tbl_uvregression() to accept survey objects (#740)

* added fn to remove survey columns

* updated to accept survey objects

* doc updates

* adding unit test

* doc update

* Increment version number

* doc updates

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: gtsummary
 Title: Presentation-Ready Data Summary and Analytic Result
     Tables
-Version: 1.3.6.9001
+Version: 1.3.6.9002
 Authors@R: 
     c(person(given = "Daniel D.",
              family = "Sjoberg",

NEWS.md

@@ -1,5 +1,7 @@
 # gtsummary (development version)
 
+* `tbl_uvregression()` now accepts both data frames and survey design objects as input. (#742)
+
 * Added function `add_vif()` to include variance inflation factors in `tbl_regression()` output. (#717)
 
 # gtsummary 1.3.6

R/tbl_svysummary.R

@@ -91,32 +91,15 @@
 tbl_svysummary <- function(data, by = NULL, label = NULL, statistic = NULL,
                         digits = NULL, type = NULL, value = NULL,
                         missing = NULL, missing_text = NULL, sort = NULL,
-                        percent = NULL, include = NULL) {
+                        percent = NULL, include = everything()) {
   # checking for survey package ------------------------------------------------
   assert_package("survey", "tbl_svysummary()")
 
   # test if data is a survey object
   if (!is_survey(data)) stop("'data' should be a survey object (see svydesign()).", call. = FALSE)
 
   # eval -----------------------------------------------------------------------
-  include <- select(data$variables, {{ include }}) %>% names()
-
-  # default selection for include
-  if (length(include) == 0) {
-    # look at data$call
-    if (is.null(data$call)) {
-      include <- names(data$variables)
-    } else {
-      exclude <- c(
-        all.vars(data$call$id),
-        all.vars(data$call$probs),
-        all.vars(data$call$strata),
-        all.vars(data$call$fpc),
-        all.vars(data$call$weights)
-      )
-      include <- setdiff(names(data$variables), exclude)
-    }
-  }
+  include <- select(.remove_survey_cols(data), {{ include }}) %>% names()
 
   # setting defaults from gtsummary theme --------------------------------------
   label <- label %||%
@@ -576,3 +559,17 @@ c_form <- function(left = NULL, right = 1) {
   right <- paste(right, collapse = "+")
   stats::as.formula(paste(left, "~", right))
 }
+
+
+# this function removes the weight/survey columns from x$variables
+# used when columns must be selected from the survey object, and we dont want users
+# to select the weighting columns
+.remove_survey_cols <- function(x) {
+  if (is.data.frame(x)) return(x)
+  x$variables %>%
+    select(-any_of(c(all.vars(x$call$id),
+                     all.vars(x$call$probs),
+                     all.vars(x$call$strata),
+                     all.vars(x$call$fpc),
+                     all.vars(x$call$weights))))
+}

R/tbl_uvregression.R

@@ -25,7 +25,9 @@
 #'
 #' @param data Data frame to be used in univariate regression modeling.  Data
 #' frame includes the outcome variable(s) and the independent variables.
-#' @param method Regression method (e.g. [lm], [glm], [survival::coxph], and more).
+#' Survey design objects are also accepted.
+#' @param method Regression method (e.g. [lm], [glm], [survival::coxph],
+#' [survey::svyglm], and more).
 #' @param y Model outcome (e.g. `y = recurrence` or `y = Surv(time, recur)`).
 #' All other column in `data` will be regressed on `y`.
 #' Specify one and only one of `y` or `x`
@@ -106,6 +108,12 @@ tbl_uvregression <- function(data, method, y = NULL, x = NULL, method.args = NUL
     )
   }
 
+  # checking input -------------------------------------------------------------
+  # data is a data frame
+  if (!is.data.frame(data) && !is_survey(data)) {
+    stop("`data` argument must be a data frame or survey object.", call. = FALSE)
+  }
+
   # setting defaults -----------------------------------------------------------
   pvalue_fun <-
     pvalue_fun %||%
@@ -138,14 +146,18 @@ tbl_uvregression <- function(data, method, y = NULL, x = NULL, method.args = NUL
   y <- rlang::enexpr(y)
   x <-
     tryCatch({
-      .select_to_varnames(select = !!x, data = data, arg_name = "x")
+      .select_to_varnames(select = !!x,
+                          data = switch(is.data.frame(data), data) %||% .remove_survey_cols(data),
+                          arg_name = "x")
     }, error = function(e) {
       rlang::expr_text(x)
     })
 
