Simulations for SARS-CoV-2

This repository contains scripts to simulate phylogenetic trees and DNA sequence alignment similar to those observed for SARS-CoV-2.

You can find a script to simulate phylogenetic trees here.

You can find a script to simulate DNA sequence alignments using a simulated phylogenetic tree here

The script that contains the epidemiological model used to simulate phyloegentic trees are here.

System Requirement

Operating System

This R package was developed and tested on a macOS High Sierra version 10.13.6

Additional R Packages Required

Note these are the version we used, however the scripts should work with other R package versions.

devtools version 2.3.2
lhs version 1.1.1
phyclust version 0.1.29
ape version 5.4.1
phydynR version 0.2.0

How to install it?

You will need to install all abovementioned R packages as below (if not alreay installed in your computer):

install.packages("devtools")
install.packages("lhs")
install.packages("phyclust")
install.packages("ape")

library(devtools)
# to install phydynR
devtools::install_github("emvolz-phylodynamics/phydynR")
# If installing phydynR from install_github does not work, and you get the 
#"#error "*** C++11 compiler required; enable C++11 mode in your compiler, or use an earlier version of Armadillo"
# then type type in R the following (but first remove the comment symbol #) and then try install phydynR again
# Sys.setenv("PKG_CXXFLAGS"="-std=c++11")
# if you still get an error, you may need to try
# devtools::install_github("emvolz-phylodynamics/phydynR", force = TRUE)

# Updated on 6 February 2023:
#If you are using the new apple M1/M2 chip, you can getting an error related to gfortran to compile/install phydyn R,
#you can have a look at the instructions described at https://github.com/RubD/Giotto_site/issues/11, 
#update gfortran as explained in the link and then try to install phydynR again. It should solve the problem.



# to install this R package
devtools::install_github(repo = "thednainus/sarscov2simulations")

# Alternatively, you can download the zip file from GitHub
# Unzip the file and run the following command on your computer (don't forget to remove the comment symbol #)
# install.packages(path_to_file, repos = NULL, type="source")
# where path_to_file is the path to the unziped directory that you downloaded from GitHub


# After installing the package:
library(sarscov2simulations)

Output Example

The aim of these scprits was to generate DNA sequence alignments consistent to a epidemiological model and phylogenetic tree. These sequence alignments were used with PhyDyn and BEAST 2 to check whether we could estimate the parameters of the epidemiological model using simulated data (see paper).

After running script DNA_seqali_simulations.R, you should get sequence alignment (all data and deduplicated data) as exemplified here. Note that sequence name is in the form of simSeq99|2020.248|_Il

where simSeq99 is the sequence name;

2020.248 is sampling date in decimal form and;

Il is the compartment the "individual" is classified, in this case it is infected with low rate of transmission.

Note that this nomenclature is following guidelines described in here for PhyDyn using BEAST 2.