Edited vignette to better explain how to set up the code and directories so that the demo code runs.
We removed examples from function documentation that do not work outside of run_cape
pracma::pinv() replaced pseudoinverse().
Added param_file argument to load_input_and_run_cape().
Added ability for cape2mpp() to recognize and format multi-parent crosses
Added ability to read in multi-parent crosses in qtl format.
Fixed display of marker effects in plot_singlescan().
Updated missing parameters from load_input_and_run_cape() documentation
Changed binary file extensions of saved files to .RData.
Additional minor bug fixes.
run_cape() now runs a full cape analysis from a yml parameter file.
Dots were replaced with underscores in all function names.
All code was refactored to S6.
qtl2cape() now accepts a covariate matrix as an argument.
Added demos starting from different file formats.
Added formatting capabilities for PLINK files.
bin_curve() was updated to handle very short vectors.
Additional minor bug fixes.
Fixed covariate handling in pairscan().