Modelling transmission dynamics of COVID-19, while accounting for presymptomatic infectiousness, time-varying ascertainment rates, transmission rates and population movements.
☆22Jul 18, 2020Updated 5 years ago
Alternatives and similar repositories for SAPHIRE
Users that are interested in SAPHIRE are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Derive social mixing matrices from survey data.☆43Updated this week
- Accompanying code for: Kucharski AJ, Russell TW et al. Early dynamics of transmission and control of COVID-19: a mathematical modelling s…☆71Dec 18, 2022Updated 3 years ago
- Code for: An investigation of transmission control measures during the first 50 days of the COVID-19 epidemic in China☆23Aug 27, 2020Updated 5 years ago
- Code for: The effect of human mobility and control measures on the COVID-19 epidemic in China☆22Dec 1, 2022Updated 3 years ago
- ☆13Nov 1, 2022Updated 3 years ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- A human mobility flow-augmented stochastic SEIR-style epidemic modeling framework is developed, which combines with data assimilation and…☆15Mar 10, 2023Updated 3 years ago
- Supplementary code for paper "Bayesian workflow for disease transmission model".☆28Feb 3, 2021Updated 5 years ago
- Approximate Bayesian Computation in python☆11Feb 19, 2015Updated 11 years ago
- Wrapper on top of LightGraphs for preserving vertex numbering☆13Aug 24, 2023Updated 2 years ago
- National and subnational estimates of the time-varying reproduction number for Covid-19☆34Nov 26, 2025Updated 4 months ago
- A pipeline to identify gene family using mutiple tools and scripts.☆11Aug 22, 2021Updated 4 years ago
- Urban Dynamics Through the Lens of Human Mobility☆17Jun 3, 2023Updated 2 years ago
- ☆11Aug 11, 2020Updated 5 years ago
- NeuronMotif: deciphering cis-regulatory codes by layerwise demixing of deep neural networks☆11Dec 3, 2023Updated 2 years ago
- Wordpress hosting with auto-scaling - Free Trial • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Code for simulating the metapopulation SEIR model. Sample network for US national simulation included.☆25Sep 3, 2025Updated 7 months ago
- R script to parse the mp3s from Radiohead's OK Computer Minidisc recordings☆12Dec 29, 2019Updated 6 years ago
- ☆23Jan 30, 2021Updated 5 years ago
- Code and description to implement Bayesian Kernel Machine Regression-Causal Mediation Analysis by Devick et al. (arXiv: 1811.10453)☆15Dec 19, 2023Updated 2 years ago
- A library of MATLAB functions for visualization, processing, and analysis of output from Bayesian models fit with Stan.☆10Dec 17, 2021Updated 4 years ago
- ☆14Jun 17, 2023Updated 2 years ago
- ☆13Mar 18, 2022Updated 4 years ago
- ☆11Aug 12, 2022Updated 3 years ago
- A package containing several useful R-functions for reading and plotting the results of Birth-Death Skyline (BDSKY) runs in BEAST2.☆12Nov 28, 2018Updated 7 years ago
- Wordpress hosting with auto-scaling - Free Trial • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Treatment of Infectious Transmissions through Agent-based Network☆17Oct 20, 2025Updated 5 months ago
- R package to run BEAST2☆11Dec 8, 2025Updated 4 months ago
- Some code for monkeypox☆10Jan 24, 2023Updated 3 years ago
- The R package 'phylosamp' implements novel tools that estimate the probability of transmission between two cases given phylogenetic linka…☆13May 23, 2023Updated 2 years ago
- Basic Tools for the Analysis of Disease Outbreaks☆12Oct 24, 2019Updated 6 years ago
- Guidelines and forecasts for a collaborative U.S. influenza forecasting project.☆39May 4, 2020Updated 5 years ago
- Python code for "Tracking R of COVID-19 A New Real-Time Estimation Using the Kalman Filter".☆27Jan 6, 2023Updated 3 years ago
- We help each other to study single-cell data☆16Jan 23, 2025Updated last year
- sftrack: Modern classes for tracking and movement data☆54Jul 27, 2023Updated 2 years ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- A small R package for finding timezone names from geographic coordinates☆12Feb 27, 2018Updated 8 years ago
- Coalescent simulation and likelihood for phylodynamic inference☆14May 15, 2025Updated 11 months ago
- ☆17Feb 23, 2021Updated 5 years ago
- ☆10Jul 9, 2020Updated 5 years ago
- Welcome to the StrainHub Repo - Files and Data - StrainHub Online:☆18Jun 26, 2022Updated 3 years ago
- Tools for querying the Withings API from R☆11Sep 2, 2025Updated 7 months ago
- RTI has developed this code for creation of synthetic populations from the U.S. Census TIGER and American Community Survey (ACS) data wit…☆21Dec 26, 2025Updated 3 months ago