reverse deprecations for tidiers with R-oldrel dependency issues (#1204)

* revert deprecation of lsmeans and emmeans
* revert emmeans and lsmeans deprecation messages
* don't install packages needing unavailable Matrix (these packages require R 4.3.0+ (maybe 4.4.0 for car and quantreg). car and quantreg use MatrixModels which uses an unavailable Matrix on oldrel-2 and previous.)
* address additional dependency conflicts
* skip Matrix ABI-dependent tests on R < 4.4.0

.github/workflows/R-CMD-check.yaml

@@ -49,7 +49,18 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck
+          extra-packages: 
+            any::rcmdcheck,
+            AER=?ignore-before-r=4.3.0,
+            car=?ignore-before-r=4.3.0,
+            cobs=?ignore-before-r=4.3.0,
+            drc=?ignore-before-r=4.3.0,
+            emmeans=?ignore-before-r=4.3.0,
+            joineRML=?ignore-before-r=4.3.0,
+            lme4=?ignore-before-r=4.3.0,
+            lsmeans=?ignore-before-r=4.3.0,
+            quantreg=?ignore-before-r=4.3.0,
+            systemfit=?ignore-before-r=4.3.0
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2

DESCRIPTION

@@ -570,6 +570,7 @@ Suggests:
     covr,
     drc,
     e1071,
+    emmeans,
     epiR,
     ergm (>= 3.10.4),
     fixest (>= 0.9.0),
@@ -595,6 +596,7 @@ Suggests:
     lme4,
     lmodel2,
     lmtest (>= 0.9.38),
+    lsmeans,
     maps,
     MASS,
     mclust,

NEWS.md

@@ -1,8 +1,6 @@
 # broom (development version)
 
-* Soft-deprecated tidiers for margins, lsmeans, and emmeans. Each package has been removed from Suggests and is no longer tested---their tidiers will raise a deprecation warning but return the same results as before.
-     - margins was archived from CRAN. In the case that the package is back on CRAN before the next package release, broom will once again Suggest and test support for the package (#1200).
-     - lsmeans and emmeans have a dependency requiring R 4.3.0 or higher. To maintain compatibility with at least 4 previous minor versions of R, broom won't test support for these packages until the release of R 4.7.x (or until lsmeans and emmeans are compatible with the R version 4 minor releases previous, #1193).
+* Soft-deprecated tidiers for margins objects, as the package was archived from CRAN in April 2024. In the case that the package is back on CRAN before the next package release, broom will once again Suggest and test support for the package (#1200).
 
 * While this broom release contains no changes to the `tidy.survfit()` method for objects from the survival package, the package has bumped the minimum required version for survival. Before survival 3.6-4, `tidy.survfit()` propagated "inconsistent" `n.censor` values from survival for multi-state models (#1195). 
 

R/emmeans-tidiers.R

@@ -3,8 +3,8 @@
 #'
 #' @param x An `lsmobj` object.
 #' @template param_confint
-#' @param ... Additional arguments passed to `emmeans::summary.emmGrid()` or
-#'   `lsmeans::summary.ref.grid()`. **Cautionary note**: misspecified arguments
+#' @param ... Additional arguments passed to [emmeans::summary.emmGrid()] or
+#'   [lsmeans::summary.ref.grid()]. **Cautionary note**: misspecified arguments
 #'   may be silently ignored!
 #'
 #' @evalRd return_tidy(
@@ -24,72 +24,62 @@
 #'   contrast, each row will contain one estimated contrast.
 #'
 #'   There are a large number of arguments that can be
-#'   passed on to `emmeans::summary.emmGrid()` or `lsmeans::summary.ref.grid()`.
+#'   passed on to [emmeans::summary.emmGrid()] or [lsmeans::summary.ref.grid()].
+#'
+#' @examplesIf rlang::is_installed(c("emmeans", "ggplot2"))
+#'
+#' # load libraries for models and data
+#' library(emmeans)
+#'
+#' # linear model for sales of oranges per day
+#' oranges_lm1 <- lm(sales1 ~ price1 + price2 + day + store, data = oranges)
+#'
+#' # reference grid; see vignette("basics", package = "emmeans")
+#' oranges_rg1 <- ref_grid(oranges_lm1)
+#' td <- tidy(oranges_rg1)
+#' td
+#'
+#' # marginal averages
+#' marginal <- emmeans(oranges_rg1, "day")
+#' tidy(marginal)
+#'
+#' # contrasts
+#' tidy(contrast(marginal))
+#' tidy(contrast(marginal, method = "pairwise"))
+#'
+#' # plot confidence intervals
+#' library(ggplot2)
+#'
+#' ggplot(tidy(marginal, conf.int = TRUE), aes(day, estimate)) +
+#'   geom_point() +
+#'   geom_errorbar(aes(ymin = conf.low, ymax = conf.high))
+#'
+#' # by multiple prices
+#' by_price <- emmeans(oranges_lm1, "day",
+#'   by = "price2",
+#'   at = list(
+#'     price1 = 50, price2 = c(40, 60, 80),
+#'     day = c("2", "3", "4")
+#'   )
+#' )
+#'
+#' by_price
+#'
+#' tidy(by_price)
+#'
+#' ggplot(tidy(by_price, conf.int = TRUE), aes(price2, estimate, color = day)) +
+#'   geom_line() +
+#'   geom_errorbar(aes(ymin = conf.low, ymax = conf.high))
+#'
+#' # joint_tests
+#' tidy(joint_tests(oranges_lm1))
 #'
-# examples no longer supplied, see #1193
-# @examplesIf rlang::is_installed(c("emmeans", "ggplot2"))
-#
-# # load libraries for models and data
-# library(emmeans)
-#
-# # linear model for sales of oranges per day
-# oranges_lm1 <- lm(sales1 ~ price1 + price2 + day + store, data = oranges)
-#
-# # reference grid; see vignette("basics", package = "emmeans")
-# oranges_rg1 <- ref_grid(oranges_lm1)
-# td <- tidy(oranges_rg1)
-# td
-#
-# # marginal averages
-# marginal <- emmeans(oranges_rg1, "day")
-# tidy(marginal)
-#
-# # contrasts
-# tidy(contrast(marginal))
-# tidy(contrast(marginal, method = "pairwise"))
-#
-# # plot confidence intervals
-# library(ggplot2)
-#
-# ggplot(tidy(marginal, conf.int = TRUE), aes(day, estimate)) +
-#   geom_point() +
-#   geom_errorbar(aes(ymin = conf.low, ymax = conf.high))
-#
-# # by multiple prices
-# by_price <- emmeans(oranges_lm1, "day",
-#   by = "price2",
-#   at = list(
-#     price1 = 50, price2 = c(40, 60, 80),
-#     day = c("2", "3", "4")
-#   )
-# )
-#
-# by_price
-#
-# tidy(by_price)
-#
-# ggplot(tidy(by_price, conf.int = TRUE), aes(price2, estimate, color = day)) +
-#   geom_line() +
-#   geom_errorbar(aes(ymin = conf.low, ymax = conf.high))
-#
-# # joint_tests
-# tidy(joint_tests(oranges_lm1))
-#
 #' @aliases emmeans_tidiers
 #' @export
 #' @family emmeans tidiers
-#' @seealso [tidy()], `emmeans::ref_grid()`, `emmeans::emmeans()`,
-#'   `emmeans::contrast()`
+#' @seealso [tidy()], [emmeans::ref_grid()], [emmeans::emmeans()],
+#'   [emmeans::contrast()]
 tidy.lsmobj <- function(x, conf.int = FALSE, conf.level = .95, ...) {
-  lifecycle::deprecate_soft(
-    "1.0.6", 
-    I("tidying a `lsmobj` object"), 
-    details = c(
-      "i" = "broom no longer tests support for emmeans output as the package 
-             requires an incompatibly recent R version.",
-      "!" = "Please interpret output with caution."
-    )
-  )
   check_ellipses("exponentiate", "tidy", "lsmobj", ...)
 
