R-universe - mrc-ide (MRC Centre for Global Infectious Disease Analysis)

Epidemiological Parameters: Ebola Bundibugyo Virus (BVD)Updated 7 days ago

A.Vicco, R. McCabe, T. Naidoo, R.K. Nash, S. Bhatia, H.J.T. Unwin, A. Cori, on behalf of the PERG group

Rendered from ebola_vignette_BVD.Rmd in epireview 1.4.8.

Naomi data modelUpdated 24 days ago

Jeff Eaton

Rendered from data-model.Rmd in naomi.zaf 999710.2.2.11.1.

Naomi Model Workflow ExampleUpdated 24 days ago

Jeff Eaton

Rendered from model-workflow.Rmd in naomi.zaf 999710.2.2.11.1.

DSL parse errorsUpdated 2 months ago

Rich FitzJohn

Rendered from dsl-errors.Rmd in monty 0.4.11.

Dealing with missed generations of infections with EpiEstimUpdated 2 months ago

Andrea Brizzi

Rendered from EpiEstim_backimputation.Rmd in EpiEstim 3.0.0.

EpiEstim VignetteUpdated 2 months ago

Rebecca Nash

Rendered from full_EpiEstim_vignette.Rmd in EpiEstim 3.0.0.

MV-EpiEstimUpdated 2 months ago

Anne Cori

Rendered from MV_EpiEstim_vignette.Rmd in EpiEstim 3.0.0.

EpiEstim for aggregated incidence dataUpdated 2 months ago

Rebecca Nash

Rendered from EpiEstim_aggregated_data.Rmd in EpiEstim 3.0.0.

EpiEstim: a demonstrationUpdated 2 months ago

Anne Cori

Rendered from short_demo.Rmd in EpiEstim 3.0.0.

P. vivax ModelUpdated 3 months ago

Giovanni Charles

Rendered from Plasmodium_vivax.Rmd in malariasimulation 3.0.0.

Parameter VariationUpdated 3 months ago

Giovanni Charles

Rendered from Parameter_variation.Rmd in malariasimulation 3.0.0.

Stochastic VariationUpdated 3 months ago

Giovanni Charles

Rendered from Variation.Rmd in malariasimulation 3.0.0.

Vector Control: Bed netsUpdated 3 months ago

Giovanni Charles

Rendered from VectorControl_Bednets.Rmd in malariasimulation 3.0.0.

Developing leapfrogUpdated 3 months ago

Robert Ashton

Rendered from development.Rmd in leapfrog 0.1.8.

Supported FunctionsUpdated 5 months ago

Rich FitzJohn

Rendered from functions.Rmd in odin2 0.3.46.

Variable naming conventionsUpdated 7 months ago

Robert Ashton

Rendered from variables.Rmd in leapfrog 0.1.8.

SHIPP toolUpdated 7 months ago

Rachel Esra

Rendered from shipp-tool.Rmd in naomi.resources 0.0.8.

DetailsUpdated 8 months ago

Rich FitzJohn

Rendered from details.Rmd in odin2 0.3.46.

AdministrationUpdated 8 months ago

Rich FitzJohn

Rendered from administration.Rmd in hipercow 1.1.8.

Using secrets on the clusterUpdated 8 months ago

Rich FitzJohn

Rendered from secrets.Rmd in hipercow 1.1.8.

Collaborative analysisUpdated 8 months ago

Rich FitzJohn

Rendered from collaboration.Rmd in orderly 2.0.3.

Creating pluginsUpdated 8 months ago

Rich FitzJohn

Rendered from plugins.Rmd in orderly 2.0.3.

Dependencies between packetsUpdated 8 months ago

Rich FitzJohn

Rendered from dependencies.Rmd in orderly 2.0.3.

DetailsUpdated 8 months ago

Rich FitzJohn

Rendered from details.Rmd in orderly 2.0.3.

Introduction to orderlyUpdated 8 months ago

Rich FitzJohn

Rendered from introduction.Rmd in orderly 2.0.3.

Migrating from orderly (1.x)Updated 8 months ago

Rich FitzJohn

Rendered from migrating.Rmd in orderly 2.0.3.

orderlyUpdated 8 months ago

Rich FitzJohn

Rendered from orderly.Rmd in orderly 2.0.3.

