EMODAnalyzeR

This package intends to help members of the Bershteyn Lab analyze results of emod. This package was developed by members of the Bershteyn lab and Edinah Mudimu.

Installation

1. Make sure you are running R 4.0 or greater

2. Make sure you have devtools installed (if not, run install.packages(“devtools”) )

3. Run library(devtools)

4. Run install_github(“BershteynLab/EMODAnalyzeR”)

As of 2022-03-10, installation problems might come up as it has mostly been tested on David Kaftan’s machine.

Usage

library(EMODAnalyzeR) data = read.simulation.results(<path to runscenarios output folder>, ‘Baseline’, c(“Infected”, “Population”), min_age_inclusive = 15, max_age_inclusive = 49) plot.prevalence(data, 2000, 2040)

EMODAnalyzeR.md

Functions

• calculate.bounds.effective_count
• calculate.bounds.two_sigma
• calculate.DALY
• calculate.incidence
• calculate.pop_scaling_factor
• calculate.prevalence
• calculate.tests.performed
• emodplot.age_prevalence
• emodplot.prevalence
• emodplot.by_gender
• read.simulation.results.bigpurple
• read.simulation.results
• report.calibration.results