---
title: "Introduction to user interface functions"
author: "Kazuki Yoshida, Yi Li"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Introduction to user interface functions}
  %\VignetteEngine{knitr::rmarkdown}
  \usepackage[utf8]{inputenc}
---

```{r, message = FALSE, tidy = FALSE, echo = F}
## knitr configuration: http://yihui.name/knitr/options#chunk_options
library(knitr)
showMessage <- FALSE
showWarning <- TRUE
set_alias(w = "fig.width", h = "fig.height", res = "results")
opts_chunk$set(comment = "##", error= TRUE, warning = showWarning, message = showMessage,
               tidy = FALSE, cache = FALSE, echo = TRUE,
               fig.width = 7, fig.height = 7,
               fig.path = "man/figures")
```

# Data preparation
The package require all variables to be numerical. So a multi-categorical factor needs to be converted to dummy variables or multiple dichotomous indicators. For survival outcome models, the indicator variable is for the event (1 = event, 0 = censored).

```{r}
library(regmedint)
library(tidyverse)
## Prepare dataset
data(vv2015)
```


# `regmedint` object
Following typical modeling workflow in R (e.g., `lm` and `glm`), a constructor function is used to create a model fit object. The `summary` method is the main user function for examining the results in the object. Lower-level methods such as `coef`, `vcov`, and `confint` are also provided for flexibility. The `print` method is mainly for meaningful implicit printing when only the object name is evaluated. All methods for the `regmedint` object has arguments `a0`, `a1`, `m_cde`, and `c_cond`. These are used to re-evaluate the results without re-fitting the underlying models.

## `regemedint()` object constructor
```{r}
regmedint_obj <- regmedint(data = vv2015,
                           ## Variables
                           yvar = "y",
                           avar = "x",
                           mvar = "m",
                           cvar = c("c"),
                           eventvar = "event",
                           ## Values at which effects are evaluated
                           a0 = 0,
                           a1 = 1,
                           m_cde = 1,
                           c_cond = 0.5,
                           ## Model types
                           mreg = "logistic",
                           yreg = "survAFT_weibull",
                           ## Additional specification
                           interaction = TRUE,
                           casecontrol = FALSE)
```
## `summary()` for `regmedint`
```{r}
summary(regmedint_obj)
summary(regmedint_obj, exponentiate = TRUE)
summary(regmedint_obj, m_cde = 0, c_cond = 1)
summary(regmedint_obj, m_cde = 0, c_cond = 1, level = 0.99)
```

## `coef()` for `regmedint`
```{r}
coef(regmedint_obj)
coef(regmedint_obj, m_cde = 0, c_cond = 1)
```

## `vcov()` for `regmedint`
```{r}
vcov(regmedint_obj)
vcov(regmedint_obj, m_cde = 0, c_cond = 1)
```

## `confint()` for `regmedint`
```{r}
confint(regmedint_obj)
confint(regmedint_obj, m_cde = 0, c_cond = 1)
confint(regmedint_obj, m_cde = 0, c_cond = 1, level = 0.99)
```

## `print()` for `regmedint`
```{r}
regmedint_obj # Implicit printing
print(regmedint_obj)
print(regmedint_obj, m_cde = 0, c_cond = 1)
```

## Methods for `summary_regmedint`
The `summary` method for the `regmedint` object returns an object of class `summary_regmedint`. To extract the mediation analysis result table as a matrix, use the `coef` method.

### `coef()` for `summary_regmedint`
```{r}
coef(summary(regmedint_obj))
```

### `print()` for `summary_regmedint`
```{r}
regmedint_summary_obj <- summary(regmedint_obj)
regmedint_summary_obj # Implicit printing
print(regmedint_summary_obj)
```