Sort by: Last updated / Name / Language
rb.test
orderly-example
Language: r
Example orderly repo for use with tests
cookiecutter-kotlin-typescript
Language: kotlin
Cookiecutter template for a Kotlin/TypeScript web application
reboot-monitor
Buffer machine requests for reboots.
interpolate
Language: js
Function Interpolation
https://reside-ic.github.io/interpolate/
logo
Language: js
style utilities for reside@ic
traduire.scripts
Language: r
What the package does (one paragraph).
vue-prototypes
Language: js
A place to stick vue component prototypes
mode-test
Language: r
beats
Language: shell
defer
Language: r
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.
https://reside-ic.github.io/defer
TreeTables
Language: js
jquery plugin extending jquery-datatables to support tree data
fstorr
Language: r
Store files by content, similar in spirit to the 'storr' package (into which this might get folded).
shiny-selenium
Language: r
Demonstrates getting shiny, selenium and travis working together.
fakerbase
Language: r
Connect to a Postgres database and generate a suite of functions that can be used to mock database tables for unit testing.
https://reside-ic.github.io/fakerbase
Used by:
  • vimc/vimpact
spud
Language: r
Enables uploading, downloading and listing of files in sharepoint.
Used by:
  • vimc/orderly.sharepoint
ids
Language: r
Generate random or human readable and pronounceable identifiers.
https://reside-ic.github.io/ids
Used by:
  • vimc/orderly.server
  • vimc/orderly
  • mrc-ide/rrq
  • mrc-ide/odin.ui
  • mrc-ide/rrq.kelp
  • mrc-ide/didehpc
  • mrc-ide/context
  • mrc-ide/kelp
  • mrc-ide/remotesave
  • mrc-ide/queuer
  • mrc-ide/hintr
vue-maps
Language: js
A library of Vue map components for model visualisation and exploration
vue-charts
Language: js
Vue components for data plotting
cookiecutter-r-package
Language: shell
:cookie::package: Template for an R package
tensor-js
Language: js
Tensor containers
porcelain
Language: r
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.
https://reside-ic.github.io/porcelain
Depends on:
  • ropensci/jsonvalidate
Used by:
  • vimc/orderly.server
  • mrc-ide/cometr
  • mrc-ide/mintr
  • mrc-ide/odin.api
  • mrc-ide/hintr
reside-ic.github.io
Language: html
Reside-IC blog
https://reside-ic.github.io/
gs2yt
Language: r
proxy-nginx
Language: shell
dfoptim
Language: js
Derivative-Free Optimisation
https://reside-ic.github.io/dfoptim/
Used by:
  • mrc-ide/odin-js
buildkite-agent-metrics
Language: shell
Build docker image from https://github.com/buildkite/buildkite-agent-metrics
constellation
Language: python
reside-hyperv-scripts
Language: powershell
random-js
Language: js
Random numbers
http://reside-ic.github.io/random-js/
traduire
Language: r
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.
https://reside-ic.github.io/traduire/
Used by:
  • mrc-ide/naomi
  • mrc-ide/hintr
cppdoc
Language: r
Provides a bridge between doxygen's XML output and vignettes written in R markdown.
https://reside-ic.github.io/cppdoc
mls
Language: r
Create multiline strings for errors, warnings and messages.
https://reside-ic.github.io/mls
youtrack-integration
Language: python
Webhook to auto-update YouTrack tickets on PR actions
vue-dynamic-form
Language: js
A metadata driven form component
logs
Language: shell
random-xoshiro256
Language: js
jsonvalidate
Language: r
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.
https://docs.ropensci.org/jsonvalidate
Used by:
  • reside-ic/porcelain
  • vimc/orderly.server
  • vimc/orderly2
  • mrc-ide/outpack
  • mrc-ide/odin
  • mrc-ide/mintr
  • mrc-ide/hintr
cyphr
Language: r
Encryption wrappers, using low-level support from 'sodium' and 'openssl'. 'cyphr' tries to smooth over some pain points when using encryption within applications and data analysis by wrapping around differences in function names and arguments in different encryption providing packages. It also provides high-level wrappers for input/output functions for seamlessly adding encryption to existing analyses.
https://docs.ropensci.org/cyphr
montagu-db-docs
Language: html
:books::bar_chart::books: Documentation for montagu-db
https://vimc.github.io/montagu-db-docs
montagu-task-queue-orderly
Language: r
db2-prototypes
Language: r
Throw away repo for prototyping and benchmarking VIMC 2.0 database
montagu-api-metrics
Language: python
Flask app to monitor montagu and reporting APIs, with /metrics endpoint for Prometheus to access (see montagu-monitor)
bb8
Language: python
Backs up files from one local server to another
universe
montagu-deploy
orderly.server
Language: r
Run orderly reports as a server.
Depends on:
  • reside-ic/ids
  • ropensci/jsonvalidate
  • vimc/orderly
  • reside-ic/porcelain
  • mrc-ide/rrq
montagu-demography-tools
Language: r
Scripts relating to the montagu demographic data
montagu-orderly-web
Language: shell
Configuration for Montagu's OrderlyWeb instance
vaultr
Language: r
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'.
https://vimc.github.io/vaultr
Used by:
  • vimc/dettl
  • vimc/orderly
  • vimc/vimpact
  • vimc/jenner
montagu-monitor
Language: python
montagu-py
Language: python
montagu-vault-py
Language: python
A small wrapper around hvac for use with montagu-vault
dettl
Language: r
Data extract, transform, test and load tool for sanitising your workflow.
https://vimc.github.io/dettl
Depends on:
  • vimc/vaultr
vpd-covid-phase-I
Language: html
Related to manuscript Health impact of routine immunisation service disruptions and mass vaccination campaign suspensions caused by the COVID-19 pandemic: Multimodel comparative analysis of disruption scenarios for measles, meningococcal A, and yellow fever vaccination in 10 low- and lower middle income countries
vault-dev
Language: python
Use vault server in development mode in tests, from python
montagu-db
Language: shell
montagu-static
Language: python
Static file server with jwt authentication
orderly
Language: r
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.
https://www.vaccineimpact.org/orderly/
Depends on:
  • reside-ic/ids
  • vimc/vaultr
Used by:
  • vimc/orderly.server
  • vimc/montagu-r
  • vimc/orderly2
  • vimc/orderly.sharepoint
  • vimc/orderlyweb
  • vimc/orderly.rstudio
  • mrc-ide/syria-covid-ascertainment
  • mrc-ide/global-lmic-meffs
  • mrc-ide/global-lmic-results
  • mrc-ide/squire.page
  • mrc-ide/india-ascertainment
metrics-utils
Language: python
Helper scripts for metric exporters
vimc.github.io
Language: html
VIMC website repo
http://www.vaccineimpact.org/
montagu-r
Language: r
Client for interacting with the montagu API, and authentication with the montagu OrderlyWeb instance. This package is part of montagu.
https://vimc.github.io/montagu-r
Depends on:
  • vimc/orderly
  • vimc/orderlyweb
orderly-web-deploy
Language: python
cached-metrics
Language: python
Metrics exporter that reads from a file cache
montagu-bb8
Language: shell
Performs local backup between our servers. This wraps bb8 with Montagu specific bits.
montagu-vault
Language: shell
Montagu Vault
montagu-machine
Language: shell
montagu-recovery
Language: shell
:face_with_head_bandage: Testing for montagu recovery
orderly-web
Language: kotlin
Web app for interfacing with orderly https://vimc.github.io/orderly/
montagu-webapps
Language: typescript
A repository for webapps built on top of the API that may need to share code. In particular, the admin portal and the modelling groups portal.
orderly-demo
Language: html
ts_data_visualisation
Language: js
The typescript / knockout implementation of the interactive reporting app
montagu-webmodels
Language: kotlin
Models (classes) that are shared between the API and the webapps
montagu
Language: python
Deployment scripts for Montagu as a constellation of Docker services
montagu-api
Language: kotlin
JSON REST API for providing data access to other applications
dataintegrity
Language: python
montagu-registry
Language: python
☁️🐳☁️ Montagu's docker registry configuration and deployment
https://docker.montagu.dide.ic.ac.uk:5000
vimc-website
Language: css
:earth_africa::loudspeaker::computer: VIMC static webpages
https://www.vaccineimpact.org/
orderly-web-py
Language: python
orderly2
Language: r
A reimplementation of the good bits of orderly using outpack.
Depends on:
  • ropensci/jsonvalidate
  • vimc/orderly
  • mrc-ide/outpack
montagu-task-queue
Language: python
montagu-db-backup
Language: python
montagu-orderly
Language: shell
A copy of orderly for running montagu reports
montagu-cert-tool
Language: kotlin
Montagu Certificate Tool
montagu-dettl
Language: shell
orderly.sharepoint
Language: r
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.
https://vimc.github.io/orderly.sharepoint
Depends on:
  • vimc/orderly
  • reside-ic/spud
orderlyweb
Language: r
Client for 'OrderlyWeb' for use from the 'orderly' package. Allows downloading of reports, running remote reports and other interaction with the remote report repository.
https://vimc.github.io/orderlyweb/
Depends on:
  • vimc/orderly
Used by:
  • vimc/montagu-r
node-docker
Language: shell
a Dockerfile and script for building an image that has both node-12 and docker installed
node-docker-openjdk
Language: shell
openjdk-libsodium
Language: shell
orderly.rstudio
Language: r
RStudio addins for orderly.
Depends on:
  • vimc/orderly
stoner
Language: r
For montagu-imports that create touchstones, or augment existing touchstones, allow the import to be as minimal as possible, towards single line extract and transform calls, in order that the review for that import can be focussed on the metadata being correct, rather than on code.
https://www.vaccineimpact.org/stoner/
demographic-data
Language: java
Scripts for parsing/transforming UNWPP demographic spreadsheets
phipps
Language: r
VIMC plotting functions.
wuenic-data
Language: r
WHO/UNICEF estimates of national immunization coverage
machine-metrics
Language: shell
Script to install and run Prometheus Node Exporter (https://github.com/prometheus/node_exporter)
vimpact
Language: r
VIMC IMPACT CALCULATION PACKAGE. This package is mainly for the VIMC Science Team to investigate vaccination impact.
http://www.vaccineimpact.org/vimpact/
Depends on:
  • reside-ic/fakerbase
  • vimc/vaultr
montagu-kodiak
Montagu wrapper around Kodiak, an S3 backup tool
montagu-shiny
Language: html
:sparkles::sparkles::sparkles: shiny server for montagu
jenner
Language: r
Helpers for Montagu.
