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GitHub - mrc-ide/mrc-ide.github.io
Contribute to mrc-ide/mrc-ide.github.io development by creating an account on GitHub.
Github.comDA: 10 PA: 26 MOZ Rank: 36
MRC-GIDA Blog
MRC-GIDA Blog ... About
Mrc-ide.github.ioDA: 17 PA: 17 MOZ Rank: 19
Framework for Specifying and Simulating Individual
Provide memory efficient, fast code for executing your model Installation The package can be installed from github using the “remotes” library library ( 'remotes') install_github ('mrc-ide/individual') Alternatively you can install individual directly from CRAN, but be aware that the CRAN version may not be the most recent version of the package:
Mrc-ide.github.ioDA: 17 PA: 12 MOZ Rank: 31
Solve Delay Differential Equations • dde - MRC-GIDA Blog
Solves ordinary and delay differential equations, where the objective function is written in either R or C. Suitable only for non-stiff equations, the solver uses a Dormand-Prince method that allows interpolation of the solution at any point. This approach is as described by Hairer, Norsett and Wanner (1993) <ISBN:3540604529>. Support is also included for iterating difference equations.
Mrc-ide.github.ioDA: 17 PA: 5 MOZ Rank: 25
GitHub - mrc-ide/nimue
Overview. Nimue is an extension to the squire package that allows vaccination to be included. For detailed information on the base model structure and parameterisation please visit the squire webpage. Nimue adds an additional dimension to the squire model, allowing us to track the vaccination status across the modelled population.
Github.comDA: 10 PA: 15 MOZ Rank: 29
GitHub - mrc-ide/dde: :clock1130: :clock9: Delay …
Dde. This package solves ordinary differential equations (ODEs), delay differential equations (DDEs) and discrete-time difference (or recursion) equations, perhaps involving delays. For all the solvers, the target function can be an R function or a compiled function.
Github.comDA: 10 PA: 12 MOZ Rank: 27
GitHub - mrc-ide/drjacoby: Flexible Markov chain monte …
DrJacoby . drjacoby is an R package for performing Bayesian inference via Markov chain monte carlo (MCMC). In addition to being highly flexible it implements some advanced techniques that can improve mixing in tricky situations. Full details can be found on the drjacoby website. So far, drjacoby has been used in the following projects: The paper Estimates of the severity of …
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GitHub - mrc-ide/didehpc: Support for the DIDE cluster
The steps below are described in more detail in the vignettes. Ensure that your project is in a directory that the cluster can see (i.e. on one of the network drives). See notes for instructions. Set your DIDE credentials up so that you can log in and tell didehpc about them. Create a "context" in which future expressions will be evaluated ...
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GitHub - mrc-ide/conan: Conan the Librarian
:package::package::arrow_right::classical_building: Conan the Librarian :crossed_swords: - GitHub - mrc-ide/conan: Conan the Librarian
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COVID-19 Vaccine Modelling • nimue - MRC-GIDA Blog
Overview. Nimue is an extension to the squire package that allows vaccination to be included. For detailed information on the base model structure and parameterisation please visit the squire webpage. Nimue adds an additional dimension to the squire model, allowing us to track the vaccination status across the modelled population.
Mrc-ide.github.ioDA: 17 PA: 7 MOZ Rank: 33
ODE Generation and Integration • odin - MRC-GIDA Blog
Odin implements a high-level language for describing and implementing ordinary differential equations in R. It provides a “domain specific language” (DSL) which looks like R but is compiled directly to C. The actual solution of the differential equations is done with the deSolve package, giving access to the excellent Livermore solvers ...
Mrc-ide.github.ioDA: 17 PA: 6 MOZ Rank: 33
SEIR transmission model of COVID-19 • squire - MRC-GIDA Blog
To run the model by providing the country we use run_explicit_SEEIR_model (): r <- run_explicit_SEEIR_model (country = "Afghanistan") The returned object is a squire_simulation object, which is a list of two ojects: output - model output. parameters - model parameters. squire_simulation objects can be plotted as follows:
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MRC-GIDA Blog - About
MRC-GIDA Blog - About ... About ...
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Issues · mrc-ide/mrc-ide.github.io · GitHub
Contribute to mrc-ide/mrc-ide.github.io development by creating an account on GitHub.
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Dashboard ⋅ mrc-ide/drjacoby - codecov.io
Highly integrated with GitHub, Bitbucket and GitLab. Docs Support Blog. Log in Sign up. mrc-ide / drjacoby. Learn more. Overview Commits Branches Pulls Compare. Showing min. min. max. per day. day. hour. month. commit. coverage for the last 6 months. last 6 months. last 3 months. last 30 days . last 7 days. last 24 hours. Coverage Chart Loading. Not enough recent commits …
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Reproducible parallel inference and... | Wellcome Open Research
This dust model and its interface is named sircovid 20, and its code and documentation can be found at https://mrc-ide.github.io/sircovid. Running with n P = 100 for 2000 steps, one MCMC chain on a laptop took around 1 hour with a single core, and showed roughly linear speedup with number of cores when used for either extra particles or extra …
Wellcomeopenresearch.orgDA: 24 PA: 15 MOZ Rank: 54
COVIDHunter - mealser.github.io
COVIDHunter An Accurate, Flexible, and Environment-Aware Open-Source COVID-19 Outbreak Simulation Model. A COVID-19 outbreak simulation model that evaluates the current mitigation measures (i.e., non-pharmaceutical intervention) that are applied to a region, environmental conditions, different variants of concern, vaccination rates, and provides insight into what …
Mealser.github.ioDA: 17 PA: 23 MOZ Rank: 56
mrc-ide/dust: Iterate Multiple Realisations of Stochastic Models
An Engine for simulation of stochastic models. Includes support for running stochastic models in parallel, either with shared or varying parameters. Simulations are run efficiently in compiled code and can be run with a fraction of simulated states returned to R, allowing control over memory usage. Support is provided for building bootstrap particle filter …
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nimue | squire package that allows vaccination
Nimue is an extension to the squire package that allows vaccination to be included. For detailed information on the base model structure and parameterisation please visit the squire webpage.
Kandi.openweaver.comDA: 20 PA: 16 MOZ Rank: 54
mrc-ide/sircovid - Overview - CodeFactor.io
Code quality results for mrc-ide/sircovid repo on GitHub. Grade: A, issues: 0, files: 57, pulls: 8, branches: 1. Improve sircovid quality by creating an account on ...
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