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remove Suggests for lsmeans and emmeans (#1194)
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simonpcouch authored Mar 20, 2024
1 parent f4fc69d commit 213daf8
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2 changes: 0 additions & 2 deletions DESCRIPTION
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Expand Up @@ -570,7 +570,6 @@ Suggests:
covr,
drc,
e1071,
emmeans,
epiR,
ergm (>= 3.10.4),
fixest (>= 0.9.0),
Expand All @@ -596,7 +595,6 @@ Suggests:
lme4,
lmodel2,
lmtest (>= 0.9.38),
lsmeans,
maps,
margins,
MASS,
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2 changes: 2 additions & 0 deletions NEWS.md
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@@ -1,5 +1,7 @@
# broom (development version)

* Removed lsmeans and emmeans as Suggested packages as the packages 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).

* Moved forward with deprecation of tidiers for objects from the sp package. See resources linked in [tidymodels/broom#1142](https://github.com/tidymodels/broom/issues/1142) for more information on migration from retiring spatial packages.

* Corrected confidence interval values for precision components in `tidy.betareg()` output (#1169).
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119 changes: 60 additions & 59 deletions R/emmeans-tidiers.R
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Expand Up @@ -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(
Expand All @@ -24,61 +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()].
#'
#' @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))
#' passed on to `emmeans::summary.emmGrid()` or `lsmeans::summary.ref.grid()`.
#'
# 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, ...) {
check_ellipses("exponentiate", "tidy", "lsmobj", ...)

Expand All @@ -103,8 +104,8 @@ 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, ...) {
check_ellipses("exponentiate", "tidy", "ref.grid", ...)

Expand All @@ -129,8 +130,8 @@ 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, ...) {
check_ellipses("exponentiate", "tidy", "emmGrid", ...)

Expand Down Expand Up @@ -163,8 +164,8 @@ 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, ...) {
check_ellipses("exponentiate", "tidy", "summary_emm", ...)
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60 changes: 5 additions & 55 deletions man/tidy.emmGrid.Rd

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60 changes: 5 additions & 55 deletions man/tidy.lsmobj.Rd

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