Changelog

Source: NEWS.md

Version 2026.8.7

Licensing

• The copyright holder is now Folkehelseinstituttet. It read “Core Surveillance”, which names the package family rather than a legal entity.
• DESCRIPTION Authors@R now declares that holder with role = "cph". It declared no copyright holder at all, and neither did any other package in the fleet. Nothing in R CMD check reports that.
• The copyright year is now 2026. It read 2023.
• CLAUDE.md now carries a Licensing section, so the year gets checked rather than silently ageing.

Corrections

• ?nowcast_evaluate_v1 claimed common random numbers, and the code does not establish them. Every method starts from the same RNG state on each as-of week, which pairs the comparison. Common random numbers would also need the methods to consume compatible variates, and nothing enforces that. The documentation now states the mechanism and stops there. vignette("pipeline") already said this. The roxygen contradicted it in three places, including a worked example.

Documentation

• Every prose file in the repository is swept to ASD-STE100 (Simplified Technical English). The sweep covers the roxygen blocks in R/, both vignettes, README.md, index.md and this file. The sweep changed no claim, number, hedge or scope qualifier, and no executable line. The one claim that did change is under Corrections above.

• Sentences over 25 words: 34 to 0 in roxygen, 80 to 0 in the vignettes. Counted per authored unit, outside fenced code and outside code-bearing roxygen tags. README.md went 3 to 0, index.md went 1 to 0, and this file went 45 to 0. Long sentences were split, not shortened, so every condition that made one true survives in the sentences that replaced it.

• SHOULD and SHOULD NOT are now capitalised in the five places that state an obligation. Three are in R/ and two are in vignette("pipeline"). A lowercase “should” reads as advice and gets treated as optional.

• The deprecation notes are unchanged in substance. They are on ?short_term_trend and ?signal_detection_hlm. Both still say the replacement is not a drop-in, that migration is a rewrite of the call site, and that the numbers will not match.

• One roxygen section gained a bulleted list, where three parallel conditions were buried in a single sentence. It is the “What it does NOT check” section on ?validate_ensemble. The three conditions are unchanged.

• 31 @param descriptions gained the terminal full stop they were missing. No wording changed. Without it a sentence counter runs straight through the boundary between one field and the next, and reports one very long sentence.

• New vignette("csalert"), the get-started page. It is an orientation and runs no analysis. It covers what the package is for, which of the two generations is current, where the csfmt_rts_data_* classes live, and what cannot be done yet. pkgdown promotes a vignette named after the package to “Get started” in the navbar, which is where the site’s primary call to action now points.

• vignette("nowcasting") is now vignette("pipeline"), retitled to “The pipeline: from incomplete counts to published numbers”. Its content, numbers and statistical claims are unchanged; the opening paragraphs were rewritten in plainer language. The 23 @seealso cross-references in R/ were updated with it, so no help page points at a vignette that no longer exists.

• vignette("short_term_trend") is deleted. It taught short_term_trend.csfmt_rts_data_v1, which is deprecated, so it was teaching new readers the route they should not take. The only worked example of that method is now the one on ?short_term_trend. Its county-map demonstration was not ported.

No behaviour change

• This release changes prose only. No exported function, argument, default or return value moved.

Bug fix

• qc_week_over_week_v1() silently dropped every HLM alert transition. signal_detection_hlm() writes naming-grammar role "hlmstatus", but the function selected only role == "status" for its $signal table. An escalation from normal to high therefore never appeared in the week-over-week review. Demonstrated on a 380-week series: a real transition from 1 to 2 at week 2025-14 returned 0 rows before the fix and 1 after. HLM needs roughly five years of history before it produces a status at all, which is why a shorter test series shows nothing.
• The same filter had a second, opposite half. $integrity excluded role != "status", so HLM status CODES were diffed as if they were continuous medians. An ordinal 1-to-2 step read as a numeric revision.
• Both halves are now driven by a new status_roles argument, which defaults to c("status", "hlmstatus"). The roles excluded from $integrity are exactly the roles whose transitions appear in $signal. Pass a different vector to narrow or widen it.
• This changes no legacy path. qc_week_over_week_v1() operates on collapsed ensemble output. Its only callers are this package’s tests and the ensemble-first pipelines. Nothing on the pre-ensemble csfmt_rts_data_v1 route reaches it.

