Age-stratified hospitalisation and death risksUpdated 1 months ago

Joshua W. Lambert

Rendered from age-strat-risks.Rmd in simulist 0.7.1.9000.
Age-structured populationUpdated 1 months ago

Joshua W. Lambert

Rendered from age-struct-pop.Rmd in simulist 0.7.1.9000.
Query parametersUpdated 1 months ago

Bubacarr Bah

Rendered from query_parameters.Rmd in readepi 1.0.6.
readepi: Reading data from health information systemsUpdated 1 months ago

Bubacarr Bah

Rendered from readepi.Rmd in readepi 1.0.6.
Package design vignette for {readepi}Updated 1 months ago

Bubacarr Bah

Rendered from design_principle.Rmd in readepi 1.0.6.
Time-varying case fatality riskUpdated 4 months ago

Joshua W. Lambert

Rendered from time-varying-cfr.Rmd in simulist 0.7.1.9000.
Wrangling simulated outbreak dataUpdated 4 months ago

Joshua W. Lambert

Rendered from wrangling-linelist.Rmd in simulist 0.7.1.9000.
Visualising simulated dataUpdated 4 months ago

Joshua W. Lambert

Rendered from vis-linelist.Rmd in simulist 0.7.1.9000.
Reporting delays and right-truncation of line list dataUpdated 4 months ago

Joshua W. Lambert

Rendered from reporting-delays-truncation.Rmd in simulist 0.7.1.9000.
Installing driversUpdated 4 months ago

Bubacarr Bah

Rendered from install_drivers.Rmd in readepi 1.0.6.
Getting Started with {simulist}Updated 7 months ago

Joshua W. Lambert

Rendered from simulist.Rmd in simulist 0.7.1.9000.
Theoretical background for epichainsUpdated 9 months ago

Sebastian Funk and James Azam

Rendered from theoretical_background.Rmd in epichains 0.1.1.9000.
Modelling time-dependence and seasonality in transmission dynamicsUpdated 10 months ago

Rosalind Eggo

Rendered from modelling_time_dependence.Rmd in epidemics 0.4.0.9000.
Design principles for epidemicsUpdated 11 months ago

Rosalind Eggo

Rendered from design-principles.Rmd in epidemics 0.4.0.9000.
Getting started with epidemic scenario modelling componentsUpdated 11 months ago

Rosalind Eggo

Rendered from epidemics.Rmd in epidemics 0.4.0.9000.
Getting started with modelling interventions targeting social contactsUpdated 11 months ago

Rosalind Eggo

Rendered from modelling_interventions.Rmd in epidemics 0.4.0.9000.
Guide to developing epidemics featuresUpdated 11 months ago

Rosalind Eggo

Rendered from developer-walkthrough.Rmd in epidemics 0.4.0.9000.
Modelling a diphtheria outbreak in a humanitarian camp settingUpdated 11 months ago

Rosalind Eggo

Rendered from model_diphtheria.Rmd in epidemics 0.4.0.9000.
Modelling intervention scenariosUpdated 11 months ago

Rosalind Eggo

Rendered from modelling_scenarios.Rmd in epidemics 0.4.0.9000.
Modelling interventions that change infection parametersUpdated 11 months ago

Rosalind Eggo

Rendered from modelling_rate_interventions.Rmd in epidemics 0.4.0.9000.
Modelling leaky vaccination and hospitalisation outcomes with VacamoleUpdated 11 months ago

Rosalind Eggo

Rendered from model_vacamole.Rmd in epidemics 0.4.0.9000.
Modelling overlapping and sequential interventions targeting social contactsUpdated 11 months ago

Rosalind Eggo

Rendered from modelling_multiple_interventions.Rmd in epidemics 0.4.0.9000.
Modelling parameter uncertaintyUpdated 11 months ago

Rosalind Eggo

Rendered from modelling_param_uncertainty.Rmd in epidemics 0.4.0.9000.
Modelling responses to a stochastic Ebola virus epidemicUpdated 11 months ago

Rosalind Eggo

Rendered from model_ebola.Rmd in epidemics 0.4.0.9000.
Modelling the effect of a vaccination campaignUpdated 11 months ago

Rosalind Eggo

Rendered from modelling_vaccination.Rmd in epidemics 0.4.0.9000.
Reducing parameters required for final size estimationUpdated 11 months ago

Rosalind Eggo

Rendered from finalsize_comparison.Rmd in epidemics 0.4.0.9000.
Estimate individual-level transmissionUpdated 11 months ago

Joshua W. Lambert

Rendered from estimate_individual_level_transmission.Rmd in superspreading 0.4.0.9000.
Introduction to cleanepiUpdated 11 months ago

Bubacarr Bah

Rendered from cleanepi.Rmd in cleanepi 1.1.2.9000.
Epidemic RiskUpdated 11 months ago

