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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12.74 score 103 stars 7 dependents 1.2k scripts 1.1k 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

12.63 score 48 stars 240 dependents 227 scripts 54k 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

10.04 score 106 stars 6 dependents 292 scripts 1.1k 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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9.85 score 11 stars 3 dependents 135 scripts 652 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

8.34 score 7 stars 7 dependents 81 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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7.83 score 116 stars 2 dependents 1 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

7.76 score 20 stars 4 dependents 59 scripts

odin2 - Next generation odin

Temporary package for rewriting odin.

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7.68 score 9 stars 1 dependents 99 scripts

malariasimulation - An individual based model for malaria

Specifies the latest and greatest malaria model.

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cpp

7.51 score 21 stars 171 scripts

naomi - Naomi Model for Subnational HIV Estimates

This package implements the Naomi model for subnational HIV estimates.

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cpp

7.28 score 9 stars 2 dependents 59 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

7.23 score 33 stars 1 dependents 81 scripts 13 downloads

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

7.21 score 6 dependents 113 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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6.44 score 36 stars 12 scripts

rrq - Simple Redis Queue

Simple Redis queue in R.

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clusterinfrastructure

6.31 score 25 stars 2 dependents 15 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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5.86 score 11 stars 126 scripts

hipercow - High Performance Computing

Set up cluster environments and jobs. Moo.

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5.83 score 1 stars 1 dependents 58 scripts

hintr - R API for calling naomi district level HIV model

R API for calling naomi district level HIV model.

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5.52 score 2 stars 1 dependents 2 scripts

leapfrog - Multistate Population Projection Model for Demographic and HIV Estimation

Leapfrog is a multistate population projection model for estimating population, demographic indicators, and HIV epidemic. The model combines a standard cohort component model of population projection (CCMPP) with a multistate model for HIV infection, disease progression, and treatment. Statistical tools are implemented for joint inference from multiple demographic and epidemiologic data sources.

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cpp

5.29 score 18 scripts

eppasm - Age-structured EPP Model for HIV Epidemic Estimates

Age-structured EPP Model for HIV Epidemic Estimates.

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5.24 score 6 stars 4 dependents 24 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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4.92 score 4 stars 3 scripts

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.

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4.86 score 4 stars 2 dependents 1 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

4.60 score 8 scripts

gonovax - Deterministic Compartmental Model of Gonorrhoea with Vaccination

Model for gonorrhoea vaccination, using odin.

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3.90 score 4 stars 1 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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3.86 score 4 dependents 1 scripts

naomi.resources - Data dependencies for Naomi output generation

Makes data for Naomi output generation as an R package.

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3.78 score 2 scripts

mpoxseir - Stochastic compartmental model of mpox transmission

Stochastic compartmental model of mpox transmission in odin.dust.

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cppopenmp

3.62 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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3.30 score 1 scripts

jenner - Internal Montagu Helpers

Helpers for Montagu.

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2.60 score 3 scripts

hipercow.dide - HPC Support for the DIDE cluster

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

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2.48 score 1 stars 1 scripts

malariaEquilibriumVivax - Return equilibrium solution to malaria transmission model (P. vivax)

Often we are interested in the state of a given malaria transmission model at equilibrium. However, some models (e.g. the Griffin et al. 2014 model, the White et al. 2018 model) are quite complex, and can result in equilibrium solutions that are fairly in-depth. In these situations it is useful to have a "canonical" equilibrium solution that is tried and tested, and can be used reliably by multiple users. This package complement the malariaEquilibriumVivax package to store canonical equilibrium solutions for Plasmodium vivax malaria models.

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2.48 score 1 dependents 2 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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2.44 score 1 stars 11 scripts

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.

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databaseduckdbolapcpp

13.38 score 212 stars 84 dependents 2.5k scripts 137k 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

10.70 score 52 stars 51 dependents 48 scripts 18k downloads

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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7.31 score 19 stars 1 dependents 100 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 744 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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6.59 score 18 stars 2 dependents 36 scripts 439 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

5.95 score 8 stars 7 dependents 2 scripts 1.1k 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).

