Athlytics: Sports Physiology Analytics from Local Activity Files and 'Strava' Exports

[HzaCode]

Submitting Author Name: Zhiang He
Submitting Author Github Handle: @HzaCode
Repository: https://github.com/HzaCode/Athlytics
Version submitted: 1.0.0
Submission type: Standard
Editor: TBD
Reviewers: TBD

Archive: TBD
Version accepted: TBD
Language: en

---

• Paste the full DESCRIPTION file inside a code block below:

Package: Athlytics
Title: Academic R Package for Sports Physiology Analysis from Local 'Strava' Data
Version: 1.0.0
Author: Zhiang He [aut, cre]
Maintainer: Zhiang He <ang@hezhiang.com>
Authors@R:
    person("Zhiang", "He", email = "ang@hezhiang.com", role = c("aut", "cre"))
Description: An open-source computational framework for longitudinal analysis of 
    exercise physiology metrics using local 'Strava' data exports. Designed 
    for personal analysis and sports science applications, this package provides 
    standardized functions to calculate and visualize key physiological indicators 
    including Acute:Chronic Workload Ratio (ACWR), Efficiency Factor (EF), and 
    training load metrics.
License: MIT + file LICENSE
URL: https://hezhiang.com/Athlytics/, https://github.com/HzaCode/Athlytics
BugReports: https://github.com/HzaCode/Athlytics/issues
Encoding: UTF-8
LazyData: true
Depends:
    R (>= 3.6.0)
Imports:
    dplyr (>= 1.0.0),
    ggplot2,
    lubridate,
    purrr,
    readr,
    rlang (>= 0.4.0),
    tidyr,
    viridis,
    zoo,
    R.utils,
    tools,
    utils
Suggests:
    devtools,
    knitr,
    pkgdown,
    rmarkdown,
    testthat (>= 3.0.0),
    mockery,
    XML,
    rStrava,
    xml2
Remotes:
    grimbough/FITfileR
VignetteBuilder: knitr
RoxygenNote: 7.3.3
Roxygen: list(markdown = TRUE)
NeedsCompilation: no

Scope

• Please indicate which category or categories from our [package fit policies](https://devguide.ropensci.org/softwarereview_policies.html#package-categories) this package falls under: (Please check an appropriate box below. If you are unsure, we suggest you make a pre-submission inquiry.):

  • data retrieval
  • data extraction
  • data munging
  • data deposition
  • data validation and testing
  • workflow automation
  • version control
  • citation management and bibliometrics
  • scientific software wrappers
  • field and lab reproducibility tools
  • database software bindings
  • geospatial data
  • translation

• Explain how and why the package falls under these categories (briefly, 1-2 sentences):

Athlytics provides a standardized, reproducible offline workflow for local Strava exports, covering cleaning/QC, computation of key physiology metrics (ACWR, EF, training load), and visualization. It emphasizes validation, automated pipelines, and research-grade reproducibility.

• Who is the target audience and what are scientific applications of this package?

Sports scientists, exercise physiologists, coaches, and researchers analyzing endurance training. Applications include workload monitoring (ACWR), aerobic efficiency tracking (EF), decoupling assessment, and cohort benchmarking for longitudinal studies.

• Are there other R packages that accomplish the same thing? If so, how does yours differ or meet [our criteria for best-in-category](https://ropensci.github.io/dev_guide/policies.html#overlap)?

rStrava focuses on API retrieval; trackeR/activatr provide general activity analytics. Athlytics is API-free and privacy-first, offering an end-to-end, reproducible analysis pipeline with built-in physiological models tailored for research settings.

• (If applicable) Does your package comply with our guidance around Ethics, Data Privacy and Human Subjects Research?

Yes. Analyses operate solely on user-owned local exports; no external personal data collection. Documentation encourages de-identification and minimal-data practices.

• If you made a pre-submission inquiry, please paste the link to the corresponding issue, forum post, or other discussion, or @tag the editor you contacted.

Pre-submission inquiry:
rOpenSci discussion #702 (Sports Analytics category).
JOSS submission (review paused):openjournals/joss-reviews#9075

• Explain reasons for any pkgcheck items which your package is unable to pass.

None — all required pkgcheck items pass.

Technical checks

Confirm each of the following by checking the box.

• I have read the rOpenSci packaging guide.
• I have read the [author guide](https://devguide.ropensci.org/softwarereview_author.html) and I expect to maintain this package for at least 2 years or to find a replacement.