Depends on:
  • vimc/vaultr
singapore_shortcourse_2022
Language: r
Repo for the Singapore Shortcourse 2022
beers
Language: r
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.
Used by:
  • mrc-ide/leapfrog
  • mrc-ide/specio
FoI_bayesian
Language: r
Fitting force-of-infection (models) to age-(sero)prevalence data, incorporating diagnostic uncertainty (sensitvity and specificity) for single datasets and multiple datasets utilising a common diagnostic test.
outpack
Language: r
Create a portable package of output from a computational experiment.
https://mrc-ide.github.io/outpack
Depends on:
  • ropensci/jsonvalidate
Used by:
  • vimc/orderly2
shinyq
Language: r
:star2::walking::walking::walking::star2: shiny application with a queue
YFburden
Language: r
The package takes estimates of the force of infection in each country, projected vaccination coverage, historic vaccination coverage, and projected population sizes to calculate the number of infections. It also takes estimates of disability weights and probability of severe infections to calculate the number of severe infections, deaths and DALYS.
Used by:
  • mrc-ide/YFestimation
hint-deploy
Language: python
Deployment tool for hint
mics-datasets
Language: html
Repository of MICS survey datasets
Contact_matrix_data
Language: r
Collated contact matrix data by country
global_covid_vaccine_booster
Language: r
sircovid-gpu-hack
Language: c++
msc-idm-2019
Language: r
YF_mcstate_example
Language: c++
Example of yellow fever model fitting implemented using mcstate
syria-covid-ascertainment
Language: r
Code repository for analysis into under-ascertainment of COVID-19 mortality in Damascus
Depends on:
  • vimc/orderly
  • mrc-ide/squire
rtss_vacc_antibody_model
Language: r
Implementation of the RTS,S vaccine antibody model developed by MT White (https://doi.org/10.1016/S1473-3099(15)00239-X).
global-lmic-meffs
Language: r
More about what it does (maybe more than one line) Use four spaces when indenting paragraphs within the Description.
Depends on:
  • vimc/orderly
  • mrc-ide/squire
shiny90
Language: r
Shiny tool for the first 90 HIV model (https://github.com/mrc-ide/first90)
https://shiny90.unaids.org/
squire_js
Language: js
A javascript implementation of the squire COVID-19 model
universe
db
Language: r
One paragraph description of what the package does as one or more full sentences.
om
Language: r
om can be used to find solutions to budget-optimisation challenges.
https://mrc-ide.github.io/om/
hint-adr-poc
Proof of concept for SSO integration
naomi.extensions
Language: r
This package implements the Naomi model for subnational HIV estimates.
Depends on:
  • mrc-ide/naomi
shinyrob
Language: r
snapalette
Language: r
What the package does (one paragraph).
rrq
Language: r
Simple Redis queue in R.
https://mrc-ide.github.io/rrq/
Depends on:
  • reside-ic/ids
Used by:
  • vimc/orderly.server
  • mrc-ide/rrq.kelp
  • mrc-ide/didehpc
  • mrc-ide/spimalot
  • mrc-ide/hintr
gasworks
Language: r
Models of Group A Streptococcus (GAS) Transmission.
Depends on:
  • mrc-ide/dust
  • mrc-ide/mcstate
  • mrc-ide/odin
  • mrc-ide/odin.dust
pika
Language: r
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.
Depends on:
  • mrc-ide/EpiEstim
hiv-orderly
Language: dockerfile
Docker image build for HIV orderly
ckan-extrafields
Language: python
An extra field customisation for departmental use of CKAN 2.9.0
covid-mortality-ascertainment
Language: r
Code repository for analysis into under-ascertainment of COVID-19 mortality.
Depends on:
  • mrc-ide/squire
nimue_global_fits
malariasimulation
Language: r
Specifies the latest and greatest malaria model.
https://mrc-ide.github.io/malariasimulation
Depends on:
  • mrc-ide/individual
  • mrc-ide/malariaEquilibrium
Used by:
  • mrc-ide/cali
  • mrc-ide/nlcali
  • mrc-ide/msvalidation
  • mrc-ide/site
  • mrc-ide/msio
comet
Language: typescript
comet
sarscov2-transmission-england
Language: r
YellowFeverDynamics
Language: r
A package for running a dynamic, stochastic SEIRV model of yellow fever, creating input data and processing output data. The package can also be used to fit values of epidemiological parameters of the model to different types of data on yellow fever burden in one or more regions.
Depends on:
  • mrc-ide/dust
  • mrc-ide/odin
  • mrc-ide/odin.dust
MIPanalyzer
Language: r
Filtering and analysis of MIP data.
https://mrc-ide.github.io/MIPanalyzer/
contact_patterns
Language: r
🤝🤧 Systematic review of contact surveys relevant to transmission of respiratory pathogens 🤧🤝
conan
Language: r
Create libraries. For us, there is no spring. Just the wind that smells fresh before the storm.
https://mrc-ide.github.io/conan/
Used by:
  • mrc-ide/didehpc
mode
Language: r
Solve multiple ODEs in parallel.
https://mrc-ide.github.io/mode/
Depends on:
  • mrc-ide/dde
  • mrc-ide/dust
Used by:
  • mrc-ide/odin.dust
  • mrc-ide/mcstate
naomi.docker
Language: dockerfile
Docker base image for naomi & hintr
covid_vaccine_allocation
Language: r
Within-country prioritisation, global allocation, and public health impact of a vaccine against SARS-CoV-2: A modelling study
reactidd
Language: r
hint-proxy
Language: shell
EpiEstim
Language: r
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>.
Used by:
  • mrc-ide/pika
  • mrc-ide/spimalot
  • mrc-ide/sircovid
novel-data-streams
PhyDyn
Language: java
PhyDyn: Epidemiological modelling in BEAST
cometr
Language: r
Run 'nimue' (and eventually other models, such as an individual based model) and expose results over an HTTP API.
Depends on:
  • mrc-ide/dde
  • mrc-ide/eigen1
  • mrc-ide/nimue
  • reside-ic/porcelain
  • mrc-ide/squire
global-lmic-reports-orderly
Language: r
COVID-19 forecast reports for LMICs
DRpower
Language: r
Can be used to analyse prevalence data typical of drug- and diagnostic-resistance studies (i.e. pfhrp2/3 deletions in malaria). Uses a Bayesian approach to estimate both the prevalence and the level of intra- cluster correlation. Also estimates the power via simulation for a given sample size, making it possible to choose a sample size to achieve a given desired power.
demogsurv
Language: r
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.
covid19-forecasts-orderly
Language: r
shortcourse-2019
Language: r
https://shiny.dide.imperial.ac.uk/shortcourse-2019/
OmicronSeverity
Language: r
Source code to accompany Lancet Paper, Nyberg, Ferguson et al, March 2022
individual
Language: r
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.
https://mrc-ide.github.io/individual
Used by:
  • mrc-ide/malariasimulation
  • mrc-ide/safir2
  • mrc-ide/safir
  • mrc-ide/hypatia
drjacoby_submission
Language: html
Scripts to carry out all analysis and reproduce tables and figures for the drjacoby manuscript submission.
odin.dust
Language: r
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).
https://mrc-ide.github.io/odin.dust
Depends on:
  • mrc-ide/dde
  • mrc-ide/dust
  • mrc-ide/mode
  • mrc-ide/odin
Used by:
  • mrc-ide/gasworks
  • mrc-ide/YellowFeverDynamics
  • mrc-ide/sircovid
  • mrc-ide/mcstate
  • mrc-ide/gonovaxdust
safir2
Language: r
'safir2' is an upgraded and refactored version of 'safir', which implements a stochastic individual based model of SARS-CoV-2 transmission. The model takes into account individual level immunity and neutralizing antibody titre, as well as allowing for complex vaccine allocation schemes.
https://mrc-ide.github.io/safir2/
Depends on:
  • mrc-ide/individual
  • mrc-ide/nimue
  • mrc-ide/squire
ring
Language: r
Circular / ring buffers in R and C. There are a couple of different buffers here with different implementations that represent different trade-offs.
https://mrc-ide.github.io/ring
Used by:
  • mrc-ide/odin
  • mrc-ide/dde
bootstrap4-collapse
Language: js
Bootstrap 4 collapse css and js
COVID19_surveillance_sensitivity
Language: r
global_lmic_projections_esft
get-unstuck
hint-generic-chart-prototypes
Language: js
dust-bench
Language: r
apothecary
Language: r
An extended model of the SEIR model available in the squire package (available at: https://github.com/mrc-ide/squire) extended to explore the impact of different pharmaceutical therapeutics.
Depends on:
  • mrc-ide/dde
  • mrc-ide/odin
  • mrc-ide/squire
DENV_risk_maps
Language: r
:world_map: Global mapping of dengue transmission intensity
hivmappr
Language: r
Small-area estimation of HIV prevalence, ART coverage, and HIV incidence
safir
Language: r
Implements an individual-based model of COVID-19 transmission. Derives from previous work in 'squire'.
https://mrc-ide.github.io/safir/
Depends on:
  • mrc-ide/individual
  • mrc-ide/nimue
  • mrc-ide/squire
comet-deploy
Language: shell
vaccinequity_litreview
Language: r
tfpbrowser
Shiny app for tfpscanner
hivmodels.net
Language: js
Static assets for hivmodel.net
MINT_data_selector
Language: r
Data and function to quickly select data for the MINT web interface
alphaepi
Language: r
What the package does (one paragraph).
genescaper
Language: r
Inputs data consisting of allele frequencies at sampling sites along with their latitude/longitude values. Fits a model of smoothly varying allele frequencies in space (a Gaussian Random Field) via Bayesian MCMC. Uses the fitted model to predict allele frequencies at any given point in space, and also to generate a null distribution for pairwise genetic distances between sites. This null distribution can then be used to detect outliers, which may represent sites that are more/less connected than we would expect by chance.
