r-code-reference.qmd

---
title: "R Code Reference"
author: "Win Khaing"
format: pdf
editor: visual
---

```{r include=FALSE}
knitr::opts_chunk$set(message=FALSE)
```

```{r}
if (!require("pacman")) install.packages("pacman")
  pacman::p_load(ggplot2, tidyr, dplyr, tidyverse, knitr, finalfit, here)
```

## Contigency Table (2x2 Table)

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

data(CO2)
head(CO2)

# basic summary table
CO2 %>% select(!c(Plant, conc)) %>% tbl_summary()

# summary split by a categorical variable
CO2 %>% select(!c(Plant, conc)) %>% tbl_summary(by = Type)

# summary split by a categorical variable with p-value
CO2 %>% select(!c(Plant, conc)) %>%
  tbl_summary(by = Type) %>% add_p()

# include overall, extra heading, custom stats
CO2 %>% select(!c(Plant, conc)) %>%
  tbl_summary(
    by = Type,
    statistic = list(
      all_continuous() ~ "{mean} ({sd})",
      all_categorical() ~ "{n} / {N} ({p}%)"
    ),
    digits = all_continuous() ~ 2
  ) %>%
  add_p() %>% add_overall() %>%
  modify_spanning_header(c("stat_1", "stat_2") ~ "**Location**") %>%
  bold_labels()

# crosstabs
CO2 %>%
  tbl_cross(
    row = Type,
    col = Treatment, percent = "cell"
  ) %>%
  add_p() %>%
  bold_labels()
```