Orderly query DSLUpdated 8 months ago

Rich FitzJohn

Rendered from query.Rmd in orderly 2.0.3.

Outpack metadataUpdated 8 months ago

Rich FitzJohn

Rendered from metadata.Rmd in orderly 2.0.3.

TroubleshootingUpdated 8 months ago

Rich FitzJohn

Rendered from troubleshooting.Rmd in orderly 2.0.3.

IntroductionUpdated 8 months ago

Rich FitzJohn

Rendered from orderly_db.Rmd in orderly.db 0.1.5.

Getting started with odin2Updated 9 months ago

Rich FitzJohn

Rendered from odin2.Rmd in odin2 0.3.46.

Odin parse errorsUpdated 9 months ago

Rich FitzJohn

Rendered from errors.Rmd in odin2 0.3.46.

Writing samplersUpdated 10 months ago

Rich FitzJohn

Rendered from writing-samplers.Rmd in monty 0.4.11.

ContributingUpdated 10 months ago

Giovanni Charles

Rendered from Contributing.Rmd in individual 0.1.18.

orderlyUpdated 11 months ago

Rich FitzJohn

Rendered from orderly.Rmd in orderly1 1.7.2.

orderly bundlesUpdated 11 months ago

Rich FitzJohn

Rendered from bundles.Rmd in orderly1 1.7.2.

orderly changelogUpdated 11 months ago

Rich FitzJohn

Rendered from changelog.Rmd in orderly1 1.7.2.

orderly patternsUpdated 11 months ago

Rich FitzJohn

Rendered from patterns.Rmd in orderly1 1.7.2.

orderly remotesUpdated 11 months ago

Rich FitzJohn

Rendered from remote.Rmd in orderly1 1.7.2.

Fitting odin2 models to dataUpdated 11 months ago

Rich FitzJohn

Rendered from fitting.Rmd in odin2 0.3.46.

Migrating from odin 1.x.xUpdated 11 months ago

Rich FitzJohn

Rendered from migrating.Rmd in odin2 0.3.46.

Writing dust2 systemsUpdated 1 years ago

Rich FitzJohn

Rendered from writing.Rmd in dust2 0.3.28.

DetailsUpdated 1 years ago

Rich FitzJohn

Rendered from details.Rmd in hipercow 1.1.8.

The DIDE ClusterUpdated 1 years ago

Rich FitzJohn

Rendered from dide-cluster.Rmd in hipercow 1.1.8.

EnvironmentsUpdated 1 years ago

Rich FitzJohn

Rendered from environments.Rmd in hipercow 1.1.8.

hipercowUpdated 1 years ago

Rich FitzJohn

Rendered from hipercow.Rmd in hipercow 1.1.8.

Migration from didehpcUpdated 1 years ago

Rich FitzJohn

Rendered from migration.Rmd in hipercow 1.1.8.

Packages and provisioningUpdated 1 years ago

Rich FitzJohn

Rendered from packages.Rmd in hipercow 1.1.8.

Parallel TasksUpdated 1 years ago

Rich FitzJohn

Rendered from parallel.Rmd in hipercow 1.1.8.

TroubleshootingUpdated 1 years ago

Rich FitzJohn

Rendered from troubleshooting.Rmd in hipercow 1.1.8.

Using INLA on WindowsUpdated 1 years ago

Rich FitzJohn

Rendered from INLA.Rmd in hipercow 1.1.8.

Using stanUpdated 1 years ago

Rich FitzJohn

Rendered from stan.Rmd in hipercow 1.1.8.

WorkersUpdated 1 years ago

Rich FitzJohn

Rendered from workers.Rmd in hipercow 1.1.8.

Using vimpact for estimating vaccine impact - internalUpdated 1 years ago

Rob Ashton, Xiang Li, Katy Gaythorpe

Rendered from internal-impact.Rmd in vimpact 0.1.6.

Using vimpact for estimating vaccine impactUpdated 1 years ago

Rob Ashton, Xiang Li, Katy Gaythorpe

Rendered from using-vimpact.Rmd in vimpact 0.1.6.

Introduction to jsonvalidateUpdated 1 years ago

Rich FitzJohn

Rendered from jsonvalidate.Rmd in jsonvalidate 1.5.0.

Metadata driven UIUpdated 1 years ago

Robert Ashton

Rendered from metadata.Rmd in hintr 1.2.21.

