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plot_rri_properties() no longer places the composite
RRI on a fifth spoke. RRI is built from the plant, soil and microbial
domains; Capacity, Connectivity, Kinetics and Memory are property
descriptors built from different inputs. Drawing them on one radar
invited the polygon to be read as averaging across incommensurable
quantities.
The chart now has four axes. The centre shows the mean of the resolved property axes, with the count of resolved axes beneath it, so a mean resting on two axes is not mistaken for one resting on four. An axis whose supporting measurement was absent is excluded from the mean rather than counted as zero. The composite is reported in the subtitle for reference.
simulate_redox_holobiont() now defaults to
seed = NULL rather than seed = 123, so no
function in the package touches the random stream unless a seed is
requested. This is what the CRAN Cookbook recommends, and the earlier
justification for keeping a fixed default did not survive checking:
every call in the package’s own examples, tests and vignettes passes a
seed explicitly, so nothing depended on it. Users who called the
simulator with no arguments and relied on reproducible output should now
pass seed themselves.benchmark_hrri() now restores the RNG kind as well
as .Random.seed, so all three functions that seed behave
identically. It could not previously change the kind, so no behaviour
depended on this, but the uniformity makes the guarantee checkable at a
glance rather than function by function.
tests/testthat/test-pipeline-partial.R collected
warnings by superassignment. It now accumulates them in an environment,
so a search for <<- across the package sources and
tests returns nothing at all.
inst/scripts/check_model_accuracy.R wrote its
figures to a directory created under the working directory. It now
writes to tempdir() unless the HRRI_OUT
environment variable names somewhere else, and prints the destination.
Nothing shipped with the package writes outside the temporary directory
unless asked to.
benchmark_hrri() no longer uses
<<-. The assignment resolved to the function’s own
frame rather than to .GlobalEnv, so it was not a policy
violation, but confirming that required reading the surrounding code.
The tryCatch() handler now returns the failure as a classed
value and the caller records it. Behaviour is unchanged; the package now
contains no <<-.
The only remaining references to .GlobalEnv are the
blocks that save and restore .Random.seed.
.Random.seed lives in .GlobalEnv, so any
function that seeds necessarily writes there; these blocks put it back
exactly as found, including on an error exit.
tests/testthat/test-api-surface.R required a
\value section on every Rd topic. That is wrong for a
narrative page: HRRI_workflow_example has no
\usage and returns nothing, so the test failed on a
correctly written topic. \value is now required only of
function topics, which is the rule R CMD check itself
applies.unzip -o overwrites files but never deletes them.
Release 1.0.0 renamed R/data-redoxrri_example.R to
R/HRRI_workflow_example.R, so a tree updated by extracting
over the old one keeps both, and both .Rd files claim
\alias{redoxrri_example}. Duplicate aliases make
R CMD INSTALL fail, and pkgdown::build_site()
then renders vignettes against whatever older copy of the package is
already installed, producing a confusing “could not find function” for a
function that is plainly present in the sources.
sync_package.sh, distributed alongside the release,
compares a tree against package_manifest.txt and reports or
removes the leftovers.
rri_o2_demand() no longer fails obscurely when every
reduced-species column the caller names is absent from
soil_df. The numeric coercion ran before the validity
check, and with no matching columns it attempted a zero-column
replacement, so [<-.data.frame raised a cryptic error
instead of the informative “none of the specified reduced-species
columns were found” message a few lines below. The coercion is now
guarded.rri_o2_demand() cited “Ghotbi et al. (2026)” in its
details and example while the reference entry carries no year, the
mechanistic review being unpublished. The in-text citations now read
“submitted”, matching the reference.First release candidate. No change to any calculation; this release completes the packaging, documentation and infrastructure.
_pkgdown.yml rebuilt from the actual Rd topics and
grouped by task rather than alphabetically: scoring pipelines, the four
hidden states, recovery signatures, model checking, figures, simulation.
All 36 topics are listed exactly once, which is what the previous index
failed at when rri_accuracy(),
plot_rri_accuracy() and rri_domain_influence()
were added without entries and the site build stopped.
GitHub Actions workflows for R CMD check (five
platform and version combinations, run with
--as-cran --run-donttest) and for the pkgdown site.
