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Changelog

Source: NEWS.md

Version 2026.10.23

  • An NA count in the identity family of rolling_slope_matrix(), and so of the ensemble short_term_trend(), gives NA only in the windows that hold its week. Before, the cumulative sums carried it into every later window, also those of each later series in the same ensemble. The other two families were already local.
  • short_term_trend_v4() with one draw calls stats::qt() once per distinct degrees of freedom, not once per row. The growth-rate percentiles are identical.
  • In the identity family, an Inf or -Inf count counts as NA, local to its windows. Before, it made every later window NaN.
  • The rebuild of a compressed v4 ensemble gives each base measure its own u, from a seed from its name and seed 4. Before, every measure of a row shared one u, so a numerator and its denominator were perfectly rank-correlated, while nowcast_ecdf_v4() draws them independently. The test triangle of test-v4_nowcast_ecdf.R has 9 nowcast weeks. There, the interquartile range of the rebuilt rate was 0.017 to 0.13 times that of the full rate. It is now 0.91 to 1.13 times.
  • The rebuild of a compressed v4 ensemble interpolates between the stored percentiles on the log1p() scale. It does so in each row whose 9 percentiles are all 0 or more. Before, a straight line on the original scale put too many draws in the upper tail of a right-skewed row.
  • On a luftvei replay of 1,272 newest weeks, HLM P(high) from rebuilt draws was within 0.05 of the full draws in 95.0%, against 92.3% before. The mean signed error fell from 0.0074 to 0.0054. At older horizons the agreement stayed 100%.
  • The rebuilt draws of two measures are now independent, also where the full draws were dependent. vignette("v4") says when to read a stored rate and when to add it again from its parts.

Version 2026.10.22

  • The identity family of the ensemble short_term_trend() takes denominator and per, as ens_add_rate() does. With a denominator, the residual variance has a floor at the Poisson variance of the rate, mean(rate) * per / mean(denominator). Without one, there is no floor, as before. For a count, pass a denominator of 1 and per = 1.
  • rolling_slope_matrix() takes the same floor as rate_denominator and per. A denominator MUST be 0 or more and finite, or NA. A 0 or NA week affects only the windows that hold it. Before, values on an exact line always got a standard error of 0, and P(increasing) of exactly 0 or 1.
  • On the percent-positive rate of vignette("pipeline"), which now passes its denominator, the floor set the standard error in 62% of the window-draws. It raised the median standard error 1.18 times.
  • signal_detection_hlm() on a csfmt_ensemble_v3, and signal_detection_hlm_v4(), flag a draw above the limit as high, as the v1 method does. Before, a draw at the limit was high. In 2026.10.18, this rule alone separated v4 from v1 in 965 NorSySS weeks with a rate and a limit of 0.
  • signal_detection_hlm_v4() stops when a series is not one row per ISO week, as short_term_trend_v4() does. Its baseline counts back 52 rows a year, so a missing week shifted the baseline without a warning.
  • vignette("csalert"), the README and the home page mention the v4 functions. The vignette heading “Use the ensemble methods” is now “Which methods to use”, because it covers the table methods too.
  • Config/roxygen2/version is 8.1.1, the roxygen2 that writes the help pages. roxygen2::roxygenise() moved it from 8.0.0 in 2026.10.16, and the package keeps it.

Version 2026.10.19

  • mem_thresholds_v4() writes the post-epidemic threshold, the season start and the season length, as <measure>_mem_thr_postepidemic, <measure>_mem_season_start and <measure>_mem_season_weeks. These are the fields that norsyss.cs9 uses from its v1 MEM fit. On the 17 national r80 seasons that both versions fit, the start and the length equal v1. The post-epidemic threshold is within 0.017% of v1.
  • The probability columns of signal_detection_hlm_v4() and mem_thresholds_v4() are NA, not NaN, in a row where every draw is NA.