Depends on:
  • mrc-ide/drjacoby
MissingCases
Language: r
This package uses next generation matrices to estimate the number of missing cases from a surveillance system.
covid_npi_lifting_manuscript
malaria_optimal_allocation
Language: r
covid19_South_Korea_report
Data to run the analysis of the Imperial College London Report on South Korea's response to COVID-19
ATACCC-kinetic-model-and-data
Language: r
ATACCC kinetic model and data
odin.ui
Language: r
A user interface for 'odin', using Shiny.
Depends on:
  • mrc-ide/dde
  • reside-ic/ids
  • mrc-ide/odin
  • mrc-ide/remotesave
rrq.kelp
Language: r
An offload file store for rrq. Using kelp API to interact with SeaweedFS, this can be used to save large input or output data to a distributed file store.
Depends on:
  • reside-ic/ids
  • mrc-ide/kelp
  • mrc-ide/rrq
china-exit-covid-19
Language: r
Code, data, and supplemental material for the analysis of China's exit from their strict social distancing policy
who_rfp_topic_IV
Language: r
cali
Language: r
Cali is a package to help calibrate malariasimulation model runs. For example to set EIR to match a given prevalence at a specific timepoint.
https://mrc-ide.github.io/cali/
Depends on:
  • mrc-ide/malariasimulation
didehpc
Language: r
DIDE HPC support.
http://mrc-ide.github.io/didehpc
Depends on:
  • mrc-ide/conan
  • mrc-ide/context
  • reside-ic/ids
  • mrc-ide/queuer
  • mrc-ide/rrq
covid-titre-efficacy
Language: r
tfpscanner
Language: r
A pipeline for scanning a SARS-CoV-2 phylogeny for clades with outlying growth patterns and high evolutionary rates. Original methods developed in emvolz-phylodynamics/variantAnalysis
treasure
Language: r
The goal of treasure is to provide basic, generic unit-costing help for malariasimulation.
https://mrc-ide.github.io/treasure/
renamer
nlcali
Language: r
What the package does (one paragraph).
Depends on:
  • mrc-ide/malariasimulation
drjacoby
Language: r
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.
https://mrc-ide.github.io/drjacoby/
Used by:
  • mrc-ide/genescaper
  • mrc-ide/squire
  • mrc-ide/COVIDCurve
  • mrc-ide/malariaModelFit
netz
Language: r
Helper functionality to set up bed nets for use in malariasimulation. Also used to cost bed net programmes.
https://mrc-ide.github.io/netz/
covid19-forecasts-orderly-shiny
Shiny app collating the outputs of mrc-ide/covid19-forecasts-orderly
covid19-short-term-forecasts
Language: html
Short term forecasts of COVID-19 deaths in multiple countries
dust-js
Language: js
Dust-like interface for js
https://mrc-ide.github.io/dust-js
GF-RTSS-CE
Language: r
Cost-effectiveness of RTS,S vs. scale-up of existing interventions.
epiestims
Language: html
naomi-troubleshooting
Language: html
https://mrc-ide.github.io/naomi-troubleshooting/
covid19-si-orderly
Language: r
agestructuredEPICYST_analysis
Language: r
Analysis code to support producing results (plots and tables) for manuscript submitted (Dixon et al. 2022) utilising age-structured EPICYST.
public-events-zombie-sim2-java
Language: java
markovid
Language: r
MCMC package for preliminary fits of hospital progression parameters (transition probabilities and durations in each state). The outputs of these fits are passed up to the larger mechanistic model as priors or relative risks for a further level of fitting. NB, this package is essentially a re-purpose of the drjacoby package, and still contains some legacy code.
who_covid_vacc_rfp
Language: r
context
Language: r
Contexts for evaluating R expressions.
http://mrc-ide.github.io/context
Depends on:
  • reside-ic/ids
Used by:
  • mrc-ide/didehpc
  • mrc-ide/queuer
first90release
Language: r
Implements the Shiny90 model for estimating progress towards the UNAIDS "first 90" target for HIV awareness of status in sub-Saharan Africa.
tmb.example
Language: r
What the package does (one paragraph).
early-japan
Repository of data used for study into the early phase of the COVID-19 epidemic in Japan
twinkle
Language: r
:star::arrow_right::sparkles::sparkles::sparkles::sparkles::dizzy: Load balanced shiny server
Brazil_COVID19_distributions
Language: python
This repository contains code and data for the "Inference of COVID-19 epidemiological distributions from Brazilian hospital data" manuscript
covfefe
Language: r
More about what it does (maybe more than one line) Use four spaces when indenting paragraphs within the Description.
https://mrc-ide.github.io/covfefe/
mockcpp
Language: r
A header only library integrating 'testthat' with 'trompeoeil' to provide mocking for C++ code in R packages. Mocking is a technique for making a fake version of a software service. You can mock services to test that your code interacts correctly with external interfaces, to make your tests deterministic, or to break your tests down into smaller units. 'testthat' provides a testing framework for R and C++ code in R packages. 'trompeoeil' is a C++ header only library for mocking.
PlasmoMAPI_submission
Language: r
Holds scripts etc. needed to reproduce all figures and tables from the PlasmoMAPI submission.
serialization
Language: kotlin
A kotlin package for de/serializing large CSV files with variable column headers into fixed types
gonovax
Language: r
Model for gonorrhoea vaccination, using odin.
https://mrc-ide.github.io/gonovax
Depends on:
  • mrc-ide/mcstate
  • mrc-ide/odin
Used by:
  • mrc-ide/gonovaxdust
dust-random-bench
Language: c++
dengue_meta_analysis
Language: r
odin
Language: r
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.
https://mrc-ide.github.io/odin
Depends on:
  • mrc-ide/cinterpolate
  • mrc-ide/dde
  • ropensci/jsonvalidate
  • mrc-ide/ring
Used by:
  • mrc-ide/gasworks
  • mrc-ide/YellowFeverDynamics
  • mrc-ide/odin.dust
  • mrc-ide/apothecary
  • mrc-ide/odin.ui
  • mrc-ide/gonovax
  • mrc-ide/sircovid
  • mrc-ide/squire
  • mrc-ide/ivRmectin
  • mrc-ide/siR
  • mrc-ide/gonovaxdust
  • mrc-ide/nimue
  • mrc-ide/epicyst
  • mrc-ide/odin.api
  • mrc-ide/deterministic-malaria-model
  • mrc-ide/squire.page
  • mrc-ide/excalibur
mintr
Language: r
Provides an API for use by 'MINT'.
Depends on:
  • ropensci/jsonvalidate
  • reside-ic/porcelain
infectiousdiseasemodels-2021
Language: r
Introduction to Mathematical Models of the Epidemiology & Control of Infectious Diseases - 2021
https://shiny.dide.imperial.ac.uk/infectiousdiseasemodels-2021/
spimalot
Language: r
Code that supports that use of sircovid for our regular workflows (weekly SPI-M analyses, medium term projections) and forward simulation. Unlike 'sircovid', this package is intended to be more rapidly iterated, contains no compiled code, and will be significantly less tested because it must bend around ever-changing data and requirements for plotting/analysis.
https://mrc-ide.github.io/spimalot/
Depends on:
  • mrc-ide/EpiEstim
  • mrc-ide/dust
  • mrc-ide/mcstate
  • mrc-ide/rrq
  • mrc-ide/sircovid
stochasticity-practical
Language: r
:sparkles::chart_with_upwards_trend::sparkles: Shiny application for stochasticity practical
https://shiny.dide.imperial.ac.uk/stochasticity-practical/
git_demo
Language: r
sarscov2-b.1.1.7
Language: html
Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England (peer-reviewed)
dde
Language: r
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.
https://mrc-ide.github.io/dde
Depends on:
  • mrc-ide/ring
Used by:
  • mrc-ide/mode
  • mrc-ide/cometr
  • mrc-ide/odin.dust
  • mrc-ide/apothecary
  • mrc-ide/odin.ui
  • mrc-ide/odin
  • mrc-ide/squire
  • mrc-ide/ivRmectin
  • mrc-ide/nimue
  • mrc-ide/deterministic-malaria-model
covid-italy-dashboard
Language: r
naomi
Language: r
This package implements the Naomi model for subnational HIV estimates.
https://mrc-ide.github.io/naomi
Depends on:
  • mrc-ide/eppasm
  • reside-ic/traduire
Used by:
  • mrc-ide/naomi.extensions
  • mrc-ide/hintr
  • mrc-ide/threemc
naomi-pipelines
Repo for naomi buildkite pipelines
didehpc-cmdline-tool
Command-line tools wrapping MS HPC Pack for job management
hint
Language: typescript
HIV Indicators Tool for district level estimates of HIV epidemic indicators
YF_climateChange
Language: r
gavi_covid_forecast
Language: r
weighter
Language: r
This package implementes model averaging.
sircovid
Language: r
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.
https://mrc-ide.github.io/sircovid
Depends on:
  • mrc-ide/EpiEstim
  • mrc-ide/dust
  • mrc-ide/eigen1
  • mrc-ide/mcstate
  • mrc-ide/odin
  • mrc-ide/odin.dust
Used by:
  • mrc-ide/spimalot
global_raster_tools
Language: java
:earth_africa: :world_map: Tools for handling shape files/rasterisation globally at 1/120 degree resolution
msc-idm-2020
Language: r
covid-uk-mobility-report
Language: r
Code to plot the figures and run the statistical analysis in: Anonymised & aggregated crowd level mobility data from mobile phones suggests initial compliance with COVID19 social distancing interventions was high & geographically consistent across UK
iccm
Integrated Community Case Management
epihawkes
Language: r
This package can be used to model infectious disease outbreaks. There are functions available for both fitting the model parameters to real outbreak data as well as simulating outbreaks from given parameters.
shiny_dide
Language: shell
:star2::hospital::star2: DIDE shiny server configuration
https://shiny.dide.ic.ac.uk
YellowFeverModelEstimation2019
Language: r
flodia
Language: r
Tools to create compartmental model flow diagrams in base R.
https://mrc-ide.github.io/flodia
squire
Language: r
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.
https://mrc-ide.github.io/squire/
Depends on:
  • mrc-ide/dde
  • mrc-ide/drjacoby
  • mrc-ide/odin
Used by:
  • mrc-ide/syria-covid-ascertainment
  • mrc-ide/global-lmic-meffs
  • mrc-ide/covid-mortality-ascertainment
  • mrc-ide/cometr
  • mrc-ide/safir2
  • mrc-ide/apothecary
  • mrc-ide/safir
  • mrc-ide/global-lmic-results
  • mrc-ide/nimue
  • mrc-ide/squire.page
  • mrc-ide/hypatia
  • mrc-ide/india-ascertainment
spatialbranchr
Language: r
spatialbranchr implements a spatially explicit branching process model.
leapfrog
Language: r
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.
