added plotting method for reg and uvreg objects (ddsjoberg#825)

* added plotting method for reg and uvreg objects

* Update plot.R

* doc updates

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: gtsummary
 Title: Presentation-Ready Data Summary and Analytic Result
     Tables
-Version: 1.3.7.9008
+Version: 1.3.7.9009
 Authors@R: 
     c(person(given = "Daniel D.",
              family = "Sjoberg",
@@ -85,6 +85,7 @@ Suggests:
     effectsize,
     flextable (>= 0.5.10),
     geepack,
+    GGally (>= 2.1.0), 
     Hmisc,
     huxtable (>= 5.0.0),
     kableExtra,

NAMESPACE

@@ -25,6 +25,8 @@ S3method(inline_text,tbl_survival)
 S3method(inline_text,tbl_svysummary)
 S3method(inline_text,tbl_uvregression)
 S3method(knit_print,gtsummary)
+S3method(plot,tbl_regression)
+S3method(plot,tbl_uvregression)
 S3method(print,gtsummary)
 S3method(tbl_regression,brmsfit)
 S3method(tbl_regression,default)

NEWS.md

@@ -1,5 +1,7 @@
 # gtsummary (development version)
 
+* Adding coefficient `plot()` methods for `tbl_regression()` and `tbl_uvregression()`
+
 * Bug fix for spanning headers with kableExtra output. The spanning header was misplaced when the header text was sandwhiched between two blank spanning headers.
 
 * Added _The Quarterly Journal of Economics_ to `theme_gtsummary_journal()`. This journal theme will be updated again after the gt package updates `cols_merge()` with a rows argument and allows for line breaks within cell.

R/plot.R

@@ -0,0 +1,46 @@
+#' Plot Regression Coefficients
+#'
+#' The `plot()` function extracts `x$table_body` and passes the it to
+#' `GGally::ggcoef_plot()` along with a formatting options.
+#'
+#' \lifecycle{experimental}
+#' @param x 'tbl_regression' or 'tbl_uvregression' object
+#' @param remove_header_rows logical indicating whether to remove header rows
+#' for categorical variables. Default is `TRUE`
+#' @param remove_reference_rows logical indicating whether to remove reference rows
+#' for categorical variables. Default is `FALSE`.
+#' @param ... arguments passed to `GGally::ggcoef_plot(...)`
+#'
+#' @return a ggplot
+#' @name plot
+#'
+#' @examples
+#' if (requireNamespace("GGally"))
+#'   glm(response ~ marker + grade, trial, family = binomial) %>%
+#'     tbl_regression(
+#'       add_estimate_to_reference_rows = TRUE,
+#'       exponentiate = TRUE
+#'     ) %>%
+#'     plot()
+NULL
+
+#' @rdname plot
+#' @export
+plot.tbl_regression <- function(x,
+                                remove_header_rows = TRUE,
+                                remove_reference_rows = FALSE, ...) {
+  assert_package("GGally", fn = "plot.tbl_regression()", version = "2.1.0")
+
+  df_coefs <- x$table_body
+  if (isTRUE(remove_header_rows))
+    df_coefs <- df_coefs %>% filter(!.data$header_row %in% TRUE)
+  if (isTRUE(remove_reference_rows))
+    df_coefs <- df_coefs %>% filter(!.data$reference_row %in% TRUE)
+
+  df_coefs %>%
+    GGally::ggcoef_plot(exponentiate = x$inputs$exponentiate, ...)
+}
+
+#' @rdname plot
+#' @export
+plot.tbl_uvregression <- plot.tbl_regression

R/tbl_strata.R

@@ -102,7 +102,7 @@ nest_df_and_svy <- function(data, strata) {
   tibble(strata_var = pluck(data, "variables", strata) %>% unique()) %>%
     rowwise() %>%
     mutate(
-      data = data[data$variables[[.env$strata]] %in% strata_var, ] %>% list()
+      data = data[data$variables[[.env$strata]] %in% .data$strata_var, ] %>% list()
     ) %>%
     ungroup() %>%
     set_names(c(strata, "data"))

pkgdown/_pkgdown.yml

@@ -93,6 +93,7 @@ reference:
       - add_q
       - add_significance_stars
       - add_vif
+      - plot
 
   - title: Inline Reporting
   - contents: