R packages by mrc-ide

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'.

Last updated 30 days ago

randomrandom-distributionsrandom-generationrandom-samplingrng

42 stars 13.18 score 3 dependencies 173 dependents

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>.

Last updated 1 months ago

94 stars 12.35 score 56 dependencies 7 dependents

duckdb - DBI Package for the DuckDB Database Management System

The DuckDB project is an embedded analytical data management system with support for the Structured Query Language (SQL). This package includes all of DuckDB and a R Database Interface (DBI) connector.

Last updated 12 months ago

databaseduckdbolap

120 stars 11.89 score 1 dependencies 45 dependents

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 3 months ago

infrastructure

104 stars 10.03 score 8 dependencies 2 dependents

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.

Last updated 7 months ago

jsonjson-validationjsonvalidate

48 stars 9.72 score 5 dependencies 41 dependents

orderly - 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.

Last updated 1 years ago

117 stars 9.63 score 34 dependencies 4 dependents

orderly2 - Orderly Next Generation

Reimplementation of orderly based on outpack.

Last updated 6 days ago

7 stars 8.05 score 21 dependencies 2 dependents

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 4 days ago

18 stars 7.77 score 15 dependencies 3 dependents

malariasimulation - An individual based model for malaria

Specifies the latest and greatest malaria model.

Last updated 3 days ago

16 stars 7.74 score 42 dependencies

naomi - Naomi Model for Subnational HIV Estimates

This package implements the Naomi model for subnational HIV estimates.

Last updated 4 days ago

9 stars 7.64 score 135 dependencies 2 dependents

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 3 months ago

19 stars 7.30 score 22 dependencies

rrq - Simple Redis Queue

Simple Redis queue in R.

Last updated 18 days ago

clusterinfrastructure

24 stars 7.23 score 24 dependencies 3 dependents

context - Contexts for evaluating R expressions

Contexts for evaluating R expressions.

Last updated 1 years ago

clusterinfrastructure

5 stars 6.84 score 9 dependencies 2 dependents

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 11 months ago

22 stars 6.72 score 10 dependencies 1 dependents

hipercow - High Performance Computing

Set up cluster environments and jobs. Moo.

Last updated 2 months ago

1 stars 6.39 score 10 dependencies 1 dependents

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.

Last updated 3 days ago

2 stars 6.38 score 4 dependencies 2 dependents

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.

Last updated 3 months ago

12 stars 6.26 score 69 dependencies

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>.

Last updated 19 days ago

infrastructure

9 stars 6.01 score 0 dependencies 3 dependents

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 13 days ago

15 stars 5.97 score 2 dependencies

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 4 days ago

3 stars 5.83 score 31 dependencies

didehpc - DIDE HPC Support

DIDE HPC support.

Last updated 1 years ago

clusterinfrastructure

10 stars 5.72 score 30 dependencies

eppasm - Age-structured EPP Model for HIV Epidemic Estimates

What the package does (one paragraph).

Last updated 4 months ago

6 stars 5.04 score 39 dependencies 3 dependents

porcelain - Turn a Package into an HTTP API

Wrapper around the plumber package to turn a package into an HTTP API. This adds some conventions that we find useful, such as some testing infrastructure and automatic validation of responses against a json schema.

Last updated 7 months ago

4 stars 5.03 score 29 dependencies 3 dependents

odin2 - Next generation odin

Temporary package for rewriting odin.

Last updated 2 days ago

1 stars 4.89 score 7 dependencies

mockr - Mocking in R

Provides a means to mock a package function, i.e., temporarily substitute it for testing. Designed as a drop-in replacement for the now deprecated 'testthat::with_mock()' and 'testthat::local_mock()'.

Last updated 2 years ago

4.83 score 2 dependencies

vimpact - Vaccine Impact Calculation

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

Last updated 6 months ago

2 stars 4.80 score 41 dependencies

hintr - R API for calling naomi district level HIV model

R API for calling naomi district level HIV model.

Last updated 4 days ago

2 stars 4.78 score 170 dependencies 1 dependents

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.

Last updated 2 days ago

4.76 score 5 dependencies 1 dependents

traduire - Internationalisation on the Fly

Internationalisation ('i18n') support for R, switching languages at runtime, based on the 'i18next' 'JavaScript' library. This provides an alternative approach to internationalisation than supported directly by R.

Last updated 5 days ago

5 stars 4.48 score 6 dependencies 4 dependents

first90 - The first90 model

Implements the Shiny90 model for estimating progress towards the UNAIDS "first 90" target for HIV awareness of status in sub-Saharan Africa.

Last updated 2 months ago

5 stars 4.43 score 29 dependencies 3 dependents

popim - POPulation IMmunity: Run a Demographic Model of Vaccine Exposure Over Time

Tools for setting up an age-structured population, applying vaccination activities to it, and tracking vaccine-induced immunity through time.

Last updated 3 months ago

1 stars 4.34 score 36 dependencies

beers - Calculate Beers Ordinary Interpolation

Calculate Beers Interpolation (both Ordinary and Modified method); a six-term formula which minimizes the fifth differences of the interpolated results. See p877 of The Methods and Materials of Demography, Volume 2, referring to Beers, The Record of the American Institute of Actuaries, 34, Part I (69):59-60, June 1945.