Depends on:
  • mrc-ide/beers
  • mrc-ide/eppasm
global-lmic-results
Language: r
More about what it does (maybe more than one line) Use four spaces when indenting paragraphs within the Description.
Depends on:
  • vimc/orderly
  • mrc-ide/squire
public-events-microbit-epidemic
Language: java
:computer::radio::syringe::chart_with_upwards_trend: Proximity-driven epidemic over bluetooth
2019-nCoV
ivRmectin
Language: r
A deterministic version of the Imperial College Malaria Model, adapted to explore the impact of novel endectocides on malaria transmission. Derived from the model developed and presented in Slater et al., Journal of Infectious Diseases 2014 (https://academic.oup.com/jid/article/210/12/1972/2908666) and Slater et al., Lancet Infectious Diseases, 2020 (https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(19)30633-4/fulltext).
Depends on:
  • mrc-ide/dde
  • mrc-ide/odin
covid_booster_analysis_safir
Language: r
msc-idm-2021
Language: r
auth-api
Language: kotlin
An API for issuing authentication and authorization tokens
outpack.orderly
Language: r
Description of the pacakge in more than one full sentence.
msvalidation
Language: r
Builds long running validation vignettes for the malariasimulation model.
https://mrc-ide.github.io/msvalidation/
Depends on:
  • mrc-ide/malariaEquilibrium
  • mrc-ide/malariasimulation
odin-js
Language: js
odin js/ts support
https://mrc-ide.github.io/odin-js/
Depends on:
  • reside-ic/dfoptim
mcstate
Language: r
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.
https://mrc-ide.github.io/mcstate
Depends on:
  • mrc-ide/dust
  • mrc-ide/mode
  • mrc-ide/odin.dust
Used by:
  • mrc-ide/gasworks
  • mrc-ide/gonovax
  • mrc-ide/spimalot
  • mrc-ide/sircovid
mint-deploy
Language: shell
public-events-zombie-sim-c
Language: c++
The Zombie Spatial Simulator Core
naomi_bot
Language: python
site
Language: r
This package converts a parameterised "site file" into malariasimulation model input parameter list.
Depends on:
  • mrc-ide/malariasimulation
siR
Language: r
Exploring the design and running of IBM in R and Rcpp with simple examples. Including demography.
Depends on:
  • mrc-ide/odin
covid_booster_analysis_safir_refit
nimue_js
Language: js
A javascript implementation of the nimue COVID-19 model
naomi-dev
Language: r
hiv-orderly-proxy
Language: shell
ccmpp.tmb
Language: r
Leapfrog is a multistate population projection model for estimating population and demographic indicators. The model implements a cohort component model of population projection (CCMPP) and statistical fitting of Wheldon et al.'s Bayesian Population Reconstruction framework in the R package Template Model Builder (TMB).
covid-vaccine-impact-orderly
Language: r
mrc-ide-vault
Language: shell
eigen1
Language: r
What the package does (one paragraph).
Used by:
  • mrc-ide/cometr
  • mrc-ide/sircovid
RECON_TB_to_odin
Language: r
Re-writing the RECON TB practical (https://www.reconlearn.org/post/practical-tb.html) to run in the odin web interface
dopri-js
Language: js
Dormand–Prince methods
https://mrc-ide.github.io/dopri-js/
global-lmic-reports-staging
Language: html
Daily updated LMIC COVID-19 reports (Staging)
https://mrc-ide.github.io/global-lmic-reports-staging
POLICI_africa_south_america
Language: r
Shiny app to show African and South American YF coverage
cart
Language: r
Extract population, prevalence and vector cartographic information for use with malarisimulation.
https://mrc-ide.github.io/cart/
umbrella
Language: r
Download CHIRPS rainfall rasters. Extract rainfall by place. Estimate seaosnality profiles.
https://mrc-ide.github.io/umbrella/
mrc-imperial-poster-template
Language: tex
gonovaxdust
Language: r
Stochastic compartmental model of gonorrhoea vaccination, using odin.dust.
https://mrc-ide.github.io/gonovaxdust/
Depends on:
  • mrc-ide/dust
  • mrc-ide/gonovax
  • mrc-ide/odin
  • mrc-ide/odin.dust
covid19_mainland_China_report
Language: html
us-covid19-forecasts-orderly
Language: r
US forecasts
malariaEquilibrium
Language: r
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.
Used by:
  • mrc-ide/malariasimulation
  • mrc-ide/msvalidation
  • mrc-ide/malariaModelFit
rtss_impact_cea_2021
Language: r
An update of the RTS,S vaccine impact and cost-effectiveness analysis first implented in Penny et al 2015 (https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(15)00725-4/fulltext).
didehpc-pkgs
Language: r
YFestimation
Language: r
Estimates ecological niche model (GLM) and two transmission models (SERO) for yellow fever. The GLM is estimated using conventional MCMC and the two transmission models are estimated with product space MCMC allowing the user to find the model evidence for one relative to the other. Models are based on Garske et al. (2014) and Jean et al. (2019).
Depends on:
  • mrc-ide/YFburden
specio
Language: r
Read data from Spectrum PJNZ file into R consumable format for EPP.
https://mrc-ide.github.io/specio/
Depends on:
  • mrc-ide/beers
Used by:
  • mrc-ide/hintr
public-events-herd-immunity-android_v2
Language: java
V2 of Herd Immunity Android Controller
hiv-docs
Documentation for HIV group
drat
Language: html
:package::package::package: drat repository
https://mrc-ide.github.io/drat
msc-istda-2019
Language: html
Introduction to Statistical Thinking and Data Analysis, MSc Epidemiology and MSc Health Data Analytics 2019
wodin-demo
Language: js
Demo instance of wodin
malaria-tools
Language: html
New version of Malaria Tools being developed in 2018
outbreakteachR
Language: r
Importing and analysing data sheet created within teaching "paper outbreak". Tools include visualisation and animation of the outbreak dynamics, example simualtion methods.
mipmapper
Language: r
Molecular inversion probes (MIPs) are a tool for genomic partitioning, which result in datasets of SNP genotypes. mipmapper is a package to help assist in filtering the raw output from these sequencing efforts, and conducting population genetic analyses.
https://mrc-ide.github.io/mipmapper/
monkeypox-orderly-web
Language: shell
threemc-orderly
Language: r
Orderly project for mrc-ide/circumcision-coverage
glodide
Language: r
Submission of Global LMIC Reports via Orderly To DIDE Cluster
nimue
Language: r
Extension of the squire (https://github.com/mrc-ide/squire) COVID-19 model for simulating vaccine impact.
https://mrc-ide.github.io/nimue/
Depends on:
  • mrc-ide/dde
  • mrc-ide/odin
  • mrc-ide/squire
Used by:
  • mrc-ide/cometr
  • mrc-ide/safir2
  • mrc-ide/safir
  • mrc-ide/squire.page
covid19-si
Language: r
hint-db
Language: shell
Web application database for the HIV Indicators Tool
welcome
:wave::wave::wave: Get started at mrc-ide
R-for-IDM-Intro
Language: html
hiv-orderly-web
Language: shell
Orderly web configuration for hiv-orderly
covid19-forecasts-orderly-image
Language: dockerfile
global_covid_vaccine_booster_paper
Language: r
kelp
Language: r
R client for calling SeaweedFS.
Depends on:
  • reside-ic/ids
Used by:
  • mrc-ide/rrq.kelp
COVID19_CFR_submission
Language: r
Repository for all scripts required to replicate the CFR analysis for paper submission.
covid_global_impact
Language: r
covid_global_impact
auth-db
Language: shell
A dockerised postgres database with a schema to support authentication and authorization for any app
rmnist
Language: r
Interface with the 'MNIST' collection of handwritten digits.
jointlyr
Language: r
Provides a Stan implementation of a method to jointly estimate incidence and reproduction number.
mint-mockups
Language: html
mint
Language: typescript
Malaria Indicators Tool
syncr
Language: r
Syncronise directories using rsync.
eppasm
Language: r
What the package does (one paragraph).
Used by:
  • mrc-ide/naomi
  • mrc-ide/leapfrog
remotesave
Language: r
Saves arbitrary state remotely to a 'Redis' server. Designed for use within shiny applications, but possibly more general.
Depends on:
  • reside-ic/ids
Used by:
  • mrc-ide/odin.ui
infectiousdiseasemodels-brazil
Language: html
Brazil 2022 short course
PlasmoMAPI
Language: r
Genetic data from Plasmodium parasites can tell us something about the spatial connectivity of parasite populations. Infections that trace back to a common ancestor in the recent past tend to be highly related, meaning we can use estimates of pairwise relatedness between sampling locations to infer levels of gene flow in the population, and to identify barriers and corridors of migration. PlasmoMAPI does this in a statistically robust way, accounting for the natural fall-off of relatedness with distance to identify significant discontinuities in the overall spatial pattern.
https://mrc-ide.github.io/PlasmoMAPI/
google-form-post-cordova-plugin
Language: js
Cordova plugin that submits a response to a google form
Zika_vaccine
Language: r
Designing clinical disease vaccine efficacy trials for Zika
epicyst
Language: r
Contains ODEs for Cysticercosis/Pork tapeworm model.
https://mrc-ide.github.io/epicyst/
Depends on:
  • mrc-ide/odin
mrc-ide-redis
Language: shell
human_tsol_FoI_modelling
Language: r
Project to fit catalytic models to human taenia solium age-(sero)prevalence data to estimate per-capita seroconversion / infection rates (force-of infection; FoI) and seroreversion / infection loss rates.
git-example
Language: r
covid_vaccine_dose_analysis
Language: r
referenced-TI
Language: python
Code for the referenced thermodynamic integration (TI) method of calculating model evidence
odin.api
Language: r
API server for odin models, using porcelain/plumber.
