regression models in r output table to word

Question

I have been using sjplot to create a combined table. This creates a HTML table. I would like to make a table that can be exported to word.

I have reviewed this post which discusses copy and pasting into word, but this alters the formatting of the columns and lines. Output several regression tables into multiple pages of a Word document in R

n1 <- glm(N  ~ Age_2 , data = n_data, family = "binomial")
g1 <- glm(G  ~ Age_2 , data = g1_data, family = "binomial")
ga1 <- glm(G_1  ~ Age_2 , data = ga1_data, family = "binomial")
l1 <- glm(L_1  ~ Age_2 , data = l1_data, family = "binomial")
c1 <- glm(C_1  ~ Age_2 , data = c1_data, family = "binomial")
m1 <- glm(m  ~ Age_2 , data = m1_data, family = "binomial")

tab_model (n1,g1,ga1,l1,c1,m1)

Also is it possible to add a line with the number that had the outcome (ie. number of N), in addition to the total number of observations per group?

Any suggestions? Willing to try other packages.

Answer 1

Since sjPlot outputs to html, it's very hard to get it into a Word document directly. Here's an example of how to do something similar to what you want to do using knitr , rmarkdown , jtools , and huxtable . I'm using RStudio with an rmarkdown document, which I knit to a Word document.

---
title: "jtools to Output Logistic Regression Models"
author: "sar"
date: "`r format(Sys.time(), '%d %B %Y')`"
output: word_document
---

```{r setup, include=FALSE}
library(knitr)
library(jtools)
library(huxtable)

knitr::opts_chunk$set(echo=FALSE, warning = FALSE)

```

# Introduction

This is a test document to demonstrate how knitr and rmarkdown can be used to put output from jtools
into a Word Document

```{r OutputTable}
set.seed(1234)
logistic_s <- data.frame(N=rbinom(200,1,0.5),
                         G=rbinom(200,1,0.5),
                         G_1=rbinom(200,1,0.5),
                         L_1=rbinom(200,1,0.5),
                         C_1=rbinom(200,1,0.5),
                         m=rbinom(200,1,0.5),
                         Age_2=round(rnorm(200,40,6)))

n1 <- glm(N  ~ Age_2 , data = logistic_s, family = "binomial")
g1 <- glm(G  ~ Age_2 , data = logistic_s, family = "binomial")
ga1 <- glm(G_1  ~ Age_2 , data = logistic_s, family = "binomial")
l1 <- glm(L_1  ~ Age_2 , data = logistic_s, family = "binomial")
c1 <- glm(C_1  ~ Age_2 , data = logistic_s, family = "binomial")
m1 <- glm(m  ~ Age_2 , data = logistic_s, family = "binomial")

model_summs <- export_summs(n1,g1,ga1,l1,c1,m1,
                            error_format = "({conf.low}, {conf.high})",
                            model.names = c("N","G","G_1","L_1","C_1","m"))

col_width(model_summs) = c(0.84,rep(0.95,6))

model_summs
```

Answer 2

We can do this with the gtsummary package. By default, gtsummary prints tables with the gt packages that does not support Word output. But we can convert any gtsummary object to a type supported by Word. In the example below, we'll convert to a flextable.

I provided 2 formats for your solution: one long table, and one (very) wide table. Here's what the long table looks like:

The wide format looks like this:

We get the number of events for each model using the add_nevent() function. Here's the full code for the R Markdown file. NOTE: The as_flextable() is new, and you'll need to install the dev version of gtsummary remotes::install_github("ddsjoberg/gtsummary") http://www.danieldsjoberg.com/gtsummary/index.html

---
title: "Regression Tables with gtsummary"
output: word_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

## Data 

```{r}
set.seed(324524)
logistic_s <- data.frame(N=rbinom(200,1,0.5),
                         G=rbinom(200,1,0.5),
                         G_1=rbinom(200,1,0.5),
                         L_1=rbinom(200,1,0.5),
                         C_1=rbinom(200,1,0.5),
                         m=rbinom(200,1,0.5),
                         Age_2=round(rnorm(200,40,6)))
```

## Long Table

Create a table that is one line per model

```{r}
library(gtsummary)
library(tidyverse)

# build models
tbl_uvregression(
  data = logistic_s,
  x = Age_2,
  method = glm,
  method.args = list(family = binomial),
  exponentiate = TRUE
) %>%
  modify_header(label = "**Model Outcome**") %>%
  # add the number of evenets
  add_nevent() %>%
  # export as flextable instead of gt table
  as_flextable()
```

## Wide Table

Create a table that wide

```{r cars}
# list all outcomes
outcomes <- c("N", "G", "G_1", "L_1", "C_1", "m") 

# map over each outcome to make a model and table
list_regression_tables <- 
  map(outcomes,
      # make a model for each outcome
      ~glm(
        formula = as.formula(paste(.x, "Age_2", sep = "~")),
        data = logistic_s,
        family = binomial
      ) %>%
        # putting model in table with tbl_regression
        tbl_regression(exponentiate = TRUE) %>%
        # add the number of evenets
        add_nevent() 
  )

# merging all tables together
tbl_merge(tbls = list_regression_tables,
          tab_spanner = outcomes) %>%
  # export as flextable instead of gt table
  as_flextable()
```

Happy Coding!