Migration from mcstateUpdated 1 years ago

Rich FitzJohn

Rendered from migration.Rmd in monty 0.4.11.

Probabilistic DSLUpdated 2 years ago

Rich FitzJohn

Rendered from dsl.Rmd in monty 0.4.11.

SamplersUpdated 2 years ago

Rich FitzJohn

Rendered from samplers.Rmd in monty 0.4.11.

Working with samplesUpdated 2 years ago

Rich FitzJohn

Rendered from samples.Rmd in monty 0.4.11.

Naomi Model Workflow ExampleUpdated 2 years ago

Jeff Eaton

Rendered from model-workflow.Rmd in naomi 2.10.20.

Migrating from dust 1.x.xUpdated 2 years ago

Rich FitzJohn

Rendered from migrating.Rmd in dust2 0.3.28.

Fault toleranceUpdated 2 years ago

Rich FitzJohn

Rendered from fault-tolerance.Rmd in rrq 0.7.23.

messagesUpdated 2 years ago

Rich FitzJohn

Rendered from messages.Rmd in rrq 0.7.23.

rrqUpdated 2 years ago

Rich FitzJohn

Rendered from rrq.Rmd in rrq 0.7.23.

DebuggingUpdated 2 years ago

Rich FitzJohn

Rendered from debugging.Rmd in odin2 0.3.46.

Packaging odin modelsUpdated 2 years ago

Rich FitzJohn

Rendered from packaging.Rmd in odin2 0.3.46.

Comparing dust systems to dataUpdated 2 years ago

Rich FitzJohn

Rendered from data.Rmd in dust2 0.3.28.

Introduction to dustUpdated 2 years ago

Rich FitzJohn

Rendered from dust2.Rmd in dust2 0.3.28.

DetailsUpdated 2 years ago

Rich FitzJohn

Rendered from details.Rmd in dust2 0.3.28.

Packaging dust systemsUpdated 2 years ago

Rich FitzJohn

Rendered from packaging.Rmd in dust2 0.3.28.

Principles and design of dustUpdated 2 years ago

Rich FitzJohn

Rendered from design.Rmd in dust2 0.3.28.

Introduction to montyUpdated 2 years ago

Rich FitzJohn

Rendered from monty.Rmd in monty 0.4.11.

Antimalarial ResistanceUpdated 2 years ago

Giovanni Charles

Rendered from Antimalarial_Resistance.Rmd in malariasimulation 3.0.0.

DemographyUpdated 2 years ago

Giovanni Charles

Rendered from Demography.Rmd in malariasimulation 3.0.0.

Mass Drug Administriation and ChemopreventionUpdated 2 years ago

Giovanni Charles

Rendered from MDA.Rmd in malariasimulation 3.0.0.

Matching EIR to PfPR~2-10~Updated 2 years ago

Giovanni Charles

Rendered from EIRprevmatch.Rmd in malariasimulation 3.0.0.

MetapopulationUpdated 2 years ago

Giovanni Charles

Rendered from Metapopulation.Rmd in malariasimulation 3.0.0.

Model IntroductionUpdated 2 years ago

Giovanni Charles

Rendered from Model.Rmd in malariasimulation 3.0.0.

Modifying the carrying capacityUpdated 2 years ago

Giovanni Charles

Rendered from Carrying-capacity.Rmd in malariasimulation 3.0.0.

Mosquito speciesUpdated 2 years ago

Giovanni Charles

Rendered from SetSpecies.Rmd in malariasimulation 3.0.0.

TreatmentUpdated 2 years ago

Giovanni Charles

Rendered from Treatment.Rmd in malariasimulation 3.0.0.

VaccinesUpdated 2 years ago

Giovanni Charles

Rendered from Vaccines.Rmd in malariasimulation 3.0.0.

Vector Control: Indoor Residual SprayingUpdated 2 years ago

Giovanni Charles

Rendered from VectorControl_IRS.Rmd in malariasimulation 3.0.0.

Periodic variables detailsUpdated 2 years ago

Rich FitzJohn

Rendered from periodic.Rmd in dust2 0.3.28.

PerformanceUpdated 2 years ago

Giovanni Charles

Rendered from Performance.Rmd in individual 0.1.18.