Joshua W. Lambert

Rendered from epidemic_risk.Rmd in superspreading 0.4.0.9000.
Design Principles for {superspreading}Updated 11 months ago

Joshua W. Lambert

Rendered from design-principles.Rmd in superspreading 0.4.0.9000.
Getting started with {superspreading}Updated 11 months ago

Joshua W. Lambert

Rendered from superspreading.Rmd in superspreading 0.4.0.9000.
Outbreaks in heterogeneous networksUpdated 11 months ago

Joshua W. Lambert

Rendered from heterogeneous_network_outbreaks.Rmd in superspreading 0.4.0.9000.
Pathogen evolution in the emergence of infectious disease outbreaksUpdated 11 months ago

Joshua W. Lambert

Rendered from emergence.Rmd in superspreading 0.4.0.9000.
Methods for calculating the proportion of transmissionUpdated 11 months ago

Joshua W. Lambert

Rendered from proportion_transmission.Rmd in superspreading 0.4.0.9000.
Package Design vignette for {cleanepi}Updated 11 months ago

Bubacarr Bah

Rendered from design_principle.Rmd in cleanepi 1.1.2.9000.
sivirepUpdated 1 years ago

Geraldine Gómez-Millán

Rendered from sivirep.Rmd in sivirep 1.0.2.
Modelling in multiple populationsUpdated 1 years ago

Rosalind Eggo

Rendered from modelling_populations.Rmd in epidemics 0.4.0.9000.
Software permissions and regulationsUpdated 1 years ago

Chris Hartgerink

Rendered from software-permissions.Rmd in linelist 2.0.1.9000.
Design Principles for {simulist}Updated 1 years ago

Joshua W. Lambert

Rendered from design-principles.Rmd in simulist 0.7.1.9000.
An introduction to linelistUpdated 1 years ago

Chris Hartgerink

Rendered from linelist.Rmd in linelist 2.0.1.9000.
Compatibility with dplyrUpdated 1 years ago

Chris Hartgerink

Rendered from compat-dplyr.Rmd in linelist 2.0.1.9000.
Estimating fatality risk from individual level dataUpdated 1 years ago

Adam Kucharski

Rendered from estimate_from_individual_data.Rmd in cfr 0.2.0.9000.
Ready reckoner for ReffUpdated 1 years ago

Rosalind Eggo

Rendered from r_eff_reckoner.Rmd in finalsize 0.2.1.9000.
Design Principles for {ColOpenData}Updated 1 years ago

Maria Camila Tavera-Cifuentes

Rendered from design_principles.Rmd in ColOpenData 0.3.1.
A Deep Dive into Colombian Demographics Using ColOpenDataUpdated 1 years ago

Maria Camila Tavera-Cifuentes

Rendered from demographic_data.Rmd in ColOpenData 0.3.1.
Documentation and DictionariesUpdated 1 years ago

Maria Camila Tavera-Cifuentes

Rendered from documentation_and_dictionaries.Rmd in ColOpenData 0.3.1.
How to download climate data using ColOpenDataUpdated 1 years ago

Maria Camila Tavera-Cifuentes

Rendered from climate_data.Rmd in ColOpenData 0.3.1.
Maps and plots with ColOpenDataUpdated 1 years ago

Maria Camila Tavera-Cifuentes

Rendered from geospatial_data.Rmd in ColOpenData 0.3.1.
Calculating the final size of an epidemicUpdated 1 years ago

Rosalind Eggo

Rendered from finalsize.Rmd in finalsize 0.2.1.9000.
Data Collation and Synthesis ProtocolUpdated 1 years ago

Joshua W. Lambert

Rendered from data_protocol.Rmd in epiparameter 0.4.1.9000.
A primer on working with delay distributionsUpdated 1 years ago

Adam Kucharski

Rendered from delay_distributions.Rmd in cfr 0.2.0.9000.
Introduction to cohort design with vaccineffUpdated 2 years ago

Zulma M. Cucunubá

Rendered from cohort_design.Rmd in vaccineff 1.0.1.
vaccineffUpdated 2 years ago

Zulma M. Cucunubá

Rendered from vaccineff.Rmd in vaccineff 1.0.1.
Design Principles for {epiparameter}Updated 2 years ago

Joshua W. Lambert

Rendered from design_principles.Rmd in epiparameter 0.4.1.9000.
Integration of Geospatial and Demographic dataUpdated 2 years ago

Maria Camila Tavera-Cifuentes

Rendered from merge_geo_demographic.Rmd in ColOpenData 0.3.1.
Population Projections with ColOpenDataUpdated 2 years ago

Maria Camila Tavera-Cifuentes

Rendered from population_projections.Rmd in ColOpenData 0.3.1.
Current databaseUpdated 2 years ago

Joshua W. Lambert

Rendered from database.Rmd in epiparameterDB 0.1.0.9000.
Design Principles for {epiparameterDB}Updated 2 years ago

