merge pr #1057: v0.7.10

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: broom
 Title: Convert Statistical Objects into Tidy Tibbles
-Version: 0.7.9.9001
+Version: 0.7.10
 Authors@R:
     c(person(given = "David",
              family = "Robinson",
@@ -539,7 +539,8 @@ Imports:
     rlang,
     stringr,
     tibble (>= 3.0.0),
-    tidyr (>= 1.0.0)
+    tidyr (>= 1.0.0),
+    ggplot2
 Suggests:
     AER,
     akima,
@@ -565,7 +566,6 @@ Suggests:
     gam (>= 1.15),
     gee,
     geepack,
-    ggplot2,
     glmnet,
     glmnetUtils,
     gmm,

NEWS.md

@@ -1,12 +1,14 @@
-# broom 0.7.9.9001
+# broom 0.7.10
 
 To be released as broom 0.7.10.
 
 * Clarifies error when `pysch::mediate` output is dispatched to `tidy.mediate` (`#1037` by `@LukasWallrich`).
 * Allows user to specify confidence level for `tidy.rma` (`#1041` by `@TarenSanders`)
 * Clarifies documentation related to usage of `augment_columns()`; most package users should use `augment()` in favor of `augment_columns()`. See `?augment_columns` for more details.
 * Extends support for `emmeans` by fixing non-standard column names in case of asymptotically derived inferential statistics. (`#1046` by `@crsh`)
-* Fixes use of index columns in `augment.mlogit`. (`#1045` and `#1053` by `@jamesrrae` and `@gregmacfarlane`)
+* Fixes use of index columns in `augment.mlogit` and adds `.resid` column to
+output. (`#1045`, `#1053`, `#1055`, and `#1056` by `@jamesrrae` and
+`@gregmacfarlane`)
 * Correct column naming of standard error measures in `glance.survfit()`.
 * Various bug fixes and improvements to documentation.
 

R/aer-tidiers.R

@@ -23,7 +23,9 @@
 #' )
 #'
 #' @examples
-#'
+#' 
+#' if (requireNamespace("AER", quietly = TRUE)) {
+#' 
 #' library(AER)
 #'
 #' data("CigarettesSW", package = "AER")
@@ -45,6 +47,9 @@
 #' augment(ivr, newdata = CigarettesSW)
 #'
 #' glance(ivr)
+#' 
+#' }
+#' 
 #' @export
 #' @seealso [tidy()], [AER::ivreg()]
 #' @family ivreg tidiers

R/auc-tidiers.R

@@ -7,6 +7,8 @@
 #' @evalRd return_tidy("cutoff", "tpr", "fpr")
 #'
 #' @examples
+#' 
+#' if (requireNamespace("AUC", quietly = TRUE)) {
 #'
 #' library(AUC)
 #' data(churn)
@@ -36,6 +38,9 @@
 #'
 #' ggplot(rocs, aes(fpr, tpr, color = algorithm)) +
 #'   geom_line()
+#'   
+#' }
+#' 
 #' @export
 #' @aliases auc_tidiers roc_tidiers
 #' @seealso [tidy()], [AUC::roc()]

R/bbmle-tidiers.R

@@ -8,6 +8,8 @@
 #' @evalRd return_tidy(regression = TRUE)
 #'
 #' @examples
+#' 
+#' if (requireNamespace("bbmle", quietly = TRUE)) {
 #'
 #' library(bbmle)
 #'
@@ -20,6 +22,9 @@
 #' )
 #'
 #' tidy(fit)
+#' 
+#' }
+#' 
 #' @export
 #' @seealso [tidy()], [bbmle::mle2()], [tidy_optim()]
 #' @aliases mle2_tidiers bbmle_tidiers

R/betareg-tidiers.R

@@ -17,6 +17,8 @@
 #'   At least one term will have been used to model the precision `phi`.
 #'
 #' @examples
+#' 
+#' if (requireNamespace("betareg", quietly = TRUE)) {
 #'
 #' library(betareg)
 #' data("GasolineYield", package = "betareg")
@@ -31,6 +33,9 @@
 #' augment(mod)
 #'
 #' glance(mod)
+#' 
+#' }
+#' 
 #' @export
 #' @seealso [tidy()], [betareg::betareg()]
 #' @family betareg tidiers

