ofemeantest 1.0.0
ofemeantest 0.0.900
Breaking changes
ofemt() no longer accepts
nmin_cell or alpha_bonferroni. Both
were kept as deprecated aliases; they are now removed. Use
min_per_cell instead of nmin_cell, and
p_adjust_method = "bonferroni" instead of
alpha_bonferroni = TRUE. Since the package has never been
on CRAN, the disruption should be limited to a rename in existing
scripts. Note that dropping the two arguments also shifts the
positional order of the remaining ones, so calls that relied on
argument position (rather than name) need to be revisited.p_adj is now the median of the per-run adjusted
p-values. Previously the median p-value was computed first and
adjusted afterwards. Now stats::p.adjust() is applied
within each sampling run, across that run’s pairwise comparisons, and
the reported p_adj is the median of the resulting
distribution. This keeps p_value and p_adj on
the same footing — both medians over the n_s runs — and
makes the median line in plot_pvalue_hist() agree with the
table. Numeric results change when
p_adjust_method != "none".keep_components = "light" now stores the complete
ofe_grid object (full grid, selection, per-cell stats and
parameters) rather than only the selected cells, so the result can be
plotted directly.
Bug fixes
- Treatment labels are no longer rewritten internally. Spaces used to
be replaced by dots (
"Bortrac + Zintrac" became
"Bortrac.+.Zintrac"), which leaked into
Means comparison, Cells per treatment and the
Comparison column, and could produce NA
letters when a label collided with the separator used by
multcompView::multcompLetters(). Labels are now mapped to
internal placeholders for the whole computation and restored on output,
so any label — spaces, +, -, parentheses,
accents — is reported verbatim. The same rewriting is gone from
select_grid(), where it could collapse two genuinely
different treatments into one and make a mixed cell look
single-treatment.
- The compact letter display now follows the ordering of the means:
treatments are sorted by decreasing median response before the letters
are assigned, so
"a" always marks the highest-yielding
group.
- The upper bound passed to
spdep::dnearneigh() is
exclusive, so the one cell whose nearest-neighbour distance
defined dmax was being dropped from its own
neighbour graph. The bound is now nudged to include it. This silently
degraded Rho, Moran’s I and the ESS on every analysis; on
the bundled ofe_f2 example the corrected values are ESS 97
/ Rho 0.652 / Moran’s I 0.548 (previously 99 / 0.646 / 0.529).
ofemt() no longer flips spdep’s global
ZeroPolicyOption as a side effect when an empty neighbour
set is encountered; the policy is passed explicitly to the calls that
need it.- Response and treatment column names are quoted before being used in
a formula, so columns whose names contain spaces or other special
characters (
"Rinde kg/ha (seco)") no longer fail. Point
coordinates are stored under dot-prefixed names, so user columns
literally named X or Y are no longer
shadowed.
- Sampling a treatment that contributes a single cell no longer falls
into
sample()’s length-one trap (sample(5, 1)
sampling from 1:5).
Reporting and plotting
spdep’s “neighbour object has N sub-graphs”
warnings are muffled. They are expected for OFE trial shapes and carry
no consequence for the diagnostics. What is now reported instead is the
condition that actually matters: an error when no cell has any neighbour
(the distance threshold is too small for the selection), and a warning
naming how many cells were left isolated.plot_grid_selection() accepts an
ofemt_result directly, and plot() methods are
provided for both ofe_grid and ofemt_result.
On a result produced with keep_components = "full" a bare
plot(res) draws the full grid, the selected cells and the
observations, with no further arguments — the view needed to judge the
effect of cellsize, shift,
angle_deg and buffer. Selected cells are
shaded translucently so the points underneath stay visible, and the plot
title repeats the grid parameters so successive calls can be
compared.- Both plotting functions gained an
engine argument,
"ggplot2" (default) or "base". The ggplot2
engine places the legend outside the plotting panel, so it can
never sit on top of the data and the result no longer depends on the
size of the graphics device — the base engine has to fit the legend
inside the panel, which on a dense grid or a small window left it
unreadable. ggplot2 stays in Suggests: when it
is not installed both functions fall back to "base" with a
message.
plot_grid_selection() gained point_size
(and legend_pos, which accepts base-style corner keywords
under either engine). Yield-monitor data runs to tens of thousands of
observations, where the default dot size still reads as a solid mass;
lowering it brings the cell boundaries back.- Unselected grid cells are now filled a very light grey instead of
left transparent, so they read as cells rather than as page background
and their legend key is visible.
plot_pvalue_hist() now draws a solid line at the median
of the distribution in addition to the dashed line at
alpha, and defaults to the adjusted p-values whenever the
analysis used a p_adjust_method (override with
which = "raw" or which = "adjusted").print() reports the total number of grid cells
alongside the number selected, states which adjustment produced
p_adj, and notes that the means table is sorted by
decreasing mean.?ofemt now documents every component of the returned
object — including perm_runs, the per-run empirical p-value
distribution the method is built on — and spells out what each
keep_components level stores and costs.
Other changes
ofemt() exposes a seed argument that
controls reproducibility of the permutation sampling. Default is
seed = 7L; pass NULL to let results vary
across runs.ofemt() accepts a pre-built grid via the
grid argument. When grid = NULL the function
builds one internally with make_ofe_grid(); the two paths
are interchangeable when called with matching arguments.make_ofe_grid() exported as the canonical way to
construct and inspect the analysis grid before running the test.plot_grid_selection() and
plot_pvalue_hist() added for visual checks of the grid
selection and the permutation p-value distribution.
plot_pvalue_hist() has a base R fallback when
ggplot2 is not installed.print() method for ofemt_result objects
provides a concise console summary.- Two new vignettes:
vignette("getting-started") (user
manual) and vignette("methodology") (technical description
of the protocol).
pkgdown website at https://ppaccioretti.github.io/ofemeantest/.- Dependencies reduced: dropped
dplyr,
magrittr and tidyr from Imports.
ggplot2 moved to Suggests.
ofemt() rewritten on top of the new grid pipeline;
cells are filtered once in select_grid(), not twice.- Moran’s I is now extracted by name
(
$estimate["Moran I statistic"]) instead of by position,
with a dependency-contract test guarding against future renames in
spdep.
- Test suite added (
testthat 3rd edition) covering grid
construction, end-to-end ofemt() on ofe_f2,
reproducibility from seed, error paths, and contracts with
upstream dependencies.
- Continuous integration on GitHub Actions:
R CMD check
on Ubuntu/macOS/Windows times R release+devel+oldrel; pkgdown site
deployed on push to main.