Version 2026.8.6

Bug fix

• short_term_trend() on an ensemble broke the data.table’s self-reference, so the NEXT stage warned. It added its P(increasing) column with base [[<-, which copies the table. Any later stage assigning with := then emitted data.table’s ten-line “shallow copy was taken” advisory. Bisected: rate -> hlm is clean, rate -> trend -> hlm warns. That is the canonical order, so every production pipeline running a trend before another ensemble stage saw it on every run. Now uses data.table::set(). Proven causally red: reverting the one line reproduces the warning.

Documentation

• vignette("nowcasting") now runs the whole canonical chain on one synthetic triangle with a denominator. The stages are nowcast, replay validation, reporting completion, rate, short-term trend, MEM intensity, HLM signal detection, and the terminal collapse. It opens by stating the rule the architecture turns on. Every analytical stage takes a csfmt_ensemble_v3 and returns one, and ens_collapse() is terminal. A collapsed table is therefore output and never input. ens_add_rate(), mem_thresholds_v1() and signal_detection_hlm() were previously named in prose but never run; production depends on all three.

Deprecated

• short_term_trend.csfmt_rts_data_v1() and signal_detection_hlm.csfmt_rts_data_v1() are deprecated. They are the pre-ensemble architecture. Both still work and NEITHER WARNS AT RUN TIME, so existing pipelines are undisturbed; the mark is a signpost for new work.
• The replacement is not a drop-in. The v1 methods take numerator, denominator, prX and the naming-prefix arguments, and return a status label. The ensemble methods take one measure and return a per-draw slope, growth rate and P(increasing), with no classification. Migrating is a rewrite of the call site and the numbers will not match.
• short_term_trend() and signal_detection_hlm() now have csfmt_rts_data_v3 methods that only stop(), naming the architecture instead of failing with a bare UseMethod error. A collapsed table carries quantiles, not draws, so a per-draw trend cannot be recovered from one.

Version 2026.8.5

Bug fix

• reporting_completion_v1(triangle, max_delay = 1) returned nonsense, silently. With a single delay column apply(M, 1, cumsum) returns a vector rather than a matrix. The transpose then produced a 1-by-n_settled matrix. The function emitted one pct_delay column PER SETTLED WEEK instead of one in total, with complete_by_md far below 1. Measured on a 30-week triangle: 30 completion columns and complete_by_md of 0.033, where both should be 1. No error was raised. Fixed, with a regression test that also pins the column count to max_delay at horizons 1 through 4.

Documentation

• vignette("nowcasting") is now a four-stage end-to-end pipeline on one seeded synthetic triangle: nowcast, replay validation, reporting completion, short-term trend. Every chunk executes under R CMD check. The reporting-completion section answers the question the old text left open: is the first completion column the reference week or the week after? It walks a named ISO week day by day. It shows that delay is measured in whole ISO weeks, so a Monday run and a Friday run bucket every report identically.
• nowcast_truth()’s description was off by one, in both bounds. It said it summed “all delays up to max_delay” and kept weeks “at least max_delay weeks before” the as-of. The code sums delays 0 .. max_delay - 1 and keeps age >= max_delay - 1. Measured: at max_delay = 3 the newest settled reference week is 2 weeks before as-of, not 3. Corrected.