This package:

• does not violate the Terms of Service of any service it interacts with.
• has a CRAN and OSI accepted license.
• contains a [README with instructions for installing the development version](https://ropensci.github.io/dev_guide/building.html#readme).
• includes [documentation with examples for all functions, created with roxygen2](https://ropensci.github.io/dev_guide/building.html#documentation).
• contains a vignette with examples of its essential functions and uses.
• has a [test suite](https://ropensci.github.io/dev_guide/building.html#testing).
• has [continuous integration](https://ropensci.github.io/dev_guide/ci.html), including reporting of test coverage.

Publication options

• Do you intend for this package to go on CRAN?

• Do you intend for this package to go on Bioconductor?

• Do you wish to submit an Applications Article about your package to [Methods in Ecology and Evolution](http://besjournals.onlinelibrary.wiley.com/hub/journal/10.1111/%28ISSN%292041-210X/)? If so:

MEE Options

• The package is novel and will be of interest to the broad readership of the journal.
• The manuscript describing the package is no longer than 3000 words.
• You intend to archive the code for the package in a long-term repository which meets the requirements of the journal (see [MEE's Policy on Publishing Code](https://besjournals.onlinelibrary.wiley.com/hub/journal/2041210x/policyonpublishingcode.html))
• (Scope: Do consider MEE's [Aims and Scope](http://besjournals.onlinelibrary.wiley.com/hub/journal/10.1111/%28ISSN%292041-210X/aims-and-scope/read-full-aims-and-scope.html) for your manuscript. We make no guarantee that your manuscript will be within MEE scope.)
• (Although not required, we strongly recommend having a full manuscript prepared when you submit here.)
• (Please do not submit your package separately to Methods in Ecology and Evolution)

Code of conduct

• I agree to abide by [rOpenSci's Code of Conduct](https://ropensci.org/code-of-conduct/) during the review process and in maintaining my package should it be accepted.

[ropensci-review-bot]

Thanks for submitting to rOpenSci, our editors and @ropensci-review-bot will reply soon. Type @ropensci-review-bot help for help.

[ropensci-review-bot]

🚀

The following problem was found in your submission template:

• URL = [https://github.com/HzaCode/Athlytics] is not valid
  The package could not be checked because of problems with the URL.
  Editors: Please ensure these problems are rectified, and then call @ropensci-review-bot check package.

👋

[mpadge]

Sorry for any confusion @HzaCode, but you'll need to update the "Repository" field in the template metadata from what you've currently got:

Repository:  <!--repourl-->[https://github.com/HzaCode/Athlytics](https://github.com/HzaCode/Athlytics)<!--end-repourl-->

to just a plain URL:

Repository:  <!--repourl-->https://github.com/HzaCode/Athlytics<!--end-repourl-->

Once you've done that, please call @ropensci-review-bot check package to start the checks. Thanks!

[HzaCode]

@ropensci-review-bot check package

[HzaCode]

Hi @mpadge — thank you for the earlier note!

I’ve updated the submission so that the Repository field now contains a plain URL and the template tags are intact.

When convenient, could you please trigger @ropensci-review-bot check package to rerun the pkgcheck?

Much appreciated for your time and help!

[mpadge]

@ropensci-review-bot check package

[ropensci-review-bot]

Thanks, about to send the query.

[ropensci-review-bot]

🚀

Editor check started

👋

[mpadge]

@HzaCode I've no idea why your check package command didn't trigger the checks, but all seems good now anyway. You can definitely issue that call yourself at any stage.

[ropensci-review-bot]

Checks for Athlytics (v1.0.0)

git hash: 4b0dcffa

• ✔️ Package is already on CRAN.
• ✔️ has a 'codemeta.json' file.
• ✔️ has a 'contributing' file.
• ✔️ uses 'roxygen2'.
• ✔️ 'DESCRIPTION' has a URL field.
• ✔️ 'DESCRIPTION' has a BugReports field.
• ✔️ Package has at least one HTML vignette
• ✔️ All functions have examples.
• ✖️ Package has no continuous integration checks.
• ✔️ Package coverage is 84.3%.
• ✔️ R CMD check found no errors.
• ✖️ R CMD check found 1 warning.
• 👀 Some goodpractice linters failed.
• 👀 Package depends on the following obsolete packages: [XML]
• 👀 Function names are duplicated in other packages
• 👀 Examples should not use \dontrun{} unless really necessary.

Important: All failing checks above must be addressed prior to proceeding

(Checks marked with 👀 may be optionally addressed.)

