| Estimates of the risk of large or long-lasting outbreaks of Middle East respiratory syndrome after importations outside the Arabian Peninsula (link) |
|
10.1016/j.epidem.2016.04.002 |
overdispersion, maximum likelihood, risk assessment, detection |
| Accurate estimation of influenza epidemics using Google search data via ARGO (link) |
argo (R) |
10.1073/pnas.1515373112 |
web sources, big-data, real-time, influenza, methods, hmm, prediction, markov hidden models |
| Diagnostic test evaluation methodology: A systematic review of methods employed to evaluate diagnostic tests in the absence of gold standard-An update (link) |
bcROCsurface (R) |
10.1371/journal.pone.0223832 |
continuous diagnostic tests, bias-corrected estimation methods, roc surface, volume under roc surfaces, missing at random |
| Deep-sequence phylogenetics to quantify patterns of HIV transmission in the context of a universal testing and treatment trial – BCPP/Ya Tsie trial (link) |
bumblebee (R) |
10.7554/eLife.72657 |
transmission pairs, phylogenetics, deep-sequence data, transmission flows within and between population groups accounting for sampling heterogeneity |
| Estimating the overdispersion in COVID-19 transmission using outbreak sizes outside China (link) |
COVID19_clustersize (R), COVID19_clustersize (Python) |
10.12688/wellcomeopenres.15842.3 |
covid-19, overdispersion, superspreading, branching process |
| Hierarchical Modeling for Diagnostic Test Accuracy Using Multivariate Probability Distribution Functions (link) |
CopulaDTA (R), CopulaREMADA (R) |
10.3390/math9111310 |
copula based bivariate beta-binomial model, diagnostic test accuracy studies, copula mixed models, multivariate meta-analysis, diagnostic test accuracy studies, case-control and cohort studies, d-vine copula mixed model, multinomial quadrivariate d-vine copula mixed model, one-factor copula mixed model, meta-analysis of multiple diagnostic tests |
| Practical considerations for measuring the effective reproductive number, Rt (link) |
|
10.1371/journal.pcbi.1008409 |
simulation, compartmental models, bias, estimation |
| International risk of yellow fever spread from the ongoing outbreak in Brazil, December 2016 to May 2017 (link) |
epiflows (R) |
10.2807/1560-7917.ES.2017.22.28.30572 |
prediction, visualization, flows, diffusion, exportations, importations |
| EpiModel: An R Package for Mathematical Modeling of Infectious Disease over Networks (link) |
EpiModel (R) |
10.18637/jss.v084.i08 |
abm, networks, sna, ergm |
| A Flexible and General Agent-Based Model Engine (link) |
epiworldR (R), epiworld (C++) |
|
abm, simulation, mcmc |
| Estimating the generation interval and inferring the latent period of COVID-19 from the contact tracing data (link) |
|
10.1016/j.epidem.2021.100482 |
general interval, incubation period, latent period, contact tracing data, gamma model |
| Incubation period for COVID-19: a systematic review and meta-analysis (link) |
|
10.1007/s10389-021-01478-1 |
meta analysis |
| The Incubation period of COVID-19: A meta-analysis (link) |
|
10.1016/j.ijid.2021.01.069 |
incubation period, meta-analysis |
| Estimating the Latent Period of Coronavirus Disease 2019 (COVID-19) (link) |
|
10.1093/cid/ciab746 |
latent period, incubation period, gamma, weibull model, log-normal model |
| Meta-analysis of diagnostic performance of serology tests for COVID-19: impact of assay design and post-symptom-onset intervals (link) |
meta4diag (R) |
10.1080/22221751.2020.1826362 |
diagnostic tests, meta-analysis, bayesian inference analysis, integrated nested laplace approximation |
| Diagnostic efficacy of anti-SARS-CoV-2 IgG/IgM test for COVID-19: A meta-analysis (link) |
meta4diag (R) |
10.1002/jmv.26211 |
diagnostic tests, meta-analysis, bayesian inference analysis, integrated nested laplace approximation |
| Estimating the relative probability of direct transmission between infectious disease patients (link) |
nbTransmission (R) |
10.1093/ije/dyaa031 |
naive bayes, estimation, methods, transmission probability, snp, whole genome sequence, relative transmission probabilities, naive bayes, generation/serial interval, reproductive number |
| Diagnostic test accuracy network meta-analysis methods: A scoping review and empirical assessment (link) |
CopulaDTA (R), mada (R), NMADiagT (R) |
10.1016/j.jclinepi.2022.02.001 |
copula based bivariate beta-binomial model, diagnostic test accuracy studies, meta-analysis, diagnostic accuracy, network meta-analysis, multiple diagnostic tests, hierarchical summary receiver operating characteristic, missing data framework |
| Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data (link) |
outbreaker2 (R) |
10.1371/journal.pcbi.1003457 |
importations, mutation rate, genomics, methods, network |
| Maximum Likelihood Estimation of the Negative Binomial Dispersion Parameter for Highly Overdispersed Data, with Applications to Infectious Diseases (link) |
|
10.1371/journal.pone.0000180 |
overdispersion, estimation, maximum likelihood, bias |
| The impact of long-term nonpharmaceutical interventions on COVID-19 epidemic dynamics and control: the value and limitations of early models (link) |
pomp (R) |
10.1098/rspb.2021.0811 |
partially observed markov processes, particle filtering, trajectory matching, approximate bayesian sequential monte carlo, approximate bayesian computation, iterated filtering, probe-matching, nonlinear forecasting, ensemble kalman filter, ensemble adjustment kalman filter, power-spectrum-matching |
| 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) |
|
10.1136/bmjopen-2020-039856 |
infectious period, meta analysis, gamma distribution, guassian distribution |
| Inference of R0 and Transmission Heterogeneity from the Size Distribution of Stuttering Chains (link) |
n/a (Matlab) |
10.1371/journal.pcbi.1002993 |
dispersion, estimation, final size, chain |
| Superspreading and the effect of individual variation on disease emergence (link) |
|
|
superspreading, dispersion, control, estimation |
| High variability in transmission of SARS-CoV-2 within households and implications for control (link) |
householdTransmission (R) |
10.1371/journal.pone.0259097 |
covid-19, overdispersion, household transmission, maximum likelihood |
