wepidemics

By parameter

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INDEX

D diagnostic test accuracy, diagnostic test sensitivity, diagnostic test specificity, dispersion, duration

G generation time

H household attack rate, household importation rate

I incubation period, incubation, infectiousness

L latent period duration, latent period

R r0, reproductive number, rt

S serial interval

T transmission flows, transmission rate

Details

diagnostic test accuracy

  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))
  2. Hierarchical Modeling for Diagnostic Test Accuracy Using Multivariate Probability Distribution Functions (link) (software: CopulaDTA (R), CopulaREMADA (R))
  3. Meta-analysis of diagnostic performance of serology tests for COVID-19: impact of assay design and post-symptom-onset intervals (link) (software: meta4diag (R))
  4. Diagnostic efficacy of anti-SARS-CoV-2 IgG/IgM test for COVID-19: A meta-analysis (link) (software: meta4diag (R))
  5. Diagnostic test accuracy network meta-analysis methods: A scoping review and empirical assessment (link) (software: CopulaDTA (R), mada (R), NMADiagT (R))

diagnostic test sensitivity

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

diagnostic test specificity

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

dispersion

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

duration

  1. Estimating the generation interval and inferring the latent period of COVID-19 from the contact tracing data (link)
  2. Incubation period for COVID-19: a systematic review and meta-analysis (link)
  3. The Incubation period of COVID-19: A meta-analysis (link)
  4. Estimating the Latent Period of Coronavirus Disease 2019 (COVID-19) (link)
  5. 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)

generation time

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

household attack rate

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

household importation rate

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

incubation period

  1. Estimating the generation interval and inferring the latent period of COVID-19 from the contact tracing data (link)
  2. Incubation period for COVID-19: a systematic review and meta-analysis (link)

incubation

  1. The Incubation period of COVID-19: A meta-analysis (link)

infectiousness

  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)

latent period duration

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

latent period

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

r0

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

reproductive number

  1. Estimating the relative probability of direct transmission between infectious disease patients (link) (software: nbTransmission (R))
  2. 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))

rt

  1. Estimates of the risk of large or long-lasting outbreaks of Middle East respiratory syndrome after importations outside the Arabian Peninsula (link)
  2. Practical considerations for measuring the effective reproductive number, Rt (link)
  3. A Flexible and General Agent-Based Model Engine (link) (software: epiworldR (R), epiworld (C++))
  4. Estimating the relative probability of direct transmission between infectious disease patients (link) (software: nbTransmission (R))

serial interval

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

transmission flows

  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 rate

  1. Estimating the relative probability of direct transmission between infectious disease patients (link) (software: nbTransmission (R))
  2. 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))