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actverse

🏃‍♀️ A Tidyverse-Style Toolbox for Actigraphy Data Analysis

https://github.com/danielvartan/actverse

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Keywords

accelerometry actigraphy actimetry actogram biomedical-data-science chronobiology data-interpolation health-data periodograms physiological-monitoring physiology r r-packages rstats sensor-data sleep spectograms time-series time-series-analysis wearables
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🏃‍♀️ A Tidyverse-Style Toolbox for Actigraphy Data Analysis

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Topics
accelerometry actigraphy actimetry actogram biomedical-data-science chronobiology data-interpolation health-data periodograms physiological-monitoring physiology r r-packages rstats sensor-data sleep spectograms time-series time-series-analysis wearables
Created over 5 years ago · Last pushed 7 months ago
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README.md

actverse

Project Status: Active - The project has reached a stable, usable state and is being actively developed. R-CMD-check.yaml Codecov test coverage License: MIT Contributor Covenant <!-- badges: end -->

Overview

actverse is an R package that offers a comprehensive toolkit for processing, analyzing, and visualizing actigraphy data. It is designed to support sleep and chronobiology researchers by streamlining workflows and enhancing reproducibility in actigraphy research.

The package is built on tidyverse principles and integrates seamlessly with the tidyverse ecosystem, ensuring a consistent and user-friendly experience for data manipulation and analysis.

If you find this project useful, please consider giving it a star!   GitHub repo stars

Installation

You can install actverse using the remotes package:

r remotes::install_github("danielvartan/actverse")

Usage

The R ecosystem offers a wide variety of time series standards, and selecting the right one was an important decision in developing actverse. A consistent standard for time objects is essential, as time can be represented in many ways and may be based on different numerical systems. For packages that follow tidyverse principles, we believe the tsibble package provides the best time series standard. As its name suggests, tsibble extends the tidyverse tibble object for time series data.

Most actverse functions require your data to be in the tsibble format. Converting your data is straightforward and can significantly improve your experience working with time series in R. Please refer to the tsibble documentation for guidance on adapting your data.

Read/Write

Example:

r file <- get_from_zenodo( doi = "10.5281/zenodo.4898822", dir = tempdir(), file = "processed.txt" )

r data <- file |> read_acttrust(tz = "America/Sao_Paulo")

``` r library(dplyr)

data |> glimpse()

> Rows: 51,806

> Columns: 17

> $ timestamp 2021-04-24 04:14:00, 2021-04-24 04:15:00, 202…

> $ pim 7815, 2661, 3402, 4580, 2624, 3929, 5812, 3182…

> $ tat 608, 160, 243, 317, 255, 246, 369, 270, 373, 1…

> $ zcm 228, 64, 80, 125, 33, 105, 171, 54, 189, 64, 6…

> $ orientation 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…

> $ wrist_temperature 26.87, 27.18, 27.68, 27.86, 28.04, 28.13, 28.2…

> $ external_temperature 24.62, 25.06, 25.50, 25.75, 25.94, 26.06, 26.3…

> $ light 3.58, 5.23, 3.93, 4.14, 3.16, 3.63, 11.53, 2.4…

> $ ambient_light 1.45, 2.12, 1.59, 1.68, 1.28, 1.47, 4.67, 0.97…

> $ red_light 0.57, 0.86, 0.64, 0.67, 0.51, 0.56, 3.22, 0.37…

> $ green_light 0.66, 0.95, 0.71, 0.75, 0.57, 0.68, 3.49, 0.44…

> $ blue_light 0.24, 0.36, 0.26, 0.28, 0.21, 0.30, 1.48, 0.20…

> $ ir_light 0.17, 0.25, 0.20, 0.20, 0.16, 0.18, 1.00, 0.13…

> $ uva_light 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…

> $ uvb_light 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…

> $ event 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…

> $ state 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…

```

Sleep Statistics

  • sri(): Compute Phillips et al. Sleep Regularity Index (SRI).
  • state_prop(): Compute the proportion of time spent in a specific state (e.g., Sleeping, Awake).