Breaking change

• reporting_completion_v1() renames its completion columns from pct_wN to pct_delayD, and they are now 0-based and indexed by DELAY. With max_delay = 3 the columns were pct_w1, pct_w2, pct_w3; they are now pct_delay0, pct_delay1, pct_delay2.
• The old names were indexed by weeks-observed, counting the reference week itself as week 1, so pct_w1 held delay 0. The number in the name never equalled the delay it represented. Next to a reporting triangle whose columns are delays 0, 1, 2, it read as “the week after”. pct_delay0 says outright that it is the reference week itself.
• The new names match the max_delay argument: the column count equals max_delay and the highest index is max_delay - 1.
• Update any code that reads these columns. The old names are gone rather than redefined, so stale code fails with an unknown-column error instead of silently returning a different week. reporting_completion_trend_v1() passes the columns through and changes with it.

Version 2026.8.4

Documentation

• Every exported function now has a runnable example. 21 of the 34 exports had none; they already had a title, a description, @param and @returns, but nothing a reader could run. The new examples all execute under R CMD check. None is wrapped in \dontrun{} or \donttest{}, because nothing in the package needs a live database, a credential or a mounted share to demonstrate. The nowcast pipeline examples share one 40-week synthetic reporting triangle, right-truncated so the newest weeks are genuinely incomplete.
• Every exported function now carries an @seealso that says which vignette covers it, including when the honest answer is “neither”. Only eight exports are actually run inside a vignette code chunk. ens_add_rate(), mem_thresholds_v1() and signal_detection_hlm() are named in the closing “Where next” list of the nowcasting vignette, but not demonstrated there. The @seealso now says so rather than implying coverage.
• Eight @family groups added as topical navigation, so the reference pages cross-link. The groups are ensemble format functions, reporting triangle functions, naming grammar functions, nowcast engines, nowcast diagnostics, nowcast calibration functions, ensemble operations, and reporting completion functions. These group functions by the concept they belong to, not by a shared call signature. Only nowcast engines is a set of interchangeable implementations. The other seven are pipeline stages or helpers around one concept, and each member’s @seealso states its own specific role. The two qc_* functions were deliberately not made a family. qc_surveillance_data_v1() screens one input feed and returns a verdict. qc_week_over_week_v1() diffs two finished runs and returns two tables. They are cross-linked with @seealso instead.
• compare_results() gained an “Identity columns” section. It finds its value columns with csfmt_interpret(). An identity column outside the csfmt structural schema — location rather than location_code — is therefore read as a value column. cur/prv then come back as character instead of numeric. qc_week_over_week_v1() then fails outright with Error in cur - prv : non-numeric argument to binary operator. The nowcasting vignette teaches exactly those non-schema names, so this is easy to hit.
• README grown from 23 words to a landing page. It covers what the package is, the two routes through it, installation, one quick start, a which-function-do-I-want table, and links to the pkgdown site. It copies no passage from either vignette; the longest shared run of consecutive words is three. It does necessarily summarise the same pipeline the nowcasting vignette explains in full.

Corrected statistical documentation

No behaviour changed. Each of these help pages described a model, or a guarantee, that the code does not implement. An adversarial review found them.

