flex_print_table_one: Print table one using flextable

In emilelatour/latable: Latour's Table Functions and Helpers

Print table one using flextable

Description

Helper function for printing output from latable::create_table_one() using flextable.

Usage

flex_print_table_one(
  x,
  font_name = "Arial",
  font_size = 11,
  align = c("llcr"),
  align_j = NULL,
  auto_fit = FALSE,
  width = NULL,
  width_j = NULL,
  width_unit = "in",
  col_nms = NULL,
  col_lbls = NULL,
  title = NULL,
  subtitle = NULL,
  footer = NULL,
  title_size = 16,
  subtitle_size = 11,
  footer_size = 11,
  strata_lbl = "Treatment group",
  t1_default_cols = c("Category", "level", "num_not_miss", "Overall", "p"),
  t1_default_lbls = c("Characteristic", "", "Number available", "All subjects",
    "p-value")
)

Arguments

x	A tibble from latable::create_table_one() results
font_name	single character value, the font family name. With Word and PowerPoint output, the value specifies the font to be used to format characters in the Unicode range (U+0000-U+007F). For "all" table parts.
font_size	integer value (points). For "all" table parts.
align	Column alignment: a character vector consisting of 'l' (left), 'c' (center), 'r' (right), and/or 'j' (justify). By default or if align = NULL, numeric columns are right-aligned, and other columns are left-aligned. If length(align) == 1L, the string will be expanded to a vector of individual letters, e.g. 'clc' becomes c('c', 'l', 'c').
align_j	Column selection for align argument. Default is 1:length(align).
auto_fit	Logical (Default is FALSE). See flextable::autofit()
width	width in inches as a character vector.
width_j	columns selection for width.
width_unit	unit for width, one of "in", "cm", "mm".
col_nms	Names of columns to be labelled.
col_lbls	Labels to apply to columns different from column names.
title	The text for the title.
subtitle	The text for the subtitle which will be displayed below the title.
footer	The text for the footer which will be displayed below the body of the table.
title_size	Font size for the title. Default is 16.
subtitle_size	Font size for the subtitle. Default is 11.
footer_size	Font size for the footer Default is 11.
strata_lbl	The text to use for the strata title displayed above the groups.
t1_default_cols	Character vector of default column names that come from latable::create_table_one(). Can be changed.
t1_default_lbls	Character vector of default column labels. Can be changed.

Value

A flextable

Examples

# Load some packages for the example
library(survival)
library(dplyr)
library(tibble)

library(latable)

# Data set comes from the survival package
data(pbc)

## Vector of variables to summarize
myVars <- c("time", "status", "trt", "age", "sex", "ascites", "hepato",
            "spiders", "edema", "bili", "chol", "albumin", "copper", "alk.phos",
            "ast", "trig", "platelet", "protime", "stage")
## Vector of categorical variables that need transformation
catVars <- c("status", "trt", "ascites", "hepato",
             "spiders", "edema", "stage")

# With labels
library(labelled)

# Tibble with labels
var_labels <- tibble::tribble(
  ~vars,                                      ~labels,
  "id",                                "Case Number",
  "time",          "Number of days since registration",
  "status",                         "Status at endpoint",
  "trt",                            "Treatment group",
  "age",                              "Age, in years",
  "sex",                                        "Sex",
  "ascites",                        "Presence of ascites",
  "hepato", "Presence of hepatomegaly or enlarged liver",
  "spiders",     "Blood vessel malformations in the skin",
  "edema",                          "Presence of edema",
  "bili",                   "Serum bilirunbin (mg/dl)",
  "chol",                  "Serum cholesterol (mg/dl)",
  "albumin",                       "Serum albumin (g/dl)",
  "copper",                      "Urine copper (ug/day)",
  "alk.phos",             "Alkaline phosphotase (U/liter)",
  "ast",          "Aspartate aminotransferase (U/ml)",
  "trig",                      "Triglycerides (mg/dl)",
  "platelet",                             "Platelet count",
  "protime",           "Standardised blood clotting time",
  "stage", "Histologic stage of disease (needs biopsy)"
)

labels_list <- setNames(as.list(var_labels$labels), var_labels$vars)

# Apply labels
labelled::var_label(pbc) <- labels_list

# No Strata
foo2 <- create_table_one(data = pbc,
                         # strata = "trt",
                         vars = myVars,
                         fct_vars = catVars,
                         keep_test = FALSE,
                         show_smd = FALSE,
                         var_labels = TRUE)


# Table one with strata
foo <- create_table_one(data = pbc,
                        strata = "trt",
                        vars = myVars,
                        fct_vars = catVars,
                        keep_test = FALSE,
                        show_smd = FALSE,
                        var_labels = TRUE)


flex_print_table_one(x = foo)

flex_print_table_one(x = foo2)

flex_print_table_one(x = foo, 
                     font_name = "Lato", 
                     title = "Edgar Anderson's Iris Data", 
                     title_size = 16, 
                     subtitle = "Just the head")

flex_print_table_one(x = foo2, 
                     font_name = "Lato", 
                     title = "Edgar Anderson's Iris Data", 
                     title_size = 16)

emilelatour/latable documentation built on Sept. 14, 2023, 9:32 a.m.