inst/data/README.md

In thednainus/senegalHIVmodel: Analysis of HIV data from Senegal

This directory contains data files used in R scripts.

HIV_subtypes_summary_CGR.csv

File containing the metadata for the close global sequences (CGR) or "source" sequences.

HIV_subtypes_summary_SENEGAL_noDups.csv

File containing the metadata for the Senegal HIV data.

bindTree_CGR_GTR+Gp12+3_droppedTip.tre

Dated phylogenetic tree used in the phylodynamic analyses for the combined data (when including subtypes B, C and CRF 02_AG). This tree was dated using treedater. I also dropped sequences from Children, risk group = NA and sex = NA.

bindTree_CGR_GTR+Gp12+3_droppedTip_sts.RDS

This file contain the estimated dates for each tip in the phylogenetic tree (bindTree_CGR_GTR+Gp12+3_droppedTip.tre) estimated using treedater.

thednainus/senegalHIVmodel documentation built on Oct. 14, 2024, 5:46 a.m.