Getting startedUpdated 2 years ago

Lilith Whittles

Rendered from getting_started.Rmd in gonovax 0.4.23.

Basic ExampleUpdated 2 years ago

Bob Verity and Pete Winskill

Rendered from example.Rmd in drjacoby 1.5.4.

Double wellUpdated 2 years ago

Bob Verity and Pete Winskill

Rendered from checks_double_well.Rmd in drjacoby 1.5.4.

Getting Model FitsUpdated 2 years ago

Bob Verity and Pete Winskill

Rendered from getting_model_fits.Rmd in drjacoby 1.5.4.

Installing drjacobyUpdated 2 years ago

Bob Verity and Pete Winskill

Rendered from installation.Rmd in drjacoby 1.5.4.

Parallel TemperingUpdated 2 years ago

Bob Verity and Pete Winskill

Rendered from metropolis_coupling.Rmd in drjacoby 1.5.4.

Running in ParallelUpdated 2 years ago

Bob Verity and Pete Winskill

Rendered from parallel.Rmd in drjacoby 1.5.4.

popimUpdated 2 years ago

Tini Garske

Rendered from popim.Rmd in popim 0.0.1.

popim technical documentationUpdated 2 years ago

Tini Garske

Rendered from technical_doc.Rmd in popim 0.0.1.

C++ APIUpdated 2 years ago

Ralf Stubner

Rendered from cpp-api.Rmd in dqrng 0.4.1.1.

Parallel RNG usageUpdated 2 years ago

Ralf Stubner

Rendered from parallel.Rmd in dqrng 0.4.1.1.

Fast Pseudo Random Number Generators for RUpdated 2 years ago

Ralf Stubner

Rendered from dqrng.Rmd in dqrng 0.4.1.1.

Saving and restoring simulation stateUpdated 2 years ago

Giovanni Charles

Rendered from Checkpoint.Rmd in individual 0.1.18.

Using vaultr in packagesUpdated 3 years ago

Rich FitzJohn

Rendered from packages.Rmd in vaultr 1.2.0.

vaultrUpdated 3 years ago

Rich FitzJohn

Rendered from vaultr.Rmd in vaultr 1.2.0.

Porting from odinUpdated 3 years ago

Rich FitzJohn

Rendered from porting.Rmd in odin.dust 0.3.13.

Fitting a continuous-time modelUpdated 3 years ago

Rich FitzJohn

Rendered from continuous.Rmd in mcstate 0.9.22.

Fast sampling methodsUpdated 3 years ago

Ralf Stubner

Rendered from sample.Rmd in dqrng 0.4.1.1.

Guide to odin docsUpdated 3 years ago

Rich FitzJohn

Rendered from guide.Rmd in odin 1.5.12.

Comparing models and dataUpdated 3 years ago

Rich FitzJohn

Rendered from data.Rmd in dust 0.15.3.

odinUpdated 3 years ago

Rich FitzJohn

Rendered from odin.Rmd in odin 1.5.12.

ddeUpdated 3 years ago

Rich FitzJohn

Rendered from dde.Rmd in dde 1.0.7.

Introduction to dustUpdated 3 years ago

Rich FitzJohn

Rendered from dust.Rmd in dust 0.15.3.

Using RNGs from packagesUpdated 3 years ago

Rich FitzJohn

Rendered from rng_package.Rmd in dust 0.15.3.

Alternative software for estimating the reproduction numberUpdated 3 years ago

Anne Cori

Rendered from alternative_software.Rmd in EpiEstim 3.0.0.

Principles and design of dustUpdated 3 years ago

Rich FitzJohn

Rendered from design.Rmd in dust 0.15.3.

debuggingUpdated 3 years ago

Rich FitzJohn

Rendered from debugging.Rmd in odin 1.5.12.

Restarting pMCMCUpdated 4 years ago

Rich FitzJohn

Rendered from restart.Rmd in mcstate 0.9.22.

SIR models with odin, dust and mcstateUpdated 4 years ago

Rich FitzJohn

Rendered from sir_models.Rmd in mcstate 0.9.22.

Validation of SMC using a Kalman filterUpdated 4 years ago

Rich FitzJohn

Rendered from kalman.Rmd in mcstate 0.9.22.

SIR modelsUpdated 4 years ago

Rich FitzJohn

Rendered from sir_models.Rmd in odin.dust 0.3.13.

