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computational-infectious-disease

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The companion repository to Computational Modeling of Infectious Disease by Chris von Csefalvay

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# The Computational Modeling of Infectious Disease

The companion repository to [Computational Modeling of Infectious Disease by Chris von Csefalvay (Elsevier/Academic Press, 2023)](https://www.elsevier.com/books/computational-modeling-of-infectious-diseases/csefalvay/978-0-323-95389-4).

# Buy the book

* [Directly from Elsevier](https://www.elsevier.com/books/computational-modeling-of-infectious-diseases/csefalvay/978-0-323-95389-4)
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# Table of contents

| Chapter | Computational Note |                                                                                                                                                                                                                             |
|---------|--------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| 
| 1 	     | 	                  | **Introduction**                               	                                                                                                                                                                            |
| 2 	     | 	                  | **Simple compartmental models**                	                                                                                                                                                                            |
|         | 2.1                | [ODE solvers](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch02/sir_models/SIR%20and%20related%20models.ipynb)                                                                           |
|         | 2.2                | [Solving ODEs in Python](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch02/sir_models/SIR%20and%20related%20models.ipynb)                                                                |
|         | 2.3                | [Phase portraits](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch02/phase_space/Phase%20space%20and%20stability.ipynb)                                                                   |                            |
|         | 2.4                | [Setting initial parameters](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch02/sir_models/SIR%20and%20related%20models.ipynb)                                                            |
|         | 2.5                | [Waning immunity](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch02/sir_models/SIR%20and%20related%20models.ipynb)                                                                       |
|         | 2.6                | [Solving SEIR models](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch02/sir_models/SIR%20and%20related%20models.ipynb)                                                                   |
|         | 2.7                | [Solving SIRC models](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch02/sir_models/SIR%20and%20related%20models.ipynb)                                                                   |
|         | 2.8                | [Solving SIRC models with reduced infectiousness](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch02/sir_models/SIR%20and%20related%20models.ipynb)                                       |
|         | 2.9                | [Symbolic computation of R_0 in a complex model](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch02/symbolic_r0/Symbolic%20determination%20of%20R0.ipynb)                                 |
|         | 2.10               | Contact tracing data with `NetworkX`                                                                                                                                                                                        |
|         | 2.11               | [Symbolic determination of the moment-generation function](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch02/symbolic_mgf/Symbolic%20moment%20generation%20function.ipynb)               |
|         | 2.12               | [Estimating R_t](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch02/rt_estimation/Rt%20estimation.ipynb)                                                                                  |
|         | 2.13               | [Multi-parameter estimation with `lmfit` and Emcee](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch02/multiparameter/Multiparameter%20fitting.ipynb)                                     |
|         |                    | [Funerary transmission](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch02/funerary_transmission/SIRFD.ipynb)                                                                             |
| 3 	     | 	                  | **Host factors**                               	                                                                                                                                                                            |
|         | 3.1                | [Calculating the R_0 of complex stratified models](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch03/stratified_r0/R_0%20of%20stratified%20system.ipynb)                                 |
|         | 3.2                | [Calculating the mixing matrix from a contact network](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch03/contact_waifw/WAIFW%20from%20network.ipynb)                                     |
|         | 3.3                | [Age differential SIR model](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch03/age_differential_sir/Age%20differential%20SIR.ipynb)                                                      |
|         | 3.4                | [Inference of mixing matrices](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch03/contact_matrix/Contact%20matrix%20inference.ipynb)                                                      |
|         | 3.5                | [Subcompartmental models](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch03/subcompartmental_models/Subcompartmental%20models.ipynb)                                                     |
|         | (Fig. 3.2)         | [Risk-stratified SIR model and coupling](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch03/risk_stratified_sir/Risk%20stratified%20SIR%20model.ipynb)                                    |
| 4 	     | 	                  | **Host-vector and multi-host interactions**    	                                                                                                                                                                            |
|         | 4.1                | [Implementing the Ross-MacDonald model](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch04/ross_macdonald/Ross-Macdonald%20model.ipynb)                                                   |
|         | 4.2                | [Creating streamplots](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch04/ross_macdonald/Ross-Macdonald%20model.ipynb)                                                                    |