• nowcast_quasipoisson_v1() is not fitted without an intercept. The documentation said “no intercept” in two places. But the formula is built as y ~ d1 + d2 + ..., which carries R’s default intercept. An inline comment in the source already said # + intercept. The documented model now matches the fitted one.
• “Honestly dispersed” removed from the same engine. Simulating from a fitted model and truncating at the observed count does not establish calibrated coverage. The documentation now says calibration is an empirical question about a given series and points at nowcast_evaluate_v1(), which exists to measure it.
• The calibration functions no longer claim split conformal or nominal coverage. The estimator takes the ordinary type-7 quantile of |truth - median| / halfwidth, not the conformal order statistic. That symmetric residual is only faithful for intervals roughly symmetric about the median. There is no finite-sample guarantee. coverage_raw is now documented as what the engine did on the replayed weeks, not as a property of the engine.
• complete_by_md is documented as identically 1. It was described as detecting reporting that continues past the horizon. It cannot: reporting_triangle_matrix() discards delays at or beyond max_delay before the total is formed. The final cumulative fraction of that truncated total is therefore always 1, and pct_delay<max_delay-1> is always 100. To look for a tail, re-run with a larger max_delay. This is a source defect left unfixed and now documented.
• q_value() is no longer described as the inverse of q_label(). The label format holds two integer-percent digits, so q_label(1) gives "q100x0", which q_value() returns NA for. The round trip holds on [0, 1).
• csfmt_parse() is no longer described as the inverse of csfmt_var(). It strips a role from the right against a fixed vocabulary. On the package’s own rate name numerator_nowcasted_vs_denominator_nowcasted_pr100 it eats the denominator’s _nowcasted as the role, and returns denom = "denominator". A new section documents the limit with that exact name.
• validate_ensemble() is retitled “Check a csfmt_ensemble_v3’s structural shape”. It checks class, two column names, and that each draw matrix has one row per row of $data — the row COUNT only. Permuting the rows of $data or of a draw matrix passes, as do a missing key, a broken time_series_internal_id and a deleted time_series_label. The page previously implied it was a safety net for hand-edited objects. It now says to rebuild with csfmt_ensemble_v3() instead, and its example demonstrates a permutation passing.
• qc_week_over_week_v1() cannot see HLM transitions. signal_detection_hlm() writes role "hlmstatus" while the check selects role "status", so only mem_thresholds_v1() output reaches qc$signal. The example said otherwise and now records the gap.

Packaging

• ^pkgdown$ and ^Rplots\.pdf$ added to .Rbuildignore. pkgdown::build_site() leaves a pkgdown/favicon/ directory behind, and an example that draws a plot leaves an Rplots.pdf. Both otherwise ship in the tarball and raise a non-standard-top-level-file NOTE.

Version 2026.7.1

Trend uncertainty

• short_term_trend() can now propagate the slope’s own sampling error. The growth rate is 100 * beta1 / Y. Until now only the uncertainty of the level Y reached it, and the OLS standard error of beta1 was computed and discarded. So every trend interval reflected nowcast uncertainty alone. A passthrough (single-draw) series got a zero-width interval and a P(increasing) of exactly 0 or 1. That is a bare sign test on a three-point slope presented as certainty. propagate_slope_error = TRUE adds se * t_(width-2) per draw, widening the trend’s own draw axis to n_sim when the incoming ensemble is degenerate. Defaults to FALSE, so published numbers are unchanged until it is switched on deliberately. Note the degrees of freedom are trend_isoyearweeks - 2: at the default window of 3 that is a Cauchy, so widen the window first.

Nowcast calibration, restored as a diagnostic

• nowcast_estimate_calibration_v1() / nowcast_apply_calibration_v1() are back, after being removed earlier in this release cycle. They are available to check an engine with, not applied to published numbers. The estimator reports a per-horizon factor. So “your 90% interval would need to be 1.4x wider to actually cover 90%” is readable straight off the backtest. That is a far more actionable red flag than a bare coverage fraction, and it keeps the published number the model’s own.
• Their tests now run against nowcast_quasipoisson_v1. The old assertions (factor > 1 everywhere, raw coverage below 0.82) encoded the removed nowcast_survrtrunc_v1’s behaviour. The current engine covers about 0.87 on the same drifting-delay synthetic, close enough to nominal that no widening is warranted.

Bug fixes

• prediction_interval.glm is now registered with S3method(). It resolved when the package was installed, but not under devtools::load_all(). The method’s own test therefore failed in a dev tree while passing in R CMD check.

