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anova_spd() split-plot ANOVA: the main-plot error term
(Error a) and the sub-plot sum of squares are now extracted from the
ANOVA table by term name rather than by fixed row position. Because R
orders main-effect terms ahead of interaction terms, the previous
positional extraction swapped the sub-plot effect with Error(a), which
produced incorrect main-plot and sub-plot F-tests and an incorrect
Error(a) mean square, main-plot standard error, critical difference and
CV(a). Sub-plot standard error, critical difference and CV(b), and the
returned ANOVA table itself, were not affected.anova_spd_ab_main(),
anova_spd_c_main_ab_sub(), anova_spd_ab_cd()
and anova_sspd() now test each effect against its correct
error term. Previously these functions reported the raw combined ANOVA,
in which the main-plot (and, for the split-split design, sub-plot)
factors were tested against the residual rather than against the
properly pooled main-plot / sub-plot error. The returned
anova_table now gives the correct F-values and p-values for
every stratum, and the objects carry the corresponding error mean
squares, degrees of freedom and CVs. Verified against independent
aov() Error()-strata models.anova_spd_pooled() and anova_sspd_pooled()
(combined analysis over environments) now test each source against the
correct pooled error. Both functions previously reported a
single-stratum anova() table in which every effect was
tested against one residual, so the environment main effect and the
main-plot (and, for the split-split design, sub-plot) factors were
tested against the sub-sub-plot residual rather than against their own
pooled errors. Treating environments as fixed and replications as random
within environment, the environment effect is now tested against the
environment/replication error (E:Rep), the main-plot factors against the
pooled main-plot error, and the sub-plot and sub-sub-plot factors
against their respective pooled errors. The returned
anova_table gives the correct F- and p-values for every
stratum, the objects now carry per-stratum coefficients of variation,
and anova_sspd_pooled() now returns factor means for
plotting. Verified against independent aov()
Error()-strata models.perform_posthoc() can now be called directly without
pre-computing the error mean square and error degrees of freedom. When
mse or df_error are not supplied they are
derived from the fitted model. This fixes errors in the Bonferroni
method and in the manual (no agricolae) fallbacks for LSD
and Tukey.multcomp is
installed.verbose = FALSE is now fully respected by
anova_crd(), anova_rbd() and
anova_latin(); these no longer print post-hoc and
assumption-check output when silent operation is requested. Result
objects are unchanged and still contain the full post-hoc and diagnostic
components regardless of verbose.arid_plot() now draws factor or treatment means for
every ANOVA design (factorial, three-way factorial, Latin square, all
split-plot and split-split-plot variants, strip-plot, alpha lattice and
the pooled designs), not only CRD and RBD. Designs with several factors
are shown as a multi-panel bar chart, one panel per factor, with
standard-deviation whiskers where available. Objects that expose no
factor-means table return quietly with an informative message instead of
an error.arid_plot() produces plots using base graphics for
correlation objects (a heatmap of the correlation matrix) and stability
objects (a bar chart of the integrated stability ranking); it previously
returned without plotting.export_results() now supports
format = "csv" in addition to "xlsx" and
raises a clear error for unsupported formats.grDevices, graphics,
stats and utils to Imports.These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.