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EpiEstim - EpiEstim: a package to estimate time varying reproduction numbers from epidemic curves

This package provides tools to quantify transmissibility throughout an epidemic from the analysis of time series of incidence.

Last updated

11.41 score 104 stars 7 dependents 1.3k scripts 1.2k downloads

odin - ODE Generation and Integration

Generate systems of ordinary differential equations (ODE) and integrate them, using a domain specific language (DSL). The DSL uses R's syntax, but compiles to C in order to efficiently solve the system. A solver is not provided, but instead interfaces to the packages 'deSolve' and 'dde' are generated. With these, while solving the differential equations, no allocations are done and the calculations remain entirely in compiled code. Alternatively, a model can be transpiled to R for use in contexts where a C compiler is not present. After compilation, models can be inspected to return information about parameters and outputs, or intermediate values after calculations. 'odin' is not targeted at any particular domain and is suitable for any system that can be expressed primarily as mathematical expressions. Additional support is provided for working with delays (delay differential equations, DDE), using interpolated functions during interpolation, and for integrating quantities that represent arrays.

Last updated

infrastructure

10.02 score 106 stars 6 dependents 295 scripts 1.1k downloads

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 for performing Sequential Monte Carlo (e.g., Gordon et al. 1993 <doi:10.1049/ip-f-2.1993.0015>). The core of the simulation engine is the 'xoshiro256**' algorithm (Blackman and Vigna <arXiv:1805.01407>), and the package is further described in FitzJohn et al 2021 <doi:10.12688/wellcomeopenres.16466.2>.

Last updated

cppopenmp

7.79 score 20 stars 4 dependents 64 scripts

mcstate - Monte Carlo Methods for State Space Models

Implements Monte Carlo methods for state-space models such as 'SIR' models in epidemiology. Particle MCMC (pmcmc) and SMC2 methods are planned. This package is particularly designed to work with odin/dust models, but we will see how general it becomes.

Last updated

7.32 score 19 stars 1 dependents 102 scripts

squire - SEIR transmission model of COVID-19

An extended model of the SEIR model used in the Imperial College London Report into the global impact of COVID-19 and strategies for mitigation and suppression (https://www.imperial.ac.uk/mrc-global-infectious-disease-analysis/covid-19/report-12-global-impact-covid-19/). Extensions now include healthcare treatment pathways and excess mortality.

Last updated

6.95 score 53 stars 1 dependents 141 scripts

projections - Project Future Case Incidence

Provides functions and graphics for projecting daily incidence based on past incidence, and estimates of the serial interval and reproduction number. Projections are based on a branching process using a Poisson-distributed number of new cases per day, similar to the model used for estimating R0 in 'EpiEstim' or in 'earlyR', and described by Nouvellet et al. (2017) <doi:10.1016/j.epidem.2017.02.012>.

Last updated

6.94 score 14 stars 1 dependents 174 scripts 390 downloads

vaultr - Vault Client for Secrets and Sensitive Data

Provides an interface to a 'HashiCorp' vault server over its http API (typically these are self-hosted; see <https://www.vaultproject.io>). This allows for secure storage and retrieval of secrets over a network, such as tokens, passwords and certificates. Authentication with vault is supported through several backends including user name/password and authentication via 'GitHub'.

Last updated

6.89 score 26 stars 2 dependents 2 scripts 579 downloads

dde - Solve Delay Differential Equations

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.

Last updated

6.80 score 18 stars 2 dependents 58 scripts 432 downloads

drjacoby - Flexible Markov Chain Monte Carlo via Reparameterization

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.

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cpp

5.70 score 13 stars 77 scripts

odin.dust - Compile Odin to Dust

Less painful than it sounds, this package compiles an odin model to use dust, our new stochastic model system. Supports only a subset of odin models (discrete time stochastic models with no interpolation and no delays).

Last updated

5.56 score 3 stars 174 scripts

sircovid - SIR Model for COVID-19

Mechanistic models of transmission of the SARS-Cov-2 (COVID-19) virus implemented as stochastic compartmental models in odin and dust. Uses mcstate to perfom Bayesian evidence synthesis from several surveillance data streams through the estimation of transmission parameters.

Last updated

cppopenmp

4.48 score 29 stars 15 scripts

hermione - Robust estimation of COVID-19 Serial Interval

This package implements methods to robustly estimate COVID-19 Serial Interval accounting for biases introduced due to isolation of cases.

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3.00 score 2 stars 6 scripts

odin.js - 'odin' 'JavaScript' support

Create 'JavaScript' differential equation models from an 'odin' model specification.

Last updated

2.88 score 5 stars 3 scripts

orderlyweb - Orderly Support for 'OrderlyWeb'

Client for 'OrderlyWeb' for use from the 'orderly1' package. Allows downloading of reports, running remote reports and other interaction with the remote report repository.

Last updated

2.78 score 1 dependents 1 scripts

pika - Evaluate Correlation Between Time Series

This package takes two time series as inputs and first, determines the lag for the primary time series at which the cross-correlation between the two time series is highest. Second, the rolling correlation is calculated between the lagged primary time-series and the secondary time series.

Last updated

2.72 score 4 stars 13 scripts

spud - Sharepoint upload & download

Enables uploading, downloading and listing of files in sharepoint.

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sharepoint

2.48 score 2 stars 6 scripts

orderly.sharepoint - Sharepoint Driver for Orderly

Store orderly reports on Sharepoint. Provides an orderly remote driver that can be used to share orderly reports using Sharepoint. You can use Sharepoint's access controls and use this to set up a lightweight way of using orderly within a team.

Last updated

2.00 score 2 scripts

orderly.rstudio - RStudio addins for orderly

RStudio addins for orderly.

Last updated

1.70 score 1 stars 1 scripts

fstorr - File Storage

Store files by content, similar in spirit to the 'storr' package (into which this might get folded).

Last updated

1.70 score 1 stars 1 scripts