Vignettes are built in CI, so a repeat of the ggtern incompatibility
that once broke vignette building would surface before release.
cran-comments.md, .gitignore, and a
.Rbuildignore that keeps all of the above out of the source
tarball.
tests/testthat/test-api-surface.R checks the public
interface itself: every export resolves, S3 methods are registered
rather than merely defined, argument names of the entry points are
pinned, every topic has a value and a runnable example, no example is
hidden behind \dontrun, and seeding leaves the caller’s
.Random.seed exactly as found. These guard the failure
modes that R CMD check cannot see.
simulate_redox_holobiont() keeps
seed = 123 rather than NULL, so that an
unseeded call to an illustrative generator is reproducible. The
@param entry now says so, and explains why it is safe: the
RNG kind and .Random.seed are saved on entry and restored
on exit, so the caller’s stream is untouched. The diagnostic functions
default to seed = NULL.
The topic redoxrri_example is renamed
HRRI_workflow_example. Its former name implied a dataset,
but the package ships no data/ directory and
data(redoxrri_example) would have failed; the page now
states plainly that it is a worked example rather than an object. The
old name is kept as an alias, so existing links still resolve.
Remaining references to the package’s former name, “RedoxRRI”, replaced with “HRRI” throughout the help pages.
inst/CITATION now matches the current software
manuscript: four authors and the title “HRRI: direction-aware
diagnostics for soil-plant-microbiome redox recovery across
hydroclimatic disturbances”, consistent with README and the
vignettes.
Manuscript statuses corrected throughout. The mechanistic review
is submitted to Soil Biology & Biochemistry, and the theory paper to
Communications Earth & Environment; the software paper remains in
preparation. Applied in README, the workflow vignette,
inst/CITATION and the rri_o2_demand() help
page, which cites the review for its stoichiometric table.
inst/CITATION had the software paper as “Manuscript
submitted” while README and the vignette said “in preparation”. Aligned
to in preparation, matching the wording confirmed for README. A single
line in inst/CITATION reverses this if the paper has in
fact been submitted.
Added .Rbuildignore, clearing both remaining
R CMD check NOTEs: .github under “checking for
hidden files and directories”, and LICENSE.md and
_pkgdown.yml under “checking top-level files”. These are
development and website files that belong in the repository but not in a
source tarball.
Each directory is listed in two forms, ^docs$ and
^docs/. A pattern anchored with a trailing $
matches the directory entry but not the files inside it, which is why an
earlier ^\.github$ left the hidden-files NOTE in place. The
patterns were checked against a list of representative paths before
release: every development file is excluded and all fourteen sampled
package files survive.
inst/CITATION, README and the
workflow vignette.inst/CITATION still lists the package manuscript under
its earlier title with five authors including Marco Guerreiro, while
README and the workflow vignette follow the current draft: four authors,
and the title “HRRI: direction-aware diagnostics for
soil-plant-microbiome redox recovery across hydroclimatic disturbances”.
The author list is not something to change by inference, so both forms
are left in place until confirmed. The review manuscript’s status is
likewise recorded as in preparation because it has not been
confirmed.rri_o2_demand()The interpretation section was headed “the 25-fold contrast” while its own text, and the example, said 26. The worked example is 33.75 mmol O2 per kg against a 1.3 mmol per kg stock, a ratio of 25.96, so 26 is right and the heading was wrong.
@return did not describe what the function returns.
Five elements were undocumented (n_species_observed,
species_coverage, interpretation,
ch4_unit_used, acetate_basis_used), and three
columns of components were listed under names the code does
not use: mean_inventory is really
mean_inventory_mmol, fraction_of_total_demand
is really fraction_total_demand, and
n_observed was missing. stoich_table was
described as “the full stoichiometric table” when it holds only the
species actually found. All eleven returned elements are now documented
under their real names. R CMD check cannot detect this
class of error.
The reference to the mechanistic review was updated to the current draft: four authors, and “disturbances” rather than “disturbance”.
Verified DOIs added to the two rate-law references, Stumm and Lee (1961) doi:10.1021/ie50614a030 and Millero, Sotolongo and Izaguirre (1987) doi:10.1016/0016-7037(87)90093-7.
The stoichiometry was checked against the electron balance rather than taken on trust. All eight coefficients are correct at 4 electrons per O2: Fe(II) 1 e- (0.25), Mn(II) 2 e- (0.50), HS- 8 e- (2.00), FeS 9 e- (2.25), FeS2 15 e- (3.75), NH4+ 8 e- (2.00), CH4 8 e- (2.00), acetate 8 e- (2.00) and 1.00 on a carbon basis. The pyrite equation balances on Fe, S, O and H, and releases the 4 mol H+ per mol FeS2 the text claims.