|         | 4.3                | [Inferring parameters for a vector-borne disease](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch04/host_vector_pe/Inferring%20parameters%20of%20a%20SIR-SI%20host-vector%20model.ipynb) |
|         | 4.4                | [Managing complex models with structures](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch04/ross_macdonald/Ross-Macdonald%20model.ipynb)                                                 |
|         | 4.5                | [Time dependence in ODE solvers](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch04/zoonosis/Zoonosis.ipynb)                                                                              |
| 5 	     | 	                  | **Multi-pathogen dynamics**                    	                                                                                                                                                                            |
|         | 5.1                | [Solving multi-pathogen compartmental models with transition matrices](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch05/transition_matrix/Transition%20matrix.ipynb)                    |
|         | 5.2                | [Modeling the no-coinfection no-cross immunity interaction](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch05/transition_matrix/Transition%20matrix.ipynb)                               |
|         |                    | [Complete cross-immunity](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch05/complete_cross_immunity/Complete%20cross-immunity.ipynb)                                                     |
|         |                    | [No-coinfection no-cross immunity simplified](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch05/nc_nci/No-coinfection%20no-cross%20immunity.ipynb)                                       |
| 6 	     | 	                  | **Modeling the control of infectious disease** 	                                                                                                                                                                            |
|         | 6.1                | [Targeted vaccination](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch06/rtv/Risk%20targeted%20vaccination.ipynb)                                                                        |
|         | 6.2                | [Solving delay differential equations computationally](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch06/waning_dde/Vaccine%20waning%20immunity%20DDE%20model.ipynb)                     |
|         | 6.3                | [Modeling the effect of different quarantine regimes](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch06/quarantine/General%20quarantine.ipynb)                                           |
|         | 6.4                | [Iterative stateful evaluation](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch06/circuit_breaker/Circuit%20breaker.ipynb)                                                               |
| 7 	     | 	                  | **Temporal dynamics of epidemics**             	                                                                                                                                                                            |
|         | 7.1                | [Symbolic identification of equilibria](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch07/sir_stability/SIR%20numeric%20equilibrium%20and%20stability.ipynb)                             |
|         | 7.2                | [Numeric equilibrium of a SIR model](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch07/sir_stability/SIR%20numeric%20equilibrium%20and%20stability.ipynb)                                |
|         | 7.3                | [Symbolic equilibrium analysis of SEIR models](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch07/seir_stability/SEIR%20symbolic%20stability.ipynb)                                       |
|         | 7.4                | [Time series decomposition](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch07/ts_decomposition/Time%20series%20decomposition%20of%20influenza%20incidence.ipynb)                         |
|         | 7.5                | [Plotting time series decompositions](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch07/ts_decomposition/Time%20series%20decomposition%20of%20influenza%20incidence.ipynb)               |
|         | 7.6                | [Continuous Wavelet spectral analysis](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch07/cwt/Pertussis%20vs%20measles%20wavelet.ipynb)                                                   |
|         | 7.7                | [Discrete Lyapunov exponents to estimate chaos](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch07/discrete_lyapunov/Discrete%20Lyapunov%20exponents.ipynb)                               |
|         |                    | [Birth pulsing](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch07/birth_pulsing/Birth%20pulse.ipynb)                                                                                     |
|         |                    | [Sinusoidal temporal forcing](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch07/sinusoidal_forcing/Sinusoidal%20temporal%20forcing.ipynb)                                                |
| 8 	     | 	                  | **Spatial dynamics of epidemics**              	                                                                                                                                                                            |
|         | 8.1                | [Simple spatial lattices](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch08/spatial_lattice/Spatial%20lattice.ipynb)                                                                     |
|         | 8.2                | [Indexing and manipulation of multi-dimensional arrays](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch08/spatial_lattice/Spatial%20lattice.ipynb)                                       |
|         | 8.3                | [Kernel neighbourhoods](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch08/kernel_neighbourhoods/Kernel%20neighbourhoods.ipynb)                                                           |
|         | 8.4                | [A neighbourhood model of influence](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch08/filtering/Filtering.ipynb)                                                                        |
|         | 8.5                | [Minimum-filtered spatial lattice](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch08/filtering/Filtering.ipynb)                                                                          |
|         | 8.6                | [Spatial autocorrelation of COVID-19](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch08/morans_i/Moran's%20I.ipynb)                                                                      |
|         | 8.7                | [Modeling the pandemic that never was](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch08/reston_virus/Reston%20virus.ipynb)                                                              |
