Description

Package detsims is a framework and model for running deterministic simulations of resistance evolution in mosquitoes. It is designed to fully reproduce the results in Madgwick & Kanitz 2021 "Comparison of resistance-management strategies with new insecticides for mosquito control using bed-nets", from model definitions, simulation executions and visualization of results, including published figures.

The final version of the publication can be found here

Installation

# You will need devtools to install evolveR. If you do not have it yet, run:
install.packages("devtools")

# Install the Syngenta development version from GitLab:
devtools::install_github("syngenta/Madgwick-Kanitz-detsims", ref='main')

Package structure

This package follows a traditional R-package setup, with its functions defined under folder 'R', their associated help files in 'man'. Importantly though, we used also used a folder called 'scripts' here: the files contained in this folder are pure R scripts designed to execute an example run or the simulations in 'OneShot.R'; and the full range of results into ./data/ with 'Simulator.R'. Please, use the latter with caution as it would execute 1 million simulations on the machine it's been called from, using the parameter definitions given at the beginning of the script under section 'meta-parameters'.

Note also that there are 4 inheritance definitions (Nuclear, Mitochondrial):

• NN - c(n,n)
• MM - c(m,m)
• MN - c(m,n)
• NM - c(n,m)

And 6 strategy numbers as follows:

1. soloA
2. soloB
3. Combination (Mosaic in the main text)
4. Mixture
5. Rotation
6. Sequence

These can be combined in all possible ways, but in the paper, we report a subset of 15 of these inheritance-strategy combinations. See the paper for more details.

We have executed these simulations in a high-performance computer cluster. Additional information and assistance on this can be provided on demand (see contact information below in section 'Issues')

The script for generating all figures in the paper and supplement (plus extras) is also under 'vignettes': 'Figures.R'. Use with caution as this is compilation of all visualization explored in the development of this work leading to a fair amount of computing time, as well.

Issues

Issues in this package can be reported using GitHub's Issues above. Other inquiries can be made by e-mail to Ricardo(dot)Kanitz(at)syngenta(dot)com and Philip(dot)Madgwick(at)syngenta(dot)com.