Every documented function now carries an explicit
@title. Twenty-nine roxygen blocks had been relying on the
implicit first-line title; six S3 methods documented with
@rdname or @describeIn correctly do not have
one, since they inherit the parent topic’s title and a second
@title would conflict.
DESCRIPTION cites six published methods references
in the form CRAN asks for, authors (year) <doi:...>
with no space after doi:. Every DOI was resolved against
Crossref before being added; none is a placeholder.
The three companion manuscripts are described in README, the
workflow vignette and inst/CITATION, each marked in
preparation, with a note that entries are provisional until publication.
They are deliberately absent from DESCRIPTION: CRAN asks
that field to carry only references a reader can retrieve, so
unpublished work belongs in these files instead.
README gained a table mapping each published reference to the specific part of HRRI that rests on it, so a reader can see why each is cited rather than taking the list on trust.
rri_accuracy() no longer modifies the user’s global
environment. set.seed() writes .Random.seed
into .GlobalEnv, so calling it without restoring the
previous state silently resets a random stream the caller may have been
relying on. The RNG kind and seed are now saved on entry and put back
with on.exit(), matching the pattern
simulate_redox_holobiont() and
benchmark_hrri() have always used. This was the only place
in the package that seeded without restoring.Audited against the CRAN Cookbook “Code Issues” chapter. Clean on
every recipe: no T/F for
TRUE/FALSE; every set.seed() is
behind a user-supplied argument defaulting to NULL; all
cat()/print() calls sit inside
print/summary methods or behind a
verbose/print argument; par() is
saved with no.readonly = TRUE and restored via
on.exit(); nothing writes to the home filespace or the
working directory; no tempfile() detritus, no
installed.packages(), no options(warn = -1),
no parallelism, no software installation from package code.
Both vignettes now restore the ggplot2 theme they set.
theme_set() changes state that persists for the rest of the
session; vignettes build in their own process so nothing outside was
affected, but it is the same courtesy CRAN asks for with
par() and options().
All \dontrun{} example wrappers replaced with
\donttest{}. \dontrun is for code that
cannot run – code needing credentials, external software or
hardware. None of these examples was in that category, and the wrapper
meant R CMD check never executed them, so they could drift
out of step with the code without anyone noticing. They are now run
under R CMD check --run-donttest and by CRAN.
The plot_RRI_ternary() example is additionally
guarded on the ggplot2 version. Unguarded it would error under ggplot2
>= 4.0.0, where ggtern cannot be used; it now skips instead.
DESCRIPTION cites the methodological reference and
the two sources for the agreement statistics, as CRAN policy asks. The
framework citation is a repository URL until the manuscript has a DOI,
at which point it should be replaced with
<doi:...>.
Vignette building failed with
Error in `plot_theme()`:
! The `tern.axis.ticks.length.major` theme element must be a <rel> object.The cause is ggtern, not the figure that happened to
trigger it. ggtern patches ggplot2’s internal element tree when its
namespace is loaded, not when a ternary plot is drawn. Under
ggplot2 >= 4.0.0, which rewrote the plot object on S7, that patch
leaves elements in a form ggplot2 rejects, and every subsequent
ggplot in the session fails in
plot_theme().
The previous guard called requireNamespace("ggtern") and
wrapped the plot in try(). That is too late:
requireNamespace() loads the namespace, which is the
damage, and try() only catches the ternary plot’s own
failure. Since R CMD build builds vignettes in one R
session, the gallery vignette’s probe brought down the workflow vignette
that followed it.
The ggplot2 version is now checked before ggtern is touched,
in a new internal helper hrri_ggtern_ok(), which never
calls requireNamespace("ggtern") on an incompatible
ggplot2. Applied in plot_RRI_ternary(), the gallery
vignette, the redoxrri_example example and
tests/testthat/test-plot_rri_ternary.R – the test had the
same defect, because skip_if_not_installed() also loads the
namespace and would have poisoned every later test file.
Where ggtern cannot be used the ternary panel is skipped with an explanation, and the same composition is reported numerically, as before.
rri_accuracy() assesses how closely a score tracks a
reference target using statistics appropriate to repeated observations
of the same units. A pooled row-wise correlation over a longitudinal
panel is not a valid precision claim: 480 rows that are 12 trajectories
sampled 40 times carry far less information than 480 independent
observations. The function reports the intra-class correlation, the
design effect 1 + (m - 1) * ICC, and the effective sample
size, and obtains intervals by resampling whole trajectories. It also
reports the naive row-resampled interval alongside, so the cost of
ignoring the clustering is shown rather than asserted.
