A toolbox to streamline the creation of landscape-scale simulations using the coalescent simulator ms. msLandscape comprises an R package and a toolbox of other scripts that work seamlessly together with the R package.
The main msLandscape webpage is here
To install the R package easily, make sure the devtools package is installed (using the command install.packages("devtools") in R if necessary). In R, then type devtools::install_github("hahnlab/msLandscape"). The package should load automatically.
For a full walkthrough guide on how to use msLandscape to automatically generate landscape-scale ms flag files and the workflow for editing and 'sculpting' these landscapes to meet the desired shape, sampling patterns, and migration patterns for the landscape, including using them to run ms, see the linked tutorial here.
For a guide to using the scripts in the msLandscape toolbox to help convert ms output data to formats that smartPCA (for running PCA), un-PC, SpaceMix, and EEMS can use as input, see the linked tutorial here.
For a tutorial about how to use the msLandscape_layerPNGImages function in msLandscape to create layered composite images of multiple input images (e.g. SpaceMix, EEMS, or un-PC results from different scenarios) that allow direct comparisons between them, see the linked tutorial here.
The toolbox of other (non-R) scripts that are part of msLandscape are found in the msLandscape_toolboxScripts directory.