---
title: "readme"
date: "`r format(Sys.time(), '%d %B %Y')`"
output: html_document
---
#Readme for Dropout Meta-analysis
##Introduction
This readme describes the files and data for the dropout meta-analysis.

##To reproduce the results:
* Make sure all files listed below are in the same directory (HTML files can be omitted)
* Open `dropout.Rmd`
* Knit the file

**Note** that re-kniting the files may potentially overwrite the output files in the folder.

**Note** that the knitting needs to occur from `dropout.Rmd` all at once. Knitting chunks in `dropout.Rmd` that call on child `.Rmd` files such as `substances.Rmd` fails when run interactively.

##Files
The following table describes all of the files in the directory. The output in the `*.html` files includes information about the system that was used for for the latest run of the `dropout.Rmd` file.

File | Description | Output |
----------|------------------------|------------------------------
`categorical.Rmd`|Knitr child file. <br> Is called from `dropout.Rmd`. <br> Evaluates study-level categorical variables.|Returns the knited analyses of study-level categorical variables, including plots and diagnostics as specified in `dropout.Rmd`. <br> Depends on the values in the parent environment created by `dropout.Rmd`.
`continuous.Rmd`|Knitr child file. <br> Is called from `dropout.Rmd`. <br> Evaluates study-level continuous variables.|Returns the knited analyses of study-level continuous variables, including plots and diagnostics as specified in `dropout.Rmd`. <br> Depends on the values in the parent environment created by `dropout.Rmd`.
`Data Dictionary.xlsx`|Excel file that includes the variable names, their descriptions, and their possible values, in human-readable format.|NA.
`datadictionary.R`|R code that facilitates translating the variable names in the `Meta Dataset` file into human readable names embedded into the output generated rom the `*.Rmd` files.|NA. When called, it creates a series of matrices that are used by the other `*.Rmd` files.
`diagnoses.Rmd`|Knitr child file. <br> Is called from `dropout.Rmd`. <br> Evaluates the study-arm-level comorbid diagnoses variable.|Returns the knited analyses of the study-arm-level comorbid diagnoses variable, including plots and diagnostics as specified in `dropout.Rmd`. <br> Depends on the values in the parent environment created by `dropout.Rmd`.
`dropout long.html`|Output from `dropout.Rmd` using the `long=TRUE` option. This includes more of the code, diagnostics, profile plots, and other inputs and outputs.|NA. It is output. Inclusion of plots is dependent on setting `plots=TRUE`.
`dropout short.html`|Output from `dropout.Rmd` using the `long=FALSE` option. This includes less of the code and diagnostics, excludes profile plots, and limits the printing of some inputs and outputs to make it more easy to evaluate|NA. It is output. Inclusion of plots is dependent on setting `plots=TRUE`.
`dropout.Rmd`|Parent knitr file. <br> Includes the parent rmarkdown and loops for calling the child knitr files.|Outputs the synthesis of everything from `dropout.Rmd` and the child knitr files. <br> Output saves as `dropout.html`, and is manually renamed to one of the `dropout long.html` or `dropout short.html` filenames.^[Programmatically kniting `dropout.Rmd` to rename the html output ran into errors with duplicate chunk names from the knitting of child files. The code therefore outputs by default to `dropout.html` based on the `.Rmd` filename, and the `dropout.html` file is manually renamed.]
`functions.R`|All of the custom functions, convenience functions, and function wrappers used in the `*.Rmd` files.|Depends on the functions called.
`Meta Dataset.xlsx`|The input dataset for analysis.<br>Includes the data dictionary.|NA: data set.
`readme.html`|The output from `readme.Rmd`.|NA: it is output.
`readme.Rmd`|The file that constructs the readme information.|`readme.html`
`substances.Rmd`|Knitr child file. <br> Is called from `dropout.Rmd`. <br> Evaluates study-arm-level substance use and use pattern variables.|Returns the knited analyses of study-arm-level substance use and use pattern variables, including plots and diagnostics as specified in `dropout.Rmd`. <br> Depends on the values in the parent environment created by `dropout.Rmd`.

