wepidemics

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INDEX

A abm, approximate bayesian computation, approximate bayesian sequential monte carlo

B bayesian inference analysis, bias-corrected estimation methods, bias, big-data, branching process

C case-control and cohort studies, chain, compartmental models, contact tracing data, continuous diagnostic tests, control, copula based bivariate beta-binomial model, copula mixed models, covid-19

D d-vine copula mixed model, deep-sequence data, detection, diagnostic accuracy, diagnostic test accuracy studies, diagnostic tests, diffusion, dispersion

E ensemble adjustment kalman filter, ensemble kalman filter, ergm, estimation, exportations

F final size, flows

G gamma distribution, gamma model, gamma, general interval, generation/serial interval, genomics, guassian distribution

H hierarchical summary receiver operating characteristic, hmm, household transmission

I importations, incubation period, infectious period, influenza, integrated nested laplace approximation, iterated filtering

L latent period, log-normal model

M markov hidden models, maximum likelihood, mcmc, meta analysis, meta-analysis of multiple diagnostic tests, meta-analysis, methods, missing at random, missing data framework, multinomial quadrivariate d-vine copula mixed model, multiple diagnostic tests, multivariate meta-analysis, mutation rate

N naive bayes, network meta-analysis, network, networks, nonlinear forecasting

O one-factor copula mixed model, overdispersion

P partially observed markov processes, particle filtering, phylogenetics, power-spectrum-matching, prediction, probe-matching

R real-time, relative transmission probabilities, reproductive number, risk assessment, roc surface

S simulation, sna, snp, superspreading

T trajectory matching, transmission flows within and between population groups accounting for sampling heterogeneity, transmission pairs, transmission probability

V visualization, volume under roc surfaces

W web sources, weibull model, whole genome sequence

Details

abm

  1. EpiModel: An R Package for Mathematical Modeling of Infectious Disease over Networks (link) (software: EpiModel (R))
  2. A Flexible and General Agent-Based Model Engine (link) (software: epiworldR (R), epiworld (C++))

approximate bayesian computation

  1. The impact of long-term nonpharmaceutical interventions on COVID-19 epidemic dynamics and control: the value and limitations of early models (link) (software: pomp (R))

approximate bayesian sequential monte carlo

  1. The impact of long-term nonpharmaceutical interventions on COVID-19 epidemic dynamics and control: the value and limitations of early models (link) (software: pomp (R))

bayesian inference analysis

  1. Meta-analysis of diagnostic performance of serology tests for COVID-19: impact of assay design and post-symptom-onset intervals (link) (software: meta4diag (R))
  2. Diagnostic efficacy of anti-SARS-CoV-2 IgG/IgM test for COVID-19: A meta-analysis (link) (software: meta4diag (R))

bias-corrected estimation methods

  1. Diagnostic test evaluation methodology: A systematic review of methods employed to evaluate diagnostic tests in the absence of gold standard-An update (link) (software: bcROCsurface (R))

bias

  1. Practical considerations for measuring the effective reproductive number, Rt (link)
  2. Maximum Likelihood Estimation of the Negative Binomial Dispersion Parameter for Highly Overdispersed Data, with Applications to Infectious Diseases (link)

big-data

  1. Accurate estimation of influenza epidemics using Google search data via ARGO (link) (software: argo (R))

branching process

  1. Estimating the overdispersion in COVID-19 transmission using outbreak sizes outside China (link) (software: COVID19_clustersize (R), COVID19_clustersize (Python))

case-control and cohort studies

  1. Hierarchical Modeling for Diagnostic Test Accuracy Using Multivariate Probability Distribution Functions (link) (software: CopulaDTA (R), CopulaREMADA (R))

chain

  1. Inference of R0 and Transmission Heterogeneity from the Size Distribution of Stuttering Chains (link) (software: n/a (Matlab))

