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tbl.now

1.2.0Package record

Tidy Data and Workflow Layer for Epidemic Nowcasting

0packages depend
570downloads / year
84.2%test coverage
10/13flavors OK

Overview

About
Maintained by Rodrigo Zepeda-TelloCRAN page ↗GitHub ↗Website ↗Issues ↗Declared funder: Columbia University in the City of New York

Defines tidy data structures and package-agnostic workflows for epidemiological nowcasting. The 'tbl_now' class records event, report, and revision dates alongside strata, covariates tagged by model component, censoring, and reporting-delay metadata while remaining compatible with 'dplyr'. Tools support validation, manipulation, diagnostics, visualization, format conversion, retrospective evaluation, and multiple modelling engines. The 'tbl_nowcast' class standardizes probabilistic predictions for plotting, scoring, comparison, and ensembling.

Changes in 1.2.0

Breaking: calendar effects follow the calendar (#99)

temporal_effects(week_of_year = TRUE), month_of_year = TRUE and seasons

were coded relative to the data rather than the calendar: the week and month

were offsets from the date in the object's **first row** (so January was month

3 for data starting in November, and the code even depended on row order), and

the Fourier terms counted time from the earliest event date. The same calendar

week therefore got a different code in every series, stratum and backtest

window, and a coefficient labelled "week 7" was not epiweek 7.

Now, on every date axis:

  • month_of_year is the calendar month: a factor with levels 1 (January) to 12 (December).
  • week_of_year is the MMWR epidemiological week, [lubridate::epiweek()]: a factor with levels 1 to 53. Week 53, which only some years have, keeps a level of its own instead of being folded into another week.
Show all changes in 1.2.0Hide the rest of the changes in 1.2.0
  • seasons count time from 1970-01-01 in the data's units, so a date gets the same sine and cosine values whatever the first date of the series. Fourier terms for report dates are still counted in the event units, as before. A numeric (non-date) axis has no calendar and still counts from its first event.

Column names are unchanged, but their values change, so models refitted with

these effects code them differently. A model's fit with Fourier seasons

alone is unaffected in principle -- shifting the phase rotates the sine and

cosine pair onto the same span -- while models with week_of_year or

month_of_year now use January / epiweek 1, rather than the first period in

the data, as the reference level. tbl_now_to_epinowcast() derives the

effects on its completed grid from the calendar too, so its values match

compute_temporal_effects() wherever the grid starts.

add_temporal_effects.data.frame() no longer needs numeric_col for seasons on

a date column (an explicit numeric_col still takes precedence) and gains

season_units, the units the Fourier periods are counted in.

nowcast_ensemble() can take the median (#100)

nowcast_ensemble(type = "median") combines the members' predictive quantiles

by their median, level by level, as the COVID-19 and FluSight forecast hubs'

quantile median ensembles do. One outlying member cannot drag it the way it

drags the average (type = "quantile"). The weights still apply: any weights

other than "equal", including "inverse_score" and "optim" from a

backtest, give a weighted median. With two equally weighted members the median

equals the average, so it needs three or more to differ.

epidist comes from CRAN

epidist in Suggests is now >= 1.0.0, its first CRAN release, so it

installs without an extra repository. tidy.epidist_fit() uses the interface

that epidist 0.5.0 introduced, delay_parameter_draws() and

add_summaries(), in place of the removed predict_delay_parameters() and

add_mean_sd(), which had made tidy() fail on every fit and R CMD check

warn about missing objects. Because the new draws carry every column of the

model data, all numeric, the reported terms are taken from the fit's family

(mu and sigma for a lognormal, say) plus mean and sd, rather than from

whatever numeric column is left after dropping a list of bookkeeping names.

baselinenowcast in Suggests is relaxed to >= 0.2.0, the version on CRAN.

diagnose() reports fractional delays under units / delay again

1.1.0 accidentally moved the fractional-.delay finding of diagnose() and

validate_tbl_now() from scope "delay" to "report". It is back under

"delay".

From NEWS.md in the release

Install

Health

CRAN checks
3NOTE10OK
Check messages
NOTERd cross-referencesr-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-patched-linux-x86_64
Packages unavailable to check Rd xrefs: ‘diseasenowcasting’, ‘epinowcast’
Unknown package ‘almanac’ in Rd xrefs

CRAN check page ↗

Slowest check: 12.8 min · r-release-macos-x86_64
Status changes
  • NOTE10 OK, 3 NOTENow
  • NOTE11 OK, 2 NOTE2026-10-22
  • WARNING12 OK, 1 WARNING2026-10-01
  • OK5 OK2026-09-22
Advisories

none known

Documentation

In release 1.2.0
READMEYes · 886 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.2.0Citation fileNoWebsiteYes · pkgdown

The repository also keeps web-only articles.