Depends on:
  • mrc-ide/odin
  • reside-ic/porcelain
deterministic-malaria-model
Language: r
Deterministic implementations of the Imperial College malaria transmission model using the pacakge odin.
https://mrc-ide.github.io/deterministic-malaria-model/index
Depends on:
  • mrc-ide/dde
  • mrc-ide/odin
africa_LSM_impact
Language: r
Looking at the impact of larval source management for Ellies paper (working title) "The potential of larval source management for malaria control across Africa"
squire.page
Language: r
Contains miscellaneous functions used in the repo global-lmic-reports-orderly and other packages that utilise squire or nimue fits. These functions are kept externally to keep them consistent across multiple repositories and multiple orderly tasks.
https://mrc-ide.github.io/squire.page/
Depends on:
  • mrc-ide/nimue
  • mrc-ide/odin
  • vimc/orderly
  • mrc-ide/squire
gf
Language: r
Contains functionality and associated documentation for both pre- and post- modelling workflows for modelling to support the Global Fund's replenishment for the period 2024 - 2026.
https://mrc-ide.github.io/gf/
PlasmoSim
Language: r
A basic Plasmodium simulator. Contains functions to simulate epidemiological and genetic data from a simple model of Plasmodium falciparum transmission.
typochallenge
Language: r
:ballot_box_with_check::calendar::negative_squared_cross_mark: Typo challenge
https://shiny.dide.imperial.ac.uk/typochallenge
promed-covid
Language: r
skygrowth
Language: r
This package provides methods for inferring effective population size for time-scaled phylogenies using Bayesian MCMC and maximum a priori. The growth rate of effective population sizes is modeled as a simple Brownian motion.
outpack-py
Language: python
queuer
Language: r
Queue tasks to number of backends.
https://mrc-ide.github.io/queuer
Depends on:
  • mrc-ide/context
  • reside-ic/ids
Used by:
  • mrc-ide/didehpc
msio
Language: r
This package samples malariasimulation inputs and calculates corresponding outputs for surrogate modelling.
Depends on:
  • mrc-ide/malariasimulation
child_covid19_lit_review
Language: html
Code and results associated with systematic literature review
repatriation-covid-19
Collated data on repatriation flights from Wuhan, China, between 29th Jan - 27th Feb
wodin
Language: typescript
odin on the web
shiny
:star2::books::star2: documentation and (eventually) scripts for our shiny setup
public-events-zombie-sim-android
Language: java
Android app to control Zombie Sim 2 remotely
COVIDCurve
Language: r
In many settings, individual-based (i.e. "line-list") data are often unavailable or unreliable. Here we provide a model framework that relies on aggregated death counts and seroprevalence data to infer the infection fatality ratio, or the probability of death givin infection. Models are fit within a Bayesian framework and account for onset-outcome delays and serologic test characteristics.
https://mrc-ide.github.io/COVIDCurve
Depends on:
  • mrc-ide/drjacoby
AMMS2022
Language: html
This repository holds all of the code for the Applied Malaria Molecular Surveillance (AMMS) 2022 workshop, held at the EPHI in Addis Ababa, 5-7 August 2022.
spam.mpxv
Language: r
Implements a stochastic dynamic variable degree model within the edge-based-compartmental modelling framework. Three contact types based on duration of partnerships.
odin-app
Language: r
Vo_serology
Language: r
hiv-inference-website
Language: html
HIV Inference Group Website
https://hiv-inference.org/
reestimate_covidIFR_analysis
Language: r
Repo for work on ICL Report 34 and subsequent Comm Med Methods Paper
viralload
Language: r
Estimate viral load using time varying sampling from time varying functions.
https://mrc-ide.github.io/viralload/
Depends on:
  • mrc-ide/dust
covid19-forecasts-orderly-web
Language: shell
EPIONCHO-IBM-CTS
Language: r
alphavirus-panama
Language: r
Endemic Alphavirus in Panama
coop
Language: r
Coop is a generalised heuristic for budget constrained optimisations using simulated annealing. You can use coop to search for optimal combinations of scenarios (e.g. intervention mixes in different areas) which minimise a target outcome (e.g. cases or deaths).
virtual-ecology-workbench
Language: java
Toolkit for creating agent-based simulations of plankton ecosystems
naomi.utils
Language: r
This package contains utility functions for creating and manipulating datasets for the Naomi model and related projects.
threemc-orderly-image
Language: shell
Docker image build for threemc orderly
covid-sim
Language: c++
This is the COVID-19 CovidSim microsimulation model developed by the MRC Centre for Global Infectious Disease Analysis hosted at Imperial College, London.
peeps
Language: r
What the package does (one paragraph).
cinterpolate
Language: r
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>.
https://mrc-ide.github.io/cinterpolate
Used by:
  • mrc-ide/odin
SIMPLEGEN
Language: r
Forwards-in time simulation of Plasmodium falciparum genetic data can be computationally intensive, as many genotypes are tracked but ultimately lost. SIMPLEGEN avoids this problem by splitting simulation into three steps - first, simulating transmission under a simple individual-based model, second, pruning the infection history to focus on nodes that contribute to the final sample, and third, simulating genetic data. A secondary advantage is that any third-party epidemiological simulator can be used for the first step as long as it outputs in the correct format. The major limitation of SIMPLEGEN is that assumes the epidemiological and genetic processes are seperable, and hence is limited to neutral variation, and cannot model selection.
https://mrc-ide.github.io/SIMPLEGEN/
global-lmic-reports
Language: html
Global LMIC COVID-19 reports. Updated to include HICs. Previous data is periodically backed up at https://mrcdata.dide.ic.ac.uk/global-lmic-reports/
https://mrc-ide.github.io/global-lmic-reports
hintr
Language: r
R API for calling naomi district level HIV model.
Depends on:
  • reside-ic/ids
  • ropensci/jsonvalidate
  • mrc-ide/naomi
  • reside-ic/porcelain
  • mrc-ide/rrq
  • mrc-ide/specio
  • reside-ic/traduire
inference-data
Language: r
inference-data-orderly-image
Language: dockerfile
Docker image build for inference-data orderly
sarscov2-roadmap-england
Language: r
commal
Language: r
Severe malaria anaemia in the community
malariasimulation_comp
Language: r
Sandbox for malaria model version comparison
rtss_prioritisation
Language: r
rincewind
Language: r
This package contains utility functions for processing forecasts matrices.
bhrp
Language: r
Code for linking Bellman Harris with Renewal Processes
threemc
Language: r
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>.
Depends on:
  • mrc-ide/naomi
ppmcmc
Language: r
What the package does (one paragraph).
https://mrc-ide.github.io/ppmcmc/
malariaModelFit
Language: r
Contains functions for re-fitting the model of Griffin et al. 2014 to data using MCMC. (Griffin et al. 2014, Nature Communications 5. "Estimates of the changing age-burden of Plasmodium falciparum malaria disease in sub-Saharan Africa").
Depends on:
  • mrc-ide/drjacoby
  • mrc-ide/malariaEquilibrium
simpleepp
Language: r
Simplified stylized implementation of UNAIDS Estimation and Projection Package (EPP) model
mlesky-experiments
Language: r
excalibur
Language: r
Exploring the impact of calibrations on using ODE epidemic models to forcast future scenarios. Uses odin from Imperials' MRC-IDE to implement models, with the intention to look at calibrations in squire/nimue.
Depends on:
  • mrc-ide/odin
MAP_raster_to_admin
Language: r
Repo for converting MAP ITN use (or other raster data) to admin data
decart
Language: java
Domestic case Estimates from Cases Among Returning Travellers - Java application
hermione
Language: r
This package implements methods to robustly estimate COVID-19 Serial Interval accounting for biases introduced due to isolation of cases.
typochallengedata
Language: r
Analysing data collected in typo challenge
fertility-orderly-image
Language: r
Docker image build for osymandius/fertility_orderly
frogger
Language: r
Frogger 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.
covid_vaccine_hesitancy
Language: r
covid19-si-shiny
Language: r
dust
Language: r
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>.
https://mrc-ide.github.io/dust
Used by:
  • mrc-ide/gasworks
  • mrc-ide/YellowFeverDynamics
  • mrc-ide/mode
  • mrc-ide/odin.dust
  • mrc-ide/spimalot
  • mrc-ide/sircovid
  • mrc-ide/mcstate
  • mrc-ide/gonovaxdust
  • mrc-ide/viralload
matchGADM
Language: r
This package contains two main functions which both map from one shapefile to another through matching the area. The resulting output is a data frame of proportions from each admin unit in the old to the new. This can be used to convert population sizes from one map to another.
hypatia
Language: r
Implements an individual-based model of COVID-19 transmission. Derives from previous work in 'squire'.
https://mrc-ide.github.io/hypatia
Depends on:
  • mrc-ide/individual
  • mrc-ide/squire
csavr-mortality
Language: r
infectiousdiseasemodels-2019
Language: r
Introduction to Mathematical Models of the Epidemiology & Control of Infectious Diseases
https://shiny.dide.imperial.ac.uk/infectiousdiseasemodels-2019/
india-ascertainment
Language: r
Code repository for analysis into under-ascertainment of COVID-19 mortality in India
Depends on:
  • vimc/orderly
  • mrc-ide/squire

The following are research outputs, authored directly by researchers in the department

Sort by: Last updated / Name / Language
hivmappr
Language: r
Small-area estimation of HIV prevalence, ART coverage, and HIV incidence
malariaModelFit
Language: r
Contains functions for re-fitting the model of Griffin et al. 2014 to data using MCMC. (Griffin et al. 2014, Nature Communications 5. "Estimates of the changing age-burden of Plasmodium falciparum malaria disease in sub-Saharan Africa").
