Modified files for strain-specific residual variance option #269
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… option similar to cvt
…eplaced in the math with the null Ve
Small formatting change to -residvar
Updated resid_var math to CalcQi
Updated most functions except MphEM and remaining P-val functions
Continued to make appropriate math changes to MphCalcSigma, UpdateV, MphCalcLogL, MphEM, MphCalcP, MphCalcBeta, and other functions.
Finished theoretical changes in other functions and replaced all "eps_eval" entries with "eval_vec, sigmasq".
Replaced any lingering mentions of "eps_eval" with "eval_vec, sigmasq".
Changed mentions of "eps_eval" with "sigmasq". Still need to figure out how to get eigenvectors from the same place "eval" is derived.
Changed mention of eps_eval as a vector to "gsl_matrix *sigmasq"
Changed the one mention of "eps_eval" to "eval_vec" and "sigmasq". May actually need to return to this file in order for the code to actually run.
eps_eval --> eval_vec, sigmasq
Changed eps_eval to sigmasq and corrected any identified regions where dimensions did not match.
Replaced input of CopyResid from eps_eval to sigmasq
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These changes include the modifications to the math inside mvlmm, and attempts to add an option for the user to input their own strain-specific residual variance column within the files gemma_io.cpp and param.cpp. Thanks for your help!