Page last updated by Matthew Denwood on 13th March 2021
Control of soil-transmitted helminths depends on the use of preventive chemotherapy with anthelmintic compounds. The continued potential for development of anthelmintic resistance is therefore a major concern to public health. We have developed software tools to aid in the design of surveys intended to monitor anthelmintic efficacy in the field.
eggSim is an R package developed by Matt Denwood and Luc Coffeng to assess different survey designs for faecal egg count reduction tests, in terms of their cost efficiency, precision and expected statistical bias. The code is open-source and freely available for use via our public GitHub repository, although it is currently under active development so expect new features to be added over time. We also welcome feedback and contributions to the project.
Using the eggSim package currently requires installation and basic usage of the statistical programming software R - this is freely available from the CRAN website. In the future we hope to provide an online interactive tool to facilitate usage by practitioners without programming experience. Please feel free to contact us if you would be interested in using (or contributing to) a tool such as this.
The simplest method of using eggSim is to install the pre-compiled package of the latest release version of the package from our Drat repopsitory. Enter the following commands into R:
install.packages("eggSim", repos=c(CRAN="https://cran.rstudio.com/", "ku-awdc"="https://ku-awdc.github.io/drat/"))
This should download and install the R package along with the required dependencies. You can then launch an introductory vignette to help you get started with the package using the following code:
vignette("eggSim", package="eggSim")
More advanced users may wish to use the development version of the R package directly from the GitHub repository. This can be installed using the following R code:
remotes::install_github("ku-awdc/eggSim")
Note that this does NOT install the vignettes by default. Alternatively, you can also inspect the R code directly from the GitHub repository.
L.E. Coffeng, B. Levecke, J. Hattendorf, M. Walker, and M.J. Denwood. 2021. Survey design to monitor drug efficacy for the control of soil-transmitted helminthiasis and schistosomiasis. Clin. Infect. Dis. (in Press).
The software used by this website is open source and freely available under the General Public License (version 2). All advice contained on this website and given by the linked web applications is provided freely under the same license, and absolutely without any form of warranty or guarantee.
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