Help pages
91 (3 internal)includes a package overview page
Examples that run
100%87 run in a plain check (22 of them under a condition)
Exported functions with examples
98%
Documented parameters
93%
Return-value docs
98%
Help pages citing references
7%

Downloads

570
CRAN downloads in the past year
Rank #22,964 · ~2/day · ~48/mo
Daily download trend is not available in this view yet.
53730 days
57090 days
5701 year
Compare downloads with other packages →
Also on5 r2u2 autocran

Repository

2Stars
0Forks
10Open issues
0Open PRs
37Releases
351Commits
2Commit identities
data-analysisepidemiologynowcastnowcastingpublic-healthrrpackagetibbles
351 commits · Last activity 2026-10-16
Responsiveness
How these are sampled
PRs merged (all time)
90%
Median days to close, 50 most recently updated closed issues
3
Median days to close, 50 most recently updated closed PRs
0

Releases over time

2026-09-22 · 342026-10-16 · 37
PracticesBeta

10 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/rodrigozepeda/tbl.now on 2026-10-22.

Continuous integration (2)
GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows

Docs source (4)
README.Rmdpkgdown

GitHub Pages site last deployed 2026-10-16 · The repository has a site deploy workflow

pkgdown site last built 2026-10-16

Coverage (1)
Coverage reporting (Codecov)
Reproducibility and dev environment (1)
data-raw/
Show all practicesHide 2 practices
CRAN release process (1)
cran-comments.md
Lint, format, editor (1)
RStudio project
How this is detected·Detection ruleset v4 (2026-10-20)
AI coding toolsBeta

This repository shows signs of AI coding tools.

  • Claude Codefirst seen 2026-04-26
    Named in .Rbuildignore: .claude
    Pull request it wrote: opened by a project member
    Commits: 4 by its own account · at least 44 crediting it in the message
  • GitHub Copilotfirst seen 2026-08-21
    Commits: at least 3 crediting it in the message
Models named in its commits
  • Claude Opus 535 commits · Aug to Sep 2026
  • Claude Sonnet 5.54 commits · Sep 2026
  • Claude Opus 5.52 commits · Oct 2026
  • Claude Opus 4.81 commit · Jul 2026
  • Claude Sonnet 4.61 commit · Apr 2026

1 more model not listed.

Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies
34 external dependencies (excludes base and recommended)

Installing tbl.now adds 31 packages (17 with compiled code, 29 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, isoband 1.5 MB.

Depends (1)
R >= 4.2.0
LinkingTo (0)
none
Enhances (0)
none
Reverse dependencies
0direct
0indirect

Nothing depends on this yet.

Datasets

People & History

People (6)
Author, Maintainer since 1.0.0 (2026)
Author
Contributor
Contributor
Releases (2)

Pick two releases to compare their code metrics.

  • 1.2.0Latest
    record
    2026-10-16 · current release · diff ↗ ·
    added 16 exports
    add_event_covariates, add_report_covariates, add_revision_covariates, backtest_combine, change_event_covariates, change_report_covariates, change_revision_covariates, get_event_covariates, get_report_covariates, get_revision_covariates, remove_all_event_covariates, remove_all_report_covariates, remove_all_revision_covariates, remove_event_covariates, remove_report_covariates, remove_revision_covariates
    ·
    listed once in CRAN's queue
    Seen in one reading of CRAN's incoming queue, at 2026-10-16 17:07 UTC, so it stayed less than the time between readings.
  • 1.0.0
    record
    2026-09-21
  • R
    R 4.6.0 released · 2026-04-24
Across CRAN, the median accepted release of the past year spent 23 hours in the queue, 90% under 11 days.How queue time is measured

Package metadata

First published
2026-09-21
Total releases
2 / 1 yrs
License
MIT + file LICENSE OSI
Minimum R
≥ 4.2.0
Bundled data
630 KB / 7 files
Download size
2.0 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("tbl.now")
Zepeda-Tello, R., Columbia University in the City of New York, Perini, M., Shaman, J., Yaari, R., & Yamana, T. (2026). tbl.now: Tidy Data and Workflow Layer for Epidemic Nowcasting (Version 1.2.0) [Computer software]. https://doi.org/10.32614/CRAN.package.tbl.now

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

APA

Balamuta, J. J. (2026). R Observatory: Metrics for tbl.now version 1.2.0 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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