Package License: MIT + file LICENSE

---

1. Package Dependencies

Details of Package Dependency Usage (click to open)

The table below tallies all function calls to all packages ('ncalls'), both internal (r-base + recommended, along with the package itself), and external (imported and suggested packages). 'NA' values indicate packages to which no identified calls to R functions could be found. Note that these results are generated by an automated code-tagging system which may not be entirely accurate.

type	package	ncalls
internal	base	596
internal	Athlytics	56
internal	stats	40
internal	graphics	7
internal	grDevices	1
imports	ggplot2	251
imports	dplyr	38
imports	zoo	38
imports	lubridate	36
imports	utils	21
imports	purrr	13
imports	tidyr	7
imports	readr	5
imports	viridis	4
imports	R.utils	3
imports	rlang	2
imports	tools	2
suggests	XML	37
suggests	devtools	NA
suggests	knitr	NA
suggests	pkgdown	NA
suggests	rmarkdown	NA
suggests	testthat	NA
suggests	mockery	NA
suggests	rStrava	NA
suggests	xml2	NA
linking_to	NA	NA

Click below for tallies of functions used in each package. Locations of each call within this package may be generated locally by running 's <- pkgstats::pkgstats(<path/to/repo>)', and examining the 'external_calls' table.

base

if (44), c (42), return (41), list (37), data.frame (32), nrow (27), as.numeric (24), date (24), tryCatch (24), length (21), numeric (21), sum (14), character (13), min (13), is.na (12), max (12), Sys.Date (12), is.null (11), names (11), colnames (10), load (10), ifelse (7), labels (7), by (6), diff (6), round (6), for (5), paste (5), apply (4), col (4), ncol (4), pi (4), seq (4), setdiff (4), abs (3), as.character (3), as.POSIXct (3), ceiling (3), lapply (3), paste0 (3), range (3), remove (3), switch (3), which (3), cos (2), do.call (2), file.path (2), format (2), integer (2), log (2), logical (2), match.arg (2), rbind (2), sapply (2), sin (2), sprintf (2), sqrt (2), tolower (2), all (1), atan2 (1), basename (1), cummin (1), difftime (1), floor (1), grep (1), grepl (1), gsub (1), matrix (1), mean (1), replace (1), sample (1), t (1), tempdir (1), tempfile (1), unique (1)

ggplot2

element_text (75), aes (42), ggplot (21), margin (14), scale_x_date (13), geom_point (11), annotate (8), geom_smooth (7), geom_hline (6), element_blank (5), scale_color_manual (5), theme_minimal (5), element_line (4), geom_ribbon (4), coord_cartesian (3), element_rect (3), facet_wrap (3), geom_abline (3), geom_line (3), margi (3), scale_shape_manual (3), guide_legend (2), guides (2), scale_color_viridis_d (2), scale_y_continuous (2), unit (2)

Athlytics

safe_as_numeric (26), english_month_year (5), bootstrap_acwr_ci (2), explicit_english_month_year (2), add_reference_bands (1), athlytics_colors_acwr_zones (1), athlytics_colors_ef (1), athlytics_colors_training_load (1), athlytics_palette_academic (1), athlytics_palette_cell (1), athlytics_palette_nature (1), athlytics_palette_science (1), athlytics_palette_vibrant (1), calc_distance (1), calculate_acwr (1), calculate_acwr_ewma (1), calculate_acwr_ewma_internal (1), calculate_acwr_ra_internal (1), calculate_daily_load (1), calculate_single_decoupling (1), extract_trackpoint (1), extract_trkpt (1), find_best_effort (1), FUN (1), parse_activity_file (1)

stats

time (10), power (6), quantile (6), df (5), sd (4), dist (3), median (3), end (2), dt (1)

dplyr

first (6), lag (6), summarise (6), select (4), tibble (4), left_join (3), mutate (3), n_distinct (2), all_of (1), bind_rows (1), case_when (1), filter (1)

zoo

rollmean (33), rollapply (5)

XML

xmlValue (14), xpathSApply (14), getNodeSet (4), xmlGetAttr (2), xmlParse (2), xmlRoot (1)

lubridate

as_date (21), days (8), as_datetime (4), month (1), seconds_to_period (1), year (1)

utils

data (13), unzip (5), getFromNamespace (2), packageDescription (1)

purrr

map_dfr (13)

graphics

title (7)

tidyr

pivot_wider (6), drop_na (1)

readr

cols (3), read_csv (2)

viridis

scale_color_viridis (4)

R.utils

gunzip (3)

rlang

expr (2)

tools

file_ext (1), toTitleCase (1)

grDevices

colors (1)

---

2. Statistical Properties

This package features some noteworthy statistical properties which may need to be clarified by a handling editor prior to progressing.

