Pre-submission inquiry: brapiR2 - BrAPI v2 client for plant breeding databases

[josh45-source]

Submitting Author Name: Joash Joshua Ayo
Submitting Author Github Handle: @josh45-source
Repository: https://github.com/josh45-source/brapiR2
Submission type: Pre-submission
Language: en

---

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

Package: brapiR2
Title: A Tidyverse-Native Client for the BrAPI v2 (Breeding API) Specification
Version: 0.1.0
Authors@R: 
    person("Joash Joshua", "Ayo", , "joashjoshua789@gmail.com", role = c("aut", "cre"))
Description: Provides pipe-friendly, stateless access to every endpoint in the 
    Breeding API (BrAPI) v2.1 specification. Covers all four BrAPI modules -- 
    Core, Germplasm, Phenotyping, and Genotyping -- returning tidy tibbles ready 
    for analysis. Features include automatic pagination, async search handling, 
    response caching, parallel batch fetching, and convenience functions for 
    genomic selection workflows (e.g. dosage matrix extraction). Designed for 
    plant breeders and bioinformaticians who need programmatic access to 
    BreedBase, BMS, EBS, GIGWA, Germinate, and any BrAPI-compliant server.
License: MIT + file LICENSE
URL: https://github.com/josh45-source/brapiR2
BugReports: https://github.com/josh45-source/brapiR2/issues
Depends:
    R (>= 4.1.0)
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Imports: 
    cli (>= 3.6.0),
    dplyr (>= 1.1.0),
    glue (>= 1.6.0),
    httr2 (>= 1.0.0),
    jsonlite (>= 1.8.0),
    purrr (>= 1.0.0),
    rlang (>= 1.1.0),
    tibble (>= 3.2.0),
    tidyr (>= 1.3.0),
    tidyselect (>= 1.2.0)
Suggests: 
    furrr (>= 0.3.0),
    future (>= 1.33.0),
    httptest2,
    knitr,
    rappdirs,
    rmarkdown,
    testthat (>= 3.0.0),
    withr
Config/testthat/edition: 3
VignetteBuilder: knitr

Scope

• Please indicate which category or categories from our package fit policies or statistical package categories this package falls under. (Please check one or more appropriate boxes below):

  *Data Lifecycle Packages

  • 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

  *Statistical Packages

  • Bayesian and Monte Carlo Routines
  • Dimensionality Reduction, Clustering, and Unsupervised Learning
  • Machine Learning
  • Regression and Supervised Learning
  • Exploratory Data Analysis (EDA) and Summary Statistics
  • Spatial Analyses
  • Time Series Analyses
  • Probability Distributions

• Explain how and why the package falls under these categories (briefly, 1-2 sentences). Please note any areas you are unsure of:

brapiR2 is a data retrieval package that provides programmatic access to plant breeding databases via the Breeding API (BrAPI) v2.1 specification. It retrieves phenotypic trial data, genotypic variant data, germplasm records, and pedigree information from BrAPI-compliant servers (BreedBase, BMS, EBS, GIGWA, Germinate) and returns them as tidy tibbles ready for analysis in R.

• If submitting a statistical package, have you already incorporated documentation of standards into your code via the srr package?

N/A — this is not a statistical package.

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

The target audience is plant breeders, quantitative geneticists, and bioinformaticians who need programmatic, reproducible access to breeding databases. BrAPI is adopted by CGIAR centers, national breeding programs, and private breeding companies worldwide.

Scientific applications include

• Pulling phenotypic trial data for spatial analysis and multi-environment modeling

• Extracting genotypic data as dosage matrices for genomic prediction (rrBLUP, BGLR, sommer)

• Batch retrieval of germplasm pedigree information for genetic studies

• Building reproducible data access pipelines (replacing manual web portal downloads)

• Are there other R packages that accomplish the same thing? If so, how does yours differ or meet our criteria for best-in-category?

