`")
+  )
+  infl <- stats::influence(model, do.coef = FALSE)
+  data$.hat <- infl$hat
+  data$.sigma <- infl$sigma
+  data$.cooksd <- stats::cooks.distance(model, infl)
+
+  data$.fitted <- stats::predict(model)
+  data$.resid <- stats::resid(model)
+  data$.stdresid <- stats::rstandard(model, infl)
+
+  data
+}
+
 #' Fortify methods for objects produced by \pkg{multcomp}
 #'
 #' @description