CRAN resubmission fixes. No computational changes; cards are identical to 0.7.2 output apart from the version stamp.
latent_class_fit() example had an unnecessary
\dontrun{} wrapper; the four \donttest{}
wrappers elsewhere dated from when those code paths were slower. Every
example now completes in under a second.?grass_roadmap (a
stray LaTeX-style thousands separator).The open-calibration release. The calibration’s remaining bounds are compute limits rather than method limits, and the package now includes the machinery for anyone to remove them.
Three new functions:
grass_calibration_manifest() – the 2,166 open
calibration blocks (null tail top-ups, a prevalence-stratified null,
intermediate rater counts), each a seeded bite-sized cell.grass_contribute() – benchmarks the machine, answers
“what would five hours buy?” (dry_run = TRUE), runs
selected blocks from their declared seeds, and writes a submission
bundle with checksums and session information. Runs are bit-reproducible
at a pinned package version. No network access; writes only to the
caller’s directory.grass_verify_contribution() – checks a bundle by
checksum, completeness, and seed replay, for contributors before
submission and maintainers at intake.Submissions land as pull requests on the repository’s
calibration-contrib branch; see CONTRIBUTING.md (new).
Every block’s seed (20300000 + block_id) is disjoint from the shipped
programs’ seeds, so contributed draws can never replay shipped
draws.
The vignette gains a closing section, “Extending the calibration”, that walks the contributor path from the bundled manifest to the pull request.
The card-redesign release. The headline reading changes from a
nearest-cell surface percentile with a four-band adjective to a pooled
percentile plus a consistency band on panel quality, and
delta_hat becomes an implied-quality spread. Supersedes the
0.7.0 tarball.
The reporting-card and methods-companion
vignettes are merged into one: vignette("grassr") carries
the whole story, from why fixed labels mislead through two synthetic
worked panels, the full API, and the calibration machinery behind the
flag.
position_on_surface() now evaluates the observed
coefficient against every calibrated quality level at the matched design
– a sweep – and reports three read-outs of one object:
p(q) = P(coefficient <= obs | quality q, this design)
over the calibrated quality axis: the coefficient’s position within the
design’s achievable agreement range, monotone in the coefficient by
construction. This retires the nearest-q_hat-cell percentile, whose
cohort selection by a statistic derived from the coefficient made it a
non-monotone sawtooth (7-9 full 0-100 cycles across the PABAK range at
k=8-10, N=200; five-agent panel review 2026-07-05).q_hat: the quality levels whose sampling
distributions are consistent with the observed value at this design.
q_hat is promoted to the card via this band (previously
internal scaffolding, never printed).sweep – the full p(q)
profile (the sweep-ridgeline graphic).The stipulated four-band partition (Poor / Moderate / Strong /
Excellent) and the modal-band bootstrap qualifier (decisive / moderate /
weak), with their 0.60 / 0.90 cuts, are retired. The bands
and band_labels arguments are removed from
position_on_surface() and grass_report()
outright, along with the legacy delta_thresholds override
on check_asymmetry() / grass_report() and the
never-wired grass_spec_*() constructor family (and the
internal spec-dispatch and retired classify() machinery
behind it). None of this ever shipped in a CRAN release, so it is gone
without deprecation shims.
grass_report(), so the per-rater confidence intervals on a
card are deterministic: the same rating matrix always prints the same
card. latent_class_fit() restores the caller’s RNG state
after a seeded call.delta_hat becomes the max-min spread of the agreement
family’s implied panel qualities (PABAK, mean AC1, Fleiss
kappa), in quality percentage points: each coefficient inverts to its
own q_hat on the shared (q, pi_+) reference, and their
spread measures cross-coefficient model discordance in interpretable
units (Option B, ratified 2026-07-05). The previous definition – spread
of surface percentiles across four coefficients including Krippendorff
alpha – ran through the retired sawtooth machinery. Krippendorff alpha
left the panel at 0.6.0 and does not re-enter; ICC is never in
delta_hat. The flag convention (percentile on the matched
(k, N, q_hat) null, >= 95th caution, >= 99th divergent) is
unchanged in form.
delta_null_ecdf carries the 385 k >= 3 ridges on a fine
1% + 99.5% probability grid. At k = 2 the two-coefficient family implies
identical quality by construction (the null is a point mass at zero on
all draws), so delta_hat reports
not_applicable there and asymmetry assessment routes to the
pairwise/bounds path. Tie runs (point masses) use the mid-p convention.