Depends on:
  • mrc-ide/drjacoby
  • mrc-ide/malariaEquilibrium
covfefe
Language: r
More about what it does (maybe more than one line) Use four spaces when indenting paragraphs within the Description.
https://mrc-ide.github.io/covfefe/
hermione
Language: r
This package implements methods to robustly estimate COVID-19 Serial Interval accounting for biases introduced due to isolation of cases.
PlasmoMAPI
Language: r
Genetic data from Plasmodium parasites can tell us something about the spatial connectivity of parasite populations. Infections that trace back to a common ancestor in the recent past tend to be highly related, meaning we can use estimates of pairwise relatedness between sampling locations to infer levels of gene flow in the population, and to identify barriers and corridors of migration. PlasmoMAPI does this in a statistically robust way, accounting for the natural fall-off of relatedness with distance to identify significant discontinuities in the overall spatial pattern.
https://mrc-ide.github.io/PlasmoMAPI/
coop
Language: r
Coop is a generalised heuristic for budget constrained optimisations using simulated annealing. You can use coop to search for optimal combinations of scenarios (e.g. intervention mixes in different areas) which minimise a target outcome (e.g. cases or deaths).
YFburden
Language: r
The package takes estimates of the force of infection in each country, projected vaccination coverage, historic vaccination coverage, and projected population sizes to calculate the number of infections. It also takes estimates of disability weights and probability of severe infections to calculate the number of severe infections, deaths and DALYS.
Used by:
  • mrc-ide/YFestimation
hypatia
Language: r
Implements an individual-based model of COVID-19 transmission. Derives from previous work in 'squire'.
https://mrc-ide.github.io/hypatia
Depends on:
  • mrc-ide/individual
  • mrc-ide/squire
YFestimation
Language: r
Estimates ecological niche model (GLM) and two transmission models (SERO) for yellow fever. The GLM is estimated using conventional MCMC and the two transmission models are estimated with product space MCMC allowing the user to find the model evidence for one relative to the other. Models are based on Garske et al. (2014) and Jean et al. (2019).
Depends on:
  • mrc-ide/YFburden
MIPanalyzer
Language: r
Filtering and analysis of MIP data.
https://mrc-ide.github.io/MIPanalyzer/
eigen1
Language: r
What the package does (one paragraph).
Used by:
  • mrc-ide/cometr
  • mrc-ide/sircovid
spatialbranchr
Language: r
spatialbranchr implements a spatially explicit branching process model.
rrq.kelp
Language: r
An offload file store for rrq. Using kelp API to interact with SeaweedFS, this can be used to save large input or output data to a distributed file store.
Depends on:
  • reside-ic/ids
  • mrc-ide/kelp
  • mrc-ide/rrq
excalibur
Language: r
Exploring the impact of calibrations on using ODE epidemic models to forcast future scenarios. Uses odin from Imperials' MRC-IDE to implement models, with the intention to look at calibrations in squire/nimue.
Depends on:
  • mrc-ide/odin
rtss_impact_cea_2021
Language: r
An update of the RTS,S vaccine impact and cost-effectiveness analysis first implented in Penny et al 2015 (https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(15)00725-4/fulltext).
naomi.extensions
Language: r
This package implements the Naomi model for subnational HIV estimates.
Depends on:
  • mrc-ide/naomi
glodide
Language: r
Submission of Global LMIC Reports via Orderly To DIDE Cluster
gonovaxdust
Language: r
Stochastic compartmental model of gonorrhoea vaccination, using odin.dust.
https://mrc-ide.github.io/gonovaxdust/
Depends on:
  • mrc-ide/dust
  • mrc-ide/gonovax
  • mrc-ide/odin
  • mrc-ide/odin.dust
sarscov2-transmission-england
Language: r
demogsurv
Language: r
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.
sarscov2-roadmap-england
Language: r
viralload
Language: r
Estimate viral load using time varying sampling from time varying functions.
https://mrc-ide.github.io/viralload/
Depends on:
  • mrc-ide/dust
MissingCases
Language: r
This package uses next generation matrices to estimate the number of missing cases from a surveillance system.
gf
Language: r
Contains functionality and associated documentation for both pre- and post- modelling workflows for modelling to support the Global Fund's replenishment for the period 2024 - 2026.
https://mrc-ide.github.io/gf/
eppasm
Language: r
What the package does (one paragraph).
Used by:
  • mrc-ide/naomi
  • mrc-ide/leapfrog
naomi.utils
Language: r
This package contains utility functions for creating and manipulating datasets for the Naomi model and related projects.
malariaEquilibrium
Language: r
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.
Used by:
  • mrc-ide/malariasimulation
  • mrc-ide/msvalidation
  • mrc-ide/malariaModelFit
skygrowth
Language: r
This package provides methods for inferring effective population size for time-scaled phylogenies using Bayesian MCMC and maximum a priori. The growth rate of effective population sizes is modeled as a simple Brownian motion.
rincewind
Language: r
This package contains utility functions for processing forecasts matrices.
spimalot
Language: r
Code that supports that use of sircovid for our regular workflows (weekly SPI-M analyses, medium term projections) and forward simulation. Unlike 'sircovid', this package is intended to be more rapidly iterated, contains no compiled code, and will be significantly less tested because it must bend around ever-changing data and requirements for plotting/analysis.
https://mrc-ide.github.io/spimalot/
Depends on:
  • mrc-ide/EpiEstim
  • mrc-ide/dust
  • mrc-ide/mcstate
  • mrc-ide/rrq
  • mrc-ide/sircovid
epihawkes
Language: r
This package can be used to model infectious disease outbreaks. There are functions available for both fitting the model parameters to real outbreak data as well as simulating outbreaks from given parameters.
malariasimulation
Language: r
Specifies the latest and greatest malaria model.
https://mrc-ide.github.io/malariasimulation
Depends on:
  • mrc-ide/individual
  • mrc-ide/malariaEquilibrium
Used by:
  • mrc-ide/cali
  • mrc-ide/nlcali
  • mrc-ide/msvalidation
  • mrc-ide/site
  • mrc-ide/msio
gonovax
Language: r
Model for gonorrhoea vaccination, using odin.
https://mrc-ide.github.io/gonovax
Depends on:
  • mrc-ide/mcstate
  • mrc-ide/odin
Used by:
  • mrc-ide/gonovaxdust
epicyst
Language: r
Contains ODEs for Cysticercosis/Pork tapeworm model.
https://mrc-ide.github.io/epicyst/
Depends on:
  • mrc-ide/odin
ivRmectin
Language: r
A deterministic version of the Imperial College Malaria Model, adapted to explore the impact of novel endectocides on malaria transmission. Derived from the model developed and presented in Slater et al., Journal of Infectious Diseases 2014 (https://academic.oup.com/jid/article/210/12/1972/2908666) and Slater et al., Lancet Infectious Diseases, 2020 (https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(19)30633-4/fulltext).
Depends on:
  • mrc-ide/dde
  • mrc-ide/odin
reactidd
Language: r
alphaepi
Language: r
What the package does (one paragraph).
YellowFeverDynamics
Language: r
A package for running a dynamic, stochastic SEIRV model of yellow fever, creating input data and processing output data. The package can also be used to fit values of epidemiological parameters of the model to different types of data on yellow fever burden in one or more regions.
Depends on:
  • mrc-ide/dust
  • mrc-ide/odin
  • mrc-ide/odin.dust
sircovid
Language: r
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.
https://mrc-ide.github.io/sircovid
Depends on:
  • mrc-ide/EpiEstim
  • mrc-ide/dust
  • mrc-ide/eigen1
  • mrc-ide/mcstate
  • mrc-ide/odin
  • mrc-ide/odin.dust
Used by:
  • mrc-ide/spimalot
PlasmoSim
Language: r
A basic Plasmodium simulator. Contains functions to simulate epidemiological and genetic data from a simple model of Plasmodium falciparum transmission.
genescaper
Language: r
Inputs data consisting of allele frequencies at sampling sites along with their latitude/longitude values. Fits a model of smoothly varying allele frequencies in space (a Gaussian Random Field) via Bayesian MCMC. Uses the fitted model to predict allele frequencies at any given point in space, and also to generate a null distribution for pairwise genetic distances between sites. This null distribution can then be used to detect outliers, which may represent sites that are more/less connected than we would expect by chance.
Depends on:
  • mrc-ide/drjacoby
cart
Language: r
Extract population, prevalence and vector cartographic information for use with malarisimulation.
https://mrc-ide.github.io/cart/
nimue
Language: r
Extension of the squire (https://github.com/mrc-ide/squire) COVID-19 model for simulating vaccine impact.
https://mrc-ide.github.io/nimue/
Depends on:
  • mrc-ide/dde
  • mrc-ide/odin
  • mrc-ide/squire
Used by:
  • mrc-ide/cometr
  • mrc-ide/safir2
  • mrc-ide/safir
  • mrc-ide/squire.page
SIMPLEGEN
Language: r
Forwards-in time simulation of Plasmodium falciparum genetic data can be computationally intensive, as many genotypes are tracked but ultimately lost. SIMPLEGEN avoids this problem by splitting simulation into three steps - first, simulating transmission under a simple individual-based model, second, pruning the infection history to focus on nodes that contribute to the final sample, and third, simulating genetic data. A secondary advantage is that any third-party epidemiological simulator can be used for the first step as long as it outputs in the correct format. The major limitation of SIMPLEGEN is that assumes the epidemiological and genetic processes are seperable, and hence is limited to neutral variation, and cannot model selection.
https://mrc-ide.github.io/SIMPLEGEN/
reestimate_covidIFR_analysis
Language: r
Repo for work on ICL Report 34 and subsequent Comm Med Methods Paper
COVIDCurve
Language: r
In many settings, individual-based (i.e. "line-list") data are often unavailable or unreliable. Here we provide a model framework that relies on aggregated death counts and seroprevalence data to infer the infection fatality ratio, or the probability of death givin infection. Models are fit within a Bayesian framework and account for onset-outcome delays and serologic test characteristics.
https://mrc-ide.github.io/COVIDCurve
Depends on:
  • mrc-ide/drjacoby

The following are software utilities, primarily authored by researcher software engineers in the department

Sort by: Last updated / Name / Language
traduire.scripts
Language: r
What the package does (one paragraph).
vue-prototypes
Language: js
A place to stick vue component prototypes
defer
Language: r
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.
https://reside-ic.github.io/defer
fstorr
Language: r
Store files by content, similar in spirit to the 'storr' package (into which this might get folded).
fakerbase
Language: r
Connect to a Postgres database and generate a suite of functions that can be used to mock database tables for unit testing.
https://reside-ic.github.io/fakerbase
Used by:
  • vimc/vimpact
spud
Language: r
Enables uploading, downloading and listing of files in sharepoint.
