---
title: "Examples of Longitudinal Mediation Models"
output: rmarkdown::html_vignette
description: > 
  This vignette provides a comprehensive exploration and practical demonstrations of the `getMediation()` function. This function is designed to construct longitudinal mediation models, which evaluate how a baseline or longitudinal predictor affect the outcome process, mediated by an intermediary process.
vignette: >
  %\VignetteIndexEntry{getMediation_examples}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
has_data <- nzchar(system.file("extdata", "getMediation_examples.RData", package = "nlpsem"))
knitr::opts_chunk$set(eval = has_data)
```

## Load nlpsem package, dependent packages and set CSOLNP as the optimizer
```{r, message = FALSE}
library(nlpsem)
mxOption(model = NULL, key = "Default optimizer", "CSOLNP", reset = FALSE)
```

## Load pre-computed models
```{r, message = FALSE}
load(system.file("extdata", "getMediation_examples.RData", package = "nlpsem"))
```

## Load example data and preprocess data
```{r, message = FALSE, eval = FALSE}
# Load ECLS-K (2011) data
data("RMS_dat")
RMS_dat0 <- RMS_dat
# Re-baseline the data so that the estimated initial status is for the
# starting point of the study
baseT <- RMS_dat0$T1
RMS_dat0$T1 <- RMS_dat0$T1 - baseT
RMS_dat0$T2 <- RMS_dat0$T2 - baseT
RMS_dat0$T3 <- RMS_dat0$T3 - baseT
RMS_dat0$T4 <- RMS_dat0$T4 - baseT
RMS_dat0$T5 <- RMS_dat0$T5 - baseT
RMS_dat0$T6 <- RMS_dat0$T6 - baseT
RMS_dat0$T7 <- RMS_dat0$T7 - baseT
RMS_dat0$T8 <- RMS_dat0$T8 - baseT
RMS_dat0$T9 <- RMS_dat0$T9 - baseT
RMS_dat0$ex1 <- scale(RMS_dat0$Approach_to_Learning)
xstarts <- mean(baseT)
```

## Example 1: Fit  longitudinal mediation model with a bilinear spline functional form to assess how the baseline teacher-reported approach to learning influences the development of mathematics ability, mediated through the development of reading ability.
```{r, message = FALSE, eval = FALSE}
Med2_LGCM_BLS <- getMediation(
  dat = RMS_dat0, t_var = rep("T", 2), y_var = "M", m_var = "R",
  x_type = "baseline", x_var = "ex1", curveFun = "bilinear spline",
  records = list(1:9, 1:9), tries = 10,
  paramOut = TRUE
  )
```

```{r}
Med2_LGCM_BLS@Estimates
```

## Example 2: Fit  longitudinal mediation model with a bilinear spline functional form to assess how the development of reading ability influences the development of science ability, mediated through the development of mathematics ability.
```{r, message = FALSE, eval = FALSE}
set.seed(20191029)
Med3_LGCM_BLS <- getMediation(
  dat = RMS_dat0, t_var = rep("T", 3), y_var = "S", m_var = "M", x_type = "longitudinal",
  x_var = "R", curveFun = "bilinear spline", records = list(2:9, 1:9, 1:9),
  tries = 10, paramOut = TRUE
  )
```

```{r}
Med3_LGCM_BLS@Estimates
```