Divergent-flag power at the same asymmetry roughly doubles relative to
the retired percentile-spread definition (e.g. TPR 0.82 at mean-norm A =
0.20 pooled over designs, vs 0.38 at the modal design previously);
realized null flag rates are slightly conservative (caution 3.7% vs
nominal 5%, divergent 0.6% vs 1%).delta_null_percentile() now resolves a value at or below
the null’s lowest stored quantile to the TOP of the zero/floor plateau.
At small N the null often has a point mass at delta_hat = 0
reaching well past the 1st percentile; 0.7.0 reported a value at the
plateau’s lowest prob, so identical raters printed “1.0 percentile” on
cells where P(D <= 0) was ~35%.grass_report() lme4 NA-skip. A missing
lme4 (Suggests) or a failed glmer no longer hard-errors
grass_report(): non-finite panel entries (e.g. ICC when
lme4 is unavailable) are dropped before positioning and the coefficient
degrades to “absent from the panel”. 0.7.0’s NEWS claimed this fix, but
the 0.7.0 code landed it in check_asymmetry() only; the
grass_report() positioning loop still errored. It is
genuinely fixed here.check_asymmetry(),
grass_report(), position_on_surface(), and
?grass_roadmap, and the README were still describing the
0.6.x conventions (per-(k, N) size-alpha thresholds
c(9.25, 11.75), the four-band adjective, the
four-coefficient percentile spread). All corrected to the 0.7.1 card
convention. Suggests-dependent examples wrapped in
\donttest{}." 2" file strays from the
source tree.inst/preview/ and dev-scratch example scripts excluded
from the build via .Rbuildignore.data-raw/round_sysdata_for_release.R skips sysdata
objects that are absent (the retired
delta_thresholds_lookup) instead of erroring.The calibration release. Two structural changes, both from the v0.7.0 calibration program (July 2026).
The per-(k, N) threshold table is retired.
check_asymmetry() and grass_report() now
report delta-hat as its percentile on the null distribution of
delta-hat at the matched (k, N, q-hat) cell, with flags as
conventions on that percentile (>= 95th caution, >= 99th
divergent). Motivation: recalibration across panel quality showed the
old single-quality (q = 0.85) thresholds were mis-sized off their
calibration point, and at small N the null’s extreme quantiles are not
stably invertible; the ECDF-position reading is stable, holds its
false-positive rate at every quality by construction, and matches how
every other quantity on the card is read.
delta_null_ecdf: 440 (k, N, q) null
ECDFs generated through the production pipeline (24.85M panels, >=
50k draws per cell), with per-cell instability metadata.delta$delta_percentile,
delta$matched_null; delta$thresholds now
carries the implied pp cuts (95th/99th of the matched null) as
context.delta_thresholds argument deprecated (honored with
legacy semantics plus a warning); delta_thresholds_lookup
removed.check_asymmetry(); non-finite panel entries are dropped
before positioning.empirical_q_hat_surface grows from 10,140 to 44,616
cells: N in {15, 20, 30, 50, 75, 100, 150, 200, 300, 500, 1000} (was
{50, 200, 1000}) and a unified 13-point q-grid at every k. Lookups that
previously clamped (e.g. N = 22 -> 50) now resolve to near cells.
sysdata is 6.91 MB (storage-precision reduction to follow before any
CRAN submission of this line).
CRAN resubmission release. No changes to package functionality.
The 0.6.1 incoming pretest failed on CRAN’s Windows R-devel machine with silent process deaths in the test and vignette-rebuild steps (no diagnostics in either log; the same tarball checks clean on the same R revision – 2026-07-03 r90206 ucrt – on independent Windows infrastructure, and on the Debian pretest). 0.6.2 minimizes what CRAN machines execute, which is recommended practice regardless:
.Rmd.orig sources (kept in the repository, regenerated with
knitr::knit()); CRAN machines render static markdown
only.delta_thresholds_lookup in sysdata is now a plain
data.frame; it previously carried a stray data.table class
from its build script although the package never depended on
data.table.CRAN resubmission release. No functional changes.
