Estimating fatality risk from individual level dataUpdated 12 hours ago

Adam Kucharski

Rendered from estimate_from_individual_data.Rmd in cfr 0.2.0.
An introduction to serofoiUpdated 23 hours ago

Zulma M. Cucunubá

Rendered from serofoi.Rmd in serofoi 1.0.2.
Reporting delays and right-truncation of line list dataUpdated 2 days ago

Joshua W. Lambert

Rendered from reporting-delays-truncation.Rmd in simulist 0.4.0.9000.
Visualising simulated dataUpdated 2 days ago

Joshua W. Lambert

Rendered from vis-linelist.Rmd in simulist 0.4.0.9000.
Wrangling simulated outbreak dataUpdated 2 days ago

Joshua W. Lambert

Rendered from wrangling-linelist.Rmd in simulist 0.4.0.9000.
Design Principles for {simulist}Updated 3 days ago

Joshua W. Lambert

Rendered from design-principles.Rmd in simulist 0.4.0.9000.
Ready reckoner for ReffUpdated 8 days ago

Rosalind Eggo

Rendered from r_eff_reckoner.Rmd in finalsize 0.2.1.9000.
Age-structured populationUpdated 10 days ago

Joshua W. Lambert

Rendered from age-struct-pop.Rmd in simulist 0.4.0.9000.
Introduction to cleanepiUpdated 14 days ago

Karim Mané

Rendered from cleanepi.Rmd in cleanepi 1.0.2.9000.
Design Principles for {ColOpenData}Updated 15 days ago

Maria Camila Tavera-Cifuentes

Rendered from design_principles.Rmd in ColOpenData 0.3.1.
A Deep Dive into Colombian Demographics Using ColOpenDataUpdated 16 days ago

Maria Camila Tavera-Cifuentes

Rendered from demographic_data.Rmd in ColOpenData 0.3.1.
Documentation and DictionariesUpdated 16 days ago

Maria Camila Tavera-Cifuentes

Rendered from documentation_and_dictionaries.Rmd in ColOpenData 0.3.1.
How to download climate data using ColOpenDataUpdated 16 days ago

Maria Camila Tavera-Cifuentes

Rendered from climate_data.Rmd in ColOpenData 0.3.1.
Maps and plots with ColOpenDataUpdated 16 days ago

Maria Camila Tavera-Cifuentes

Rendered from geospatial_data.Rmd in ColOpenData 0.3.1.
Package Design vignette for {cleanepi}Updated 16 days ago

Karim Mané

Rendered from design_principle.Rmd in cleanepi 1.0.2.9000.
Design Principles for {superspreading}Updated 25 days ago

Joshua W. Lambert

Rendered from design-principles.Rmd in superspreading 0.3.0.
Epidemic RiskUpdated 25 days ago

Joshua W. Lambert

Rendered from epidemic_risk.Rmd in superspreading 0.3.0.
Estimate individual-level transmissionUpdated 25 days ago

Joshua W. Lambert

Rendered from estimate_individual_level_transmission.Rmd in superspreading 0.3.0.
Getting started with {superspreading}Updated 25 days ago

Joshua W. Lambert

Rendered from superspreading.Rmd in superspreading 0.3.0.
Methods for calculating the proportion of transmissionUpdated 25 days ago

Joshua W. Lambert

Rendered from proportion_transmission.Rmd in superspreading 0.3.0.
Outbreaks in heterogeneous networksUpdated 25 days ago

Joshua W. Lambert

Rendered from heterogeneous_network_outbreaks.Rmd in superspreading 0.3.0.
Age-stratified hospitalisation and death risksUpdated 1 months ago

Joshua W. Lambert

Rendered from age-strat-risks.Rmd in simulist 0.4.0.9000.
Getting Started with {simulist}Updated 1 months ago

Joshua W. Lambert

Rendered from simulist.Rmd in simulist 0.4.0.9000.
Time-varying case fatality riskUpdated 1 months ago

Joshua W. Lambert

Rendered from time-varying-cfr.Rmd in simulist 0.4.0.9000.
Calculating the final size of an epidemicUpdated 1 months ago

Rosalind Eggo

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

Joshua W. Lambert

Rendered from data_protocol.Rmd in epiparameter 0.4.1.9000.
A primer on working with delay distributionsUpdated 3 months ago

Adam Kucharski

Rendered from delay_distributions.Rmd in cfr 0.2.0.
sivirepUpdated 3 months ago

Geraldine Gómez-Millán

Rendered from sivirep.Rmd in sivirep 1.0.1.
Introduction to cohort design with vaccineffUpdated 3 months ago

Zulma M. Cucunubá

Rendered from cohort_design.Rmd in vaccineff 1.0.0.9000.
vaccineffUpdated 3 months ago