Simplification

• reporting_completion_trend_v1 returns the completion curve by calendar year (all) + by month (last N, per series), with a scope column. That is the year/month trend the luftveis pipeline used to assemble by hand.
• nowcast_evaluate_v1 is now the single entry point for scoring nowcasts. Give it a triangle and one method, or a NAMED list. It replays each – paired by a shared seed – and returns one per-horizon table of interval coverage + point-estimate revision, with a method column. It subsumes the former nowcast_score (coverage, via scoringutils), nowcast_revision, nowcast_compare and nowcast_validate. Coverage is read straight off the interval quantiles, so scoringutils is no longer a dependency (WIS was dropped).
• Removed the unused nowcast_survrtrunc_v1 engine, and its flexsurv dependency. Also removed the conformal calibration functions (nowcast_estimate_calibration_v1 / _apply_ / print.nowcast_calibration). Both were already dropped from the production pipeline.
• Renamed mem_thresholds -> mem_thresholds_v1 (versioned-engine convention).

Documentation

• New vignette “Nowcasting a reporting triangle with csfmt_ensemble_v3” — a runnable end-to-end walk-through (synthetic triangle -> nowcast -> collapse -> backtest coverage/revision/completion -> naming grammar).
• Documented the previously-bare print.csfmt_ensemble_v3 method; added the missing @returns to the ensemble/nowcast S3 methods (mem_thresholds_v1, short_term_trend, signal_detection_hlm, nowcast_quasipoisson_v1).
• Added runnable @examples to the naming-grammar functions (csfmt_var, csfmt_parse, q_label, q_value) and to the nowcast analysis functions (nowcast_evaluate_v1, reporting_completion_trend_v1).
• Fixed unescaped % in the nowcast / reporting_completion roxygen that had been corrupting their generated .Rd, plus copy-paste errors in the simulation-helper docs.

csfmt_ensemble_v3 surveillance engine

A new draw-parallel ensemble format and the full analysis pipeline built on it (reporting triangle -> nowcast -> trend -> MEM thresholds -> quantile collapse).