   y <-
     tryCatch({
-      .select_to_varnames(select = !!y, data = data, arg_name = "y")
+      .select_to_varnames(select = !!y,
+                          data = switch(is.data.frame(data), data) %||% .remove_survey_cols(data),
+                          arg_name = "y")
     }, error = function(e) {
       rlang::expr_text(y)
     })
@@ -163,19 +175,19 @@ tbl_uvregression <- function(data, method, y = NULL, x = NULL, method.args = NUL
   include <-
     .select_to_varnames(
       select = {{ include }},
-      data = data,
+      data = switch(is.data.frame(data), data) %||% .remove_survey_cols(data),
       arg_name =  "include"
     )
   exclude <-
     .select_to_varnames(
       select = {{ exclude }},
-      data = data,
+      data = switch(is.data.frame(data), data) %||% .remove_survey_cols(data),
       arg_name =  "exclude"
     )
   show_single_row <-
     .select_to_varnames(
       select = {{ show_single_row }},
-      data = data,
+      data = switch(is.data.frame(data), data) %||% .remove_survey_cols(data),
       arg_name =  "show_single_row"
     )
 
@@ -205,7 +217,7 @@ tbl_uvregression <- function(data, method, y = NULL, x = NULL, method.args = NUL
   label <-
     .formula_list_to_named_list(
       x = label,
-      data = data,
+      data = switch(is.data.frame(data), data) %||% .remove_survey_cols(data),
       arg_name = "label"
     )
 
@@ -214,12 +226,6 @@ tbl_uvregression <- function(data, method, y = NULL, x = NULL, method.args = NUL
     stop("Each `label` specified must be a string of length 1.", call. = FALSE)
   }
 
-  # data -----------------------------------------------------------------------
-  # data is a data frame
-  if (!is.data.frame(data)) {
-    stop("`data` argument must be a data frame.", call. = FALSE)
-  }
-
   # will return call, and all object passed to in table1 call
   # the object func_inputs is a list of every object passed to the function
   tbl_uvregression_inputs <- as.list(environment())
@@ -229,7 +235,7 @@ tbl_uvregression <- function(data, method, y = NULL, x = NULL, method.args = NUL
 
   # get all vars not specified -------------------------------------------------
   all_vars <-
-    names(data) %>%
+    names(switch(is.data.frame(data), data) %||% .remove_survey_cols(data)) %>%
     # removing x or y variable
     setdiff(paste(c(y, x), "~ 1") %>% stats::as.formula() %>% all.vars()) %>%
     # removing any other variables listed in the formula
@@ -263,10 +269,17 @@ tbl_uvregression <- function(data, method, y = NULL, x = NULL, method.args = NUL
       formula_chr = glue(formula),
       model = map(
         .data$formula_chr,
-        ~list(method, formula = as.formula(.x), data = data) %>%
+        function(.x) {
+          call_list1 <- # defining formula and data call (or formula and design)
+            switch(is.data.frame(data),
+                   list(method, formula = as.formula(.x), data = data)) %||%
+            list(method, formula = as.formula(.x), design = data)
+
+          call_list1 %>%
           c(as.list(method.args)[-1]) %>%
           as.call() %>%
           eval()
+        }
       ),
       # removing backticks
       y = switch(is.null(.env$y), all_vars) %||% y,

inst/WORDLIST

@@ -54,6 +54,7 @@ saddlepoint
 sig
 survfit
 svychisq
+svyglm
 svyranktest
 svysummary
 svyttest
@@ -68,4 +69,3 @@ tidyselect's
 tidyverse
 unhide
 uvregression
-varnames

tests/testthat/test-tbl_uvregression.R

@@ -277,3 +277,25 @@ test_that("tbl_uvregression throw error with odd variable names in `data=`", {
     trial %>% dplyr::rename(`age person` = age) %>% tbl_uvregression(method = lm, y = `age person`)
   )
 })
+
+test_that("tbl_uvregression works with survey object", {
+  svy <- survey::svydesign(ids = ~1, data = trial, weights = ~1)
+
+  expect_error(
+    tbl_uvreg <-
+      svy %>%
+      tbl_uvregression(
+        y = response,
+        method = survey::svyglm,
+        method.args = list(family = binomial),
+        hide_n = TRUE,
+        include = c(response, age, marker, grade)
+      ),
+    NA
+  )
+
+  expect_equal(
+    tbl_uvreg$tbls$age$model_obj %>% broom::tidy(),
+    survey::svyglm(response ~ age, design = svy, family = binomial) %>% broom::tidy()
+  )
+})