Used by:
  • vimc/orderly.sharepoint
ids
Language: r
Generate random or human readable and pronounceable identifiers.
https://reside-ic.github.io/ids
Used by:
  • vimc/orderly.server
  • vimc/orderly
  • mrc-ide/rrq
  • mrc-ide/odin.ui
  • mrc-ide/rrq.kelp
  • mrc-ide/didehpc
  • mrc-ide/context
  • mrc-ide/kelp
  • mrc-ide/remotesave
  • mrc-ide/queuer
  • mrc-ide/hintr
porcelain
Language: r
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.
https://reside-ic.github.io/porcelain
Depends on:
  • ropensci/jsonvalidate
Used by:
  • vimc/orderly.server
  • mrc-ide/cometr
  • mrc-ide/mintr
  • mrc-ide/odin.api
  • mrc-ide/hintr
dfoptim
Language: js
Derivative-Free Optimisation
https://reside-ic.github.io/dfoptim/
Used by:
  • mrc-ide/odin-js
constellation
Language: python
traduire
Language: r
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.
https://reside-ic.github.io/traduire/
Used by:
  • mrc-ide/naomi
  • mrc-ide/hintr
cppdoc
Language: r
Provides a bridge between doxygen's XML output and vignettes written in R markdown.
https://reside-ic.github.io/cppdoc
mls
Language: r
Create multiline strings for errors, warnings and messages.
https://reside-ic.github.io/mls
jsonvalidate
Language: r
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.
https://docs.ropensci.org/jsonvalidate
Used by:
  • reside-ic/porcelain
  • vimc/orderly.server
  • vimc/orderly2
  • mrc-ide/outpack
  • mrc-ide/odin
  • mrc-ide/mintr
  • mrc-ide/hintr
cyphr
Language: r
Encryption wrappers, using low-level support from 'sodium' and 'openssl'. 'cyphr' tries to smooth over some pain points when using encryption within applications and data analysis by wrapping around differences in function names and arguments in different encryption providing packages. It also provides high-level wrappers for input/output functions for seamlessly adding encryption to existing analyses.
https://docs.ropensci.org/cyphr
orderly.server
Language: r
Run orderly reports as a server.
Depends on:
  • reside-ic/ids
  • ropensci/jsonvalidate
  • vimc/orderly
  • reside-ic/porcelain
  • mrc-ide/rrq
vaultr
Language: r
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'.
https://vimc.github.io/vaultr
Used by:
  • vimc/dettl
  • vimc/orderly
  • vimc/vimpact
  • vimc/jenner
montagu-py
Language: python
dettl
Language: r
Data extract, transform, test and load tool for sanitising your workflow.
https://vimc.github.io/dettl
Depends on:
  • vimc/vaultr
vault-dev
Language: python
Use vault server in development mode in tests, from python
orderly
Language: r
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.
https://www.vaccineimpact.org/orderly/
Depends on:
  • reside-ic/ids
  • vimc/vaultr
Used by:
  • vimc/orderly.server
  • vimc/montagu-r
  • vimc/orderly2
  • vimc/orderly.sharepoint
  • vimc/orderlyweb
  • vimc/orderly.rstudio
  • mrc-ide/syria-covid-ascertainment
  • mrc-ide/global-lmic-meffs
  • mrc-ide/global-lmic-results
  • mrc-ide/squire.page
  • mrc-ide/india-ascertainment
orderly-web-deploy
Language: python
montagu
Language: python
Deployment scripts for Montagu as a constellation of Docker services
orderly-web-py
Language: python
orderly2
Language: r
A reimplementation of the good bits of orderly using outpack.
Depends on:
  • ropensci/jsonvalidate
  • vimc/orderly
  • mrc-ide/outpack
orderly.sharepoint
Language: r
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.
https://vimc.github.io/orderly.sharepoint
Depends on:
  • vimc/orderly
  • reside-ic/spud
orderlyweb
Language: r
Client for 'OrderlyWeb' for use from the 'orderly' package. Allows downloading of reports, running remote reports and other interaction with the remote report repository.
https://vimc.github.io/orderlyweb/
Depends on:
  • vimc/orderly
Used by:
  • vimc/montagu-r
orderly.rstudio
Language: r
RStudio addins for orderly.
Depends on:
  • vimc/orderly
stoner
Language: r
For montagu-imports that create touchstones, or augment existing touchstones, allow the import to be as minimal as possible, towards single line extract and transform calls, in order that the review for that import can be focussed on the metadata being correct, rather than on code.
https://www.vaccineimpact.org/stoner/
phipps
Language: r
VIMC plotting functions.
vimpact
Language: r
VIMC IMPACT CALCULATION PACKAGE. This package is mainly for the VIMC Science Team to investigate vaccination impact.
http://www.vaccineimpact.org/vimpact/
Depends on:
  • reside-ic/fakerbase
  • vimc/vaultr
jenner
Language: r
Helpers for Montagu.
Depends on:
  • vimc/vaultr
beers
Language: r
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.
Used by:
  • mrc-ide/leapfrog
  • mrc-ide/specio
outpack
Language: r
Create a portable package of output from a computational experiment.
https://mrc-ide.github.io/outpack
Depends on:
  • ropensci/jsonvalidate
Used by:
  • vimc/orderly2
db
Language: r
One paragraph description of what the package does as one or more full sentences.
om
Language: r
om can be used to find solutions to budget-optimisation challenges.
https://mrc-ide.github.io/om/
snapalette
Language: r
What the package does (one paragraph).
rrq
Language: r
Simple Redis queue in R.
https://mrc-ide.github.io/rrq/
Depends on:
  • reside-ic/ids
Used by:
  • vimc/orderly.server
  • mrc-ide/rrq.kelp
  • mrc-ide/didehpc
  • mrc-ide/spimalot
  • mrc-ide/hintr
gasworks
Language: r
Models of Group A Streptococcus (GAS) Transmission.
Depends on:
  • mrc-ide/dust
  • mrc-ide/mcstate
  • mrc-ide/odin
  • mrc-ide/odin.dust
pika
Language: r
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.
Depends on:
  • mrc-ide/EpiEstim
conan
Language: r
Create libraries. For us, there is no spring. Just the wind that smells fresh before the storm.
https://mrc-ide.github.io/conan/
Used by:
  • mrc-ide/didehpc
mode
Language: r
Solve multiple ODEs in parallel.
https://mrc-ide.github.io/mode/
Depends on:
  • mrc-ide/dde
  • mrc-ide/dust
Used by:
  • mrc-ide/odin.dust
  • mrc-ide/mcstate
EpiEstim
Language: r
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>.
Used by:
  • mrc-ide/pika
  • mrc-ide/spimalot
  • mrc-ide/sircovid
cometr
Language: r
Run 'nimue' (and eventually other models, such as an individual based model) and expose results over an HTTP API.
Depends on:
  • mrc-ide/dde
  • mrc-ide/eigen1
  • mrc-ide/nimue
  • reside-ic/porcelain
  • mrc-ide/squire
DRpower
Language: r
Can be used to analyse prevalence data typical of drug- and diagnostic-resistance studies (i.e. pfhrp2/3 deletions in malaria). Uses a Bayesian approach to estimate both the prevalence and the level of intra- cluster correlation. Also estimates the power via simulation for a given sample size, making it possible to choose a sample size to achieve a given desired power.
individual
Language: r
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.
https://mrc-ide.github.io/individual
Used by:
  • mrc-ide/malariasimulation
  • mrc-ide/safir2
  • mrc-ide/safir
  • mrc-ide/hypatia
odin.dust
Language: r
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).
https://mrc-ide.github.io/odin.dust
Depends on:
  • mrc-ide/dde
  • mrc-ide/dust
  • mrc-ide/mode
  • mrc-ide/odin
Used by:
  • mrc-ide/gasworks
  • mrc-ide/YellowFeverDynamics
  • mrc-ide/sircovid
  • mrc-ide/mcstate
  • mrc-ide/gonovaxdust
safir2
Language: r
'safir2' is an upgraded and refactored version of 'safir', which implements a stochastic individual based model of SARS-CoV-2 transmission. The model takes into account individual level immunity and neutralizing antibody titre, as well as allowing for complex vaccine allocation schemes.
https://mrc-ide.github.io/safir2/
Depends on:
  • mrc-ide/individual
  • mrc-ide/nimue
  • mrc-ide/squire
ring
Language: r
Circular / ring buffers in R and C. There are a couple of different buffers here with different implementations that represent different trade-offs.
https://mrc-ide.github.io/ring
Used by:
  • mrc-ide/odin
  • mrc-ide/dde
hint-generic-chart-prototypes
Language: js
apothecary
Language: r
An extended model of the SEIR model available in the squire package (available at: https://github.com/mrc-ide/squire) extended to explore the impact of different pharmaceutical therapeutics.
Depends on:
  • mrc-ide/dde
  • mrc-ide/odin
  • mrc-ide/squire
safir
Language: r
Implements an individual-based model of COVID-19 transmission. Derives from previous work in 'squire'.
https://mrc-ide.github.io/safir/
Depends on:
  • mrc-ide/individual
  • mrc-ide/nimue
  • mrc-ide/squire
hivmodels.net
Language: js
Static assets for hivmodel.net
odin.ui
Language: r
A user interface for 'odin', using Shiny.
