csmGmm 0.6.0

Breaking changes

• sameDirAlt no longer has a default value in symm_fit_ind_EM() and symm_fit_ind_EM_noAssumption() (previously FALSE). Users must now set sameDirAlt = TRUE for replication analysis or sameDirAlt = FALSE for mediation and pleiotropy analysis. This prevents replication analyses from accidentally using the larger (non-replication) alternative space.
• symm_fit_cor_EM(), symm_fit_cor_EM_noAssumption(), symm_fit_cor_EM_rho(), and symm_fit_cor_EM_fulllik() gain a required sameDirAlt argument, placed before eps. Code that passed eps or checkpoint by position should now pass them by name.
• The correlated-model functions (symm_fit_cor_EM(), symm_fit_cor_EM_noAssumption(), symm_fit_cor_EM_rho(), and symm_fit_cor_EM_fulllik()) now check that testStats is a matrix with exactly two columns and stop with an informative error otherwise.

New features

• New plot_fit_hist() for checking model fit. For each dimension, it plots a histogram of the observed test statistics with the fitted marginal mixture density, the null N(0, 1) component, and the combined alternative component overlaid, plus the observed counts minus the counts expected under the fitted null. Optional nBins, zLim, and yLim arguments control the display.
• New get_marginal_mixture() collapses a fitted csmGmm into the one-dimensional marginal Gaussian mixture (means and weights) for each dimension. It is used internally by plot_fit_hist().

Documentation and minor changes

• Examples for all model-fitting functions now simulate signals in both directions and pass sameDirAlt explicitly.
• The vignette now sets sameDirAlt explicitly in every model-fitting call.