CRAN declined to release the archived name ‘GRASS’ (package names are
persistent, case-insensitively). The package is now ‘grassr’. All
function names, arguments, and behavior are unchanged – the API keeps
the grass_* prefix, matching the GRASS framework the
package implements.
The reference surfaces in R/sysdata.rda are now stored
at 5-decimal precision (previously full 64-bit doubles), shrinking the
file from 9.55 MB to 2.83 MB and the tarball to under 5 MB. The
discarded digits are Monte Carlo noise: the surfaces’ simulation error
is on the order of 1e-2, three orders of magnitude above the rounding.
No lookup, threshold, test, or reported number changes at reported
precision. The full-precision surfaces and the rounding script are
archived in data-raw/.
First CRAN release. Two behavioral changes and a legacy-API removal, plus CRAN compliance fixes.
In the binary fully-crossed designs this package targets, Krippendorff’s alpha coincides with Fleiss’ kappa asymptotically (median absolute difference 0.00024 across the 10,140-cell calibration grid; the asymptotic argument is in the accompanying paper’s Appendix A.2). The alpha row added no information to the Report Card and its small-sample deviation from Fleiss’ kappa could tip borderline delta-hat readings across a calibrated threshold on noise alone. As of 0.6.0:
compute_panel() no longer returns
krippendorff_a; the Report Card panel is PABAK / AC1 /
Cohen’s kappa at k = 2 and PABAK / AC1 / Fleiss’ kappa / ICC at k >=
3.delta_hat is the surface-percentile spread over PABAK,
mean AC1, and Fleiss’ kappa. The bundled per-(k, N) thresholds hold for
the 3-coefficient spread (sensitivity check: sub-pp shift, within
MC-SE).obs_krippendorff_alpha() is newly exported for users
who need the value for cross-study comparison, and
position_on_surface(metric = "krippendorff_a") still
positions it on its closed-form reference.The pre-0.2.0 grass_result object and its consumers were
deprecated at 0.2.0 and have been unreachable from the public API since
then (no exported constructor produced a grass_result).
Removed: grass_format_report(),
grass_methods(), grass_report_by(),
print.grass_result(), summary.grass_result(),
tidy.grass_result(),
as.data.frame.grass_result(). The modern equivalents are
print(grass_report(Y)), summary(),
as.data.frame(), and the Methods-paragraph templates in the
reporting-card vignette.
pairwise_agreement; broken Rd cross-links resolved.bootstrap_delta_B argument documented.globalVariables().Bug-fix and sysdata-correction release. The v0.5.0 / v0.5.1 bundled
empirical_q_hat_surface had a build-time mislabeling bug at
k = 2 that paired empirical q-hat distributions with the wrong scenarios
for roughly half of all k = 2 sysdata cells; a corrected k = 2 sub-grid
plus a high-q augmentation are bundled here. Internal logic is
unchanged; the 0 FAIL test posture is preserved and 12 new
regression-anchor tests pin known design points.
Cause. The script that originally built the k =
2 portion of empirical_q_hat_surface
(grass/data-raw/extend_empirical_bands_k2.R,
pre-2026-05-10) concatenated per-rep batches via
per_rep <- c(per_rep, batch) over
list.files(...) (alphabetical filename order), then
assigned names(per_rep) <- s$scenario_id assuming the
resulting list was in the same order as summaries.rds. The
two source machines (laptop / sebastian) wrote scenarios in randomized
scenario-id order within each batch, so the alphabetical concat
misaligned 864 of 1728 k = 2 entries. The empirical q-hat distribution
under scenario_id = X was, in half of all k = 2 cells,
actually the q-hat distribution from a different scenario.
Effect.
position_on_surface(metric, pi_hat, k = 2L, N, ...)
returned percentiles that were correct for ~50% of the (F-key, q_true,
N) cells and silently wrong for the rest. The most visible manifestation
was the published Soares (2021) HEART-score panel: the v0.5.0 surface
placed it at the 96th percentile; the corrected surface places it at the
~9th percentile (a structural inversion, not a small drift).