Zulma M. Cucunubá

Rendered from vaccineff.Rmd in vaccineff 1.0.0.9000.
Design Principles for {epiparameter}Updated 3 months ago

Joshua W. Lambert

Rendered from design_principles.Rmd in epiparameter 0.4.1.9000.
Design Principles for {superspreading}Updated 4 months ago

Joshua W. Lambert

Rendered from design-principles.Rmd in superspreading 0.3.0.9000.
Integration of Geospatial and Demographic dataUpdated 4 months ago

Maria Camila Tavera-Cifuentes

Rendered from merge_geo_demographic.Rmd in ColOpenData 0.3.1.
Population Projections with ColOpenDataUpdated 4 months ago

Maria Camila Tavera-Cifuentes

Rendered from population_projections.Rmd in ColOpenData 0.3.1.
Current databaseUpdated 4 months ago

Joshua W. Lambert

Rendered from database.Rmd in epiparameterDB 0.1.0.9000.
Design Principles for {epiparameterDB}Updated 4 months ago

Joshua W. Lambert

Rendered from design-principles.Rmd in epiparameterDB 0.1.0.9000.
Design Principles for {epichains}Updated 4 months ago

James M. Azam

Rendered from design-principles.Rmd in epichains 0.1.1.9000.
Modelling disease control interventionsUpdated 4 months 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 4 months ago

James Azam, Sebastian Funk

Rendered from projecting_incidence.Rmd in epichains 0.1.1.9000.
Other study designsUpdated 4 months ago

Zulma M. Cucunubá

Rendered from other_designs.Rmd in vaccineff 1.0.0.9000.
Getting started with {superspreading}Updated 4 months ago

Joshua W. Lambert

Rendered from superspreading.Rmd in superspreading 0.3.0.9000.
Methods for calculating the proportion of transmissionUpdated 4 months ago

Joshua W. Lambert

Rendered from proportion_transmission.Rmd in superspreading 0.3.0.9000.
Current databaseUpdated 5 months ago

Joshua W. Lambert

Rendered from database.Rmd in epiparameter 0.4.1.9000.
Getting Started with {epiparameter}Updated 5 months ago

Joshua W. Lambert

Rendered from epiparameter.Rmd in epiparameter 0.4.1.9000.
Parameter extraction and conversion in {epiparameter}Updated 5 months ago

Joshua W. Lambert

Rendered from extract_convert.Rmd in epiparameter 0.4.1.9000.
Building an Endemic Channel with epiCoUpdated 5 months ago

Juan D. Umaña

Rendered from endemic_channel.Rmd in epiCo 1.0.1.
Analyzing demographic data with epiCoUpdated 5 months ago

Juan D. Umaña

Rendered from demographic_vignette.Rmd in epiCo 1.0.1.
Epidemic RiskUpdated 5 months ago

Joshua W. Lambert

Rendered from epidemic_risk.Rmd in superspreading 0.3.0.9000.
Estimate individual-level transmissionUpdated 5 months ago

Joshua W. Lambert

Rendered from estimate_individual_level_transmission.Rmd in superspreading 0.3.0.9000.
Outbreaks in heterogeneous networksUpdated 5 months ago

Joshua W. Lambert

Rendered from heterogeneous_network_outbreaks.Rmd in superspreading 0.3.0.9000.
Spatiotemporal analyses with epiCoUpdated 6 months ago

Juan D. Umaña

Rendered from spatiotemporal_vignette.Rmd in epiCo 1.0.1.
Calculating a static, delay-adjusted estimate of disease severityUpdated 7 months ago

Adam Kucharski

Rendered from estimate_static_severity.Rmd in cfr 0.2.0.
Estimating disease severity while correcting for reporting delaysUpdated 7 months ago

Adam Kucharski

Rendered from cfr.Rmd in cfr 0.2.0.
Estimating how disease severity varies over the course of an outbreakUpdated 7 months ago

Adam Kucharski

Rendered from estimate_time_varying_severity.Rmd in cfr 0.2.0.
Estimating the proportion of cases that are ascertained during an outbreakUpdated 7 months ago

Adam Kucharski

Rendered from estimate_ascertainment.Rmd in cfr 0.2.0.
Handling data from {incidence2}Updated 7 months ago

Adam Kucharski

Rendered from data_from_incidence2.Rmd in cfr 0.2.0.
Compatibility with dplyrUpdated 8 months ago

Hugo Gruson

Rendered from compat-dplyr.Rmd in linelist 1.1.4.9000.
Theoretical background for epichainsUpdated 8 months ago

Sebastian Funk and James Azam

Rendered from theoretical_background.Rmd in epichains 0.1.1.9000.
An introduction to linelistUpdated 8 months ago

