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.
ginpiper uses the following packages:
- ggplot2
- R0
- scales
ginpiper can be installed in R using devtools:
install.packages("devtools")
library(devtools)
devtools::install_github("KleistLab/ginpiper")
[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