---
title: "Introduction for the tmt package"
author: "Jan Steinfeld"
date: June 27, 2019

output:
  prettydoc::html_pretty:
    smart: false
    theme: cayman
    highlight: github
    css: style.css
    fig_caption: yes
    number_sections: TRUE


vignette: >
  %\VignetteIndexEntry{Introduction for the tmt package}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}

bibliography: references.bib
csl: apa.csl
---


```{r setup, echo=FALSE, message=FALSE, warning=FALSE}
  knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>",
    fig.width = 10, 
    fig.height = 10
  )
  options(width=80)

  # includes: in_header: "header.html"
  library(tmt)
```
# Introduction
This package provides a collection of functions to simulate data, estimate item parameters and calculation of likelihood ratio test in multistage designs. 
In multistage tests, different groups of items (module) are presented to test persons depending on their response behavior to previous item groups. Multistage testing is thus a simple form of adaptive testing. If data are collected on the basis of such a multistage design and the items are estimated using the Conditional Maximum Likelihood (CML) method, @glas1988rasch has shown, that the item parameters are biased. 
While @eggen2011item propose to avoid the bias using the marginal maximum likelihood (MML) method, @zwitser2015conditional showed in their work, that taking the applied multistage design in consideration and including it in the estimation of the item parameters, the estimation of item parameters is not biased using the CML method. Their proposed solution is implemented in our package.
In this package, the approach of @zwitser2015conditional is implemented. It was ensured that the necessary specification of the multistage design is as simple as possible and will be described in detail below. For the multistage design, the elementary symmetric function has to be calculated several times, so that this is as efficient as possible, the relevant functions have been written in Rcpp [@rcpp].
In addition to estimating the item parameters for multistage designs, it is also possible to estimate the item parameters for conventional designs. In order to further increase the efficiency, the algorithm of @verhelst1984estimation was used for the elementary symmetry function.

The package is well tested, but errors can still be exist. If you find a bug, please report it to us (with an working example) preferred via github: [issues](https://github.com/jansteinfeld/tmt/issues)

# Package
Below are a few sample applications of our package, which should provide information for the start:

## Rasch model without multistage design
For the estimation of item parameters of a simple 1-PL model, the function <tt>tmt_rm</tt> must be called. Here only the data set has to be passed (as matrix or data.frame) to estimate item parameters. Additional arguments allow to turn off the estimates of the standard errors (for example, for time reasons) or to switch from "nlminb" to "optim" (as in the example below). Per default the items are normalized to sum = 0 as recommended by @glas2016.

```{r, rm_nmst, warning=FALSE}
   # simulate some data 
 dat <- tmt:::sim.rm(theta = 100,b = 10,seed = 1111)

  # estimate item parameters
 dat.rm <- tmt_rm(dat = dat, optimization = "optim")

 # print summary
 summary(dat.rm)

```

## Rasch model with simple multistage design
In order to estimate the item parameters in a multistage design, the corresponding design must first be specified. For the multistage design, it is necessary that each module is defined, as exemplified below with M1, M2, etc. The name of the module is arbitrary. The name of the module follows with "=~" the vector with the items of the respective path. If all modules have been defined, the start module(s) must be defined. The starting module(s) is/are described with a name and the sign "==" (double equal sign) followed by the particular module. Each path has a name followed by the ":=" character in the starting module and all other modules in that path. Each module must be followed in parentheses by the minimum (first number) and maximum (second number) of solved items in the respective module.

Keeping the syntax is very important, otherwise the design can not be translated.

| component         | syntax | example                                                      |
| ----------------- |:------:| ------------------------------------------------------------:|
| module            | =~     | M1 =~ c(i1, i2, i3, i4, i5)                                  |
| starting module   | ==     | Start == M2                                                  |
| path              | :=     | p1 := Start(minSolved,maxSolved)                             |
| stages            | +      | p1 := Start(minSolved,maxSolved) + M1(minSolved, maxSolved)  |

To estimate the item parameters the function <tt>tmt_rm</tt> must be called with the additional information of the multistage design. Additional arguments allow to turn off the estimates of the standard errors (for example, for time reasons) or to switch from "nlminb" to "optim" (as in the example below).

```{r, rm_mst, warning=FALSE}
  # Example for multistage-design
  mstdesign <- "
    M1 =~ c(i1, i2, i3, i4, i5)
    M2 =~ c(i6, i7, i8, i9, i10)
    M3 =~ c(i11, i12, i13, i14, i15)

    # define starting Block
    Start == M2

    # define path
    p1 := Start(0,2) + M1(0,5)
    p2 := Start(3,5) + M3(0,5)
  "
    # generate item parameters with corresponding names to the multistage design
  items <- seq(-1,1, length.out = 15)
  names(items) <- paste0("i",1:length(items))
  
    # generate random data under given multistage design
  dat <- tmt_sim(mstdesign = mstdesign, 
                      items = items, 
                      persons = 500, 
                      mean = 0, 
                      sd = 1)
    # estimate the item parameters under the given multistage-design
  dat.rm <- tmt_rm(dat = dat, 
                  mstdesign = mstdesign, 
                  optimization = "optim")
  
    # print summary of item parameters
  summary(dat.rm)
```
## Rasch model with cumulative multistage design
In order to estimate the item parameters in a cumulative multistage design, the corresponding design must first be specified. For the multistage design, it is necessary that each module is defined, as exemplified below with M1, M2, etc. The name of the module is arbitrary. The name of the module follows with "=~" the vector with the items of the respective module. If all modules have been defined, the start module(s) must be defined. The starting module(s) is/are described with a name and the sign "==" (double equal sign) followed by the particular module. Finally, all pathes must be defined. Each path has a name followed by the ":=" character in the starting module and all other modules (stages) in the path. Each module must be followed in parentheses by the minimum (first number) and maximum (second number) of solved items at that stage. For a cumulative design, the number of minimum and maximum solved items from the previous + the current module must be specified at the current stage. For this purpose the specifing character becomes "+=" instead of "+".