Last updated 4 years ago

demographyinterpolationsubdivision

2 stars 3.95 score 0 dependencies 3 dependents

specio - Read Spectrum Files

Read data from Spectrum PJNZ file into R consumable format for EPP.

Last updated 3 years ago

eppspectrum

1 stars 3.78 score 5 dependencies 2 dependents

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.

Last updated 5 days ago

3.73 score 8 dependencies 3 dependents

montagu - Interface with 'montagu'

Client for interacting with the montagu API, and authentication with the montagu OrderlyWeb instance. This package is part of montagu.

Last updated 5 years ago

2 stars 3.48 score 22 dependencies

hipercow.windows - DIDE HPC Support for Windows

Driver for using the DIDE windows cluster, via the hipercow package. Typically the user will install that package directly and this once they are requested to.

Last updated 2 months ago

1 stars 3.40 score 30 dependencies

orderly.db - Database Support for 'orderly2'

Access databases from 'orderly2' while running reports. Includes the basic 'SQL' support originally included in 'orderly' for establishing connections and setting up data for use within a report.

Last updated 8 months ago

3.30 score 17 dependencies

queuer - Queue Tasks

Queue tasks to number of backends.

Last updated 1 years ago

clusterinfrastructure

4 stars 3.26 score 20 dependencies 1 dependents

spud - Sharepoint upload & download

Enables uploading, downloading and listing of files in sharepoint.

Last updated 4 years ago

sharepoint

2 stars 3.26 score 14 dependencies 2 dependents

conan2 - Conan the Librarian

Create libraries. For us, there is no spring. Just the wind that smells fresh before the storm.

Last updated 6 months ago

3.22 score 5 dependencies 1 dependents

logwatch - Watch Logs Run

Watch a log, streaming progress to the console.

Last updated 8 months ago

3.18 score 1 dependencies 5 dependents

provisionr - Provision a Library

Provision a set of packages into a new library, possibly for use on a different architecture.

Last updated 4 years ago

clusterinfrastructure

27 stars 3.13 score 20 dependencies

threemc - (Matt's) Multi-Level Model of Male Circumcision in Sub-Saharan Africa

Functions and datasets to support, and extend to other Sub-Saharan African countries, Thomas, M. et. al., 2021, A multi-level model for estimating region-age-time-type specific male circumcision coverage from household survey and health system data in South Africa, <arXiv:2108.091422>.

Last updated 8 months ago

3.08 score 78 dependencies

naomi.resources - Data dependencies for Naomi output generation

Makes data for Naomi output generation as an R package.

Last updated 8 months ago

3.02 score 25 dependencies

demogsurv - Demographic analysis of DHS and other household surveys

This package includes tools for calculating demographic indicators from household survey data. Initially developed for for processing and analysis from Demographic and Health Surveys (DHS) and Multiple Indicator Cluster Surveys (MICS). The package provides tools to calculate standard child mortality, adult mortality, and fertility indicators stratified arbitrarily by age group, calendar period, pre-survey time periods, birth cohorts and other survey variables (e.g. residence, region, wealth status, education, etc.). Design-based standard errors and sample correlations are available for all indicators via Taylor linearisation or jackknife.

Last updated 3 years ago

6 stars 2.92 score 20 dependencies

nomad - Create Portable R Repositories

Collects together all the bits required to easily install packages from R in situations with limited internet.

Last updated 4 years ago

8 stars 2.90 score 21 dependencies

odin.js - 'odin' 'JavaScript' support

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

Last updated 2 years ago

5 stars 2.88 score 12 dependencies

orderlyweb - Orderly Support for 'OrderlyWeb'

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

Last updated 2 years ago

2.78 score 40 dependencies 1 dependents

defer - Defer Errors

Create errors that can be deferred until later. With deferrable errors, collections of errors that are not immediately fatal can be collected and reported back at once.

Last updated 5 years ago

9 stars 2.73 score 0 dependencies

syncr - Synchronise Directories

Syncronise directories using rsync.

Last updated 7 years ago

clusterinfrastructure

9 stars 2.65 score 0 dependencies

testthat.buildkite - A testthat reporter for buildkite

A testthat reporter that prints progress output in a format for use in buildkite logs.

Last updated 1 years ago

2.54 score 31 dependencies

assessr - Performance metrics for probabilitic forecasts

This package implements various metrics for assessing the performance of probabilitic forecasts.

Last updated 4 years ago

2.35 score 0 dependencies 1 dependents

heartbeatr - Heartbeat Support using 'Redis'

Simple heartbeat support for R using 'Redis'. A heartbeat is a background thread that acts as a dead-man's switch. It will create a key on Redis that will automatically expire after a number of seconds and then periodically refresh that key, even when the R process is busy. If the process dies for some reason, then the key will disappear. A heartbeat can be used to detect loss of worker processes on shared systems.

Last updated 3 years ago

2 stars 2.30 score 4 dependencies

moz.utils - Utility functions

Utility functions, for useful utilitarian uses.

Last updated 1 years ago

2.26 score 78 dependencies

jenner - Internal Montagu Helpers

Helpers for Montagu.

Last updated 6 years ago

2.18 score 33 dependencies

mode - Solve Multiple ODEs

Solve multiple ODEs in parallel.

Last updated 2 years ago

2.08 score 16 dependencies

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 1 years ago

2.00 score 17 dependencies