compartmental models

  1. Practical considerations for measuring the effective reproductive number, Rt (link)

contact tracing data

  1. Estimating the generation interval and inferring the latent period of COVID-19 from the contact tracing data (link)

continuous diagnostic tests

  1. Diagnostic test evaluation methodology: A systematic review of methods employed to evaluate diagnostic tests in the absence of gold standard-An update (link) (software: bcROCsurface (R))

control

  1. Superspreading and the effect of individual variation on disease emergence (link)

copula based bivariate beta-binomial model

  1. Hierarchical Modeling for Diagnostic Test Accuracy Using Multivariate Probability Distribution Functions (link) (software: CopulaDTA (R), CopulaREMADA (R))
  2. Diagnostic test accuracy network meta-analysis methods: A scoping review and empirical assessment (link) (software: CopulaDTA (R), mada (R), NMADiagT (R))

copula mixed models

  1. Hierarchical Modeling for Diagnostic Test Accuracy Using Multivariate Probability Distribution Functions (link) (software: CopulaDTA (R), CopulaREMADA (R))

covid-19

  1. Estimating the overdispersion in COVID-19 transmission using outbreak sizes outside China (link) (software: COVID19_clustersize (R), COVID19_clustersize (Python))
  2. High variability in transmission of SARS-CoV-2 within households and implications for control (link) (software: householdTransmission (R))

d-vine copula mixed model

  1. Hierarchical Modeling for Diagnostic Test Accuracy Using Multivariate Probability Distribution Functions (link) (software: CopulaDTA (R), CopulaREMADA (R))

deep-sequence data

  1. Deep-sequence phylogenetics to quantify patterns of HIV transmission in the context of a universal testing and treatment trial – BCPP/Ya Tsie trial (link) (software: bumblebee (R))

detection

  1. Estimates of the risk of large or long-lasting outbreaks of Middle East respiratory syndrome after importations outside the Arabian Peninsula (link)

diagnostic accuracy

  1. Diagnostic test accuracy network meta-analysis methods: A scoping review and empirical assessment (link) (software: CopulaDTA (R), mada (R), NMADiagT (R))

diagnostic test accuracy studies

  1. Hierarchical Modeling for Diagnostic Test Accuracy Using Multivariate Probability Distribution Functions (link) (software: CopulaDTA (R), CopulaREMADA (R))
  2. Diagnostic test accuracy network meta-analysis methods: A scoping review and empirical assessment (link) (software: CopulaDTA (R), mada (R), NMADiagT (R))

diagnostic tests

  1. Meta-analysis of diagnostic performance of serology tests for COVID-19: impact of assay design and post-symptom-onset intervals (link) (software: meta4diag (R))
  2. Diagnostic efficacy of anti-SARS-CoV-2 IgG/IgM test for COVID-19: A meta-analysis (link) (software: meta4diag (R))

diffusion

  1. International risk of yellow fever spread from the ongoing outbreak in Brazil, December 2016 to May 2017 (link) (software: epiflows (R))

dispersion

  1. Inference of R0 and Transmission Heterogeneity from the Size Distribution of Stuttering Chains (link) (software: n/a (Matlab))
  2. Superspreading and the effect of individual variation on disease emergence (link)

ensemble adjustment kalman filter

  1. The impact of long-term nonpharmaceutical interventions on COVID-19 epidemic dynamics and control: the value and limitations of early models (link) (software: pomp (R))

ensemble kalman filter

  1. The impact of long-term nonpharmaceutical interventions on COVID-19 epidemic dynamics and control: the value and limitations of early models (link) (software: pomp (R))

ergm

  1. EpiModel: An R Package for Mathematical Modeling of Infectious Disease over Networks (link) (software: EpiModel (R))

estimation

  1. Practical considerations for measuring the effective reproductive number, Rt (link)
  2. Estimating the relative probability of direct transmission between infectious disease patients (link) (software: nbTransmission (R))
  3. Maximum Likelihood Estimation of the Negative Binomial Dispersion Parameter for Highly Overdispersed Data, with Applications to Infectious Diseases (link)
  4. Inference of R0 and Transmission Heterogeneity from the Size Distribution of Stuttering Chains (link) (software: n/a (Matlab))
  5. Superspreading and the effect of individual variation on disease emergence (link)