Version 2026.10.18

  • New: a v4 layer that carries one ensemble, csfmt_ensemble_v4(), through every step. A full ensemble holds the draws in memory, and a compressed ensemble holds a point value and 9 percentiles for each base measure. print() shows the state.
  • vignette("v4", package = "csalert") runs the v4 layer from weekly counts to a stored table and back.
  • ens_compress_v4() returns the compressed ensemble as a plain table to store, such as in PostgreSQL. It stops with an error when a name is longer than 63 bytes, the limit of a PostgreSQL name.
  • as_ensemble_v4() reads a stored table back as a compressed ensemble. A step that needs draws rebuilds them from the percentiles, with seed 4 and an independent draw for each week.
  • The rebuild draws each week independently, because that rule gave the higher arrow agreement on a replay of luftvei data. On that replay, the trend arrow from rebuilt draws agreed with the arrow from full draws in 99.98% of 6,360 indicator-weeks. The replay covered 24 indicators, 53 as-of dates and 5 horizons.
  • csfmt_reporting_triangle_v4(), nowcast_ecdf_v4() and nowcast_passthrough_v4() build the triangle and nowcast it. With the same seed, their draws are identical to those of nowcast_delay_ecdf_v1() and nowcast_passthrough_to_ensemble_v1().
  • ens_add_rate_v4() adds a rate draw by draw. On a compressed ensemble, it rebuilds the numerator and the denominator with paired draws.
  • short_term_trend_v4() fits the trend on the quasi-Poisson kernel of 2026.10.17, with the denominator as an offset for a rate. It computes P(increasing) exactly from the fits, with no simulation.
  • signal_detection_hlm_v4() and mem_thresholds_v4() write the share of the draws at each level, as <measure>_hlm_prob_<level> and <measure>_mem_prob_<level>.
  • On 5 national NorSySS groups, a short_term_trend_v4() P(increasing) of at least 0.95 agreed with the v1 status “increasing” in 100% of 5,398 weeks.
  • On the same 5 groups, HLM “high” agreed with v1 in 99.90% of 3,150 weeks. In 965 other weeks the rate and the limit were both 0. v4 flags these weeks “high”, as v3 does, and v1 does not.
  • On the r80 national NorSySS series, the 68 MEM thresholds of the 17 seasons that both versions fit were within 0.019% of the v1 thresholds.
  • On synthetic data in the production shape of NorSySS, the v4 trend and HLM together took 0.53 times the v1 run time. The measurement used 3 groups of 614,628 rows.
  • The v1 and v3 functions do not change.

Version 2026.10.17

  • The csfmt_rts_data_v1 method of short_term_trend() fits all rolling windows of a series in one vectorised step, and it no longer calls glm2. On a synthetic group of 252 series of 1,000 weeks, it took 34 s, against 1,180 s before.
  • In that synthetic group, the statuses and forecasts did not change. 9 of 251,496 doubling days changed, and each was above 8 million days in absolute value.
  • A window still leaves out its weeks with an NA count or denominator. With fewer than 3 weeks left, it now gets NA status, NA doubling days and, as the last window, NA forecasts.
  • A window whose counts are all 0 keeps its status, but its doubling days are now NA. Before, they came from a fit that has no estimate.
  • A window gets NA status and NA doubling days when its first week, or its last week, holds every count above 0. Before, it got the status of a glm2 fit that has no estimate, and doubling days near 0. A window whose fit does not converge still gets NA.
  • A window of 2 weeks with a count above 0 now gets NA status and NA doubling days. Its fit has no degree of freedom left for the dispersion. Before, some such windows got notincreasing. A last window of 2 weeks now gives NA forecasts.
  • A window where glm2 halved the step got NA before. It now gets the estimate of the fit, when the fit converges.
  • Without a denominator, the csfmt_rts_data_v1 method no longer stops with “object ‘varname_forecast_denominator’ not found” when the last window has no fit. It returns NA forecasts, as it does with a denominator.
  • csalert no longer imports glue, because no code calls it.

