Objective Functions Functions

PO.Stats.LogSSE

Computes the sum of squared errors (SSE) in log-space between observed and predicted rate sequences. Small positive epsilon added before taking logs to avoid log(0).

PO.Stats.R2

Computes the coefficient of determination (R²) between observed and predicted sequences. R² = 1 - SSE/TSS. Returns 1.0 for perfect fit.

PO.Stats.RMSE

Computes the root mean squared error (RMSE) between observed and predicted sequences. RMSE = sqrt(SSE/n).

PO.Stats.SSE

Computes the sum of squared errors (SSE) between observed and predicted rate sequences. Returns a scalar value.

PO.Stats.WLogSSE

Computes the weighted log-space SSE between observed and predicted sequences. Small positive epsilon added before taking logs to avoid log(0).

PO.Stats.WSSE

Computes the weighted SSE between observed and predicted sequences.