Hugo Gruson

Rendered from linelist.Rmd in linelist 1.1.4.9000.
Design Principles for linelistUpdated 8 months ago

Hugo Gruson

Rendered from design-principles.Rmd in linelist 1.1.4.9000.
Literature on branching process applicationsUpdated 8 months ago

James M. Azam

Rendered from branching_process_literature.Rmd in epichains 0.1.1.9000.
Modelling uncertainty in R₀Updated 8 months ago

Rosalind Eggo

Rendered from uncertainty_params.Rmd in finalsize 0.2.1.9000.
Projecting re-emergence risk after waning or new birthsUpdated 8 months ago

Rosalind Eggo

Rendered from demographic_turnover.Rmd in finalsize 0.2.1.9000.
Package Design vignette for {readepi}Updated 9 months ago

Karim Mané

Rendered from design_principle.Rmd in readepi 0.1.0.
Design principles for epidemicsUpdated 9 months ago

Rosalind Eggo

Rendered from design-principles.Rmd in epidemics 0.4.0.9000.
Guide to developing epidemics featuresUpdated 9 months ago

Rosalind Eggo

Rendered from developer-walkthrough.Rmd in epidemics 0.4.0.9000.
Modelling the effect of a vaccination campaignUpdated 9 months ago

Rosalind Eggo

Rendered from modelling_vaccination.Rmd in epidemics 0.4.0.9000.
Getting started with epichainsUpdated 9 months ago

James M. Azam and Sebastian Funk

Rendered from epichains.Rmd in epichains 0.1.1.9000.
readepi: Reading data from health information systemsUpdated 9 months ago

Karim Mané

Rendered from readepi.Rmd in readepi 0.1.0.
Modelling intervention scenariosUpdated 10 months ago

Rosalind Eggo

Rendered from modelling_scenarios.Rmd in epidemics 0.4.0.9000.
Modelling interventions that change infection parametersUpdated 10 months ago

Rosalind Eggo

Rendered from modelling_rate_interventions.Rmd in epidemics 0.4.0.9000.
Modelling parameter uncertaintyUpdated 10 months ago

Rosalind Eggo

Rendered from modelling_param_uncertainty.Rmd in epidemics 0.4.0.9000.
Getting started with epidemic scenario modelling componentsUpdated 10 months ago

Rosalind Eggo

Rendered from epidemics.Rmd in epidemics 0.4.0.9000.
Getting started with modelling interventions targeting social contactsUpdated 10 months ago

Rosalind Eggo

Rendered from modelling_interventions.Rmd in epidemics 0.4.0.9000.
Modelling leaky vaccination and hospitalisation outcomes with VacamoleUpdated 10 months ago

Rosalind Eggo

Rendered from model_vacamole.Rmd in epidemics 0.4.0.9000.
Modelling responses to a stochastic Ebola virus epidemicUpdated 10 months ago

Rosalind Eggo

Rendered from model_ebola.Rmd in epidemics 0.4.0.9000.
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.
Guidelines for VisualisationsUpdated 10 months ago

Hugo Gruson

Rendered from guidelines.Rmd in tracetheme 0.1.0.9000.
Modelling heterogeneous susceptibilityUpdated 11 months ago

Rosalind Eggo

Rendered from varying_susceptibility.Rmd in finalsize 0.2.1.9000.
Theoretical backgroundUpdated 11 months ago

Adam Kucharski

Rendered from theoretical_background.Rmd in finalsize 0.2.1.9000.
Design Principles for tracethemeUpdated 11 months ago

Hugo Gruson

Rendered from design-principles.Rmd in tracetheme 0.1.0.9000.
Epiverse-TRACE ggplot2 theme and scale demoUpdated 11 months ago

Hugo Gruson

Rendered from demo.Rmd in tracetheme 0.1.0.9000.
Software permissions and regulationsUpdated 11 months ago

Hugo Gruson

Rendered from software-permissions.Rmd in linelist 1.1.4.9000.
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.
Reducing parameters required for final size estimationUpdated 11 months ago

Rosalind Eggo

Rendered from finalsize_comparison.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.
Software permissions and regulationsUpdated 1 years ago

Adam Kucharski

Rendered from software-permissions.Rmd in cfr 0.2.0.
Guide to constructing susceptibility matricesUpdated 1 years ago

Rosalind Eggo

Rendered from susceptibility_matrices.Rmd in finalsize 0.2.1.9000.
Modelling heterogeneous social contactsUpdated 1 years ago

Rosalind Eggo

Rendered from varying_contacts.Rmd in finalsize 0.2.1.9000.
Comparison with a compartmental modelUpdated 2 years ago

Rosalind Eggo

Rendered from compare_sir_model.Rmd in finalsize 0.2.1.9000.