VertexWiseR system requirements installation
VWRfirstrun.RdHelps the user verify if VertexWisrR's system requirements are present and install them (a suitable 'Python' or 'Miniconda' environment, 'BrainStat' toolbox and libraries). If they are installed already, nothing will be overwritten.
Arguments
- requirement
String that specifies a requirement to enquire about:
For only Python/Conda installation: 'python/conda only'
For Python/Conda and Brainstat installation: 'conda/brainstat'
For specific 'BrainStat' libraries: 'fsaverage5', 'fsaverage6', 'fslr32k', 'yeo_parcels'
For the neurosynth database: 'neurosynth'. Default is 'any' and checks everything.
- n_vert
Numeric vector indicating the number of vertices of a given surface data so that only the required templates are asked for. It will modify the requirement argument accordingly.
- promptless
A boolean object specifying whether to prompt the user for action when system requirements are missing. If TRUE, VWRfirstrun() will simply inform of what is missing and will not prompt for action. Default is FALSE.
Value
No returned value in interactive session. In non-interactive sessions, a string object informing that system requirements are missing.
Details
VertexWiseR imports and makes use of the R package 'reticulate.' 'reticulate' is a package that allows R to borrow or translate Python functions into R. Using 'reticulate', the package calls functions from the 'BrainStat' Python module. For 'reticulate' to work properly with VertexWiseR, a Python environment needs to be installed with it — the default choice offered by VWRfirstrun is to let reticulate (version 1.41.0) create an ephemeral Python virtual environment using UV and py_require(). If for a reason this is not desirable, VWRfirstrun() also gives the choice to install a 'Miniconda' (lightweight version of Python) or Python environment in a reticulate default path or a specified path. Vertex-wise statistical analyses of cortical surface require fsaverage and parcellation templates as imported by default in 'BrainStat'. The decode_surf_data() function also requires the 'Neurosynth' database to be downloaded.