Example:

Compare the results with the actogram plot shown in the following sections.

``` r sri_data <- data |> sri()

sri_data

> # A tsibble: 1,440 x 5 [1m]

> time state previous_state agreement sri

>

> 1 00'00" 77.1

> 2 01'00" 77.1

> 3 02'00" 77.1

> 4 03'00" 77.1

> 5 04'00" 77.1

> 6 05'00" 77.1

> # ℹ 1,434 more rows

```

``` r library(rutils) # github.com/danielvartan/rutils

sridata |> rutils:::statssummary("sri", threshold = NULL) |> print(n = Inf)

> # A tibble: 15 × 2

> name value

>

> 1 n 1440

> 2 nrmna 1440

> 3 n_na 0

> 4 mean 58.7795701029482

> 5 var 785.141504008496

> 6 sd 28.0203765857723

> 7 min -25

> 8 q_1 37.1428571428571

> 9 median 63.6363636363637

> 10 q_3 86.6666666666667

> 11 max 100

> 12 iqr 49.5238095238095

> 13 range 125

> 14 skewness -0.401815749365758

> 15 kurtosis 2.10073487543524

```

``` r library(ggplot2) library(scales)

sridata |> ggplot(ggplot2::aes(x = time, y = sri)) + geomsmooth(color = "#FC2913") + labs( x = "Time of day (Hour)", y = "Sleep Regularity Index (SRI)" ) + scalextime( breaks = breakswidth("6 hours"), labels = labeltime("%-H") # Use "%#H" for Windows ) + scaleycontinuous(limits = c(0, NA)) + actverse:::getactversetheme() ```

Period Functions

  • periodogram(): Compute Sokolove & Bushell’s $\chi^{2}$ periodogram.
  • spectrogram(): Create a spectrogram plot based on Sokolove & Bushell’s $\chi^{2}$ periodogram.

Example:

r data |> periodogram("pim")

r data |> spectrogram("pim")

Data Visualization

We strongly recommend using the ragg package as your backend graphics device for complex data visualizations. It is faster and produces higher quality images than R default graphics device.

  • actogram(): Create an actogram plot from actigraphy data.

r data |> actogram( col = "pim", days = -1, latitude = -23.55065, longitude = -46.63338, double_plot = TRUE )

Data Interpolation

  • na_approx() na_locf() na_overall_mean() na_overall_median() na_overall_mode() na_spline() na_weekly_mean() na_zero() na_plot(): Interpolate missing values in a numeric vector.

Example:

``` r x <- c(NA, 1, 5, 10, NA, 5, 10, 1, NA, 10, 1, 5, NA, NA) index <- seq(as.Date("2020-01-01"), as.Date("2020-01-14"), by = "day")

naapprox(x, index, fillna_tips = TRUE)

> [1] 1.0 1.0 5.0 10.0 7.5 5.0 10.0 1.0 5.5 10.0 1.0 5.0 5.0 5.0

```

r na_plot(x, index, na_approx(x, index, fill_na_tips = TRUE))

API Clients

Example:

``` r library(rutils) # github.com/danielvartan/rutils

getsunstats( latitude = -23.5489, longitude = -46.6388, tz = "America/SaoPaulo" ) |> rutils:::listas_tibble() |> print(n = Inf)

> # A tibble: 18 × 2

> name value

>

> 1 date 2025-06-05

> 2 latitude -23.5489

> 3 longitude -46.6388

> 4 tz America/Sao_Paulo

> 5 sunrise_start 06:44:16

> 6 sunrise_end 06:46:50

> 7 goldenhourend 07:17:28

> 8 solar_noon 12:06:31

> 9 goldenhourstart 16:55:34

> 10 sunset_start 17:26:13

> 11 sunset_end 17:28:46

> 12 dusk 17:53:17

> 13 nautical_dusk 18:21:18

> 14 night_start 18:48:54

> 15 nadir 00:06:31

> 16 night_end 05:24:08

> 17 nautical_dawn 05:51:44

> 18 dawn 06:19:45

```

Other Features

actverse also comes with many utility functions and provides actigraphy datasets for testing and learning purposes.

All functions are thoroughly documented, with detailed explanations of the underlying methodologies and computational guidelines. For a complete list of available functions and their documentation, click here.

Example:

``` r file |> readacttrust(regularize = FALSE) |> findepoch()

> $best_match

> [1] 60

>

> $prevalence

> # A tibble: 4 × 2

> epoch proportion

>

> 1 60 1.00

> 2 86 0.0000193

> 3 94 0.0000193

> 4 101 0.0000193

```

How to Cite

``` r citation("actverse")

> To cite {actverse} in publications use:

>

> Vartanian, D., Matias, V. A., Serrano, C. A. M., & Benedito-Silva,

> A. A. (2025). {actverse}: A Tidyverse-style toolbox for actigraphy

> data analysis [Computer software, R package].