Fix. The replacement sim
(paper1_2_merged/output/multirater_sim_k2_extension/)
writes one RDS per scenario keyed by scenario_id in the filename, so the
alphabetical-concat bug class is structurally impossible. The new
extend_empirical_bands_k2.R reads per-scenario files
directly. k = 2 q-true grid is densified from the previous 6-point set
{0.60, 0.70, 0.80, 0.85, 0.90, 0.95} to the canonical 11-point set
{0.55, 0.60, 0.65, 0.70, 0.75, 0.80, 0.85, 0.90, 0.95, 0.97, 0.99}.
F-key set densified from 16 to the canonical 52 (matches k >= 3).
Total k = 2 scenario count: 1728 -> 1716 (slightly lower because the
new sim does not include the 5 asymmetric profiles per cell that were
inappropriately mixed into the symmetric-anchor surface in v0.5.0; those
are preserved separately at
paper2/simulation_output/k2_asym_sim/ for non-surface uses
such as the §4.2 op_strong worked example and pairwise-PABAK
validation).
Migration impact. Anyone who computed grass surface percentiles on a k = 2 panel with v0.5.0 or v0.5.1 should re-run under v0.5.2. Aggregate downstream: the merged GRASS paper §5 Soares anchor was written against the buggy v0.5.0 surface and reports 96th pct; corrected reading is ~9th pct, with the Klein 2018 panels stable (50th, 51st pct unchanged) and the Hinde 2025 k = 10 panels unaffected (canonical k >= 3 surface; built correctly in v0.5.0).
Three targeted sub-sims added at v0.5.2 verify the surface lookup behaves as designed at high-quality boundary cells where per-cohort empirical distributions are tightest and grid coverage matters most. These are robustness checks of the framework’s reach into the high-q corners of the design space, not bug fixes.
k = 2 q = 0.97 (multirater_sim_k2_q097_aug/,
156 scenarios). At k = 2 with the canonical 10-point q-grid,
panels with closed-form-inverted q_hat in (0.96, 0.98) snap to
q_true_near = 0.99, where the empirical distribution is centered above
q_hat. Adding q = 0.97 to the grid lets such panels snap to a cohort
whose empirical distribution brackets q_hat, returning a centered
percentile.
k = 25 q in {0.92, 0.97}
(multirater_sim_k25_q092_097_aug/, 312 scenarios).
At k = 25 with N = 1000, per-cohort q-hat sd is ~0.003 (panels are
tightly informative), so grid spacing of 0.05 leaves cells in the gap
between adjacent cohorts. Adding q = 0.92 and q = 0.97 closes the
0.90–0.95 and 0.95–0.99 gaps.
k = 2 + k = 25 q = 0.94
(multirater_sim_q094_aug/, 312 scenarios). A
residual 0.92–0.95 midpoint gap surfaced when
tab:card_summary row 6 (k = 25, PABAK = 0.78, q_hat =
0.9416) still snapped to q = 0.95 after the q = {0.92, 0.97}
augmentation. Adding q = 0.94 to k = 2 and k = 25 lets such panels snap
to q = 0.94 cohort and return a centered percentile.
Net q-grids after all v0.5.2 augmentations: - k = 2: 12 points {0.55, 0.60, 0.65, 0.70, 0.75, 0.80, 0.85, 0.90, 0.94, 0.95, 0.97, 0.99} — canonical 10-point grid plus 0.94 and 0.97. - k = 25: 13 points {0.55, 0.60, 0.65, 0.70, 0.75, 0.80, 0.85, 0.90, 0.92, 0.94, 0.95, 0.97, 0.99} — canonical 10-point grid plus 0.92, 0.94, and 0.97. - k in {3, 5, 8, 15}: 10 points (canonical) — unchanged.
The augmentation sims use a per-scenario rds layout (kill-safe,
resume-safe) and skip glmer (the bundled surface uses only
logit_mixed_icc_oracle, not the glmer-fitted ICC; glmer was
the slow path that initially stalled the k = 25 run before being
disabled).