exportations

  1. International risk of yellow fever spread from the ongoing outbreak in Brazil, December 2016 to May 2017 (link) (software: epiflows (R))

final size

  1. Inference of R0 and Transmission Heterogeneity from the Size Distribution of Stuttering Chains (link) (software: n/a (Matlab))

flows

  1. International risk of yellow fever spread from the ongoing outbreak in Brazil, December 2016 to May 2017 (link) (software: epiflows (R))

gamma distribution

  1. Inferred duration of infectious period of SARS-CoV-2: rapid scoping review and analysis of available evidence for asymptomatic and symptomatic COVID-19 cases (link)

gamma model

  1. Estimating the generation interval and inferring the latent period of COVID-19 from the contact tracing data (link)

gamma

  1. Estimating the Latent Period of Coronavirus Disease 2019 (COVID-19) (link)

general interval

  1. Estimating the generation interval and inferring the latent period of COVID-19 from the contact tracing data (link)

generation/serial interval

  1. Estimating the relative probability of direct transmission between infectious disease patients (link) (software: nbTransmission (R))

genomics

  1. Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data (link) (software: outbreaker2 (R))

guassian distribution

  1. Inferred duration of infectious period of SARS-CoV-2: rapid scoping review and analysis of available evidence for asymptomatic and symptomatic COVID-19 cases (link)

hierarchical summary receiver operating characteristic

  1. Diagnostic test accuracy network meta-analysis methods: A scoping review and empirical assessment (link) (software: CopulaDTA (R), mada (R), NMADiagT (R))

hmm

  1. Accurate estimation of influenza epidemics using Google search data via ARGO (link) (software: argo (R))

household transmission

  1. High variability in transmission of SARS-CoV-2 within households and implications for control (link) (software: householdTransmission (R))

importations

  1. International risk of yellow fever spread from the ongoing outbreak in Brazil, December 2016 to May 2017 (link) (software: epiflows (R))
  2. Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data (link) (software: outbreaker2 (R))

incubation period

  1. Estimating the generation interval and inferring the latent period of COVID-19 from the contact tracing data (link)
  2. The Incubation period of COVID-19: A meta-analysis (link)
  3. Estimating the Latent Period of Coronavirus Disease 2019 (COVID-19) (link)

infectious period

  1. Inferred duration of infectious period of SARS-CoV-2: rapid scoping review and analysis of available evidence for asymptomatic and symptomatic COVID-19 cases (link)

influenza

  1. Accurate estimation of influenza epidemics using Google search data via ARGO (link) (software: argo (R))

integrated nested laplace approximation

  1. Meta-analysis of diagnostic performance of serology tests for COVID-19: impact of assay design and post-symptom-onset intervals (link) (software: meta4diag (R))
  2. Diagnostic efficacy of anti-SARS-CoV-2 IgG/IgM test for COVID-19: A meta-analysis (link) (software: meta4diag (R))

iterated filtering

  1. The impact of long-term nonpharmaceutical interventions on COVID-19 epidemic dynamics and control: the value and limitations of early models (link) (software: pomp (R))

latent period

  1. Estimating the generation interval and inferring the latent period of COVID-19 from the contact tracing data (link)
  2. Estimating the Latent Period of Coronavirus Disease 2019 (COVID-19) (link)

log-normal model

  1. Estimating the Latent Period of Coronavirus Disease 2019 (COVID-19) (link)

markov hidden models

  1. Accurate estimation of influenza epidemics using Google search data via ARGO (link) (software: argo (R))

maximum likelihood

  1. Estimates of the risk of large or long-lasting outbreaks of Middle East respiratory syndrome after importations outside the Arabian Peninsula (link)
  2. Maximum Likelihood Estimation of the Negative Binomial Dispersion Parameter for Highly Overdispersed Data, with Applications to Infectious Diseases (link)
  3. High variability in transmission of SARS-CoV-2 within households and implications for control (link) (software: householdTransmission (R))