Joshua W. Lambert

Rendered from design-principles.Rmd in epiparameterDB 0.1.0.9000.
Design Principles for {epichains}Updated 2 years ago

James M. Azam

Rendered from design-principles.Rmd in epichains 0.1.1.9000.
Modelling disease control interventionsUpdated 2 years ago

Sebastian Funk and James M. Azam

Rendered from interventions.Rmd in epichains 0.1.1.9000.
Projecting infectious disease incidence: a COVID-19 exampleUpdated 2 years ago

James Azam, Sebastian Funk

Rendered from projecting_incidence.Rmd in epichains 0.1.1.9000.
Other study designsUpdated 2 years ago

Zulma M. Cucunubá

Rendered from other_designs.Rmd in vaccineff 1.0.1.
Current databaseUpdated 2 years ago

Joshua W. Lambert

Rendered from database.Rmd in epiparameter 0.4.1.9000.
Getting Started with {epiparameter}Updated 2 years ago

Joshua W. Lambert

Rendered from epiparameter.Rmd in epiparameter 0.4.1.9000.
Parameter extraction and conversion in {epiparameter}Updated 2 years ago

Joshua W. Lambert

Rendered from extract_convert.Rmd in epiparameter 0.4.1.9000.
Building an Endemic Channel with epiCoUpdated 2 years ago

Juan D. Umaña

Rendered from endemic_channel.Rmd in epiCo 1.0.1.9000.
Analyzing demographic data with epiCoUpdated 2 years ago

Juan D. Umaña

Rendered from demographic_vignette.Rmd in epiCo 1.0.1.9000.
Spatiotemporal analyses with epiCoUpdated 2 years ago

Juan D. Umaña

Rendered from spatiotemporal_vignette.Rmd in epiCo 1.0.1.9000.
Calculating a static, delay-adjusted estimate of disease severityUpdated 2 years ago

Adam Kucharski

Rendered from estimate_static_severity.Rmd in cfr 0.2.0.9000.
Estimating disease severity while correcting for reporting delaysUpdated 2 years ago

Adam Kucharski

Rendered from cfr.Rmd in cfr 0.2.0.9000.
Estimating how disease severity varies over the course of an outbreakUpdated 2 years ago

Adam Kucharski

Rendered from estimate_time_varying_severity.Rmd in cfr 0.2.0.9000.
Estimating the proportion of cases that are ascertained during an outbreakUpdated 2 years ago

Adam Kucharski

Rendered from estimate_ascertainment.Rmd in cfr 0.2.0.9000.
Handling data from {incidence2}Updated 2 years ago

Adam Kucharski

Rendered from data_from_incidence2.Rmd in cfr 0.2.0.9000.
Design Principles for linelistUpdated 2 years ago

Chris Hartgerink

Rendered from design-principles.Rmd in linelist 2.0.1.9000.
Literature on branching process applicationsUpdated 2 years ago

James M. Azam

Rendered from branching_process_literature.Rmd in epichains 0.1.1.9000.
Modelling uncertainty in R₀Updated 2 years ago

Rosalind Eggo

Rendered from uncertainty_params.Rmd in finalsize 0.2.1.9000.
Projecting re-emergence risk after waning or new birthsUpdated 2 years ago

Rosalind Eggo

Rendered from demographic_turnover.Rmd in finalsize 0.2.1.9000.
Getting started with epichainsUpdated 2 years ago

James M. Azam and Sebastian Funk

Rendered from epichains.Rmd in epichains 0.1.1.9000.
Guidelines for VisualisationsUpdated 2 years ago

Hugo Gruson

Rendered from guidelines.Rmd in tracetheme 0.1.0.9000.
Modelling heterogeneous susceptibilityUpdated 2 years ago

Rosalind Eggo

Rendered from varying_susceptibility.Rmd in finalsize 0.2.1.9000.
Theoretical backgroundUpdated 2 years ago

Adam Kucharski

Rendered from theoretical_background.Rmd in finalsize 0.2.1.9000.
Design Principles for tracethemeUpdated 2 years ago

Hugo Gruson

Rendered from design-principles.Rmd in tracetheme 0.1.0.9000.
Epiverse-TRACE ggplot2 theme and scale demoUpdated 2 years ago

Hugo Gruson

Rendered from demo.Rmd in tracetheme 0.1.0.9000.
Software permissions and regulationsUpdated 2 years ago

Adam Kucharski

Rendered from software-permissions.Rmd in cfr 0.2.0.9000.
Guide to constructing susceptibility matricesUpdated 3 years ago

Rosalind Eggo

Rendered from susceptibility_matrices.Rmd in finalsize 0.2.1.9000.
Modelling heterogeneous social contactsUpdated 3 years ago

Rosalind Eggo

Rendered from varying_contacts.Rmd in finalsize 0.2.1.9000.
Comparison with a compartmental modelUpdated 3 years ago

Rosalind Eggo

Rendered from compare_sir_model.Rmd in finalsize 0.2.1.9000.