ncov-ic.r-universe.dev

[ncov-ic] pika 0.2.0

ainslie.kylie@gmail.com (Kylie Ainslie) — Thu, 02 Jul 2026 05:44:55 GMT

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.

[ncov-ic] odin 1.5.12

rich.fitzjohn@gmail.com (Rich FitzJohn) — Thu, 15 Jan 2026 17:26:10 GMT

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.

[ncov-ic] dust 0.15.3

rich.fitzjohn@gmail.com (Rich FitzJohn) — Fri, 15 Aug 2025 15:16:17 GMT

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 ). The core of the simulation engine is the 'xoshiro256**' algorithm (Blackman and Vigna ), and the package is further described in FitzJohn et al 2021 .

[ncov-ic] orderlyweb 0.1.16

rich.fitzjohn@gmail.com (Rich FitzJohn) — Mon, 14 Jul 2025 14:41:48 GMT

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

[ncov-ic] odin.dust 0.3.13

rich.fitzjohn@gmail.com (Rich FitzJohn) — Wed, 02 Oct 2024 15:02:46 GMT

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).

[ncov-ic] dde 1.0.7

rich.fitzjohn@gmail.com (Rich FitzJohn) — Mon, 23 Sep 2024 20:14:13 GMT

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) . Support is also included for iterating difference equations.

[ncov-ic] mcstate 0.9.22

rich.fitzjohn@gmail.com (Rich FitzJohn) — Mon, 01 Jul 2024 13:22:09 GMT

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.

[ncov-ic] drjacoby 1.5.4

r.verity@imperial.ac.uk (Bob Verity) — Wed, 26 Jun 2024 02:17:18 GMT

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.

[ncov-ic] sircovid 0.15.1

m.baguelin@imperial.ac.uk (Marc Baguelin) — Wed, 19 Jun 2024 08:41:01 GMT

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.

[ncov-ic] vaultr 1.2.0

rich.fitzjohn@gmail.com (Rich FitzJohn) — Thu, 09 Nov 2023 12:51:39 GMT

Provides an interface to a 'HashiCorp' vault server over its http API (typically these are self-hosted; see ). 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'.

[ncov-ic] orderly.sharepoint 0.1.5

rich.fitzjohn@gmail.com (Rich FitzJohn) — Thu, 20 Jul 2023 13:49:33 GMT

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.

[ncov-ic] odin.js 0.1.11

rich.fitzjohn@gmail.com (Rich FitzJohn) — Wed, 26 Oct 2022 09:16:04 GMT

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

[ncov-ic] squire 0.7.1

o.watson15@imperial.ac.uk (OJ Watson) — Thu, 08 Sep 2022 09:14:12 GMT

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.

[ncov-ic] orderly.rstudio 0.0.3

r.ashton@imperial.ac.uk (Robert Ashton) — Thu, 11 Mar 2021 17:18:35 GMT

RStudio addins for orderly.

[ncov-ic] spud 0.1.7

r.ashton@imperial.ac.uk (Robert Ashton) — Wed, 04 Nov 2020 16:37:04 GMT

Enables uploading, downloading and listing of files in sharepoint.

[ncov-ic] hermione 1.0.0

s.bhatia@imperial.ac.uk (Sangeeta Bhatia) — Thu, 13 Aug 2020 12:25:35 GMT

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

[ncov-ic] fstorr 0.1.0

rich.fitzjohn@gmail.com (Rich FitzJohn) — Sun, 26 Apr 2020 10:28:42 GMT

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

[ncov-ic] EpiEstim 2.1-0

a.cori@imperial.ac.uk (Anne Cori) — Mon, 11 Jun 2018 13:17:54 GMT

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

[ncov-ic] projections 0.3.0

thibautjombart@gmail.com (Thibaut Jombart) — Mon, 11 Jun 2018 13:06:48 GMT

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) .