Yes. QBMS (on CRAN, ~9,400 downloads) is the primary existing R client for BrAPI. brapiR2 differs in design philosophy and scope:

Feature	brapiR2	QBMS
Design	Stateless, functional, pipe-friendly	Stateful, menu-driven (set_program > set_trial > set_study)
BrAPI v2 coverage	Full spec — all 4 modules	Partial (phenotyping focus)
Genotyping endpoints	Native variants, callsets, allele matrices, dosage extraction	Limited (via GIGWA wrapper)
Return type	Always tibbles	Mixed lists/dataframes
Caching	Built-in with configurable TTL	None
Parallel fetching	Via furrr	Sequential

brapiR2 complements QBMS - QBMS is excellent for interactive exploration, while brapiR2 targets reproducible scripting and pipeline building. The genotyping module coverage is the strongest differentiator.

There was also an older brapi package by CIP-RIU on GitHub targeting BrAPI v1, which appears unmaintained.

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

Yes. brapiR2 accesses only plant breeding data (phenotypic measurements, genotypic markers, germplasm records). No human subjects data is involved. Authentication credentials are handled via explicit connection objects and are never stored globally or logged.

• Any other questions or issues we should be aware of?

• The package has 117 integration tests against the public BrAPI test server at https://test-server.brapi.org (guarded by skip_on_cran() and skip_if_offline())

• 3 vignettes: getting started, genomic selection pipeline, multi-environment analysis

• pkgdown documentation site: https://josh45-source.github.io/brapiR2/

• GitHub Actions CI across macOS, Windows, and Ubuntu with multiple R versions

• Built with httr2 (not httr), fully stateless (no global state or side effects)

• The BrAPI specification is open source (CC-BY license) and explicitly encourages client development

• brapiR2 has been submitted to the BrAPI compatible software registry at brapi.org

• Not yet on CRAN intending to submit after rOpenSci review

Use of Generative AI

• Generative AI tools were used to produce some of the material in this submission.

Claude Code (Anthropic's AI coding assistant) was used as a development aid throughout the package creation process. Specifically

• Code scaffolding - Claude Code generated initial function structures, roxygen2 documentation skeletons, and test file templates, which were then reviewed, tested against the live BrAPI test server, and iteratively refined.
• Debugging - Claude Code helped diagnose and fix issues found during devtools::check() and integration testing (e.g., non-ASCII characters, import directives, test expectations for cli output).
• CI/CD setup - GitHub Actions workflow files were generated with Claude Code assistance.

All generated code was verified through: (1) devtools::check() passing with 0 errors and 0 warnings, (2) 117 integration tests passing against the live BrAPI test server, and (3) manual review of all function outputs. The package architecture, API design decisions (stateless connection objects, tibble-only returns, BrAPI module organization), and scientific domain logic were directed by the author.

The full development history is visible in the git log: https://github.com/josh45-source/brapiR2/commits/main

[ropensci-review-bot]

Thanks for your pre-submission to rOpenSci, our editors will reply soon.

[ropensci-review-bot]

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---

Matches are generated by the 'pkgmatch' package, based on inverse-term frequencies; see the main function documentation for details.

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Checks for brapiR2 (v0.1.0)

