estimateRtAvg

Averages the time-level reproductive numbers within a certain range to estimate the overall
reproductive number for an oubreak.

Estimates the relative transmission probabilities between cases in an infectious disease outbreak or cluster using naive Bayes. Included are various functions to use these probabilities to estimate transmission parameters such as the generation/serial interval and reproductive number as well as finding the contribution of covariates to the probabilities and visualizing results. The ideal use is for an infectious disease dataset with metadata on the majority of cases but more informative data such as contact tracing or pathogen whole genome sequencing on only a subset of cases. For a detailed description of the methods see Leavitt et al. (2020) <doi:10.1093/ije/dyaa031>.

Sarah V Leavitt

nbTransmission

Naive Bayes Transmission Analysis

estimateRtAvg function

<dl><dt>rtData</dt>
<dd>The name of the dateset with time-level reproductive numbers.</dd>
<dt>rangeForAvg</dt>
<dd>A vector with the start and ending time period to be used to calculate the
average effective reproductive number.</dd></dl>

Arguments

Estimates the average effective reproductive number — estimateRtAvg

<dl>

<dt>rtData</dt>
<dd>The name of the dateset with time-level reproductive numbers.</dd>


<dt>rangeForAvg</dt>
<dd>A vector with the start and ending time period to be used to calculate the
average effective reproductive number.</dd>

</dl>

estimateRtAvg: Estimates the average effective reproductive number

Description

Usage

Value

Arguments

Details

See Also