---
title: "Group Regression Analysis and Visualization"
author: 
  - name: Shixiang Wang
    affiliation: Central South University
    email: wangshx@csu.edu.cn
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Group Regression Analysis and Visualization}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  out.width = "100%"
)
```

We are using the same example from the [ezcox package vignette](https://CRAN.R-project.org/package=ezcox/vignettes/ezgroup.html).

Load the package and data.

```{r setup}
library(bregr)

data <- survival::lung
data <- data |>
  dplyr::mutate(
    ph.ecog = factor(ph.ecog),
    sex = ifelse(sex == 1, "Male", "Female")
  )
```

Construct grouped batch survival models to determine if the variable `ph.ecog` has different survival effects under different sex groups.

```{r groupby-pipeline}
mds <- br_pipeline(
  data,
  y = c("time", "status"),
  x = "ph.ecog",
  group_by = "sex",
  method = "coxph"
)
```

We can examine the constructed models.

```{r get-models}
br_get_models(mds)
```

Now, display the results using a forest plot.

```{r show-forest, fig.width=9, fig.height=5, dpi=150}
br_show_forest(mds)
```

We can optimize the plot for better visualization, for example, by removing the second column of the table and eliminating the row with `NA` results.

```{r show-forest2, fig.width=8, fig.height=4, dpi=150}
br_show_forest(
  mds,
  drop = 2,
  subset = !(Group_variable == "Female" & variable == "ph.ecog" & label == 3)
)
```

To subset the data rows, we can input an R expression using variables from `br_get_results(mds)`. For example, we can use `Group_variable == "Female" & variable == "ph.ecog" & label == 3` to locate the row we want to remove, and then use `!()` to select the negated rows.

If drop `All` group is necessary, update the `subset` with:

```{r show-forest-rm-all, fig.width=8, fig.height=4, dpi=150}
br_show_forest(
  mds,
  drop = 2,
  subset = !((Group_variable == "Female" & variable == "ph.ecog" & label == 3) |
    (Group_variable == "All"))
)
```