From 607fe01f5f4736c78d947423dac9c2f533e36a12 Mon Sep 17 00:00:00 2001
From: Lukas Wallrich <lukas.wallrich@gmail.com>
Date: Thu, 16 Apr 2020 20:58:42 +0100
Subject: [PATCH 1/3] Add option to return p.values to tidy.polr

---
 R/mass-polr-tidiers.R | 30 +++++++++++++++++++++++++++++-
 1 file changed, 29 insertions(+), 1 deletion(-)

diff --git a/R/mass-polr-tidiers.R b/R/mass-polr-tidiers.R
index 2de7e8318..94b6e92ab 100644
--- a/R/mass-polr-tidiers.R
+++ b/R/mass-polr-tidiers.R
@@ -4,6 +4,8 @@
 #' @param x A `polr` object returned from [MASS::polr()].
 #' @template param_confint
 #' @template param_exponentiate
+#' @param p.values Logical. Should p-values be returned, 
+#' based on chi-squared tests from [MASS::dropterm()]. Defaults to FAlSE
 #' @template param_unused_dots
 #'   
 #' @examples
@@ -17,18 +19,30 @@
 #' glance(fit)
 #' augment(fit, type.predict = "class")
 #' 
+#' fit2 <- polr(factor(gear) ~ am + mpg + qsec, data = mtcars)
+#' tidy(fit, p.values = TRUE)
+#' 
 #' @evalRd return_tidy(regression = TRUE)
 #' 
 #' @details In `broom 0.7.0` the `coefficient_type` column was renamed to
 #'   `coef.type`, and the contents were changed as well. Now the contents
 #'   are `coefficient` and `scale`, rather than `coefficient` and `zeta`.
+#'   
+#'   Calculating p.values with the `dropterm()` function is the approach
+#'   suggested by the MASS package author 
+#'   (https://r.789695.n4.nabble.com/p-values-of-plor-td4668100.html). This
+#'   approach is computationally intensive, so that p.values are only
+#'   returned if requested explicitly. Additionally, it only works for 
+#'   models containing no variables with more than two categories. If this
+#'   condition is not met, a message is shown and NA is returned instead of 
+#'   p-values.
 #'
 #' @aliases polr_tidiers
 #' @export
 #' @seealso [tidy], [MASS::polr()]
 #' @family ordinal tidiers
 tidy.polr <- function(x, conf.int = FALSE, conf.level = 0.95,
-                      exponentiate = FALSE, ...) {
+                      exponentiate = FALSE, p.values = FALSE, ...) {
   
   ret <- as_tibble(coef(summary(x)), rownames = "term")
   colnames(ret) <- c("term", "estimate", "std.error", "statistic")
@@ -41,6 +55,20 @@ tidy.polr <- function(x, conf.int = FALSE, conf.level = 0.95,
   if (exponentiate)
     ret <- exponentiate(ret)
   
+  if (p.values) {
+    sig <- MASS::dropterm(x, test = "Chisq")
+    p <- sig %>% dplyr::select(`Pr(Chi)`) %>% dplyr::pull() %>% .[-1]
+    terms <- purrr::map(rownames(sig)[-1], function(x) 
+      ret$term[stringr::str_detect(ret$term, stringr::fixed(x))]) %>% unlist()
+    if (length(p) == length(terms)) {
+      ret <- dplyr::left_join(ret, tibble::tibble(term = terms, p.value = p), by = "term")
+    } else {
+      message("p-values can presently only be returned for models that contain 
+              no categorical variables with more than two levels")
+      ret$p.value <- NA
+    }
+  }
+  
   mutate(
     ret, 
     coef.type = if_else(term %in% names(x$zeta), "scale", "coefficient")

From 0428c7dc519d56249b6f2e7a65b83d910ccb84f4 Mon Sep 17 00:00:00 2001
From: Lukas Wallrich <lukas.wallrich@gmail.com>
Date: Fri, 24 Apr 2020 13:16:03 +0100
Subject: [PATCH 2/3] Update NEWS.md

---
 NEWS.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/NEWS.md b/NEWS.md
index 700781c7d..95cb8de03 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -150,6 +150,8 @@ pending getting `safepredict()` going urgh)
 
 - `tidy.lsmobj()` gained a `conf.int` argument for consistency with other tidiers.
 
+- `tidy.polr()` now returns p-values if  `p.values` is set to TRUE and the model does not contain factors with more than two levels.
+
 - `tidy.zoo()` now doesn't change column names that have spaces or other
 special characters (previously they were converted to data.frame friendly
 column names by `make.names`)

From 1b5d17854bad4ccf3972a316b5cb754d97adbab8 Mon Sep 17 00:00:00 2001
From: Lukas Wallrich <lukas.wallrich@gmail.com>
Date: Fri, 24 Apr 2020 13:18:51 +0100
Subject: [PATCH 3/3] Update DESCRIPTION

---
 DESCRIPTION | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 73542cd37..9787ee397 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -275,7 +275,12 @@ Authors@R:
              family = "Kuriwaki",
              role = "ctb",
              email = "shirokuriwaki@gmail.com",
-             comment = c(ORCID = "0000-0002-5687-2647")))
+             comment = c(ORCID = "0000-0002-5687-2647")),
+      person(given = "Lukas",
+             family = "Wallrich",
+             role = "ctb",
+             email = "lukas.wallrich@gmail.com",
+             comment = c(ORCID = "0000-0003-2121-5177")))
 Description: Summarizes key information about statistical
     objects in tidy tibbles. This makes it easy to report results, create
     plots and consistently work with large numbers of models at once.