Version 2026.10.16

  • The csfmt_rts_data_v1 table methods of short_term_trend() and signal_detection_hlm() are supported for counts without delayed reporting. The documentation no longer calls them deprecated, and their code does not change.
  • glue moves from Suggests to Imports, because the table method of short_term_trend() calls it. csalert no longer imports ggplot2 or suggests csmaps, because no code uses them.
  • Removed the development files in dev/ and tests/manual/, the CRAN submission files, the R-hub workflow, two unused internal data generators and commented-out code. R/nowcast_evaluate.R is now R/nowcast_score.R, named after nowcast_score_v1().

Version 2026.10.15

  • short_term_trend() floors the quasi-Poisson dispersion at 1. A window with less variation than Poisson now gets the Poisson standard error. Before, it could get a near-zero one, and a <measure>_trend_increasing_pr of exactly 0 or 1.

Version 2026.10.13

  • Removed the interval and outage_gap_days arguments of nowcast_delay_ecdf_v1(). On 52 replayed weeks of Norwegian surveillance data, neither option beat the default empirical interval by enough to matter. Output without these arguments does not change. A call that still passes either argument stops with an error, so it cannot silently get the default.

Version 2026.10.12

Version 2026.10.11

  • reporting_triangle_matrix() returns a new element, late: the count of each reference week reported at delay max_delay_days or later. These reports no longer count in the last delay column of mat.
  • nowcast_delay_ecdf_v1() estimates the count reported within max_delay_days days, and nowcast_truth() returns that count. Before, the last delay column also held every later report, so a backtest scored the nowcast against everything ever reported.
  • The published observed count keeps the late reports. original, <denominator_col>_observed and the draws of a week that is not nowcast are rowSums(mat) + late. So nowcast_passthrough_to_ensemble_v1() and reporting_completion_v1() give the same output as in 2026.10.10.
  • nowcast_delay_ecdf_v1() leaves a week out of the pool when all its reports are past the horizon, as in a bulk load of old weeks. The week stays in the output with its observed count.
  • On a triangle with no report at delay max_delay_days or later, the nowcast engines, nowcast_truth(), nowcast_backtest() and reporting_completion_v1() give output identical to 2026.10.10.

Version 2026.10.10

  • R CMD check no longer gives a NOTE for qc_week_over_week_v1(): the column it filters on in 2026.10.8 is declared as a data.table column.

Version 2026.10.9

  • Tests only: the family = "identity" kernel test of short_term_trend() compares the draws with expect_equal(tolerance = 1e-12) instead of expect_identical(). On macOS arm64 the draws differed from x86_64 in the last bits, so the r-universe macOS checks failed since at least 2026.10.7. A change of 1e-8 still fails the test.

Version 2026.10.8

  • qc_week_over_week_v1() has a new argument, model_pattern, default "_trend_(gr|beta1)_". $integrity leaves out the columns whose names match it. Before, the Monte-Carlo noise of trend estimates in settled weeks filled $integrity: 2314 growth-rate and 217 slope rows of 2599 in one weekly run, which hid the real data revisions. Roleless published medians, such as cases_q50x0, are still compared.

Version 2026.10.7

  • nowcast_delay_ecdf_v1() has two new options, outage_gap_days and interval = "log_robust". A few pool weeks with a delivery outage have extreme pool ratios T_s / O_s, and these set the upper limit of the interval. The defaults are unchanged and give output identical to 2026.9.24 for the same seed.
  • outage_gap_days removes a pool week from the pool when its delay days 0 to d hold that many or more consecutive dates with no delivery. Here d is the age in days of the reference week to nowcast. The full pool stays when that week has its own outage, or when fewer than 3 pool weeks would remain.
  • interval = "log_robust" draws the log pool ratio from a normal distribution with the median and the MAD of the log pool ratios. The median and the MAD change little when a few pool weeks have extreme ratios.
  • nowcast_score_v1() is new and exported. It scores replayed nowcast quantiles against the settled truth. The scores are the weighted interval score (WIS), the WIS after log1p(), the 95% coverage and the 95% interval width relative to the truth. Coverage alone rewards an interval that is too wide, and WIS penalises both a miss and the width.
  • nowcast_evaluate_v1() calls nowcast_score_v1() and gains the columns wis, wis_log, coverage_95 and width_95_rel_median. The earlier columns keep their values.