git hash: adfec769

• ✔️ Package name is available
• ✔️ has a 'contributing' file.
• ✔️ uses 'roxygen2'.
• ✔️ 'DESCRIPTION' has a URL field.
• ✔️ 'DESCRIPTION' has a BugReports field.
• ✔️ Package has at least one HTML vignette
• ✖️ These functions do not have examples: [brapi_allele_matrix, brapi_cache_clear, brapi_call_sets, brapi_calls, brapi_crosses, brapi_crossing_projects, brapi_events, brapi_germplasm_attributes, brapi_germplasm_detail, brapi_germplasm_pedigree, brapi_germplasm_progeny, brapi_germplasm, brapi_images, brapi_lists, brapi_locations, brapi_methods, brapi_observation_units, brapi_observation_variables, brapi_observations, brapi_people, brapi_program, brapi_reference_sets, brapi_references, brapi_samples, brapi_scales, brapi_search_calls, brapi_search_germplasm, brapi_search_observations, brapi_search_variables, brapi_search_variants, brapi_seasons, brapi_seed_lots, brapi_study, brapi_traits, brapi_trial, brapi_variant_sets, brapi_variants, print.brapi_con].
• ✖️ Repository has no website
• ✔️ Package has continuous integration checks.
• ✖️ Package coverage is 65.6% (should be at least 75%).
• ✔️ R CMD check found no errors.
• ✔️ R CMD check found no warnings.
• 👀 Some goodpractice linters failed.
• 👀 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	110
internal	brapiR2	64
internal	utils	4
imports	purrr	15
imports	rlang	15
imports	httr2	14
imports	tibble	12
imports	glue	8
imports	dplyr	3
imports	jsonlite	2
imports	tidyr	2
imports	cli	1
imports	tidyselect	1
suggests	future	3
suggests	furrr	2
suggests	AGHmatrix	NA
suggests	BGLR	NA
suggests	httptest2	NA
suggests	knitr	NA
suggests	lme4	NA
suggests	metan	NA
suggests	rappdirs	NA
suggests	rmarkdown	NA
suggests	rrBLUP	NA
suggests	sommer	NA
suggests	testthat	NA
suggests	withr	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

list (33), body (18), drop (7), dir (6), c (4), for (4), if (4), names (3), unlist (3), as.matrix (2), character (2), intersect (2), is.null (2), length (2), paste0 (2), seq_len (2), url (2), version (2), as.integer (1), as.numeric (1), lapply (1), list.files (1), order (1), q (1), row (1), seq_along (1), setdiff (1), strsplit (1)

brapiR2

brapi_req (7), brapi_observations (3), brapi_allele_matrix (2), brapi_cache_clear (1), brapi_cache_enable (1), brapi_call_sets (1), brapi_calls (1), brapi_connection (1), brapi_crosses (1), brapi_crossing_projects (1), brapi_endpoints (1), brapi_events (1), brapi_fetch_parallel (1), brapi_germplasm (1), brapi_germplasm_attributes (1), brapi_germplasm_detail (1), brapi_germplasm_pedigree (1), brapi_germplasm_progeny (1), brapi_get (1), brapi_get_dosage_matrix (1), brapi_get_marker_map (1), brapi_images (1), brapi_lists (1), brapi_locations (1), brapi_login (1), brapi_login_oauth2 (1), brapi_methods (1), brapi_observation_units (1), brapi_observation_variables (1), brapi_people (1), brapi_ping (1), brapi_post_search (1), brapi_program (1), brapi_programs (1), brapi_reference_sets (1), brapi_references (1), brapi_samples (1), brapi_scales (1), brapi_search_calls (1), brapi_search_germplasm (1), brapi_search_observations (1), brapi_search_variables (1), brapi_search_variants (1), brapi_seasons (1), brapi_seed_lots (1), brapi_server_info (1), brapi_set_token (1), brapi_studies (1), brapi_study (1), brapi_study_data (1), brapi_traits (1), brapi_trial (1), brapi_trials (1), brapi_variant_sets (1), brapi_variants (1)

purrr

compact (12), map (3)

rlang

%||% (13), hash (1), warn (1)

httr2

resp_body_json (7), request (3), resp_status (3), req_perform (1)

tibble

tibble (10), as_tibble (2)

glue

glue (8)

utils

data (4)

dplyr

bind_rows (1), filter (1), mutate (1)

future

plan (2), multisession (1)

furrr

future_map_dfr (2)

jsonlite

fromJSON (1), toJSON (1)

tidyr

pivot_wider (2)

cli

cli_abort (1)

tidyselect

where (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 10 files) and
• 1 authors
• 3 vignettes
• no internal data file
• 10 imported packages
• 59 exported functions (median 6 lines of code)
• no non-exported function in R (median 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	10	74.3
files_vignettes	3	94.2
files_tests	6	90.7
loc_R	666	77.7
loc_vignettes	386	72.8
loc_tests	403	77.1
num_vignettes	3	94.9
n_fns_r	59	88.1
n_fns_r_exported	59	92.6
n_fns_r_not_exported	0	0.0	TRUE
n_fns_per_file_r	7	88.1
num_params_per_fn	2	49.3
loc_per_fn_r	6	50.2
loc_per_fn_r_exp	6	51.2
doclines_per_fn_exp	12	45.9
fn_call_network_size	66	83.8