Keeping the syntax is very important, otherwise the design can not be translated.

| component         | syntax | example                                                      |
| ----------------- |:------:| ------------------------------------------------------------:|
| module            | =~     | M1 =~ c(i1, i2, i3, i4, i5)                                  |
| starting module   | ==     | Start == M2                                                  |
| path              | :=     | p1 := Start(minSolved,maxSolved)                             |
| stages            | +=     | p1 := Start(minSolved,maxSolved) += M1(minSolved, maxSolved) |

To estimate the item parameters the function <tt>tmt_rm</tt> must be called with the additional information of the multistage design. Additional arguments allow to turn off the estimates of the standard errors (for example, for time reasons) or to switch from "nlminb" to "optim" (as in the example below).

```{r, rm_mst_cumulative, warning=FALSE}
  # Example for multistage-design
   mstdesign <- "
    M1  =~ paste0('i',21:30)
    M2  =~ paste0('i',11:20)
    M3  =~ paste0('i', 1:10)
    M4  =~ paste0('i',31:40)
    M5  =~ paste0('i',41:50)
    M6  =~ paste0('i',51:60)
    
    # define starting module
    Start == M1

    # define path
    p1 := Start(0, 5) += M2( 0,10) += M3
    p2 := Start(0, 5) += M2(11,15) += M4
    p3 := Start(6,10) += M5( 6,15) += M4
    p4 := Start(6,10) += M5(16,20) += M6
    "
    # generate item parameters with corresponding names to the multistage design
  items <- seq(-1,1, length.out = 60)
  names(items) <- paste0("i",1:length(items))
  
    # generate random data under given multistage design
  dat <- tmt_sim(mstdesign = mstdesign, 
                      items = items, 
                      persons = 1000, 
                      mean = 0, 
                      sd = 1)
    # estimate the item parameters under the given multistage-design
  dat.rm <- tmt_rm(dat = dat, 
                  mstdesign = mstdesign, 
                  optimization = "optim")
  
    # print summary of item parameters
  summary(dat.rm)
```

## Likelihood-ratio Test
The likelihood ratio test of Andersen [@andersen1973goodness] is also implemented. The estimated item parameters either from an simple 1-PL model or from a 1-PL model with multistage design could be passed to the function <tt>tmt_lrtest</tt>. This function is also a generic function (like <tt>tmt_rm</tt>), which calls the specific function for data with/without multistage design. For the application on very large data sets it is possible to parallelize the <tt>tmt_lrtest</tt> function. For this purpose only the amount of cores has to be passed as additional argument (it is recommended to use three cores, if possible).

```{r, rm_lrtest, warning=FALSE}
    # simulate some data
  dat_nmst <- tmt:::sim.rm(theta = 100,b = 10,seed = 1111)

    # estimate item parameters
  dat_nmst_rm <- tmt_rm(dat = dat_nmst, optimization = "optim")
  
    # calculate likelihood ratio-test
  dat_lrt_nmst <- tmt_lrtest(dat_nmst_rm, optimization = "optim")
  
    # print summary
  summary(dat_lrt_nmst)
```

```{r, rm_lrtest_mst, warning=FALSE}
    # example of multistage-design
  mstdesign <- "
    M1 =~ c(i1, i2, i3, i4, i5)
    M2 =~ c(i6, i7, i8, i9, i10)
    M3 =~ c(i11, i12, i13, i14, i15)

    # define starting Block
    Start == M2

    # define path
    p1 := Start(0,2) + M1(0,5)
    p2 := Start(3,5) + M3(0,5)
  "
    # generate item parameters with corresponding names to the multistage design
  items <- seq(-1,1, length.out = 15)
  names(items) <- paste0("i",1:length(items))
  
      # generate random data under given multistage design
  set.seed(1111)
  dat_mst <- tmt_sim(mstdesign = mstdesign, 
                      items = items, 
                      persons = 500, 
                      mean = 0, 
                      sd = 1)

    # estimate the item parameters under the given multistage-design
  dat_mst_rm <- tmt_rm(dat = dat_mst, 
                  mstdesign = mstdesign, 
                  optimization = "optim")

    # calculate likelihood ratio-test
  dat_lrt_mst <- tmt_lrtest(dat_mst_rm, optimization = "optim")
  
    # print summary
  summary(dat_lrt_mst)
``` 

## Graphical model check
For a graphical comparison of estimated item parameters for each sub group, we provide a so-called graphical model check. Several options are available for further specification of the plot (internally the package ggplot2 is used)

```{r, gmt, warning=FALSE}
    # example of multistage-design
  items <- seq(-1,1,length.out = 30)
  names(items) <- paste0("i",1:30)
  persons = 100
  mean = 0
  sd = 1
  dat <- tmt:::sim.rm(theta = persons, b = items, 1111)
  
  dat.rm <- tmt_rm(dat, optimization = "optim")
  dat.lrt <- tmt_lrtest(dat.rm, split = "median", optimization = "optim")


  info <- rep(c("group_a","group_b"),each = 15)
  names(info) <- paste0("i",1:30)

  drop <- c("i1","i18","i20","i10")

  tmt_gmc(object = dat.lrt, 
    ellipse = TRUE, 
    info = info,
    drop = drop,
    title = "graphical model check",
    alpha = 0.05,
    legendtitle = "split criteria")

``` 

# References