Version 2026.9.24

  • reporting_triangle_matrix() sums the counts in a cell with na.rm = TRUE. Before, one NA count set its whole cell to 0, so the real counts in that cell were lost with no warning.
  • nowcast_backtest() returns an empty data.table when no report is inside the horizon and as_of_weeks is NULL. Before, it errored with “NA/NaN argument”.
  • isoyearweek_week_start() is exported. It returns the Monday that starts an ISO week, the day every delay counts from.
  • Documentation only: each nowcast_delay_ecdf_v1() draw is the observed count times a quantile of the pool ratio T_s / O_s. The help page and the pipeline vignette said observed / p(d), but p(d) cancels out.
  • Documentation only: the pipeline vignette no longer says every older settled week finished reporting before the extract day. That holds only because sim_reports() emits no delay beyond day 34.
  • Documentation only: the nowcast_delay_ecdf_v1() help page says that a settled pool week can still receive late reports, so a long backlog makes the nowcast run low, and that a pool week with no early reports cannot enter the pool.
  • Documentation only: the help pages render as markdown, so their links, code and lists no longer show as raw text.
  • Documentation only: every public help page has a description, a family and a vignette link.
  • Documentation only: the mem_thresholds_v1() help page says it adds the five threshold columns to $data, by reference, and not to $draws.
  • Documentation only: the signal_detection_hlm() help page says the ensemble method codes a draw 1 for null and 2 for high, not 0 and 1.
  • Documentation only: the simulate_baseline_data() help page says phi = 1 gives Poisson counts. It said phi = 0, which gives NA.
  • Documentation only: the help pages state that remove_last_isoyearweeks of the deprecated signal_detection_hlm() method has no effect.
  • Documentation only: prediction_interval() and its glm method are internal, and left the reference index. The generic was never exported.
  • Documentation only: the pipeline vignette has a quality-control section, and the Get started vignette has a simulation section.
  • Documentation only: the vignettes say that csdb cannot validate a v3 table. They said that a v3 table cannot be stored.
  • Documentation only: the README no longer says that denominator belongs only to the deprecated trend method.

Version

  • r-universe publishes 2026.9.23 from commit 75c0751, so this tree needs a higher number.

Version 2026.9.23

A late report is a report at delay max_delay_days or later, counted in days from the reference week’s Monday.

Breaking: reporting_triangle_matrix() keeps late reports

  • A late report counts in the last delay column, max_delay_days - 1. Earlier versions dropped it. The delay columns are unchanged, 0 to max_delay_days - 1.
  • The drop lowered published counts, and nothing warned. Both engines publish rowSums() of this matrix as original. Measured on 2026-09-23 in luftveisovervaking_trend with one input file, s19_hosp_sari lost every week from 2020-01 to 2025-26. That is 287 weeks and 346,306 admissions, nearly all bulk-loaded on 2025-07-30. The settled weeks lost a net 2,453 in msis_covid19, 1,367 in lab_hospitalised_sars_cov_2 and 448 in daar_sari_scd2.
  • Published numbers move wherever a series has a late report. That covers original, every nowcast, nowcast_truth(), and mean_delay and the pct_delayD curve of reporting_completion_v1(). A week whose every report was late now carries its count, where before it was absent or zero.
  • A report before the reference Monday has a negative delay, and it is still dropped.
  • A settled week is not final: a report at a delay beyond max_delay_days - 1 can still arrive and raise its count.

