Logistic growth regression models applied to HIV transmitted founder and chronic control isolates

Code to fit (and illustrate) the logistic growth models used in Sugrue et al. (2022). The apparent interferon resistance of transmitted HIV-1 is possibly a consequence of enhanced replicative fitness. PLOS Pathogens 18[11]: e1010973. doi:10.1371/journal.ppat.1010973.

Requirements

• Install the conda package manager
• All other dependencies can then be installed using:

conda env create -f environment.yml

Usage

Re-run all analyses using:

conda activate hiv_growth_rate
make