mcmc

  1. A Flexible and General Agent-Based Model Engine (link) (software: epiworldR (R), epiworld (C++))

meta analysis

  1. Incubation period for COVID-19: a systematic review and meta-analysis (link)
  2. Inferred duration of infectious period of SARS-CoV-2: rapid scoping review and analysis of available evidence for asymptomatic and symptomatic COVID-19 cases (link)

meta-analysis of multiple diagnostic tests

  1. Hierarchical Modeling for Diagnostic Test Accuracy Using Multivariate Probability Distribution Functions (link) (software: CopulaDTA (R), CopulaREMADA (R))

meta-analysis

  1. The Incubation period of COVID-19: A meta-analysis (link)
  2. Meta-analysis of diagnostic performance of serology tests for COVID-19: impact of assay design and post-symptom-onset intervals (link) (software: meta4diag (R))
  3. Diagnostic efficacy of anti-SARS-CoV-2 IgG/IgM test for COVID-19: A meta-analysis (link) (software: meta4diag (R))
  4. Diagnostic test accuracy network meta-analysis methods: A scoping review and empirical assessment (link) (software: CopulaDTA (R), mada (R), NMADiagT (R))

methods

  1. Accurate estimation of influenza epidemics using Google search data via ARGO (link) (software: argo (R))
  2. Estimating the relative probability of direct transmission between infectious disease patients (link) (software: nbTransmission (R))
  3. Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data (link) (software: outbreaker2 (R))

missing at random

  1. Diagnostic test evaluation methodology: A systematic review of methods employed to evaluate diagnostic tests in the absence of gold standard-An update (link) (software: bcROCsurface (R))

missing data framework

  1. Diagnostic test accuracy network meta-analysis methods: A scoping review and empirical assessment (link) (software: CopulaDTA (R), mada (R), NMADiagT (R))

multinomial quadrivariate d-vine copula mixed model

  1. Hierarchical Modeling for Diagnostic Test Accuracy Using Multivariate Probability Distribution Functions (link) (software: CopulaDTA (R), CopulaREMADA (R))

multiple diagnostic tests

  1. Diagnostic test accuracy network meta-analysis methods: A scoping review and empirical assessment (link) (software: CopulaDTA (R), mada (R), NMADiagT (R))

multivariate meta-analysis

  1. Hierarchical Modeling for Diagnostic Test Accuracy Using Multivariate Probability Distribution Functions (link) (software: CopulaDTA (R), CopulaREMADA (R))

mutation rate

  1. Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data (link) (software: outbreaker2 (R))

naive bayes

  1. Estimating the relative probability of direct transmission between infectious disease patients (link) (software: nbTransmission (R))

network meta-analysis

  1. Diagnostic test accuracy network meta-analysis methods: A scoping review and empirical assessment (link) (software: CopulaDTA (R), mada (R), NMADiagT (R))

network

  1. Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data (link) (software: outbreaker2 (R))

networks

  1. EpiModel: An R Package for Mathematical Modeling of Infectious Disease over Networks (link) (software: EpiModel (R))

nonlinear forecasting

  1. The impact of long-term nonpharmaceutical interventions on COVID-19 epidemic dynamics and control: the value and limitations of early models (link) (software: pomp (R))

one-factor copula mixed model

  1. Hierarchical Modeling for Diagnostic Test Accuracy Using Multivariate Probability Distribution Functions (link) (software: CopulaDTA (R), CopulaREMADA (R))

overdispersion

  1. Estimates of the risk of large or long-lasting outbreaks of Middle East respiratory syndrome after importations outside the Arabian Peninsula (link)
  2. Estimating the overdispersion in COVID-19 transmission using outbreak sizes outside China (link) (software: COVID19_clustersize (R), COVID19_clustersize (Python))
  3. Maximum Likelihood Estimation of the Negative Binomial Dispersion Parameter for Highly Overdispersed Data, with Applications to Infectious Diseases (link)
  4. High variability in transmission of SARS-CoV-2 within households and implications for control (link) (software: householdTransmission (R))