Distributed parallel random numbersUpdated 4 years ago

Rich FitzJohn

Rendered from rng_distributed.Rmd in dust 0.15.3.

Running models on GPUs with CUDAUpdated 4 years ago

Rich FitzJohn

Rendered from gpu.Rmd in dust 0.15.3.

Random number generationUpdated 4 years ago

Rich FitzJohn

Rendered from rng.Rmd in dust 0.15.3.

odin discrete modelsUpdated 4 years ago

Thibaut Jombart, Rich FitzJohn

Rendered from discrete.Rmd in odin 1.5.12.

odin functionsUpdated 4 years ago

Rich FitzJohn

Rendered from functions.Rmd in odin 1.5.12.

Changing populationUpdated 4 years ago

Giovanni Charles

Rendered from Changing_Populations.Rmd in individual 0.1.18.

Mocking with mockrUpdated 4 years ago

Kirill Müller

Rendered from mockr.Rmd in mockr 0.2.0.9002.

Using Likelihood BlocksUpdated 4 years ago

Bob Verity and Pete Winskill

Rendered from blocks.Rmd in drjacoby 1.5.4.

Deterministic modelsUpdated 4 years ago

Rich FitzJohn

Rendered from deterministic.Rmd in mcstate 0.9.22.

Inference with iterated filteringUpdated 4 years ago

Rich FitzJohn

Rendered from if2.Rmd in mcstate 0.9.22.

Nested SIR ModelsUpdated 4 years ago

Rich FitzJohn

Rendered from nested_sir_models.Rmd in mcstate 0.9.22.

Parallelisation of inferenceUpdated 4 years ago

Rich FitzJohn

Rendered from parallelisation.Rmd in mcstate 0.9.22.

Algorithms used to compute random numbersUpdated 5 years ago

Rich FitzJohn

Rendered from rng_algorithms.Rmd in dust 0.15.3.

roxygenUpdated 5 years ago

Rich FitzJohn

Rendered from roxygen.Rmd in porcelain 0.1.16.

Using vimpact for estimating vaccine impact - VIMC membersUpdated 5 years ago

Xiang Li

Rendered from vignette.Rmd in vimpact 0.1.6.

Multiple parameter setsUpdated 5 years ago

Rich FitzJohn

Rendered from multi.Rmd in dust 0.15.3.

Multilevel example with blocksUpdated 5 years ago

Bob Verity and Pete Winskill

Rendered from checks_multilevel_blocks.Rmd in drjacoby 1.5.4.

Normal modelUpdated 5 years ago

Bob Verity and Pete Winskill

Rendered from checks_normal_model.Rmd in drjacoby 1.5.4.

Return priorUpdated 5 years ago

Bob Verity and Pete Winskill

Rendered from checks_return_prior.Rmd in drjacoby 1.5.4.

cookbookUpdated 5 years ago

Rich FitzJohn

Rendered from cookbook.Rmd in porcelain 0.1.16.

porcelainUpdated 5 years ago

Rich FitzJohn

Rendered from porcelain.Rmd in porcelain 0.1.16.

APIUpdated 5 years ago

Giovanni Charles

Rendered from API.Rmd in individual 0.1.18.

TutorialUpdated 5 years ago

Giovanni Charles

Rendered from Tutorial.Rmd in individual 0.1.18.

Translating with traduireUpdated 5 years ago

Rich FitzJohn

Rendered from traduire.Rmd in traduire 0.1.1.

Using jointlyrUpdated 5 years ago

Sangeeta Bhatia

Rendered from using-jointlyr.Rmd in jointlyr 0.0.1.

Naomi data modelUpdated 5 years ago

Jeff Eaton

Rendered from data-model.Rmd in naomi 2.10.20.

Montagu API from RUpdated 7 years ago

VIMC Technical Team

Rendered from montagu_user_guide.Rmd in montagu 0.6.1.

Using cinterpolateUpdated 7 years ago

Rich FitzJohn

Rendered from cinterpolate.Rmd in cinterpolate 1.0.2.

PJNZ FilesUpdated 7 years ago

Robert Ashton

Rendered from pjnz.Rmd in specio 0.1.4.

beersUpdated 8 years ago

Wes Hinsley

Rendered from beers-vignette.Rmd in beers 0.1.0.