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    • Modeling infectious disease dynamics
    • Model Implementation
      • flepiMoP's configuration file
      • Specifying population structure
      • Specifying compartmental model
      • Specifying initial conditions
      • Specifying seeding
      • Specifying observational model
      • Distributions
      • Specifying time-varying parameter modifications
      • Other configuration options
      • Code structure
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    • Inference Description
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      • Specifying data source and fitted variables
      • (OLD) Configuration options
      • (OLD) Configuration setup
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  • 🖥️More
    • Setting up the model and post-processing
      • Config writer
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      • Create a post-processing script
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    • Advanced
      • File descriptions
      • Numerical methods
      • Additional parameter options
      • Swapping model modules
      • Using plug-ins 🧩[experimental]
  • 🛠️How To Run
    • Before any run
    • Quick Start Guide
    • Multiple Configuration Files
    • Synchronizing Files
    • Advanced run guides
      • Running with Docker locally 🛳
      • Running locally in a conda environment 🐍
      • Running on AWS 🌳
      • Running On A HPC With Slurm
    • Common errors
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  • 🗜️Development
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  • JHU Internal
    • US specific How to Run
      • Running with Docker locally (outdated/US specific) 🛳
      • Running on Rockfish/MARCC - JHU 🪨🐠
      • Running with docker on AWS - OLD probably outdated
        • Provisioning AWS EC2 instance
        • AWS Submission Instructions: Influenza
        • AWS Submission Instructions: COVID-19
      • Running with RStudio Server on AWS EC2
    • Inference scratch
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  1. gempyor: modeling infectious disease dynamics
  2. Model Implementation

Distributions

This page describes the configuration schema for specifying distributions

Distribution
Parameters
Type/Format
Description

fixed

value

Any real number

Draws all values exactly equal to value

uniform

low

Any real number

Draws all values randomly from a uniform distribution with range [low, high]

high

Any real number greater than low

poisson

lam

Any positive real number

Draws all values randomly from a Poisson distribution with rate parameter (mean) lam (lambda)

binomial

size

Any non-negative integer

Draws all values randomly from a binomial distribution with number of trials (n) = size and probability of success on each trial (p) = prob

prob

Any number in [0,1]

lognormal

meanlog

Any real number

Draws all values randomly from a lognormal distribution (natural log, base e) with mean on a log scale of meanlog and standard deviation on a log scale of sdlog

sdlog

Any non-negative real number

truncnorm

mean

Any real number

Draws all values randomly from a truncated normal distribution with mean mean and standard deviation sd, truncated to have a maximum value of a and a minimum value of b

sd

Any non-negative real number

a

Any real number, or -Inf

b

Any real number greater than a, or Inf

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Last updated 7 months ago

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