Depends on:
  • mrc-ide/dde
  • reside-ic/ids
  • mrc-ide/odin
  • mrc-ide/remotesave
cali
Language: r
Cali is a package to help calibrate malariasimulation model runs. For example to set EIR to match a given prevalence at a specific timepoint.
https://mrc-ide.github.io/cali/
Depends on:
  • mrc-ide/malariasimulation
didehpc
Language: r
DIDE HPC support.
http://mrc-ide.github.io/didehpc
Depends on:
  • mrc-ide/conan
  • mrc-ide/context
  • reside-ic/ids
  • mrc-ide/queuer
  • mrc-ide/rrq
tfpscanner
Language: r
A pipeline for scanning a SARS-CoV-2 phylogeny for clades with outlying growth patterns and high evolutionary rates. Original methods developed in emvolz-phylodynamics/variantAnalysis
treasure
Language: r
The goal of treasure is to provide basic, generic unit-costing help for malariasimulation.
https://mrc-ide.github.io/treasure/
nlcali
Language: r
What the package does (one paragraph).
Depends on:
  • mrc-ide/malariasimulation
drjacoby
Language: r
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.
https://mrc-ide.github.io/drjacoby/
Used by:
  • mrc-ide/genescaper
  • mrc-ide/squire
  • mrc-ide/COVIDCurve
  • mrc-ide/malariaModelFit
netz
Language: r
Helper functionality to set up bed nets for use in malariasimulation. Also used to cost bed net programmes.
https://mrc-ide.github.io/netz/
markovid
Language: r
MCMC package for preliminary fits of hospital progression parameters (transition probabilities and durations in each state). The outputs of these fits are passed up to the larger mechanistic model as priors or relative risks for a further level of fitting. NB, this package is essentially a re-purpose of the drjacoby package, and still contains some legacy code.
context
Language: r
Contexts for evaluating R expressions.
http://mrc-ide.github.io/context
Depends on:
  • reside-ic/ids
Used by:
  • mrc-ide/didehpc
  • mrc-ide/queuer
mockcpp
Language: r
A header only library integrating 'testthat' with 'trompeoeil' to provide mocking for C++ code in R packages. Mocking is a technique for making a fake version of a software service. You can mock services to test that your code interacts correctly with external interfaces, to make your tests deterministic, or to break your tests down into smaller units. 'testthat' provides a testing framework for R and C++ code in R packages. 'trompeoeil' is a C++ header only library for mocking.
odin
Language: r
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.
https://mrc-ide.github.io/odin
Depends on:
  • mrc-ide/cinterpolate
  • mrc-ide/dde
  • ropensci/jsonvalidate
  • mrc-ide/ring
Used by:
  • mrc-ide/gasworks
  • mrc-ide/YellowFeverDynamics
  • mrc-ide/odin.dust
  • mrc-ide/apothecary
  • mrc-ide/odin.ui
  • mrc-ide/gonovax
  • mrc-ide/sircovid
  • mrc-ide/squire
  • mrc-ide/ivRmectin
  • mrc-ide/siR
  • mrc-ide/gonovaxdust
  • mrc-ide/nimue
  • mrc-ide/epicyst
  • mrc-ide/odin.api
  • mrc-ide/deterministic-malaria-model
  • mrc-ide/squire.page
  • mrc-ide/excalibur
mintr
Language: r
Provides an API for use by 'MINT'.
Depends on:
  • ropensci/jsonvalidate
  • reside-ic/porcelain
dde
Language: r
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.
https://mrc-ide.github.io/dde
Depends on:
  • mrc-ide/ring
Used by:
  • mrc-ide/mode
  • mrc-ide/cometr
  • mrc-ide/odin.dust
  • mrc-ide/apothecary
  • mrc-ide/odin.ui
  • mrc-ide/odin
  • mrc-ide/squire
  • mrc-ide/ivRmectin
  • mrc-ide/nimue
  • mrc-ide/deterministic-malaria-model
naomi
Language: r
This package implements the Naomi model for subnational HIV estimates.
https://mrc-ide.github.io/naomi
Depends on:
  • mrc-ide/eppasm
  • reside-ic/traduire
Used by:
  • mrc-ide/naomi.extensions
  • mrc-ide/hintr
  • mrc-ide/threemc
weighter
Language: r
This package implementes model averaging.
flodia
Language: r
Tools to create compartmental model flow diagrams in base R.
https://mrc-ide.github.io/flodia
squire
Language: r
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.
https://mrc-ide.github.io/squire/
Depends on:
  • mrc-ide/dde
  • mrc-ide/drjacoby
  • mrc-ide/odin
Used by:
  • mrc-ide/syria-covid-ascertainment
  • mrc-ide/global-lmic-meffs
  • mrc-ide/covid-mortality-ascertainment
  • mrc-ide/cometr
  • mrc-ide/safir2
  • mrc-ide/apothecary
  • mrc-ide/safir
  • mrc-ide/global-lmic-results
  • mrc-ide/nimue
  • mrc-ide/squire.page
  • mrc-ide/hypatia
  • mrc-ide/india-ascertainment
leapfrog
Language: r
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.
Depends on:
  • mrc-ide/beers
  • mrc-ide/eppasm
outpack.orderly
Language: r
Description of the pacakge in more than one full sentence.
msvalidation
Language: r
Builds long running validation vignettes for the malariasimulation model.
https://mrc-ide.github.io/msvalidation/
Depends on:
  • mrc-ide/malariaEquilibrium
  • mrc-ide/malariasimulation
mcstate
Language: r
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.
https://mrc-ide.github.io/mcstate
Depends on:
  • mrc-ide/dust
  • mrc-ide/mode
  • mrc-ide/odin.dust
Used by:
  • mrc-ide/gasworks
  • mrc-ide/gonovax
  • mrc-ide/spimalot
  • mrc-ide/sircovid
naomi_bot
Language: python
site
Language: r
This package converts a parameterised "site file" into malariasimulation model input parameter list.
Depends on:
  • mrc-ide/malariasimulation
siR
Language: r
Exploring the design and running of IBM in R and Rcpp with simple examples. Including demography.
Depends on:
  • mrc-ide/odin
nimue_js
Language: js
A javascript implementation of the nimue COVID-19 model
ccmpp.tmb
Language: r
Leapfrog is a multistate population projection model for estimating population and demographic indicators. The model implements a cohort component model of population projection (CCMPP) and statistical fitting of Wheldon et al.'s Bayesian Population Reconstruction framework in the R package Template Model Builder (TMB).
umbrella
Language: r
Download CHIRPS rainfall rasters. Extract rainfall by place. Estimate seaosnality profiles.
https://mrc-ide.github.io/umbrella/
specio
Language: r
Read data from Spectrum PJNZ file into R consumable format for EPP.
https://mrc-ide.github.io/specio/
Depends on:
  • mrc-ide/beers
Used by:
  • mrc-ide/hintr
wodin-demo
Language: js
Demo instance of wodin
mipmapper
Language: r
Molecular inversion probes (MIPs) are a tool for genomic partitioning, which result in datasets of SNP genotypes. mipmapper is a package to help assist in filtering the raw output from these sequencing efforts, and conducting population genetic analyses.
https://mrc-ide.github.io/mipmapper/
kelp
Language: r
R client for calling SeaweedFS.
Depends on:
  • reside-ic/ids
Used by:
  • mrc-ide/rrq.kelp
rmnist
Language: r
Interface with the 'MNIST' collection of handwritten digits.
jointlyr
Language: r
Provides a Stan implementation of a method to jointly estimate incidence and reproduction number.
syncr
Language: r
Syncronise directories using rsync.
remotesave
Language: r
Saves arbitrary state remotely to a 'Redis' server. Designed for use within shiny applications, but possibly more general.
Depends on:
  • reside-ic/ids
Used by:
  • mrc-ide/odin.ui
odin.api
Language: r
API server for odin models, using porcelain/plumber.
Depends on:
  • mrc-ide/odin
  • reside-ic/porcelain
squire.page
Language: r
Contains miscellaneous functions used in the repo global-lmic-reports-orderly and other packages that utilise squire or nimue fits. These functions are kept externally to keep them consistent across multiple repositories and multiple orderly tasks.
https://mrc-ide.github.io/squire.page/
Depends on:
  • mrc-ide/nimue
  • mrc-ide/odin
  • vimc/orderly
  • mrc-ide/squire
outpack-py
Language: python
queuer
Language: r
Queue tasks to number of backends.
https://mrc-ide.github.io/queuer
Depends on:
  • mrc-ide/context
  • reside-ic/ids
Used by:
  • mrc-ide/didehpc
msio
Language: r
This package samples malariasimulation inputs and calculates corresponding outputs for surrogate modelling.
Depends on:
  • mrc-ide/malariasimulation
spam.mpxv
Language: r
Implements a stochastic dynamic variable degree model within the edge-based-compartmental modelling framework. Three contact types based on duration of partnerships.
peeps
Language: r
What the package does (one paragraph).
cinterpolate
Language: r
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>.
https://mrc-ide.github.io/cinterpolate
Used by:
  • mrc-ide/odin
hintr
Language: r
R API for calling naomi district level HIV model.
Depends on:
  • reside-ic/ids
  • ropensci/jsonvalidate
  • mrc-ide/naomi
  • reside-ic/porcelain
  • mrc-ide/rrq
  • mrc-ide/specio
  • reside-ic/traduire
threemc
Language: r
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>.
Depends on:
  • mrc-ide/naomi
ppmcmc
Language: r
What the package does (one paragraph).
https://mrc-ide.github.io/ppmcmc/
frogger
Language: r
Frogger 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.
dust
Language: r
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>.
https://mrc-ide.github.io/dust
Used by:
  • mrc-ide/gasworks
  • mrc-ide/YellowFeverDynamics
  • mrc-ide/mode
  • mrc-ide/odin.dust
  • mrc-ide/spimalot
  • mrc-ide/sircovid
  • mrc-ide/mcstate
  • mrc-ide/gonovaxdust
  • mrc-ide/viralload
matchGADM
Language: r
This package contains two main functions which both map from one shapefile to another through matching the area. The resulting output is a data frame of proportions from each admin unit in the old to the new. This can be used to convert population sizes from one map to another.