R/bingroup-tidiers.R

@@ -9,6 +9,8 @@
 #' )
 #'
 #' @examples
+#' 
+#' if (requireNamespace("binGroup", quietly = TRUE)) {
 #'
 #' library(binGroup)
 #' library(dplyr)
@@ -17,6 +19,9 @@
 #' bw <- binWidth(100, .1)
 #' bw
 #' tidy(bw)
+#' 
+#' }
+#' 
 #' @export
 #' @family bingroup tidiers
 #' @aliases binwidth_tidiers
@@ -39,6 +44,8 @@ tidy.binWidth <- function(x, ...) {
 #' )
 #'
 #' @examples
+#' 
+#' if (requireNamespace("binGroup", quietly = TRUE)) {
 #'
 #' library(binGroup)
 #' des <- binDesign(
@@ -53,6 +60,9 @@ tidy.binWidth <- function(x, ...) {
 #' library(ggplot2)
 #' ggplot(tidy(des), aes(n, power)) +
 #'   geom_line()
+#'   
+#' }
+#' 
 #' @export
 #' @family bingroup tidiers
 #' @aliases bindesign_tidiers
@@ -77,7 +87,9 @@ tidy.binDesign <- function(x, ...) {
 #' )
 #'
 #' @examples
-#'
+#' 
+#' if (requireNamespace("binGroup", quietly = TRUE)) {
+#' 
 #' library(binGroup)
 #' des <- binDesign(
 #'   nmax = 300, delta = 0.06,
@@ -90,6 +102,9 @@ tidy.binDesign <- function(x, ...) {
 #' library(ggplot2)
 #' ggplot(tidy(des), aes(n, power)) +
 #'   geom_line()
+#'   
+#' }
+#' 
 #' @export
 #' @family bingroup tidiers
 #' @seealso [glance()], [binGroup::binDesign()]

R/boot-tidiers.R

@@ -22,6 +22,8 @@
 #' `std.error` columns shown.
 #'
 #' @examples
+#' 
+#' if (requireNamespace("boot", quietly = TRUE)) {
 #'
 #' library(boot)
 #'
@@ -40,6 +42,9 @@
 #' bootres <- boot(clotting, bootfun, R = 999)
 #' tidy(g1, conf.int = TRUE)
 #' tidy(bootres, conf.int = TRUE)
+#' 
+#' }
+#' 
 #' @export
 #' @aliases boot_tidiers
 #' @seealso [tidy()], [boot::boot()], [boot::tsboot()], [boot::boot.ci()],

R/car-tidiers.R

@@ -11,10 +11,15 @@
 #' )
 #'
 #' @examples
+#' 
+#' if (requireNamespace("car", quietly = TRUE)) {
 #'
 #' dw <- car::durbinWatsonTest(lm(mpg ~ wt, data = mtcars))
 #' tidy(dw)
 #' glance(dw) # same output for all durbinWatsonTests
+#' 
+#' }
+#' 
 #' @name durbinWatsonTest_tidiers
 #' @family car tidiers
 #' @export
@@ -50,11 +55,15 @@ glance.durbinWatsonTest <- function(x, ...) tidy(x)
 #'
 #' @examples
 #'
+#' if (requireNamespace("car", quietly = TRUE)) {
+#' 
 #' library(car)
 #' data(Moore)
 #' lt <- with(Moore, leveneTest(conformity, fcategory))
 #' tidy(lt)
 #' glance(lt) # same output for all leveneTest
+#' 
+#' }
 #' @name leveneTest_tidiers
 #' @family car tidiers
 #' @export

R/caret-tidiers.R

@@ -18,6 +18,8 @@
 #' )
 #'
 #' @examples
+#' 
+#' if (requireNamespace("caret", quietly = TRUE)) {
 #'
 #' library(caret)
 #'
@@ -46,6 +48,9 @@
 #'
 #' tidy(six_class_cm)
 #' tidy(six_class_cm, by_class = FALSE)
+#' 
+#' }
+#' 
 #' @aliases caret_tidiers confusionMatrix_tidiers
 #' @export
 #' @seealso [tidy()], [caret::confusionMatrix()]

R/cmprsk-tidiers.R

@@ -16,6 +16,8 @@
 #' )
 #'
 #' @examples
+#' 
+#' if (requireNamespace("cmprsk", quietly = TRUE)) {
 #'
 #' library(cmprsk)
 #' lrf_time <- rexp(100) #time to loco-regional failure (lrf)
@@ -25,6 +27,8 @@
 #' x <- crr(lrf_time, lrf_event, cbind(trt, strt))
 #' tidy(x, conf.int = TRUE)
 #' glance(x)
+#' 
+#' }
 #'
 #' @aliases cmprsk_tidiers
 #' @export