Version

  • r-universe publishes 2026.9.22 from commit 2dfed42, which is this tree’s parent. This tree needs a number above it. 2026.9.23 is the release date of this tree.

Version 2026.9.22

The nowcast stack moves from a weekly delay axis to a daily one, and the default engine changes. Two of the six breaking changes below return wrong numbers rather than an error.

Breaking: the reporting axis is a Date

  • csfmt_reporting_triangle_v3() defaults reporting_col to reporting_date, and that column MUST be a Date. isoyearweek_reporting is gone. A character column raises an error naming the class it got.
  • The as_of attribute is a Date. It held the largest ISO-week string before. Code that compared as_of against an ISO week now compares two types.
  • The constructor errors on a missing reporting date, and the message names the count. One NA used to set as_of to NA. No reference week then settled, no delay pool built, and every engine returned the observed totals while labelling them a nowcast. Densification dropped the row as well, so the week’s own count was understated too. Map every missing reporting date to a date, or drop those rows, before you build the triangle.

Breaking: max_delay is now max_delay_days, and it counts DAYS

Breaking: qc_week_over_week_v1() takes max_delay_weeks, in WEEKS

  • Two parameter names, two units, on purpose. This function windows reference weeks, never delay. Its horizon sets the boundary between the settled weeks and the frontier, and that boundary counts reference weeks.
  • The nowcast engines take max_delay_days, because their axis is the delay in days. One name across both would mean days here and weeks there.
  • Do not rename max_delay_weeks to match the engines. The old name was max_delay, and each new name states its own unit.

Breaking: nowcast_quasipoisson_v1() is now nowcast_delay_ecdf_v1(), and it is a different estimator

  • Its numbers move. The new engine completes each incomplete reference week from a pooled daily delay ECDF. The old engine regressed the settled total on the observed delay columns. The interval is empirical now, taken from the pool’s own truth / estimate ratios, and no longer parametric.
  • nowcast_quasipoisson_v1() no longer exists. A call to it raises “could not find function”.
  • The model family is unchanged. The ECDF is the closed-form maximum likelihood estimator of n[ref, d] ~ Poisson(lambda[ref] * p[d]), the same Poisson delay model. It estimates the delay profile saturated, one number per delay day, rather than through a regression.
  • The old engine failed silently on complete data. Where every settled week’s delay columns sum exactly to its total, the design matrix is perfectly collinear and coef() returns NA. The engine then fell back to the observed count and labelled it a nowcast. Measured on lab_hospitalised_influensavirus: 27 of 27 replays at horizon 2.
  • The delay ECDF was measured against a quasi-Poisson GAM with a smooth in delay and a weekday term. Under a log link the two agree: every difference sits inside 0.5 percentage points over 30 replays. Under the identity link, which the old engine used, the GAM failed to converge on 30 of 30.

Version

  • r-universe publishes 2026.8.28 from commit 670fe584, which is this tree’s parent. One version must never name two trees, so this tree takes a number above it. 2026.9.22 is the release date of this tree.

Version 2026.8.28

Installation points at the r-universe

  • README.md told users to run install.packages("csalert"). With no repos set that reaches CRAN, which carries 2024.6.24 from 2024-06-24. It installs without complaint, so a reader following the README got a release two years behind and nothing said so.
  • The section now sets repos to niphr.r-universe.dev first, which builds every commit on main, and says to put that in ~/.Rprofile.
  • It also records what pak can express, measured against pak 0.11.1: a version range such as csalert@>=2026.8.27 is rejected with “Version ranges are not implemented yet”, an exact csalert@2026.8.27 pin works, and a DESCRIPTION floor of Imports: csalert (>= x) resolves through pak::local_install_deps().

No code changed. This release is documentation only.