Why three sub-sims rather than one denser grid up
front? Each boundary gap surfaced through diagnostic work on a
specific paper anchor (post-hoc figure A at k = 2; tab:card_summary row
6 at k = 25). We added grid points where the diagnostics surfaced gaps,
keeping the augmentation tight to the actual coverage need rather than
running an order-of-magnitude denser global grid. The structural fix —
bilinear interpolation across two adjacent q_true cohorts in
lookup_empirical_q_hat() — is designed in
grass/design/v0.5.3_lookup_interpolation.md and queued for
the next minor release; it would resolve the boundary-snap pathology
without requiring ever-denser grids, but the augmentations
bring the v0.5.2 surface to a defensible coverage level for the paper’s
specific anchor cells.
extend_empirical_bands_k2.R and the new
augment_empirical_bands_k2_q097.R both assert
setequal(names(per_rep), as.character(s$scenario_id)) and
!any(duplicated(names(per_rep))) after labeling. These
would have caught the original mislabeling at write time.build_empirical_bands.R (canonical k >=
3 builder) — currently safe because
multirater_sim_v3_combined_full.rds saves per_rep named by
scenario_id, but the silent positional-fallback at L171-173 could mask a
future regression.tests/testthat/test-sysdata-regression-anchors.R
(12 tests, all PASS): pins surface-percentile lookups for the merged
GRASS paper’s §4 / §5 anchors. Soares now bracketed below 20 pct (was
inflated to 96 in v0.5.0), Klein AE/PR ~50 pct, Hinde DSM-5-TR ~10 pct,
Hinde ICD-11 PTSD ~95 pct, §4.1 PABAK 40-55, §4.2 PABAK 30-50 + AC1
50-65 (the divergent split), §4.3 unclamped 30-80 (the q = 0.97
augmentation guard). Plus three structural invariants on the k = 2
index. Regenerating sysdata in the future without producing these values
will fail-fast.empirical_q_hat_surface: 9,360 -> 10,140 scenarios
after the fix and the three v0.5.2 augmentations (k = 2 went 1728 ->
1872; k = 25 went 1560 -> 2028; k in {3, 5, 8, 15} unchanged at 1560
each).R/format.R)Two render-layer changes surfaced by the 2026-05-11 paper-vs-code
audit. Neither changes computation; both affect what
print(grass_report(Y)) shows on screen.
Aligned and caution flags now render all panel
coefficients, not just the primary. Previously, under the
aligned/caution branch, format.grass_card() emitted only
the primary coefficient line; the other agreement-family coefficients
(and ICC) were computed and stored in card$panel but
suppressed in the print output. The new render lists every coefficient
with its observed value and surface percentile; the primary carries the
qualifier (decisive / moderate /
weak) inline and a <- primary marker. This
matches the §3.2 dictionary table in the paper (coefficient
field “lists every coefficient with its own percentile”) and the §3.1
Quick Start example output.
[distribution-sensitive] marker now rendered
by format.grass_card() on the ICC line. Previously
the marker was emitted only inside
print.grass_asymmetry_panel, so the Report Card a user saw
via print(grass_report(Y)) carried no marker on ICC. The
marker now renders in both the aligned/caution branch and the divergent
branch, alongside any [oracle-fallback] /
[oracle-icc] reference-source markers.
tau2_hat removed from the inline sample
header. The sample line now reads
sample = k raters, N = ..., pi_hat = ... only; the
per-panel τ̂² lives in card$sample$tau2_hat and prints in
the Notes section when a fitted-ICC F_key is picked via glmer.
fitted_icc_reference_curves) is
unchanged.delta_thresholds_lookup) is
unchanged.reference_binary lookup is unchanged.Cosmetic and documentation release. No internal-logic, sysdata, or
test changes; the 0 FAIL across 194 test files posture from
v0.5.0 is unchanged.
Print marker rename: [F-shape sensitive] →
[distribution-sensitive]. The earlier label
collided with the F-statistic / ANOVA reading. The marker references the
full subject-prevalence distribution F, not an F-statistic; the rename
matches the merged GRASS paper’s manuscript wording. Affects the
print method on grass_card and
grass_asymmetry_panel objects only. ICC panel rows now
print as no [distribution-sensitive] in the
in_delta_hat column. Downstream code that parses print
output (rare) needs an update; return values, sysdata, and signatures
are unchanged.
