comments
Respond
Comment on the article
Add a citation
Reply with an article
Start a new topic
Edit
Edit article
Delete article
Share
Invite
Link
Embed
Social media
Avatar
View
Graph
Explorer
Focus
Down
Load 1 level
Load 2 levels
Load 3 levels
Load 4 levels
Load all levels
All
Dagre
Focus
Down
Load 1 level
Load 2 levels
Load 3 levels
Load 4 level
Load all levels
All
Tree
SpaceTree
Focus
Expanding
Load 1 level
Load 2 levels
Load 3 levels
Down
All
Down
Radial
Focus
Expanding
Load 1 level
Load 2 levels
Load 3 levels
Down
All
Down
Box
Focus
Expanding
Down
Up
All
Down
Article ✓
Outline
Document
Down
All
Page
Canvas
Time
Timeline
Calendar
Updates
Subscribe to updates
Get updates
Past 24 hours
Past week
Past month
Past year
Pause updates
Contact us
spread
Infectious Disease Spread Models
RELATED ARTICLES
Explain
⌅
EIDM
EIDM ☜The Emerging Infectious Diseases Modelling Initiative (EIDM) – by the Public Health Agency of Canada and NSERC – aims to establish multi-disciplinary network(s) of specialists across the country in modelling infectious diseases to be applied to public needs associated with emerging infectious diseases and pandemics such as COVID-19. [1]☜F1CEB7
⌃
Software
Software☜Learn more about the software being used across the EIDM network.☜C78CB7
⌃
Software languages
Software languages☜☜76A4CF
⌃
R
R☜☜76A4CF
⌃
R Packages
R Packages☜List of ten most popular R packages in infectious disease modelling as measured by the pkgsearch package (on 2021-06-09).☜76A4CF
■
spread
spread☜Infectious Disease Spread Models☜C78CB7
□
EpiModel
EpiModel☜EpiModel is an R package that provides tools for simulating and analyzing mathematical models of infectious disease dynamics. Supported epidemic model classes include deterministic compartmental models, stochastic individual contact models, and stochastic network models. Disease types include SI, SIR, and SIS epidemics with and without demography, with utilities available for expansion to construct and simulate epidemic models of arbitrary complexity. [1]☜C78CB7
□
epitrix
epitrix☜A collection of small functions useful for epidemics analysis and infectious disease modelling. This includes computation of basic reproduction numbers from growth rates, generation of hashed labels to anonymize data, and fitting discretized Gamma distributions. [2]☜C78CB7
□
hhh4contacts
hhh4contacts☜Age-Structured Spatio-Temporal Models for Infectious Disease Counts – Meyer and Held (2017) present an age-structured spatio-temporal model for infectious disease counts. The approach is illustrated in a case study on norovirus gastroenteritis in Berlin, 2011-2015, by age group, city district and week, using additional contact data from the POLYMOD survey. [2]☜C78CB7
□
ibmcraftr
ibmcraftr☜Toolkits to Develop Individual-Based Models in Infectious Disease – It provides a generic set of tools for initializing a synthetic population with each individual in specific disease states, and making transitions between those disease states according to the rates calculated on each timestep. The new version 1.0.0 has C++ code integration to make the functions run faster. It has also a higher level function to actually run the transitions for the number of timesteps that users specify. [1]☜C78CB7
□
idmodelr
idmodelr☜The primary aim of idmodelr is to provide a library of infectious disease models for researchers. These models can be used to understand the underlying dynamics and as a reference point when developing models for research. idmodelr also provides a range of utilities. These include: plotting functionality; a simulation wrapper; scenario analysis tooling; an interactive dashboard; tools for handling mult-dimensional models; and both model and parameter look up tables. [1]☜C78CB7
□
pspline.inference
pspline.inference☜Estimation of Characteristics of Seasonal and Sporadic Infectious Disease Outbreaks Using Generalized Additive Modeling with Penalized Basis Splines. [1]☜C78CB7
□
shinySIR
shinySIR☜Interactive Plotting for Mathematical Models of Infectious Disease Spread – Provides interactive plotting for mathematical models of infectious disease spread. Users can choose from a variety of common built-in ordinary differential equation (ODE) models (such as the SIR, SIRS, and SIS models), or create their own. This latter flexibility allows shinySIR to be applied to simple ODEs from any discipline. [1]☜C78CB7
□
SimBIID
SimBIID☜Simulation-Based Inference Methods for Infectious Disease Model – Provides some code to run simulations of state-space models, and then use these in the Approximate Bayesian Computation Sequential Monte Carlo (ABC-SMC) algorithm of Toni et al. (2009) and a bootstrap particle filter based particle Markov chain Monte Carlo (PMCMC) algorithm (Andrieu et al., 2010). Also provides functions to plot and summarise the outputs. [1]☜C78CB7
□
socialmixr
socialmixr☜Social Mixing Matrices for Infectious Disease Modelling — Provides methods for sampling contact matrices from diary data for use in infectious disease modelling, as discussed in Mossong et al. (2008)☜C78CB7
□
Graph of this discussion
Graph of this discussion☜Click this to see the whole debate, excluding comments, in graphical form☜dcdcdc
Enter the title of your article
Enter a short (max 500 characters) summation of your article
Click the button to enter task scheduling information
Open
Enter the main body of your article
Prefer more work space? Try the
big editor
Enter task details
Message text
Select assignee(s)
Due date (click calendar)
RadDatePicker
RadDatePicker
Open the calendar popup.
Calendar
Title and navigation
Title and navigation
<<
<
July 2024
>
<<
July 2024
S
M
T
W
T
F
S
27
30
1
2
3
4
5
6
28
7
8
9
10
11
12
13
29
14
15
16
17
18
19
20
30
21
22
23
24
25
26
27
31
28
29
30
31
1
2
3
32
4
5
6
7
8
9
10
Reminder
No reminder
1 day before due
2 days before due
3 days before due
1 week before due
Ready to post
Copy to text
Enter
Cancel
Task assignment(s) have been emailed and cannot now be altered
Lock
Cancel
Save
Comment graphing options
Choose comments:
Comment only
Whole thread
All comments
Choose location:
To a new map
To this map
New map options
Select map ontology
Options
Standard (default) ontology
College debate ontology
Hypothesis ontology
Influence diagram ontology
Story ontology
Graph to private map
Cancel
Proceed
+Comments (
0
)
- Comments
Add a comment
Newest first
Oldest first
Show threads
+Citations (
1
)
- Citations
Add new citation
List by:
Citerank
Map
+About
- About
Entered by:-
David Price
NodeID:
#707869
Node type:
Resource
Entry date (GMT):
1/30/2023 10:52:00 PM
Last edit date (GMT):
1/30/2023 11:36:00 PM
Show other editors
Incoming cross-relations:
0
Outgoing cross-relations:
0
Average rating:
0
by
0
users
Enter comment
Select article text to quote
Cancel
Enter
welcome text
First name
Last name
Email
Skip
Join
x
Select file to upload