Tim Taylor

Tim Taylor

7 packages on CRAN

i2extras

cran
99.99th

Percentile

Provides functions to work with 'incidence2' objects, including a simplified interface for trend fitting and peak estimation. This package is part of the RECON (<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.

incidence

cran
99.99th

Percentile

Provides functions and classes to compute, handle and visualise incidence from dated events for a defined time interval. Dates can be provided in various standard formats. The class 'incidence' is used to store computed incidence and can be easily manipulated, subsetted, and plotted. In addition, log-linear models can be fitted to 'incidence' objects using 'fit'. This package is part of the RECON (<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.

incidence2

cran
99.99th

Percentile

Provides functions and classes to compute, handle and visualise incidence from dated events for a defined time interval. Dates can be provided in various standard formats. The class 'incidence2' is used to store computed incidence and can be easily manipulated, subsetted, and plotted. This package is part of the RECON (<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.

trendeval

cran
99.99th

Percentile

Provides a coherent interface for evaluating models fit with the trending package. This package is part of the RECON (<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.

trending

cran
99.99th

Percentile

Provides a coherent interface to multiple modelling tools for fitting trends along with a standardised approach for generating confidence and prediction intervals.

earlyR

cran
99.99th

Percentile

Implements a simple, likelihood-based estimation of the reproduction number (R0) using a branching process with a Poisson likelihood. This model requires knowledge of the serial interval distribution, and dates of symptom onsets. Infectiousness is determined by weighting R0 by the probability mass function of the serial interval on the corresponding day. It is a simplified version of the model introduced by Cori et al. (2013) <doi:10.1093/aje/kwt133>.

99.99th

Percentile

Provides functions and graphics for projecting daily incidence based on past incidence, and estimates of the serial interval and reproduction number. Projections are based on a branching process using a Poisson-distributed number of new cases per day, similar to the model used for estimating R in 'EpiEstim' or in 'earlyR', and described by Nouvellet et al. (2017) <doi:10.1016/j.epidem.2017.02.012>. The package provides the S3 class 'projections' which extends 'matrix', with accessors and additional helpers for handling, subsetting, merging, or adding these objects, as well as dedicated printing and plotting methods.