The vignettes in the vignettes folder and the
Articles tab in the darthpack
website are meant to guide you through the R code-based
functions of darthpack with a fully functional decision
model to showcase the framework described by the Decision Analysis in R for
Technologies in Health (DARTH) workgroup in the manuscript A
need for change! A coding framework for improving transparency in
decision modeling (Alarid-Escudero F
2019). For a more detailed description of the usage and
installation of darthpack, we refer the reader to the
package’s website (https://darth-git.github.io/darthpack/). The framework
is divided into different directories, described in Table 1 of the main
manuscript, that could be accessed from the RStudio project
darthpack.Rproj. We refer to the directory names of this
framework and scripts stored in these directories using italic
style. These vignettes are created with R Markdown and are located in
the vignettes directory of the framework. The figures for the
case-study can be found in the figs directory, data required to
conduct some of the analyses of the different components are in the
data and data-raw directories and the R
scripts with functions, are located in the R directory. The
main R scripts that conduct the analyses of the different
components of the framework are stored in the analysis
directory. In this document we do not show all the R code
we refer to. Therefore, it is important to follow along while reading
this document. To make sure you have all the required packages needed to
run all the code, first install all the required and suggested packages
in DESCRIPTION file in the main directory of
darthpack.
The file Shiny_framework.R in the main folder is a R
Shiny application that encompasses all our analyses for our Sick-Sicker
case study. Specifically, it contains model calibration, model
validation, probabilistic sensitivity and deterministic analysis,
sensitivity analyses, and value of information analysis. In addition, it
allows the user to modify the model structure and input parameters
including initial age of the cohort, probabilities, utilities and costs.
The summary and visualization of results are displayed in the panel upon
upon a simply click. All R code are run in the background
so the user would not have to program or run any code. Through this app,
we demonstrate how we modelers can build user-friendly, “click-based”
applications for people who wish to use our models.
To use this app, simply open Shiny_framework.R and click
the green Run App button on the top right corner of the script
window.
The book describing our Sick-Sicker case study is written in R
Markdown using the bookdown package. More about books
written in R Markdown using bookdown can be found on this
website: https://bookdown.org/yihui/bookdown/. When you like to
generate the book yourself using Markdown you need to install the
bookdown package from CRAN or GitHub:
install.packages("bookdown")
# or the development version
# devtools::install_github("rstudio/bookdown")To compile this example to PDF, you need XeLaTeX. You are recommended to install TinyTeX (which includes XeLaTeX): https://yihui.name/tinytex/.