> https://danielvartan.github.io/actverse/

>

> A BibTeX entry for LaTeX users is

>

> @Misc{,

> title = {{actverse}: A Tidyverse-style toolbox for actigraphy data analysis},

> author = {Daniel Vartanian and Vinicius Alves Matias and Cassio Almeida Mattos Serrano and Ana Amélia Benedito-Silva},

> year = {2025},

> url = {https://danielvartan.github.io/actverse/},

> note = {R package},

> }

```

License

actverse code is released under the MIT license. This means you can use, modify, and distribute the code freely, as long as you include the original license and copyright notice in any copies or substantial portions of the software.

Contributing

Contributions are welcome, including bug reports. Take a moment to review our Guidelines for Contributing.

You can also support the development of actverse by becoming a sponsor. Click here to make a donation. Please mention actverse in your donation message.

Owner

  • Name: Daniel Vartanian
  • Login: danielvartan
  • Kind: user
  • Location: São Paulo, Brazil
  • Company: @sustentarea

Academic. Passionate about #opendata and #openscience.

Citation (CITATION.cff) 

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    given-names: Hadley
    email: hadley@posit.co
  year: '2025'
  doi: 10.32614/CRAN.package.rlang
  version: '>= 1.1.6'
- type: software
  title: scales
  abstract: 'scales: Scale Functions for Visualization'
  notes: Imports
  url: https://scales.r-lib.org
  repository: https://CRAN.R-project.org/package=scales
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Pedersen
    given-names: Thomas Lin
    email: thomas.pedersen@posit.co
    orcid: https://orcid.org/0000-0002-5147-4711
  - family-names: Seidel
    given-names: Dana
  year: '2025'
  doi: 10.32614/CRAN.package.scales
  version: '>= 1.4.0'
- type: software
  title: stats
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2025'
  version: '>= 4.4'
- type: software
  title: stringr
  abstract: 'stringr: Simple, Consistent Wrappers for Common String Operations'
  notes: Imports
  url: https://stringr.tidyverse.org
  repository: https://CRAN.R-project.org/package=stringr
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2025'
  doi: 10.32614/CRAN.package.stringr
  version: '>= 1.5.1'
- type: software
  title: suncalc
  abstract: 'suncalc: Compute Sun Position, Sunlight Phases, Moon Position and Lunar
    Phase'
  notes: Imports
  url: https://github.com/datastorm-open/suncalc
  repository: https://CRAN.R-project.org/package=suncalc
  authors:
  - family-names: Thieurmel
    given-names: Benoit
    email: bthieurmel@gmail.com
  - family-names: Elmarhraoui
    given-names: Achraf
    email: achraf.elmar@gmail.com
  year: '2025'
  doi: 10.32614/CRAN.package.suncalc
  version: '>= 0.5.1'
- type: software
  title: tools
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2025'
  version: '>= 4.4'
- type: software
  title: tsibble
  abstract: 'tsibble: Tidy Temporal Data Frames and Tools'
  notes: Imports
  url: https://tsibble.tidyverts.org
  repository: https://CRAN.R-project.org/package=tsibble
  authors:
  - family-names: Wang
    given-names: Earo
    email: earo.wang@gmail.com
    orcid: https://orcid.org/0000-0001-6448-5260
  - family-names: Cook
    given-names: Di
    orcid: https://orcid.org/0000-0002-3813-7155
  - family-names: Hyndman
    given-names: Rob
    orcid: https://orcid.org/0000-0002-2140-5352
  - family-names: O'Hara-Wild
    given-names: Mitchell
    orcid: https://orcid.org/0000-0001-6729-7695
  year: '2025'
  doi: 10.32614/CRAN.package.tsibble
  version: '>= 1.1.6'
- type: software
  title: utils
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2025'
  version: '>= 4.4'
- type: software
  title: viridis
  abstract: 'viridis: Colorblind-Friendly Color Maps for R'
  notes: Imports
  url: https://sjmgarnier.github.io/viridis/
  repository: https://CRAN.R-project.org/package=viridis
  authors:
  - family-names: Garnier
    given-names: Simon
    email: garnier@njit.edu
  year: '2025'
  doi: 10.32614/CRAN.package.viridis
  version: '>= 0.6.5'
- type: software
  title: withr
  abstract: 'withr: Run Code ''With'' Temporarily Modified Global State'
  notes: Imports
  url: https://withr.r-lib.org
  repository: https://CRAN.R-project.org/package=withr
