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EpiEstim - Estimate Time Varying Reproduction Numbers from Epidemic Curves

Tools to quantify transmissibility throughout an epidemic from the analysis of time series of incidence as described in Cori et al. (2013) <doi:10.1093/aje/kwt133> and Wallinga and Teunis (2004) <doi:10.1093/aje/kwh255>.

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13.49 score 105 stars 7 dependents 1.2k scripts 4.9k downloads

dqrng - Fast Pseudo Random Number Generators

Several fast random number generators are provided as C++ header only libraries: The PCG family by O'Neill (2014 <https://www.cs.hmc.edu/tr/hmc-cs-2014-0905.pdf>) as well as the Xoroshiro / Xoshiro family by Blackman and Vigna (2021 <doi:10.1145/3460772>). In addition fast functions for generating random numbers according to a uniform, normal and exponential distribution are included. The latter two use the Ziggurat algorithm originally proposed by Marsaglia and Tsang (2000, <doi:10.18637/jss.v005.i08>). The fast sampling methods support unweighted sampling both with and without replacement. These functions are exported to R and as a C++ interface and are enabled for use with the default 64 bit generator from the PCG family, Xoroshiro128+/++/** and Xoshiro256+/++/** as well as the 64 bit version of the 20 rounds Threefry engine (Salmon et al., 2011, <doi:10.1145/2063384.2063405>) as provided by the package 'sitmo'.

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randomrandom-distributionsrandom-generationrandom-samplingrngcpp

12.99 score 50 stars 267 dependents 446 scripts 54k downloads

jsonvalidate - Validate 'JSON' Schema

Uses the node library 'is-my-json-valid' or 'ajv' to validate 'JSON' against a 'JSON' schema. Drafts 04, 06 and 07 of 'JSON' schema are supported.

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jsonjson-validationjsonvalidate

10.84 score 52 stars 57 dependents 65 scripts 16k 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.

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infrastructure

9.99 score 106 stars 6 dependents 292 scripts 817 downloads

orderly - Lightweight Reproducible Reporting

Distributed reproducible computing framework, adopting ideas from git, docker and other software. By defining a lightweight interface around the inputs and outputs of an analysis, a lot of the repetitive work for reproducible research can be automated. We define a simple format for organising and describing work that facilitates collaborative reproducible research and acknowledges that all analyses are run multiple times over their lifespans.

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9.48 score 11 stars 3 dependents 176 scripts 634 downloads

monty - Monte Carlo Models

Experimental sources for the next generation of mcstate, now called 'monty', which will support much of the old mcstate functionality but new things like better parameter interfaces, Hamiltonian Monte Carlo, and other features.

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cpp

8.16 score 7 stars 7 dependents 101 scripts

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>.

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cppopenmp

7.74 score 20 stars 4 dependents 56 scripts

malariasimulation - An individual based model for malaria

Specifies the latest and greatest malaria model.

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cpp

7.61 score 23 stars 195 scripts

odin2 - Next generation odin

Temporary package for rewriting odin.

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7.51 score 11 stars 1 dependents 118 scripts

orderly1 - Lightweight Reproducible Reporting

Order, create and store reports from R. By defining a lightweight interface around the inputs and outputs of an analysis, a lot of the repetitive work for reproducible research can be automated. We define a simple format for organising and describing work that facilitates collaborative reproducible research and acknowledges that all analyses are run multiple times over their lifespans.

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7.35 score 116 stars 2 dependents 1 scripts

individual - Framework for Specifying and Simulating Individual Based Models

A framework which provides users a set of useful primitive elements for specifying individual based simulation models, with special attention models for infectious disease epidemiology. Users build models by specifying variables for each characteristic of individuals in the simulated population by using data structures exposed by the package. The package provides efficient methods for finding subsets of individuals based on these variables, or cohorts. Cohorts can then be targeted for variable updates or scheduled for events. Variable updates queued during a time step are executed at the end of a discrete time step, and the code places no restrictions on how individuals are allowed to interact. These data structures are designed to provide an intuitive way for users to turn their conceptual model of a system into executable code, which is fast and memory efficient.

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agent-based-modelingepidemiologyindividual-based-modellinginfectious-diseasescpp

7.33 score 35 stars 1 dependents 98 scripts 27 downloads

naomi - Naomi Model for Subnational HIV Estimates

This package implements the Naomi model for subnational HIV estimates.

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cpp

7.33 score 9 stars 2 dependents 66 scripts

dust2 - Next Generation dust

Experimental sources for the next generation of dust, which will properly adopt the particle filter, have support for partial parameter updates, support for multiple parameter sets and hopefully better GPU/MPI support.

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cppopenmp

6.66 score 6 dependents 126 scripts

epireview - Tools to update and summarise the latest pathogen data from the Pathogen Epidemiology Review Group (PERG)

Contains the latest open access pathogen data from the Pathogen Epidemiology Review Group (PERG). Tools are available to update pathogen databases with new peer-reviewed data as it becomes available, and to summarise the latest data using tables and figures.

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6.43 score 37 stars 15 scripts

rrq - Simple Redis Queue

Simple Redis queue in R.

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clusterinfrastructure

6.34 score 27 stars 2 dependents 15 scripts

hipercow - High Performance Computing

Set up cluster environments and jobs. Moo.

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5.92 score 1 stars 1 dependents 71 scripts

hintr - R API for calling naomi district level HIV model

R API for calling naomi district level HIV model.

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5.43 score 2 stars 1 dependents 2 scripts

orderly2 - Compatibility Wrapper for 'orderly'

Acts as an installable package that can be used with repositories that reference 'orderly2', rather than orderly.

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5.39 score 11 stars 128 scripts

eppasm - Age-structured EPP Model for HIV Epidemic Estimates

Age-structured EPP Model for HIV Epidemic Estimates.

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4.78 score 6 stars 4 dependents 21 scripts

vimpact - Vaccine Impact Calculation

VIMC IMPACT CALCULATION PACKAGE. This package is mainly for the VIMC Science Team to investigate vaccination impact.

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4.62 score 4 stars 7 scripts

naomi.zaf - Naomi Model for Subnational HIV Estimates -- South Africa District Estimates version

This package implements the Naomi model for subnational HIV estimates. This package is a customised version with additional features for the South Africa district HIV estimates. The version number is prefixed with 999710.Y.X.X.X, with 710 reflecting the ISO-3 numeric country code for South Africa, Y representing an increment on the South Africa specific version, and X.X.X reflects the main Naomi model version.

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cpp

4.48 score 8 scripts

naomi.resources - Data dependencies for Naomi output generation

Makes data for Naomi output generation as an R package.

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3.88 score 2 scripts

naomi.options - Contains model and calibration options and helper functions for Naomi

Contains model and calibration option JSON and default values and helper functions for Naomi.

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3.56 score 4 dependents 1 scripts

mpoxseir - Stochastic compartmental model of mpox transmission

Stochastic compartmental model of mpox transmission in odin.dust.

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cppopenmp

3.15 score 4 stars 10 scripts

orderly.db - Database Support for 'orderly'

Access databases from 'orderly' while running reports. Includes the basic 'SQL' support originally included in 'orderly' for establishing connections and setting up data for use within a report.

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3.00 score 1 scripts

naomi.utils - Utility Functions For Naomi Datasets

This package contains utility functions for creating and manipulating datasets for the Naomi model and related projects.

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2.65 score 1 stars 18 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.

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7.51 score 19 stars 1 dependents 158 scripts

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'.

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6.89 score 26 stars 2 dependents 2 scripts 578 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.

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6.82 score 18 stars 2 dependents 61 scripts 566 downloads

cinterpolate - Interpolation From C

Simple interpolation methods designed to be used from C code. Supports constant, linear and spline interpolation. An R wrapper is included but this package is primarily designed to be used from C code using 'LinkingTo'. The spline calculations are classical cubic interpolation, e.g., Forsythe, Malcolm and Moler (1977) <ISBN: 9780131653320>.

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infrastructureopenblas

5.92 score 8 stars 7 dependents 2 scripts 850 downloads