partially observed markov processes

  1. The impact of long-term nonpharmaceutical interventions on COVID-19 epidemic dynamics and control: the value and limitations of early models (link) (software: pomp (R))

particle filtering

  1. The impact of long-term nonpharmaceutical interventions on COVID-19 epidemic dynamics and control: the value and limitations of early models (link) (software: pomp (R))

phylogenetics

  1. Deep-sequence phylogenetics to quantify patterns of HIV transmission in the context of a universal testing and treatment trial – BCPP/Ya Tsie trial (link) (software: bumblebee (R))

power-spectrum-matching

  1. The impact of long-term nonpharmaceutical interventions on COVID-19 epidemic dynamics and control: the value and limitations of early models (link) (software: pomp (R))

prediction

  1. Accurate estimation of influenza epidemics using Google search data via ARGO (link) (software: argo (R))
  2. International risk of yellow fever spread from the ongoing outbreak in Brazil, December 2016 to May 2017 (link) (software: epiflows (R))

probe-matching

  1. The impact of long-term nonpharmaceutical interventions on COVID-19 epidemic dynamics and control: the value and limitations of early models (link) (software: pomp (R))

real-time

  1. Accurate estimation of influenza epidemics using Google search data via ARGO (link) (software: argo (R))

relative transmission probabilities

  1. Estimating the relative probability of direct transmission between infectious disease patients (link) (software: nbTransmission (R))

reproductive number

  1. Estimating the relative probability of direct transmission between infectious disease patients (link) (software: nbTransmission (R))

risk assessment

  1. Estimates of the risk of large or long-lasting outbreaks of Middle East respiratory syndrome after importations outside the Arabian Peninsula (link)

roc surface

  1. Diagnostic test evaluation methodology: A systematic review of methods employed to evaluate diagnostic tests in the absence of gold standard-An update (link) (software: bcROCsurface (R))

simulation

  1. Practical considerations for measuring the effective reproductive number, Rt (link)
  2. A Flexible and General Agent-Based Model Engine (link) (software: epiworldR (R), epiworld (C++))

sna

  1. EpiModel: An R Package for Mathematical Modeling of Infectious Disease over Networks (link) (software: EpiModel (R))

snp

  1. Estimating the relative probability of direct transmission between infectious disease patients (link) (software: nbTransmission (R))

superspreading

  1. Estimating the overdispersion in COVID-19 transmission using outbreak sizes outside China (link) (software: COVID19_clustersize (R), COVID19_clustersize (Python))
  2. Superspreading and the effect of individual variation on disease emergence (link)

trajectory matching

  1. The impact of long-term nonpharmaceutical interventions on COVID-19 epidemic dynamics and control: the value and limitations of early models (link) (software: pomp (R))

transmission flows within and between population groups accounting for sampling heterogeneity

  1. Deep-sequence phylogenetics to quantify patterns of HIV transmission in the context of a universal testing and treatment trial – BCPP/Ya Tsie trial (link) (software: bumblebee (R))

transmission pairs

  1. Deep-sequence phylogenetics to quantify patterns of HIV transmission in the context of a universal testing and treatment trial – BCPP/Ya Tsie trial (link) (software: bumblebee (R))

transmission probability

  1. Estimating the relative probability of direct transmission between infectious disease patients (link) (software: nbTransmission (R))

visualization

  1. International risk of yellow fever spread from the ongoing outbreak in Brazil, December 2016 to May 2017 (link) (software: epiflows (R))

volume under roc surfaces

  1. Diagnostic test evaluation methodology: A systematic review of methods employed to evaluate diagnostic tests in the absence of gold standard-An update (link) (software: bcROCsurface (R))

web sources

  1. Accurate estimation of influenza epidemics using Google search data via ARGO (link) (software: argo (R))

weibull model

  1. Estimating the Latent Period of Coronavirus Disease 2019 (COVID-19) (link)

whole genome sequence

  1. Estimating the relative probability of direct transmission between infectious disease patients (link) (software: nbTransmission (R))