  authors:
  - family-names: Hester
    given-names: Jim
  - family-names: Henry
    given-names: Lionel
    email: lionel@posit.co
  - family-names: Müller
    given-names: Kirill
    email: krlmlr+r@mailbox.org
  - family-names: Ushey
    given-names: Kevin
    email: kevinushey@gmail.com
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Chang
    given-names: Winston
  year: '2025'
  doi: 10.32614/CRAN.package.withr
  version: '>= 3.0.2'
- type: software
  title: zoo
  abstract: 'zoo: S3 Infrastructure for Regular and Irregular Time Series (Z''s Ordered
    Observations)'
  notes: Imports
  url: https://zoo.R-Forge.R-project.org/
  repository: https://CRAN.R-project.org/package=zoo
  authors:
  - family-names: Zeileis
    given-names: Achim
    email: Achim.Zeileis@R-project.org
    orcid: https://orcid.org/0000-0003-0918-3766
  - family-names: Grothendieck
    given-names: Gabor
    email: ggrothendieck@gmail.com
  - family-names: Ryan
    given-names: Jeffrey A.
    email: jeff.a.ryan@gmail.com
  year: '2025'
  doi: 10.32614/CRAN.package.zoo
  version: '>= 1.8.14'
- type: software
  title: covr
  abstract: 'covr: Test Coverage for Packages'
  notes: Suggests
  url: https://covr.r-lib.org
  repository: https://CRAN.R-project.org/package=covr
  authors:
  - family-names: Hester
    given-names: Jim
    email: james.f.hester@gmail.com
  year: '2025'
  doi: 10.32614/CRAN.package.covr
  version: '>= 3.6.4'
- type: software
  title: knitr
  abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
  notes: Suggests
  url: https://yihui.org/knitr/
  repository: https://CRAN.R-project.org/package=knitr
  authors:
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  year: '2025'
  doi: 10.32614/CRAN.package.knitr
  version: '>= 1.50'
- type: software
  title: rmarkdown
  abstract: 'rmarkdown: Dynamic Documents for R'
  notes: Suggests
  url: https://pkgs.rstudio.com/rmarkdown/
  repository: https://CRAN.R-project.org/package=rmarkdown
  authors:
  - family-names: Allaire
    given-names: JJ
    email: jj@posit.co
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  - family-names: Dervieux
    given-names: Christophe
    email: cderv@posit.co
    orcid: https://orcid.org/0000-0003-4474-2498
  - family-names: McPherson
    given-names: Jonathan
    email: jonathan@posit.co
  - family-names: Luraschi
    given-names: Javier
  - family-names: Ushey
    given-names: Kevin
    email: kevin@posit.co
  - family-names: Atkins
    given-names: Aron
    email: aron@posit.co
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Cheng
    given-names: Joe
    email: joe@posit.co
  - family-names: Chang
    given-names: Winston
    email: winston@posit.co
  - family-names: Iannone
    given-names: Richard
    email: rich@posit.co
    orcid: https://orcid.org/0000-0003-3925-190X
  year: '2025'
  doi: 10.32614/CRAN.package.rmarkdown
  version: '>= 2.29'
- type: software
  title: spelling
  abstract: 'spelling: Tools for Spell Checking in R'
  notes: Suggests
  url: https://ropensci.r-universe.dev/spelling
  repository: https://CRAN.R-project.org/package=spelling
  authors:
  - family-names: Ooms
    given-names: Jeroen
    email: jeroenooms@gmail.com
    orcid: https://orcid.org/0000-0002-4035-0289
  - family-names: Hester
    given-names: Jim
    email: james.hester@rstudio.com
  year: '2025'
  doi: 10.32614/CRAN.package.spelling
  version: '>= 2.3.1'
- type: software
  title: testthat
  abstract: 'testthat: Unit Testing for R'
  notes: Suggests
  url: https://testthat.r-lib.org
  repository: https://CRAN.R-project.org/package=testthat
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2025'
  doi: 10.32614/CRAN.package.testthat
  version: '>= 3.2.3'
- type: software
  title: tibble
  abstract: 'tibble: Simple Data Frames'
  notes: Suggests
  url: https://tibble.tidyverse.org/
  repository: https://CRAN.R-project.org/package=tibble
  authors:
  - family-names: Müller
    given-names: Kirill
    email: kirill@cynkra.com
    orcid: https://orcid.org/0000-0002-1416-3412
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  year: '2025'
  doi: 10.32614/CRAN.package.tibble
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    "SystemRequirements": null