   tidy_emmeans(x, infer = c(conf.int, TRUE), level = conf.level, ...)
@@ -113,18 +103,9 @@ tidy.lsmobj <- function(x, conf.int = FALSE, conf.level = .95, ...) {
 #'
 #' @export
 #' @family emmeans tidiers
-#' @seealso [tidy()], `emmeans::ref_grid()`, `emmeans::emmeans()`,
-#'   `emmeans::contrast()`
+#' @seealso [tidy()], [emmeans::ref_grid()], [emmeans::emmeans()],
+#'   [emmeans::contrast()]
 tidy.ref.grid <- function(x, conf.int = FALSE, conf.level = .95, ...) {
-  lifecycle::deprecate_soft(
-    "1.0.6", 
-    I("tidying a `ref.grid` object"), 
-    details = c(
-      "i" = "broom no longer tests support for emmeans output as the package 
-             requires an incompatibly recent R version.",
-      "!" = "Please interpret output with caution."
-    )
-  )
   check_ellipses("exponentiate", "tidy", "ref.grid", ...)
 
   tidy_emmeans(x, infer = c(conf.int, TRUE), level = conf.level, ...)
@@ -148,18 +129,9 @@ tidy.ref.grid <- function(x, conf.int = FALSE, conf.level = .95, ...) {
 #'
 #' @export
 #' @family emmeans tidiers
-#' @seealso [tidy()], `emmeans::ref_grid()`, `emmeans::emmeans()`,
-#'   `emmeans::contrast()`
+#' @seealso [tidy()], [emmeans::ref_grid()], [emmeans::emmeans()],
+#'   [emmeans::contrast()]
 tidy.emmGrid <- function(x, conf.int = FALSE, conf.level = .95, ...) {
-  lifecycle::deprecate_soft(
-    "1.0.6", 
-    I("tidying a `emmGrid` object"), 
-    details = c(
-      "i" = "broom no longer tests support for emmeans output as the package 
-             requires an incompatibly recent R version.",
-      "!" = "Please interpret output with caution."
-    )
-  )
   check_ellipses("exponentiate", "tidy", "emmGrid", ...)
 
   tidy_emmeans(x, infer = c(conf.int, TRUE), level = conf.level, ...)
@@ -191,19 +163,10 @@ tidy.emmGrid <- function(x, conf.int = FALSE, conf.level = .95, ...) {
 #'
 #' @export
 #' @family emmeans tidiers
-#' @seealso [tidy()], `emmeans::ref_grid()`, `emmeans::emmeans()`,
-#'   `emmeans::contrast()`
+#' @seealso [tidy()], [emmeans::ref_grid()], [emmeans::emmeans()],
+#'   [emmeans::contrast()]
 
 tidy.summary_emm <- function(x, null.value = NULL, ...) {
-  lifecycle::deprecate_soft(
-    "1.0.6", 
-    I("tidying a `summary_emm` object"), 
-    details = c(
-      "i" = "broom no longer tests support for emmeans output as the package 
-             requires an incompatibly recent R version.",
-      "!" = "Please interpret output with caution."
-    )
-  )
   check_ellipses("exponentiate", "tidy", "summary_emm", ...)
 
   tidy_emmeans_summary(x, null.value = null.value)