r-code-reference/demographic report.Rmd at main · winkhaing/r-code-reference · GitHub

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---
title: "Example knitr/R Markdown document"
author: "Your name"
date: "22/5/2020"
output:
  word_document: default
---

```{r include=FALSE}
knitr::opts_chunk$set(message=FALSE)
knitr::opts_chunk$set(dpi = 300)
```

# Load necessary library

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

# Demographic Table

```{r warning=FALSE}
# Specify explanatory variables of interest
explanatory <- c("age", "sex.factor",
                "extent.factor", "obstruct.factor",
                "nodes")

colon_s %>%
  summary_factorlist("differ.factor", explanatory,
                     p=TRUE, na_include=TRUE)
```

# Generate Final Table

```{r warning=FALSE}
colon_s <- colon_s %>%
  mutate(
    nodes = ff_label(nodes, "Lymph nodes involved")
    )

table1 <- colon_s %>%
  summary_factorlist("differ.factor", explanatory,
                     p=TRUE, na_include=TRUE,
                     add_dependent_label=TRUE,
                     dependent_label_prefix = "Exposure: "
                     )
table1
```

# Logistic Regression Table

```{r warning=FALSE}
explanatory <- c( "differ.factor", "age", "sex.factor",
                "extent.factor", "obstruct.factor",
                "nodes")
dependent <- "mort_5yr"
table2 <- colon_s %>%
  finalfit(dependent, explanatory,
           dependent_label_prefix = "")
table2
```

# Odds Ratio Plot

```{r warning=FALSE}
colon_s %>%
  or_plot(dependent, explanatory,
          breaks = c(0.5, 1, 5, 10, 20, 30),
          table_text_size = 2.5)
```

# Save objects for knitr/markdown

```{r}
# creat folder
dir.create(here::here("data"), showWarnings = FALSE, recursive = TRUE)

# Verify the path
file_path <- here::here("data", "out.rda")
print(file_path)

# Save the objects
save(table1, table2, dependent, explanatory, file = file_path)
```

## Load Data

```{r}
load(here::here("data", "out.rda"))

```

## Table 1 - Demographics

```{r table1, echo = FALSE, warning=FALSE}
kable(table1, row.names=FALSE, align=c("l", "l", "r", "r", "r", "r"))
```

## Table 2 - Association between tumour factors and 5-year mortality

```{r table2, echo = FALSE, warning=FALSE}
kable(table2, row.names=FALSE, align=c("l", "l", "r", "r", "r", "r"))
```

## Figure 1 - Association between tumour factors and 5-year mortality

```{r figure1, echo = FALSE, warning=FALSE}
explanatory = c( "differ.factor", "age", "sex.factor",
                "extent.factor", "obstruct.factor",
                "nodes")
dependent = "mort_5yr"
colon_s %>%
  or_plot(dependent, explanatory, breaks = c(0.5, 1, 5, 10, 20, 30),
          table_text_size = 2.5)
```