R/drc-tidiers.R

@@ -14,6 +14,8 @@
 #'   The `curveid` column indicates the curve.
 #'
 #' @examples
+#' 
+#' if (requireNamespace("drc", quietly = TRUE)) {
 #'
 #' library(drc)
 #'
@@ -27,6 +29,9 @@
 #' glance(mod)
 #'
 #' augment(mod, selenium)
+#' 
+#' } 
+#' 
 #' @export
 #' @seealso [tidy()], [drc::drm()]
 #' @family drc tidiers

R/emmeans-tidiers.R

@@ -27,6 +27,8 @@
 #'   passed on to [emmeans::summary.emmGrid()] or [lsmeans::summary.ref.grid()].
 #'
 #' @examples
+#' 
+#' if (requireNamespace("emmeans", quietly = TRUE)) {
 #'
 #' library(emmeans)
 #' # linear model for sales of oranges per day
@@ -68,6 +70,9 @@
 #'
 #' # joint_tests
 #' tidy(joint_tests(oranges_lm1))
+#' 
+#' }
+#' 
 #' @aliases emmeans_tidiers
 #' @export
 #' @family emmeans tidiers

R/epiR-tidiers.R

@@ -21,6 +21,8 @@
 #'
 #' @examples
 #' 
+#' if (requireNamespace("epiR", quietly = TRUE)) {
+#' 
 #' library(epiR)
 #' 
 #' dat <- matrix(c(13, 2163, 5, 3349), nrow = 2, byrow = TRUE)
@@ -36,6 +38,8 @@
 #' tidy(fit, parameters = "moa")
 #' tidy(fit, parameters = "stat")
 #' 
+#' }
+#' 
 #' @export
 #' @seealso [tidy()], [epiR::epi.2by2()]
 #' @family epiR tidiers

R/ergm-tidiers.R

@@ -21,6 +21,8 @@
 #'   \item{p.value}{The two-sided p-value}
 #' 
 #' @examples
+#' 
+#' if (requireNamespace("ergm", quietly = TRUE)) {
 #'
 #' library(ergm)
 #' # Using the same example as the ergm package
@@ -43,6 +45,8 @@
 #' glance(gest, deviance = TRUE)
 #' glance(gest, mcmc = TRUE)
 #' 
+#' }
+#' 
 #' @references Hunter DR, Handcock MS, Butts CT, Goodreau SM, Morris M (2008b).
 #'   \pkg{ergm}: A Package to Fit, Simulate and Diagnose Exponential-Family
 #'   Models for Networks. *Journal of Statistical Software*, 24(3).

R/fixest-tidiers.R

@@ -26,6 +26,9 @@
 #'   \url{https://github.com/sgaure/lfe/issues/1#issuecomment-530646990})
 #'
 #' @examples
+#' 
+#' if (requireNamespace("fixest", quietly = TRUE)) {
+#' 
 #' \donttest{
 #' library(fixest)
 #' 
@@ -50,6 +53,8 @@
 #' # Approach (1) is preferred.
 #' 
 #' }
+#' 
+#' }
 #'
 #' @export
 #' @family fixest tidiers

R/gam-tidiers.R

@@ -17,12 +17,17 @@
 #'   [tidy.gam()].
 #'
 #' @examples
+#' 
+#' if (requireNamespace("gam", quietly = TRUE)) {
 #'
 #' library(gam)
 #' g <- gam(mpg ~ s(hp, 4) + am + qsec, data = mtcars)
 #'
 #' tidy(g)
 #' glance(g)
+#' 
+#' }
+#' 
 #' @export
 #' @family gam tidiers
 #' @aliases Gam_tidiers

R/geepack-tidiers.R

@@ -14,6 +14,8 @@
 #'   missingness in the data beforehand.
 #'
 #' @examples
+#' 
+#' if (requireNamespace("geepack", quietly = TRUE)) {
 #'
 #' library(geepack)
 #' data(state)
@@ -28,6 +30,9 @@
 #'
 #' tidy(geefit)
 #' tidy(geefit, conf.int = TRUE)
+#' 
+#' }
+#' 
 #' @evalRd return_tidy(regression = TRUE)
 #'
 #' @export