Details of statistical properties (click to open)

The package has:

• code in R (100% in 20 files) and
• 1 authors
• 2 vignettes
• 5 internal data files
• 12 imported packages
• 35 exported functions (median 55 lines of code)
• 66 non-exported functions in R (median 34 lines of code)

---

Statistical properties of package structure as distributional percentiles in relation to all current CRAN packages
The following terminology is used:

• loc = "Lines of Code"
• fn = "function"
• exp/not_exp = exported / not exported

All parameters are explained as tooltips in the locally-rendered HTML version of this report generated by the checks_to_markdown() function

The final measure (fn_call_network_size) is the total number of calls between functions (in R), or more abstract relationships between code objects in other languages. Values are flagged as "noteworthy" when they lie in the upper or lower 5th percentile.

measure	value	percentile	noteworthy
files_R	20	79.8
files_vignettes	2	81.7
files_tests	49	98.9
loc_R	2626	86.3
loc_vignettes	663	82.7
loc_tests	5604	97.9	TRUE
num_vignettes	2	84.9
data_size_total	34892	76.9
data_size_median	1544	66.2
n_fns_r	101	74.9
n_fns_r_exported	35	80.8
n_fns_r_not_exported	66	72.7
n_fns_per_file_r	3	45.6
num_params_per_fn	6	77.3
loc_per_fn_r	43	86.6
loc_per_fn_r_exp	55	81.6
loc_per_fn_r_not_exp	34	81.9
rel_whitespace_R	22	88.7
rel_whitespace_vignettes	44	89.6
rel_whitespace_tests	26	98.7	TRUE
doclines_per_fn_exp	34	40.7
doclines_per_fn_not_exp	0	0.0	TRUE
fn_call_network_size	46	62.9

---

2a. Network visualisation

Click to see the interactive network visualisation of calls between objects in package

---

3. goodpractice and other checks

Details of goodpractice checks (click to open)

---

3b. goodpractice results

R CMD check with rcmdcheck

R CMD check generated the following warning:

1. checking dependencies in R code ... WARNING
   'loadNamespace' or 'requireNamespace' call not declared from: ‘FITfileR’

R CMD check generated the following check_fails:

1. cyclocomp
2. no_import_package_as_a_whole
3. rcmdcheck_undeclared_loadnamespace_requirenamespace

Test coverage with covr

Package coverage: 84.32

Cyclocomplexity with cyclocomp

The following functions have cyclocomplexity >= 15:

function	cyclocomplexity
calculate_acwr	83
calculate_ef	77
calculate_decoupling	47
calculate_acwr_ewma	43
calculate_exposure	42
plot_acwr_enhanced	38
calculate_ef_from_stream	33
calculate_daily_load	30
calculate_single_decoupling	29
load_local_activities	29
calculate_pbs	27
flag_quality	25
plot_acwr	25
find_best_effort	20
plot_pbs	20
plot_ef	18
parse_activity_file	16
parse_fit_file	16
parse_tcx_file	16
plot_decoupling	16

Static code analyses with lintr

lintr found no issues with this package!

---

4. Other Checks

Details of other checks (click to open)

✖️ Package contains the following obsolete packages:

• XML

See our Recommended Scaffolding for alternatives.

✖️ The following 2 function names are duplicated in other packages:

• • calculate_exposure from optic
• • plot_exposure from mSigTools, GeoTox, rbioacc

---

Package Versions

package	version
pkgstats	0.2.0.68
pkgcheck	0.1.2.239

---

Editor-in-Chief Instructions:

Processing may not proceed until the items marked with ✖️ have been resolved.

[mpadge]

@HzaCode The R CMD check warning there seems to be genuine - click on "Details of goodpractice" to see. The ✖️ "no continuous integration" is because our checks expect standard markdown syntax for badges in the README, whereas you've got HTML. While we could update our system, README.md really is intended to be markdown, so should have all badge links in markdown format. Many commands to automatically add badges will output the markdown lines needed to display them, or you could just look at any example repo of an R package to see what most look like. Likely more importantly, many of your current badge svg links are indirect, through shields.io, while they should preferably use direct versions, for example directly from github.com for all workflow-related badges, or directly from codecov for that one. Your pkgcheck badge is an example of the confusion that can ensue from indirect badges - you don't actually have the pkgcheck-action installed here, and that action has no badge associated with it anyway. (But it will likely help you to install it regardless, so please do!)

Once you've fixed those, and confirmed ideally via local pkgcheck-action run, then feel free to ask the bot to check package again. Thanks!

[HzaCode]

@ropensci-review-bot check package

[ropensci-review-bot]

Thanks, about to send the query.

[ropensci-review-bot]

🚀

Editor check started

👋