Print format simplified: separate band = ...
line dropped. The percentile and qualifier now appear inline as
Nth pct (decisive) per the manifesto-locked Report Card
format. The internal card$coefficient$band field is still
computed and remains in the object slot for callers that need it; only
the printed rendering changed. Divergent panels print
panel-agg. = suppressed (divergent) instead of
band = suppressed.
methods-companion.Rmd expanded by ~120
lines absorbing Tier-1-cut content from the merged GRASS paper:
ref = "v0.5.1" install pin.man/*.Rd regenerated from roxygen blocks to reflect the
marker text change throughout function-level documentation.Three substantive landings drive this release. (1)
Cross-coefficient divergence delta_hat is now
computed over the agreement family only (PABAK, mean AC1,
Fleiss kappa, Krippendorff alpha). Each has a closed-form reference
depending on (q, pi_+) only, so the cross-family spread is
DGP-robust at the panel level. ICC remains on the Report Card panel rows
but does NOT enter delta_hat: ICC’s reference surface
depends on the full F-shape variance structure rather than
(q, pi_+), and a panel whose true F does not match the
bundled logit-normal reference can drift by ~20 pp at small designs. An
earlier delta_hat scope including ICC produced ~80% FPR at the diagonal
null under matched DGPs and was abandoned in favor of the
agreement-family-only construction adopted here (see § “Behavioral
change” below; paper §3 ICC scope and Appendix E for the full
quantitative case). (2) The bundled
fitted_icc_reference_curves sysdata object is rebuilt from
a unified Julia MixedModels.jl simulation extending
coverage to
k in {3, 5, 8, 15, 25} x N in {30, 50, 75, 100, 200, 300, 500, 1000}
on a 14-point q-grid spanning [0.35, 0.99]. Across 1,000
random common-applied-design panels the ICC clamp rate is 7.7% (residual
clamping concentrated at small N: 14.3% at N=30; or small k: 16.3% at
k=3). (3) The delta_thresholds_lookup table is freshly
derived under the agreement-family delta_hat definition
(4-coefficient max-min) for size-alpha calibration.
delta_hat over the agreement family
only. The panel-level card$panel data frame now
carries an in_delta_hat logical column (TRUE for PABAK,
AC1, Fleiss kappa, Krippendorff alpha; FALSE for ICC). The print method
shows the column inline so users can see which coefficients enter the
cross-family spread. The notes vector for any divergent /
caution panel records the v0.5 scope decision: ICC’s surface depends on
the full F-shape and is reported separately on the Report Card, but does
not contribute to the asymmetry signal.
ICC marked [F-shape sensitive]. The
print method labels ICC’s panel row with the
[F-shape sensitive] marker, signaling to the reader that
ICC’s percentile reading carries a misspecification cost the agreement
family does not. The cost is quantified in Appendix E of the merged
GRASS paper.
Per-(k, N) threshold lookup –
grass_report() and check_asymmetry() now
default delta_thresholds = NULL, which triggers a lookup
against the delta_thresholds_lookup table
(k in {2, 3, 5, 6, 8, 10}, N in {15, 20, 30, 50, 75, 100, 200, 500}).
When the exact (k, N) has both thresholds calibrated, those
are used directly. Otherwise the lookup searches all fully-calibrated
cells and returns the nearest one in (k, log10(N)) space
(each axis range-normalized). Falling back to the modal default
c(9.25, 11.75) is reserved for the
impossible-with-bundled-sysdata case of an empty calibration table; in
normal operation users always receive thresholds calibrated
somewhere on the grid.
The card field card$delta$thresholds_source records one
of "calibrated_at_k_N",
"snapped_to_nearest_calibrated",
"default_fallback", or
"user_supplied".
Print-method visibility – the Report Card now
shows a thresholds = (caution, divergent) [source] line
directly under the delta = ... pp (flag) line, so the user
sees which pair was applied and why.
