README.md
In wdelva/RSimpactHelp: Pre- and Post-simulation helper functions for RSimpact Cyan
The RSimpactHelper package
This repository contains R functions that facilitate post-simulation analysis in R of simulation output for models developed with SimpactCyan (https://simpactcyan.readthedocs.io/en/latest/).
SYSTEM AND SOFTWARE REQUIREMENTS
Operating system
We have only tested this code on personal computers (OS X Version 10.11.6 and Linux Ubuntu Version 16.04), and on the lengau cluster at the Cape Town Centre for High Performance Computing (CHPC) and the golett cluster of the Flemish Supercomputer Centre (VSC).
Required software
R version 3.4.4
Seq-Gen version 1.3.4. https://github.com/rambaut/Seq-Gen/releases/tag/1.3.4 Simulates viral evolution across a transmission network.
FastTree version 2.1.10. http://www.microbesonline.org/fasttree/#Install Reconstructs a phylogenetic tree from a large alignment dataset.
To install and load the package, run the following lines of code:
library(devtools)
Mac users will need to have Xcode installed, as well as Command Line Tool https://developer.apple.com/download/more/ and gfortran for MacOS: https://github.com/fxcoudert/gfortran-for-macOS/releases
install_github("wdelva/RSimpactHelp”, dependencies = TRUE)
library(RSimpactHelper)
COPYRIGHT AND LICENSING INFORMATION
All files are copyright protected and are made available under the GPL 3.0 License https://www.gnu.org/licenses/gpl-3.0.en.html. This means that this work is suitable for commercial use, that licensees can modify the work, that they must release the source alongside with Derivative Work, and that Derivative Work must be released under the same terms.
CONTACT INFORMATION
Please contact Prof Wim Delva with questions regarding the files provided and their authorized usage:
Wim Delva
Email: DELVAW@sun.ac.za
INFORMATION FOR RSIMPACTHELP DEVELOPERS
Adding package dependencies
If you want to use a function from a package, it not only needs to be listed in the NAMESPACE file, but you must also list the package as a dependency in the DESCRIPTION file.
If the package is on CRAN, it should be listed under "Imports" in the DESCRIPTION file.
If the package is hosted on another repository or website, it gets listed under "Imports", as well as "Remotes" in the DESCRIPTION file. How you list it under "Remotes" is dependent upon where you have to install it from. Here are the directions for listing it under Remotes: https://cran.r-project.org/web/packages/devtools/vignettes/dependencies.html .
If the packages is from Bioconductor you need to, first list "biocViews" before "Imports", and then include the name of package in "Imports".
wdelva/RSimpactHelp documentation built on Dec. 26, 2019, 3:42 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
The RSimpactHelper package
This repository contains R functions that facilitate post-simulation analysis in R of simulation output for models developed with SimpactCyan (https://simpactcyan.readthedocs.io/en/latest/).
SYSTEM AND SOFTWARE REQUIREMENTS
Operating system
We have only tested this code on personal computers (OS X Version 10.11.6 and Linux Ubuntu Version 16.04), and on the lengau cluster at the Cape Town Centre for High Performance Computing (CHPC) and the golett cluster of the Flemish Supercomputer Centre (VSC).
Required software
R version 3.4.4
Seq-Gen version 1.3.4. https://github.com/rambaut/Seq-Gen/releases/tag/1.3.4 Simulates viral evolution across a transmission network.
FastTree version 2.1.10. http://www.microbesonline.org/fasttree/#Install Reconstructs a phylogenetic tree from a large alignment dataset.
To install and load the package, run the following lines of code:
library(devtools)
Mac users will need to have Xcode installed, as well as Command Line Tool https://developer.apple.com/download/more/ and gfortran for MacOS: https://github.com/fxcoudert/gfortran-for-macOS/releases
install_github("wdelva/RSimpactHelp”, dependencies = TRUE)
library(RSimpactHelper)
COPYRIGHT AND LICENSING INFORMATION
All files are copyright protected and are made available under the GPL 3.0 License https://www.gnu.org/licenses/gpl-3.0.en.html. This means that this work is suitable for commercial use, that licensees can modify the work, that they must release the source alongside with Derivative Work, and that Derivative Work must be released under the same terms.
CONTACT INFORMATION
Please contact Prof Wim Delva with questions regarding the files provided and their authorized usage:
Wim Delva Email: DELVAW@sun.ac.za
INFORMATION FOR RSIMPACTHELP DEVELOPERS
Adding package dependencies
If you want to use a function from a package, it not only needs to be listed in the NAMESPACE file, but you must also list the package as a dependency in the DESCRIPTION file.
If the package is on CRAN, it should be listed under "Imports" in the DESCRIPTION file.
If the package is hosted on another repository or website, it gets listed under "Imports", as well as "Remotes" in the DESCRIPTION file. How you list it under "Remotes" is dependent upon where you have to install it from. Here are the directions for listing it under Remotes: https://cran.r-project.org/web/packages/devtools/vignettes/dependencies.html . If the packages is from Bioconductor you need to, first list "biocViews" before "Imports", and then include the name of package in "Imports".
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.