IMPACTncd_Engl is an implementation of the IMPACTncd framework, developed by Chris Kypridemos with contributions from Max Birkett, Karl Emmert-Fees, Anna Head, Brendan Collins, Martin O'Flaherty, Peter Crowther (Melandra Ltd), Maria Guzman-Castillo, Amandine Robert, Piotr Bandosz, and Adithi R. Upadhya.
Several research grants have supported its development including grants from the Health Foundation, NIHR, EU Horizon2020, Liverpool City Council, MRC, NIH, and the National Cerebral and Cardiovascular Center in Japan.
Copyright (C) 2018-2023 University of Liverpool, Chris Kypridemos.
IMPACTncd_Engl is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, see http://www.gnu.org/licenses/ or write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
A simulation consists of baseline and what-if policy scenarios (or hypotheses). Policy scenarios typically comprise populations with improved risk factors, e.g. after some future health policy, 20% of the population show
- improved body mass index (BMI), blood pressure, or cholesterol level (each by 20%).
- increased fruit and vegetable intake (by 20%).
- reduced alcohol intake (by 20%).
- reduced smoking prevalence or passive smoking (each by 20%).
- increased physical activity (by a single day).
Output data is then analysed for health improvements, e.g. in disease prevalence, incidence, or mortality.
The IMPACTncd_Engl distribution is usually installed directly from GitHub via the Git version control system, which should be installed on the target system. While not absolutely required, Git eases installation of future updates and previous releases. While earlier versions will suffice, Git 2.40.0 was the latest at release time.
The IMPACTncd_Engl model is written primarily in, and so requires installation of, the R programming language, for which version 4.2.3 was the latest at release time. Additional R packages (listed in dependencies.yaml) will be installed automatically if missing at execution time, e.g. data.table, piggyback, foreach.
IMPACTncd_Engl is installed directly from GitHub, after which a model-specific configuration is set. With multiple configurations, different policy scenarios may be tested on the same server.
To install and run IMPACTncd_Engl we need to install R on Windows / Linux; and rtools (only for Windows) before these following steps
-
To use IMPACTncd England navigate here: https://github.com/ChristK/IMPACTncd_Engl
-
Select Code on the right side corner, this will show an option of Download ZIP
- Once downloaded unzip the folder and save it in desired location
To install and run IMPACTncd_Engl we need to install R on Windows / Linux; Git; and rtools (only for Windows) before these following steps
-
To use IMPACTncd England navigate here: https://github.com/ChristK/IMPACTncd_Engl
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Select Code on the right side corner, this will present a link which can be used to download the package in local system. Copy this link
- In terminal, type git clone https://github.com/ChristK/IMPACTncd_Engl.git (which is the copied link)
Important Note : It is highly recommended to create your own copies of sim_design.yaml present in inputs folder and simulation.R in the root folder to run this model and make no changes to the original sim_design.yaml and simulation.R, as this would help reducing conflicts while pulling changes from GitHub.
- All vignettes can be viewed using the code below
vignette(package = "IMPACTncdEngl")
- The next steps can be found in the vignette which can be accessed using the code below
vignette("how_to_test_run", package = "IMPACTncdEngl")
- Use the following code to open the vignette to run different policy scenarios
vignette("how_to_run_scenarios", package = "IMPACTncdEngl")
- Use the following code to open the vignette to understand model outputs
vignette("understanding_model_outputs", package = "IMPACTncdEngl")
- To completely delete the package IMPACTncdEngl is explained in a section called How to remove IMPACTncdEngl installed package in the vignette mentioned below
vignette("how_to_test_run", package = "IMPACTncdEngl")
[^policyScenario]