ICC reference-path transparency –
position_on_surface() now records which path produced each
coefficient’s reference surface in a structured
reference_used field (one of "closed-form",
"fitted-icc", "oracle-icc-fallback",
"oracle-icc-explicit", "user-supplied"),
surfaced in card$panel$reference_used. When the fitted-ICC
reference is unavailable at the user’s (k, N) and the
function falls back to the older oracle reference, the print output now
marks the affected coefficient with [oracle-fallback] in
addition to the existing notes-vector entry. Closes a quiet fallback
that previously only showed up in the bottom-of-card notes
block.
fitted_icc_reference_curves rebuilt for the
v0.5 grid. The bundled GLMM-gap-corrected ICC reference now
covers
k in {3, 5, 8, 15, 25} x N in {30, 50, 75, 100, 200, 300, 500, 1000}
on a 14-point q-grid spanning [0.35, 0.99] – 2,080 (F_key,
k, N) lookups across 52 F_keys (logit-normal grid + 4 discrete-mixture
presets). Built from a unified Julia + MixedModels.jl
simulation averaging 500-1000 fitted-ICC reps per cell. Per-cell
mean_icc values are monotone-enforced along q (cummax) and
linearly interpolated onto the package’s 501-point internal q-grid.
Builder source: data-raw/build_fitted_icc_reference_v0.4.R.
Sysdata size ~8.9 MB (xz-compressed).
Calibrated delta_thresholds_lookup for
delta_hat_4. The per-(k, N) threshold table is
built against the agreement-family delta_hat definition
over a 1,440-cell sim grid
(k in {2, 3, 5, 6, 8, 10} x N in {15, ..., 500} x A in {0, ..., 0.30} x mu in {0.05, 0.20, 0.50, 0.80, 0.95},
1,000 reps per cell). Cells where no threshold satisfies the size-alpha
constraint at t in [0, 50] pp return NA and
the Report Card defaults to caution-by-default per-rater routing per the
paper’s Appendix D specification.
§4.1 worked example clean under v0.5 sysdata.
The §4.1 design point (k=5, N=1000, mu=-1.386, tau2=1.0)
resolves via the fitted-ICC path with no [oracle-fallback]
marker; the previously load-bearing ICC clamp at this case is
closed.
Round 5 — spec-dispatch architecture + reviewer 5/5 items.
grass_report() now
takes spec = grass_spec_binary() as its primary argument.
Metric families (binary today; ordinal, multirater, continuous planned)
are selected by the spec constructor rather than by family-specific
function names. One package, one entry point, extensible to future
families without API churn. See ?grass_roadmap.grass_spec_ordinal(), grass_spec_multirater(),
grass_spec_continuous() return valid placeholder specs so
users can write release-ready code; passing one to
grass_report() errors with a pointer to
?grass_roadmap.$spec slot
holding the spec used for the call. All downstream verbs
(print, plot, as.data.frame,
tidy, grass_methods,
grass_format_report) dispatch on
result$spec$family.reference_level argument on
grass_spec_binary() accepts
0.70 / 0.80 / 0.85 / 0.90. Each band is the analytical
Youden-J-optimal expected metric value at Se = Sp = reference_level, in
closed form under conditional independence of the two raters given the
true class. Previously only "high" (= 0.85) and
"medium" (= 0.70) were available.grass_methods(result) —
GRRAS-compliant manuscript methods paragraph pre-filled with study
numbers. Supports format = c("markdown", "latex", "plain").
Templated so that future metric families slot in without touching the
dispatcher..parallel = TRUE on
grass_report_by() — backed by
future.apply::future_lapply() with a
progressr::progressor() handler. Respects the user’s active
future::plan(). Optional dependencies; clean
install-command error if absent.?grass_roadmap help page — framework
taxonomy, ecosystem architecture, what is implemented today, what is
planned.reference_level = 0.85 vs pre-0.1.2
reference = "high" for most prevalences. Full Monte-Carlo
regeneration with empirical confidence bands is deferred to a future
release.reference = "high" / "medium" / "none"
argument on grass_report() is deprecated (soft —
emits a one-time message). "high" maps to
reference_level = 0.85, "medium" to
0.70, "none" to NULL.grass_reference(quality = ...) is
deprecated; use
grass_reference(reference_level = ...).thresholds sysdata renamed to
reference_binary (long-form: prevalence × reference_level ×
metric). grass_reference_table() now returns the long form
by default and accepts an optional reference_level filter.
Package-internal only; user impact limited to anyone previously calling
grass:::thresholds.Reviewer-driven polish (round 4).
response = argument — stats-modelling alias for
rater_cols = (wide) and rating = (long).