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5.46 score 3 stars 137 scripts

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()'.

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5.13 score 38 scripts 24k downloads

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.

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4.65 score 6 stars 5 dependents 1 scripts

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.

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demographyinterpolationsubdivision

4.08 score 2 stars 4 dependents 5 scripts

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.

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3.95 score 5 stars 4 dependents 9 scripts

specio - Read Spectrum Files

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

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eppspectrum

3.78 score 1 stars 2 dependents 1 scripts

montagu - Interface with 'montagu'

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

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3.48 score 2 stars 3 scripts

malariaEquilibrium - Return equilibrium solution to malaria transmission model

Often we are interested in the state of a given malaria transmission model at equibrium. However, some models (e.g. the Griffin et al. 2014 model) are quite complex, and can result in equilibrium solutions that are fairly in-depth. In these situations it is useful to have a "canonical" equilibrium solution that is tried and tested, and can be used reliably by multiple users. This package aims to be a place for hosting these canonical solutions, and for storing useful tests, checks and plotting functions for exploring a given solution.

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3.39 score 3 stars 1 dependents 55 scripts

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.

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3.15 score 8 stars 35 scripts

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.

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3.00 score 1 stars 4 scripts

nomad - Create Portable R Repositories

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

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2.90 score 8 stars 4 scripts

odin.js - 'odin' 'JavaScript' support

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

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2.88 score 5 stars 3 scripts

logwatch - Watch Logs Run

Watch a log, streaming progress to the console.

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2.78 score 4 dependents 1 scripts

epp - R Implementation of the EPP model for HIV epidemic estimates.

This implements the EPP r-spline and r-trend models for HIV epidemic estimates.

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2.78 score 4 stars 5 dependents 8 scripts

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.

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2.73 score 9 stars 12 scripts

syncr - Synchronise Directories

Syncronise directories using rsync.

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clusterinfrastructure

2.65 score 9 stars 2 scripts

testthat.buildkite - A testthat reporter for buildkite

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

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2.54 score 1 scripts

conan2 - Conan the Librarian

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

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2.48 score 1 dependents 1 scripts

assessr - Performance metrics for probabilitic forecasts

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

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2.41 score 1 dependents 17 scripts

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>.

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2.38 score 16 scripts

mode - Solve Multiple ODEs

Solve multiple ODEs in parallel.

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2.32 score 42 scripts

conan - Conan the Librarian

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

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2.30 score 4 stars 8 scripts

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.

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hirediscpp

2.30 score 2 stars 2 scripts 211 downloads

orderly.sharedfile - Package Title Here

Access files in shared locations from orderly.

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2.18 score 1 stars 3 scripts

anclik - Likelihood for ANC Sentinel Surveillance Data

This implements the random effects likelihood for ANC HIV prevalence described by Alkema, Raftery, Clark Ann Appl Stat 2007 (http://dx.doi.org/10.1214/07-AOAS111). This is implemented in the EPP model used by UNAIDS for generating HIV epidemic trends: http://www.unaids.org/en/dataanalysis/datatools/spectrumepp2013.

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openblas

2.18 score 5 dependents 2 scripts

moz.utils - Utility functions

Utility functions, for useful utilitarian uses.

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2.08 score 12 scripts

jointlyr - Joint estimation of initial incidence and reproduction number

Provides a Stan implementation of a method to jointly estimate incidence and reproduction number.

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cpp

2.00 score 1 scripts

buildr - buildr

Simple package build server.

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clusterinfrastructure

2.00 score 2 stars 8 scripts 267 downloads

cart - Malaria Cartographic Information

Extract population, prevalence and vector cartographic information for use with malarisimulation.

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1.70 score 1 stars 9 scripts

rincewind - Utilities for processing forecasts matrices

This package contains utility functions for processing forecasts matrices.

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1.00 score 1 stars 1 scripts

weighter - Model averaging

This package implementes model averaging.

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1.70 score 1 stars 1 scripts

ascertainr - Case Ascertainment Model

This pacakge implements a case asecertainment model.

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1.30 score 2 stars 1 scripts