Agreement is reported as Lin’s concordance correlation coefficient
next to Pearson’s r. The two differ whenever the score is
miscalibrated: a score equal to twice the target plus a constant has
r = 1 and concordance near 0.3. Calibration intercept and
slope are given so the direction of the miscalibration is visible. Mean
squared error is partitioned into squared bias, variance mismatch and
lack of correlation (Kobayashi and Salam 2000); the three components sum
to MSE exactly, and the residual is returned as an attribute so a future
regression in the arithmetic would be caught.
The permutation null exchanges whole trajectories rather than rows, so each unit keeps its temporal shape. Permuting rows would destroy the shared event-driven signal and make almost any score appear significant.
plot_rri_accuracy() draws the assessment as a
four-panel figure: calibration against the 1:1 line, a Bland-Altman
agreement plot with limits computed from cluster means, the
row-resampled and trajectory-resampled bootstrap distributions side by
side, and the exact error partition. Panels are selectable, and the
figure degrades to a list of plots rather than failing when
patchwork is absent.
man/rri_domain_influence.Rd was missing from the 0.99.3
tarball: the function was exported and had a complete roxygen block, but
no Rd file was generated, which is an “undocumented code objects”
warning under R CMD check. Added.vignettes/HRRI.R, an orphaned knitr output with
no corresponding .Rmd, which R CMD check flags
as a file in vignettes/ that builds no vignette.latent_truth; it now reports cluster-aware agreement, shows
the figure, and states plainly that a target and a score sharing a
generator establish internal consistency of the estimator and not
empirical validation.rri_domain_influence() reports the realised
contribution of each domain to the composite, as an exact variance
decomposition (phi_d = w_d Cov(S_d, R) / Var(R), summing to one).
Declared weights and realised influence diverge whenever domain scores
differ in dispersion, covary with one another, or are missing for some
rows; this function makes that visible instead of leaving it to be
inferred from a figure.plot_rri_properties() no longer draws a literal “NA”
label at the tip of an unavailable axis. The label was placed at the
same radius as the axis name and overlapped it, rendering “Capacity” as
“CNAacity”. Unavailable axes now show the short spoke only.plot_rri_properties() dropped two spurious warnings: an
invalid label.size argument passed to
annotate(), and a removed-rows warning from plotting an
NA vertex.rri_property_scores() now reports which input is
missing when a property is unavailable. Capacity requires
soil_df; omitting it is the usual reason Capacity returns
NA. The worked example shows both the complete and the
partial call.R/plot_rri_recovery_landscape.R used a literal em dash
inside a string, which is non-ASCII in executable code. Replaced with
\u2014; the rendered glyph is unchanged.rri_recovery_metrics() gains a section explaining why
k_recovery and t_half are frequently
NA. The rate fit requires at least min_pts
recovery observations that fall after the trough, below baseline, and
before the first baseline crossing; short windows routinely leave fewer.
The worked example now uses a 40-day record with a 10-day event so the
fit succeeds, and contrasts it with a short window where the rate is
correctly withheld.M) is now a holobiont state rather than a
mineralogical one. It accumulates from hydrological event load, the
Fe-crystallinity ratchet, persistent plant acclimation (aerenchyma
displacement), and microbial community displacement. Component weights
sum to the previous total (0.060), so overall accumulation rate is
unchanged while its causes are distributed across the three
domains.micro_legacy as a simulator state: it accrues
under sustained reduction and relaxes more slowly under oxic recovery,
giving the microbial component an asymmetric (hysteretic) legacy.latent_state now returns micro_legacy and
plant_legacy so the memory decomposition is auditable.latent_truth. All
figures, benchmarks and any stored simulation outputs must be
regenerated.attach_hrri_ids(): joins design identifiers onto
a score table using a unique row_id or a complete
observation key, falling back to row order only with an explicit
warning. Records the method used in the id_alignment
attribute.@importFrom declarations for all external calls and a
worked @examples block. Regenerated NAMESPACE
and all help pages.R CMD check and pkgdown deployment.test-property-scores.R and
corrected two test expectations that compared per-row
domain_coverage and n_domains columns against
scalars.hrri_infer_architecture() as a conditional
recovery-curve fit. Its fitted amplitude and rate are no longer
described as mechanistic accessibility and reservoir exchange
kinetics.rri_pipeline() now forwards domain weights and accepts
partial soil, plant or microbial panels.rri_memory_index().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.
Health stats visible at Monitor.