|         | 8.8                | [Access and distance](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch08/access_heterogeneities/Hospital%20access.ipynb)                                                                  |
|         | 8.9                | [Placing testing sites in Manhattan](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch08/testing_site_location/Testing%20site%20location.ipynb)                                            |
|         | 8.10               | [Nested interdiction](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch08/graph_interdiction/Graph%20interdiction.ipynb)                                                                   |
| 9 	     | 	                  | **Agent-based modeling**                       	                                                                                                                                                                            |
|         | 9.1                | [Using Mesa](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch09/sir_abm/Vanilla%20SIR%20ABM.ipynb)                                                                                        |
|         | 9.2                | [Initialising the model](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch09/sir_abm/Vanilla%20SIR%20ABM.ipynb)                                                                            |
|         | 9.3                | [Using enumerations to define states](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch09/sir_abm/Vanilla%20SIR%20ABM.ipynb)                                                               |
|         | 9.4                | [Creating the `Agent` blueprint](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch09/sir_abm/Vanilla%20SIR%20ABM.ipynb)                                                                    |
|         | 9.5                | [Probabilistic steps in ABMs](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch09/sir_abm/Vanilla%20SIR%20ABM.ipynb)                                                                       |
|         | 9.6                | [Creating the infectious process](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch09/sir_abm/Vanilla%20SIR%20ABM.ipynb)                                                                   |
|         | 9.7                | [Networks in Mesa](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch09/sir_abm/Vanilla%20SIR%20ABM.ipynb)                                                                                  |
|         | 9.8                | [Activations in Mesa](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch09/sir_abm/Vanilla%20SIR%20ABM.ipynb)                                                                               |
|         | 9.9                | [The `Model` class and parametrising the ABM](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch09/sir_abm/Vanilla%20SIR%20ABM.ipynb)                                                       |
|         | 9.10               | [Collection and export from ABMs](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch09/sir_abm/Vanilla%20SIR%20ABM.ipynb)                                                                   |
|         | 9.11               | [Creating seed populations](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch09/sir_abm/Vanilla%20SIR%20ABM.ipynb)                                                                         |
|         | 9.12               | [Iterative running of ABMs](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch09/sir_abm/Vanilla%20SIR%20ABM.ipynb)                                                                         |
|         | 9.13               | [The q infector](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch09/q_infector/Q%20infector.ipynb)                                                                                        |
|         | 9.14               | [An ABM for pure vector-borne disease](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch09/host_vector_abm/Host-vector%20ABM.ipynb)                                                        |
|         | 9.15               | [SI-SIRD epidemic competition](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch09/epidemic_competition/Epidemic%20competition%20SI-SIRD.ipynb)                                            |
|         | 9.16               | [Competing pathogens with a modal shift](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch09/epidemic_competition/Epidemic%20competition%20SI-SIRD.ipynb)                                  |
|         | 9.17               | [Quarantine modeling](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch09/quarantine/SEIRD%20with%20quarantine.ipynb)                                                                      |
|         | 9.18               | [Vaccination and peer influence](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch09/blocking/Modeling%20anti-vaccine%20sentiment.ipynb)                                                   |
|         | 9.19               | [Targeted prophylaxis](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch09/targeted_prophylaxis/Targeted%20prophylaxis.ipynb)                                                              |
|         | 9.20               | [Modeling anti-vaccine sentiment](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch09/blocking/Modeling%20anti-vaccine%20sentiment.ipynb)                                                  |
|         | 9.21               | [ABM of treatment effects](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch09/treatment_abm/SEIRD%20with%20treatment.ipynb)                                                               |
|         | 9.22               | [A spatial graph with movement](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch09/network_movement/Network%20with%20movement.ipynb)                                                      |
|         | 9.23               | [Homesick random-destination walks](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch09/homesick_agent/Homesick%20agent.ipynb)                                                             |
|         |                    | [Healthcare capacity contingent mortality](https://github.com/chrisvoncsefalvay/computational-infectious-disease/blob/main/ch09/hccm/Healthcare%20capacity%20contingent%20mortality.ipynb)                                  |

# About the author

[Chris von Csefalvay](https://www.chrisvoncsefalvay.com) is a data scientist and computational epidemiologist specialising in the computational dynamics of infectious diseases.
Born in Budapest, Hungary, he was educated at Oxford, Leiden and Cardiff.

He is the author of several papers. His first monograph, [_The Computational Modeling of Infectious Disease_](https://www.elsevier.com/books/computational-modeling-of-infectious-diseases/csefalvay/978-0-323-95389-4), was published by Elsevier in 2023. 
He is a Fellow of the Royal Society for Public Health, and lives in Northern Virginia with his wife and their Golden Retriever, Oliver.

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