Version

  • 2026.8.27 was published twice, from 44a33f02 and then from 0f719ece. Two trees under one version is the defect CalVer prevents, so the README tree takes a number of its own. 2026.8.28 is the release date of this tree.

Version 2026.8.27

Breaking: propagate_slope_error was removed, and the slope error is always propagated

  • short_term_trend() on a csfmt_ensemble_v3 no longer takes propagate_slope_error. The slope’s own sampling error now reaches every draw, always, and there is no way to switch it off.
  • Two things are uncertain and both belong in the draws: the level, which the incoming ensemble already carries, and the line fitted through those levels. increasing_pr is the share of draws whose slope is positive, so without the second it is a sign test on the point slope wearing the name of a probability. A threshold like > 0.975 on it then does nothing at all. That was the default behaviour, and nothing warned.
  • Published numbers change. Every _trend_beta1, _trend_gr and _trend_increasing_pr a caller was producing under the old default is different now, and the trend columns are no longer reproducible run to run without a seed. Set one if you need that.
  • $draws[["<measure>_trend_beta1"]] is no longer the point estimate. It holds the perturbed draws. Call rolling_slope_matrix() for the unperturbed slope, its standard error and its convergence flag.
  • Passing propagate_slope_error now raises an error naming the removal. The method takes ..., so without that guard a caller who had turned it off would get propagated numbers and no notice.
  • family = "identity" and family = "quasipoisson" now refuse trend_isoyearweeks = 2. Both read a dispersion off width - 2 residual degrees of freedom, so se has no value at width 2 and no error_reference repairs it. family = "binomial" fixes the dispersion at 1 and still accepts width 2.
  • n_sim moved from argument 5 to argument 4, which changes the meaning of a positional call.
  • error_reference is unchanged and still selects the reference distribution.

The csfmt_rts_data_v1 method is untouched. It fits its own GLM per window and never had this argument.

Version

  • r-universe publishes 2026.8.26 from commit 576b9c51, so this tree needs a number above it. 2026.8.27 is the release date of this tree.

Version 2026.8.26

  • short_term_trend() on a csfmt_ensemble_v3 takes family. "quasipoisson" is a log link and "binomial" is a logit link. beta1 is then the slope on the link scale. That is the coef(model)[2] the older glm() pipelines report, so the two become comparable. "identity" is the default and reproduces the previous numbers exactly.
  • The growth rate on a link scale is 100 * (exp(beta1) - 1), a percent change per week. Under "binomial" that percent change is in the odds.
  • A zero count needs no offset. The log link models E[Y] = exp(b0 + b1 t) and never takes log(Y).
  • family = "binomial" needs the new denominator argument, which names the $draws measure holding the binomial denominator. It enters the fit as the prior weight, and measure MUST then be a proportion between 0 and 1.
  • The rolling GLM stays a filter. IRLS advances every window of every draw together, and no window reaches stats::glm().

A window that cannot converge returns NA

  • A separated window has no finite slope, and the fit cannot converge. Complete or quasi-complete separation drives the IRLS slope to infinity. The iterate that maxit stops on is finite, so is.finite() never removed it. A window of c(0, 0, 0, 0, 0.2, 0.3, 0.4, 0.5) separates at width 4, with a denominator of 50. Its growth rate reached $draws as 1.06e13 percent per week. beta1, se and the growth rate are now NA_real_ there.
  • rolling_slope_matrix() returns a fourth matrix, converged. It is logical, and NA on the leading width-1 rows that hold no window.
  • beta0 is NA_real_ there too. A lone intercept beside a missing slope reads as a fitted level, and it is the same meaningless iterate.
  • An all-zero window returns NA, and stats::glm() returns a slope of 0. That is the one place the two disagree on purpose. stats::glm() stops on the relative change in the deviance, which is 0 for an all-zero window from the first iteration. This kernel stops on the coefficient step, and that step never settles: the intercept marches to -Inf as the fitted mean goes to 0. An all-zero window identifies no slope, and NA says so.
  • The warning reports the iteration the batch stopped on, and names maxit separately. It claimed maxit iterations before. A batch holding a missing-value window can settle earlier, because the stopping rule drops that window with na.rm.
  • The two GLM families warn once per call, with the count of window fits that did not converge. A run of zero weeks followed by a rise is ordinary early-season surveillance data, so the warning will fire.