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  "fileSize": "2001.231KB",
  "citation": [
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      "@type": "CreativeWork",
      "datePublished": "2025",
      "author": [
        {
          "@type": "Person",
          "givenName": "Daniel",
          "familyName": "Vartanian",
          "email": "danvartan@gmail.com",
          "@id": "https://orcid.org/0000-0001-7782-759X"
        },
        {
          "@type": "Person",
          "givenName": "Vinicius Alves",
          "familyName": "Matias",
          "email": "viniciusmatias@usp.br",
          "@id": "https://orcid.org/0000-0002-2047-5420"
        },
        {
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          "givenName": "Cassio Almeida Mattos",
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          "email": "cassio.serrano@usp.br",
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        },
        {
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          "givenName": "Ana Amlia",
          "familyName": "Benedito-Silva",
          "email": "aamelia@usp.br",
          "@id": "https://orcid.org/0000-0003-0667-9504"
        }
      ],
      "name": "{actverse}: A Tidyverse-style toolbox for actigraphy data analysis",
      "url": "https://danielvartan.github.io/actverse/",
      "description": "R package"
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  "releaseNotes": "https://github.com/danielvartan/actverse/blob/master/NEWS.md",
  "readme": "https://github.com/danielvartan/actverse/blob/main/README.md",
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    "https://app.codecov.io/gh/danielvartan/actverse?branch=main"
  ],
  "developmentStatus": "https://www.repostatus.org/#active",
  "keywords": [
    "actigraphy",
    "sleep",
    "chronobiology",
    "r",
    "rstats",
    "physiology",
    "actogram",
    "data-interpolation",
    "periodograms",
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    "time-series",
    "time-series-analysis",
    "accelerometry",
    "biomedical-data-science",
    "health-data",
    "r-packages",
    "sensor-data",
    "wearables",
    "physiological-monitoring",
    "actimetry"
  ]
}

GitHub Events

Total
  • Create event: 1
  • Release event: 1
  • Issues event: 2
  • Watch event: 1
  • Push event: 20
Last Year
  • Create event: 1
  • Release event: 1
  • Issues event: 2
  • Watch event: 1
  • Push event: 20

Issues and Pull Requests

Last synced: over 1 year ago

All Time
  • Total issues: 37
  • Total pull requests: 7
  • Average time to close issues: 7 months
  • Average time to close pull requests: 6 months
  • Total issue authors: 1
  • Total pull request authors: 2
  • Average comments per issue: 0.08
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • danielvartan (24)
Pull Request Authors
  • matiasvinicius (3)
  • danielvartan (1)
Top Labels
Issue Labels
enhancement (14) incomplete (13)
Pull Request Labels
enhancement (3)

Dependencies

DESCRIPTION cran
  • R >= 4.0 depends
  • checkmate >= 2.0.0 imports
  • cli >= 3.2.0 imports
  • dplyr >= 1.0.8 imports
  • ggplot2 >= 3.3.5 imports
  • hms >= 1.1.1 imports
  • lifecycle >= 1.0.1 imports
  • lubridate >= 1.8.0 imports
  • magrittr >= 2.0.3 imports
  • purrr >= 0.3.4 imports
  • rlang >= 1.0.2 imports
  • stats >= 4.0.0 imports
  • tsibble >= 1.1.1 imports
  • viridis >= 0.6.2 imports
  • withr >= 2.5.0 imports
  • covr >= 3.5.1 suggests
  • curl >= 4.3.2 suggests
  • jsonlite >= 1.8.0 suggests
  • knitr >= 1.37 suggests
  • mockr >= 0.1 suggests
  • parallel >= 4.0.0 suggests
  • plotly >= 4.10.0 suggests
  • readr >= 2.1.2 suggests
  • rmarkdown >= 2.13 suggests
  • spelling >= 2.2 suggests
  • suncalc >= 0.5.0 suggests
  • testthat >= 3.1.2 suggests
  • tibble >= 3.1.6 suggests
  • tools >= 4.0.0 suggests
  • utils >= 4.0.0 suggests
  • zoo >= 1.8 suggests
.github/workflows/check-pak.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/pkgdown-pak.yaml actions
  • actions/checkout v2 composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite
  • r-lib/actions/setup-r-dependencies v1 composite
.github/workflows/test-coverage-pak.yaml actions
  • actions/checkout v3 composite
  • actions/upload-artifact v3 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite