EpiEstim specifications

Information


Unique identifier OMICS_23626
Name EpiEstim
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.1.2
Stability Stable
Source code URL https://cran.r-project.org/src/contrib/EpiEstim_1.1-2.tar.gz
Maintained Yes

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Maintainer


  • person_outline Anne Cori <>

Publication for EpiEstim

EpiEstim in publications

 (5)
PMCID: 5871640
PMID: 28351674
DOI: 10.1016/j.epidem.2017.02.012

[…] distribution to these observed serial intervals by maximum likelihood (). using this serial interval distribution, the instantaneous reproduction number (rt) was estimated on a daily basis using the epiestim r package () with a 2-week sliding window. this reproduction number provided insights into the trend in transmissibility, but was not used for forecasting., additionally, for each patient, […]

PMCID: 5821398
PMID: 29420641
DOI: 10.1371/journal.ppat.1006885

[…] the arithmetic mean weighted by the sample size of the study. we then generated discretized gamma distributions of the generation time distribution, using the function discrsi from the r package epiestim []., studies describing the mutation rate were identified using the search terms ‘mutation rate or substitution rate or spontaneous mutation’. the arithmetic mean was calculated to summarise […]

PMCID: 5598245
PMID: 28703921
DOI: 10.1111/irv.12467

[…] tree method estimates reproduction numbers using transmission tree based only on the gaps in symptom‐onset dates between patients. these four methods are coded in the r0 package. , package “epiestim” , which was based on the nowcasting method that takes censoring into account, provides a method to estimate the instantaneous reproductive number (r t) smoothing by averaging […]

PMCID: 4945720
PMID: 27433381
DOI: 10.3947/ic.2016.48.2.108

[…] estimated from this study, the serial interval (12.6 days ± 2.8 days) from the previous analysis was also used for sensitivity analysis []. daily rc and rt were estimated over a one-day window using epiestim in r []., this study analyzed the publicly available data with private information deidentified, so this study was not subject to the approval of the institutional review board., data […]

PMCID: 3900386
PMID: 24465202
DOI: 10.1371/journal.pcbi.1003457

[…] s2). we used a generation time distribution modeled as a discretized gamma distribution with a mean of 8.4 days and a standard deviation of 3.8 days , using the function discrsi from the r package epiestim . the same distribution was used for the the time to collection. details of the parameters used to run outbreaker are provided in supporting methods. the statistical confidence […]


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EpiEstim institution(s)
Department of Infectious Disease Epidemiology, MRC Centre for Outbreak Analysis and Modelling, Imperial College London, London, UK
EpiEstim funding source(s)
Supported by the United Kingdom Medical Research Council methodology project G0800596, the FP7 European Management Platform for Emerging and Reemerging Infectious Disease Entities project, and the National Institute of General Medical Sciences Models of Infectious Disease Agent Study program, by the Research Council United Kingdom and a fellowship supported by the Royal Society.

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