---

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)

3a. Continuous Integration Badges

GitHub Workflow Results

id	name	conclusion	sha	run_number	date
28698697846	pkgdown	success	adfec7	2	2026-07-04
28698697864	R-CMD-check	success	adfec7	3	2026-07-04

---

3b. goodpractice results

Test coverage with covr

Package coverage: 65.59

The following files are not completely covered by tests:

file	coverage
R/auth.R	9.09%
R/cache.R	43.59%
R/core.R	66.67%
R/germplasm.R	20%
R/phenotyping.R	64.91%

Cyclocomplexity with cyclocomp

The following functions have cyclocomplexity >= 15:

function	cyclocomplexity
brapi_allele_matrix	23
brapi_get	20
brapi_get_dosage_matrix	16
brapi_post_search	15

Static code analyses with lintr

lintr found the following 30 potential issues:

message	number of times
Construct file paths with file.path(...) instead of paste0(x, "/", y, "/", z).	2
Don't nest pipes inside other calls.	1
expect_type(x, t) is better than expect_true(is.(x))	1
Lines should not be more than 80 characters.	8
Use "brapi/v2/programs" with fixed = TRUE here.	1
Use expect_identical(x, y) by default; resort to expect_equal() only when needed, e.g.	17

Other goodpractice checks

✖️ Exported functions have \examples in .Rd
✖️ Documented functions have @export, @nord, or @Rdname
✖️ Avoid duplicated @param documentation across functions
✖️ No misspelled words in documentation

---

Package Versions

package	version
pkgstats	0.2.3.2
pkgcheck	0.1.3.6

---

Editor-in-Chief Instructions:

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

This package has some noteworthy properties, see 'Package Statistics' details above.

[josh45-source]

Thanks for the insightful feedback, I will work on fixing the gaps in the software.

[josh45-source]

Thanks for the detailed review. I've addressed all flagged items in commit 985d532

Examples (✖️ → ✔️) = Added working @examples to all 37 exported functions that lacked them. Network-dependent examples use \donttest{} (not \dontrun{}), and all were verified against the live BrAPI test server. Functions that don't require network access (e.g. brapi_connection(), brapi_set_token(), brapi_cache_enable()) have fully runnable examples.

Repository website (✖️ → ✔️) = Added the pkgdown site URL to both the DESCRIPTION URL field and the GitHub repository metadata: https://josh45-source.github.io/brapiR2/

Test coverage (✖️ → ✔️) = Increased from 65.6% to 97.69% by adding 114 new mocked test cases (231 total, all passing). New tests cover auth flows, pagination, async search polling, cache hit/miss/expiry, all genotyping convenience functions, phenotyping wide-pivot, and parallel fetching — all using local_mocked_bindings() so they run deterministically without network access.

goodpractice linters (👀 → ✔️) = Fixed all flagged issues including function complexity (split three >50-line functions into smaller helpers), line lengths, expect_equal → expect_identical conversions, and @noRd tags on internal helpers.

\dontrun → \donttest (👀 → ✔️) = Replaced all instances package-wide.

devtools::check() passes with 0 errors, 0 warnings. Ready for re-check when convenient. @maurolepore @ropensci-review-bot

[mpadge]

Thanks for the prompt response @josh45-source. Could you please install our pkgcheck-action GitHub workflow in your repo to confirm locally that everything is okay? Once your checks pass there, feel free to trigger our bot checks again here with:

@ropensci-review-bot check package

👍

[josh45-source]

Thanks @mpadge. The pkgcheck action is installed and passing (7/7 checks green on commit b103723). All pkgcheck results show ✔ across the board, including 98.1% coverage.

@ropensci-review-bot check package