The slope-error reference is now an argument

  • short_term_trend() on a csfmt_ensemble_v3 takes error_reference. "auto" is the default. It gives "identity" and "quasipoisson" a t on trend_isoyearweeks - 2 degrees of freedom. Both estimate a dispersion from that many residual degrees of freedom. That is the case summary.glm() refers to a t.
  • "binomial" keeps a standard normal under "auto", because that family fixes the dispersion at 1 and leaves nothing to estimate.
  • Pass error_reference = "normal" to match a pipeline whose interval comes from stats::confint(), which profiles the deviance against an asymptotic chi-squared. "t" forces the other direction on every family.
  • propagate_slope_error = TRUE now needs trend_isoyearweeks >= 3 under family = "identity" and family = "quasipoisson", whatever the error_reference. Both read a dispersion off width - 2 residual degrees of freedom, so at width 2 se is NaN under identity and Inf under quasi-Poisson. The growth rate then reached $draws missing, or as a random -100 percent. family = "binomial" fixes the dispersion at 1 and still accepts width 2.
  • family = "identity" is unchanged. It drew se * t_(width-2) before and it still does.

Static checks

  • R/ passes the shared static-checks gate. The gate arrived with the workflow pin two releases ago and reported 127 findings across 23 of the 24 code files. Every one is now fixed.
  • Every stop() and warning() names call. = FALSE, because the message goes to a user who cannot act on the call. Every function returns explicitly. seq_len() and seq_along() replace 1:n, && and || replace & and | inside a condition, and TRUE and FALSE replace T and F.
  • Seven functions were over 15 cyclomatic complexity and gave their branches to named helpers. In short_term_trend_ensemble.R, rolling_irls_slope() gave up irls_check_response(), irls_working() and irls_wald_se(), and short_term_trend.csfmt_ensemble_v3() gave up stt_prior_weights() and stt_error_reference().
  • No behaviour changes. One user-facing message reads “0.05, 0.25, 0.5, 0.75 and 0.95” where it read “0.05/0.25/0.5/0.75/0.95”, because the slashes read as a file path.

Version

  • r-universe published 2026.8.23 from commit ed0749b8, so this tree cannot reuse that number. 2026.8.26 is the release date of this tree.

Version 2026.8.23

  • The 51-name utils::globalVariables() list is gone. Each NSE column name is now declared as NULL at the top of the one function that uses it: 18 declarations across 12 files. Only . stays package-wide, because it is read as an undefined function and no local binding fixes that.
  • The old list was both too wide and too narrow. level, method, period, role and truth are also formal arguments of other functions, so declaring them package-wide suppressed the note for a genuine undefined variable anywhere in the package. coverage_raw and horizon were declared and used nowhere.
  • R/csfmt_ensemble.R already used this idiom at set_time_series_id(). The package now uses it everywhere.

Version 2026.8.22

  • The package drops magrittr. Every %>% is now the base pipe |>, and magrittr is gone from DESCRIPTION.

  • The rewrite is a relocation, not an edit. Each %>% call was transformed the way R’s parser transforms |>, and the resulting tree was required to match the tree parsed from the rewritten file. A file whose trees disagreed was left untouched and converted by hand instead.

  • The version runs one day ahead of the calendar on purpose. r-universe already published today’s number from a different commit, and one version must never name two trees.

Version 2026.8.21

  • R/globals.R declares ".". R CMD check read data.table’s .(), its alias for list(), as an undefined function rather than an undefined variable, so the file’s existing declarations did not cover it.

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