covidhm

covidm-alpha

testing version of covidm package

datadelay

R package for implementing delay functions

data_science_skills_practice

Contains my learning material and practice files for data science and machine learning concepts.

donskerclass.github.io

epi.branch.sim

Stochastic epidemiological branching simulation

epicontacts

Handling, Visualisation and Analysis of Epidemiological Contacts

epidist-paper

epiestim

A tool to estimate time varying instantaneous reproduction number during epidemics

epinow2

Estimate Realtime Case Counts and Time-varying Epidemiological Parameters

epinowcast

Tools to enable flexible and efficient hierarchical nowcasting of epidemiological time-series using a semi-mechanistic Bayesian model with support for a range of reporting and generative processes.

epiparameter

R package with epidemiological parameters for infectious diseases

epiparameterdashboard

A dashboard for visualising the epidemiological parameters stored in the epiparameter package.

epireview

evidence-bank

fitr

Functions for model fitting and inference

flu-evidence-synthesis

Code for reconstructing influenza dynamics from surveillance data using evidence synthesis techniques

forecast.vocs

Contains models and tools to produce short-term forecasts for both case and sequence notifications assuming circulation of either one or two variants. Tools are also provided to allow the evaluation of the use of sequence data for short-term forecasts in both real-world settings and in user generated scenarios.

free-data-science

🛠️ 🌐 Thematic list of high-quality data science resources

git-example

good-first-issues

Good first issues for the hpc.social community!

h5n1_uk_scenario_modelling

helpful_stan_functions

hettmo_01

R-package based on Stan to efficiently implement time-dependent transmission and stratification

immunity.thresholds

Code accompanying the manuscript "Combining serological and contact data to derive target immunity levels for achieving and maintaining measles elimination".

incidence2

Compute and visualise incidence (reworking of the original incidence package)

jamesmbaazam

Personal profile

jamesmbaazam.github.io

Personal website

kmisc

A collection of functions for common data reshaping operations, as well as functions for table and plot generation for R Markdown documents.

linelist

An R package to import, clean, and store case data