Modelling transmission dynamics of COVID-19, while accounting for presymptomatic infectiousness, time-varying ascertainment rates, transmission rates and population movements.
☆22Jul 18, 2020Updated 6 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:
- Basic Epidemic, Activity, and Response COVID-19 model☆31Jul 6, 2020Updated 6 years ago
- 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
- Covid19 microsimulation☆14May 6, 2020Updated 6 years ago
- Derive social mixing matrices from survey data.☆44Sep 28, 2026Updated last month
- Code for: The effect of human mobility and control measures on the COVID-19 epidemic in China☆22Dec 1, 2022Updated 3 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Contemporary statistical inference for infectious disease models using Stan☆16Mar 3, 2019Updated 7 years ago
- Synthetic Populations and Ecosystems of the World☆14Nov 3, 2017Updated 9 years ago
- Bayesian estimation of Rt (C code)☆13Mar 18, 2020Updated 6 years ago
- This project holds a line-list data (including mobility and exposure history, as well as epidemiological Timelines) of 10,000+ COVID-19 c…☆14Apr 28, 2023Updated 3 years ago
- A human mobility flow-augmented stochastic SEIR-style epidemic modeling framework is developed, which combines with data assimilation and…☆14Mar 10, 2023Updated 3 years ago
- ☆13Nov 1, 2022Updated 4 years ago
- SEIR transmission model of COVID-19. Documentation at:☆53Feb 15, 2024Updated 2 years ago
- Supplementary code for paper "Bayesian workflow for disease transmission model".☆29Feb 3, 2021Updated 5 years ago
- ☆11Aug 11, 2020Updated 6 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Agent Based Model for COVID 19 transmission dynamics☆11Nov 2, 2020Updated 6 years ago
- Wrapper on top of LightGraphs for preserving vertex numbering☆13Aug 24, 2023Updated 3 years ago
- An implementation of the Grammar of Graphics in R☆10Jun 15, 2022Updated 4 years ago
- National and subnational estimates of the time-varying reproduction number for Covid-19☆34Nov 26, 2025Updated 11 months ago
- Urban Dynamics Through the Lens of Human Mobility☆18Jun 3, 2023Updated 3 years ago
- A pipeline to identify gene family using mutiple tools and scripts.☆12Aug 22, 2021Updated 5 years ago
- an attention mechanism-based deep neural network for protein lysine lactylation site prediction in Rice (Oryza sativa)☆11Jan 22, 2022Updated 4 years ago
- https://epidemiology-stan.github.io/☆10Mar 12, 2022Updated 4 years ago
- Code for simulating the metapopulation SEIR model. Sample network for US national simulation included.☆25Sep 3, 2025Updated last year
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- The book aims to describe programming good practices and introduce common tools used in software development to guarantee reproducibility…☆14Jan 2, 2023Updated 3 years ago
- ☆12Oct 11, 2022Updated 4 years ago
- R script to parse the mp3s from Radiohead's OK Computer Minidisc recordings☆12Dec 29, 2019Updated 6 years 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…☆14May 23, 2023Updated 3 years ago
- R package to run BEAST2☆11Dec 8, 2025Updated 10 months ago
- ☆14Jun 17, 2023Updated 3 years ago
- ☆23Jan 30, 2021Updated 5 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
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- ☆12Aug 12, 2022Updated 4 years ago
- Shiny app providing estimates of future bed occupancy given recent admissions☆12Jul 2, 2020Updated 6 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
- We design a method for heritability estimation, namely LD Eigenvalue Regression (LDER), which extends the LDSC method and provides more a…☆13Aug 20, 2025Updated last year
- ☆13Mar 18, 2022Updated 4 years ago
- Causal Mediation analysis☆12Oct 13, 2026Updated 3 weeks ago
- hazard and excess hazard modelling with multidimensional penalized splines☆12Mar 25, 2026Updated 7 months ago