• csfmt_ensemble_v3: S3 container ($data data.table + per-measure $draws matrices) with invariants enforced by validate_ensemble.
• Naming grammar: csfmt_var / csfmt_parse (order-independent parse of trailing coordinates), q_label / q_value, and csfmt_interpret for self-describing datasets.
• csfmt_reporting_triangle_v3: reference-by-delay input format with a reshape that completes the reference axis.
• nowcast(): reporting triangle -> ensemble via flexsurv survrtrunc + negbin (no epinowcast dependency). Can nowcast a denominator alongside the numerator (full % positive -> MEM path) and surface the observed denominator total. The reporting-before-reference check is NA-safe.
• observed_ensemble(): passthrough (degenerate single-draw) ensemble for indicators that should not be nowcasted.
• collapse(): ensemble -> quantile summary; collapse(heal = TRUE) heals the result into cstidy csfmt_rts_data_v3.
• add_rate(): numerator-vs-denominator rate (% positive).
• short_term_trend.csfmt_ensemble: batched, shared-design-matrix kernel that also emits P(increasing).
• mem_thresholds.csfmt_ensemble_v3: MEM intensity thresholds with provisional seasons. exclude_seasons drops anomalous seasons from the baseline. Training is capped to the most recent i.seasons before na.omit. A non-zero-season guard plus a quiet memmodel wrapper prevent sparse indicators from erroring.
• signal_detection_hlm.csfmt_ensemble_v3: per-draw exceedance detection.
• add_holiday_effect for the ensemble format.
• Input QC: qc_surveillance_data (generic input QC, verdict only) and qc_week_over_week (A/B revision comparison across runs).
• add_rate and collapse are renamed to ens_add_rate / ens_collapse. They are now S3 generics dispatching on csfmt_ensemble_v3 (the ens_ family), so the ensemble class carries the “operates on an ensemble” meaning. Behaviour is unchanged. (add_holiday_effect is a simulation-data helper on a plain data.table and keeps its name).
• nowcast and observed_ensemble are renamed to nowcast_survrtrunc_v1 and nowcast_passthrough_to_ensemble_v1 – concrete, VERSIONED nowcast engines that share the contract f(reporting_triangle, ...) -> csfmt_ensemble_v3. Behaviour is unchanged; the _vN suffix versions the algorithm (a future nowcast_stan_v1 or nowcast_simple_v2 slots in beside them), selected by a caller-side registry. The validation harness (nowcast_backtest/score/compare/validate/censor/truth) is generic tooling and is NOT versioned.
• nowcast_survrtrunc_v1 gains delay_window (default 26 weeks): the reporting-delay distribution is estimated from only the most recent weeks, so a non-stationary / drifting delay (e.g. a backfilled history then live prospective reporting) is tracked instead of averaged into a stale pooled curve. Fixes the median bias that caused sub-nominal interval coverage. Residual under-coverage (plug-in delay) is documented by the calibration test, and awaits per-draw delay uncertainty or backtest-driven recalibration. NULL restores the old pool-all-history behaviour.
• Calibration test (test-nowcast-calibration.R): empirical interval coverage vs nominal on synthetic data, with a stationary case (calibrated) and a drifting-delay case (reproduces the real-data under-coverage synthetically).
• nowcast_simple_v1 renamed to nowcast_survrtrunc_v1 (the name now states the method: right-truncated survival delay + negbin completion).
• New engine nowcast_quasipoisson_v1: a discriminative (regression) nowcast. For each horizon, regress the settled TOTAL on the counts reported so far, on the recent settled weeks. The regression is total ~ n[delay 0] + n[delay 1] + ..., quasipoisson/identity, no intercept. Then simulate the incomplete weeks (parameter uncertainty from the fit + a dispersion-matched negbin). No per-week magnitude parameter, so it is robust for the recent weeks and honestly dispersed. Drifting-delay synthetic coverage is ~0.79, vs the plug-in survrtrunc’s ~0.72 (nominal 0.90). Base stats only; same f(triangle) -> ensemble contract -> drops into the registry as a candidate key.
• Backtest-driven recalibration. nowcast_estimate_calibration_v1 learns a per-group (default horizon) conformal interval-scaling correction from past nowcasts vs settled truth. nowcast_apply_calibration_v1 applies it, so a method’s intervals hit nominal coverage regardless of internal misspecification. A nowcast_calibration S3 object with a print method sits between. Turns the backtest into calibration data: engine -> backtest -> estimate -> apply -> honest intervals. Distribution-free (split conformal); estimate on past backtests, apply to the current nowcast.
• Nowcast validation harness (method-agnostic, replay-based). nowcast_censor reconstructs what was known as-of a past week from the reporting triangle. nowcast_truth gives settled totals. nowcast_backtest replays any f(triangle) -> ensemble across as-of weeks into tidy quantile nowcasts. nowcast_evaluate_v1 scores one or several methods on interval coverage + point-estimate revision by horizon – see the Simplification section above.
• reporting_completion: the empirical reporting-delay summary of a triangle. From the settled weeks it gives the mean delay, and the weeks-observed to reach 25/50/75/90/95% of a reference week’s cases. It also gives the fraction actually in by max_delay. period = "year" / "month" stratifies the settled weeks in time, by the ISO year / midweek-day month. A drift in reporting speed then shows up as a trend in mean delay, instead of being averaged away.

version 2024.6.24

CRAN release: 2024-06-24

• Inclusion of short_term_trend_sts_v1.

Version 2023.6.22

• First inclusion of signal_detection_hlm.

Version 2023.5.23

• Updating to be in line with the latest cstidy version.

Version 2022.5.6

• short_term_trend now allows for vectorized prX and statistics_naming_prefix.

Version 2022.4.22

• short_term_trend now allows for granularity_time==‘isoweek’ and denominators.

Version 2022.4.21

• short_term_trend created to allow for easy estimation of short-term trends (increasing/decreasing/null), doubling time in days, and short-term forecasting with prediction intervals.
• prediction_interval created to allow for easy estimation of prediction intervals after fitting glms (family = poisson and quasipoisson) based on Farrington 1996.

Version 2022.4.10

• Package is created