Conflicting canonical + alias errors with a “disagree” message.grass_format_report(ci_width = TRUE) — appends
"; kappa CI width = 0.26, wide" with half-width cutpoints
calibrated for kappa: tight < 0.10,
moderate < 0.20, wide >= 0.20. Default
FALSE (opt-in). Kappa Wilson-logit CIs run 2-2.5x wider
than component Se/Sp CIs at the same N, so these cutpoints are higher
than the Se/Sp conventions from diagnostic accuracy reporting.broom::tidy.grass_result() long-form — 9 rows (3
metrics × 3 quantities: estimate, reference,
distance). Columns: metric,
quantity, value, conf.low,
conf.high, n, prevalence.
conf.low/conf.high populated only on kappa
estimate. value (not estimate) is the generic
column so reference/distance rows do not read as point estimates without
CIs. Plots via
ggplot(aes(metric, value, colour = quantity)) without a
reshape.grass_report_by(data, group, ...) — splits
data by group (bare symbol or string), runs
grass_report() per subset, returns a tidy data.frame with
.cohort column carrying the group value. Uses
as.data.frame(compact = TRUE) internally.as.data.frame(r, compact = TRUE) argument (already in
earlier 0.1.1 draft; surface again here).id_col = hint when
exactly one column is non-binary: “Column ‘xxx’ looks like an
identifier; you could try id_col = 'xxx'.” No hint
when ambiguous (all columns binary-looking).reset_grass_warnings() — clears the once-per-session
message cache so loops over many studies with consistently named columns
re-emit the fallthrough warning.?grass_report now has a “Sample size caveats” section
documenting the two N thresholds (N < 10 warning,
N < 30 print note).format is now "wide" (was
"matrix") across grass_report(),
grass_compute(), grass_prevalence(). Users
passing a data.frame no longer need to name the format.grass_format_report() default is now
ascii = TRUE (was FALSE). Safer for Slack,
Markdown, and non-UTF-8 locales. Pass ascii = FALSE for a
Unicode kappa in an RStudio console.validate_prevalence() now errors on exactly
0 or 1 (degenerate cases with no reference
defined). Values in (0, 0.01) and (0.99, 1)
still warn and clamp.id_col = NULL argument on format = "wide"
— drop a subject-identifier column before the two-rater detection.
Example: grass_report(df, id_col = "subject_id").as.data.frame.grass_result() now returns 19 columns
including kappa_ref, kappa_distance,
PABAK_ref, PABAK_distance,
AC1_ref, AC1_distance,
reference_quality, and regime_note. Pass
compact = TRUE to drop regime_note when
binding many rows.print.grass_result() prints a “sensitive to sampling
noise” caveat in the reference-comparison section when
N < 30. (This is distinct from the
N < 10 warning on grass_compute(), which
flags the metrics themselves as unreliable at very small N.)pick_positive() now
escalates from a message() to a one-time
warning() with explicit override guidance. This prevents
silent prevalence inversion when rater levels are clinical terms (e.g.,
"abnormal", "normal") that fall outside the
yes / 1 / true /
positive keyword list. Flagged by Dr. M. Chen.rater_cols = c(...) and id_col = "...") and
lists the actual column names present, without guessing which are
raters. Flagged by J. Okafor.grass_compute(), grass_report(),
grass_reference(), grass_reference_table(),
grass_prevalence(), grass_format_report(),
grass_plot().
Initial local draft.
grass_compute() — raw metric panel from 2x2 or rater
datagrass_report() — contextual profile: metrics + PI + BI
+ regime + referencegrass_reference() — look up reference curves at a given
prevalencegrass_reference_table() — full internal reference-curve
table (23 prevalence points, High and Medium calibration levels)grass_prevalence() — estimate prevalence from rater
marginalsgrass_format_report() — one-line paper-ready summary of
a resultgrass_plot() — plot a grass objectgrass_report() returns a contextual profile (metrics +
PI + BI + regime + signed distance from the reference curve). Regime is
one of balanced, prevalence-dominated,
bias-dominated, mixed; each carries a short
structural-implication note describing what the algebra of that regime
forces on the metrics.plot.grass_result() landing plot and regime
scatter, plot.grass_reference() curves,
theme_grass(). Inline or legend curve labels via
labels = c("auto", "inline", "legend").grass-intro,
skewed-examples.reference throughout its public API to signal that the
values serve as comparison points reported alongside PI and BI, rather
than as cutoffs for a binary verdict.