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rtestim

Estimate the Effective Reproductive Number with Trend Filtering

v1.0.1 · Oct 24, 2025 · MIT + file LICENSE

Description

Use trend filtering, a type of regularized nonparametric regression, to estimate the instantaneous reproduction number, also called Rt. This value roughly says how many new infections will result from each new infection today. Values larger than 1 indicate that an epidemic is growing while those less than 1 indicate decline. For more details about this methodology, see Liu, Cai, Gustafson, and McDonald (2024) <doi:10.1371/journal.pcbi.1012324>.

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  installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   6.0Mb
NOTE r-oldrel-macos-x86_64

installed package size

  installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   6.0Mb
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NOTE 12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 9, 2026
NOTE r-oldrel-macos-arm64

installed package size

  installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   6.0Mb
NOTE r-oldrel-macos-x86_64

installed package size

  installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   6.0Mb

Dependency Network

Dependencies Reverse dependencies checkmate cli dspline ggplot2 Matrix Rcpp rlang tibble tvdenoising vctrs rtestim

Version History

new 1.0.1 Mar 9, 2026