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.