ginpiper - Package for smooth curve estimation, R_e computation and plotting

This R package is used by GInPipe [1] - Genome-based Incidence Estimation Pipeline - to draw a smooth incidence trajectory estimate, calculate the corresponding effective reproduction number and make correspoonding plots and tables.

Dependencies

ginpiper uses the following packages:

• ggplot2
• R0
• scales

Installation

ginpiper can be installed in R using devtools:

install.packages("devtools")

library(devtools)
devtools::install_github("KleistLab/ginpiper")

Reference

[1] Smith, M. R. and Trofimova, M., et al. (2021). Rapid incidence estimation from SARS-CoV-2 genomes reveals decreased case detection in Europe during summer 2020. medRxiv, https://github.com/KleistLab/GInPipe