ohun

[maRce10]

Date accepted: 2023-09-13

Submitting Author Name: Marcelo Araya-Salas
Submitting Author Github Handle: @maRce10
Repository: https://github.com/maRce10/ohun
Version submitted: 0.1.0
Submission type: Standard
Editor: @jhollist
Reviewers: @sammlapp, @robitalec

Archive: TBD
Version accepted: TBD
Language: en

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

Package: ohun
Type: Package
Title: Optimizing Acoustic Signal Detection
Version: 0.1.0
Maintainer: Marcelo Araya-Salas <marcelo.araya@ucr.ac.cr>
Description: Facilitates the automatic detection of acoustic signals, 
  providing functions to diagnose and optimize the performance of detection 
  routines. Detections from other software can also be explored and optimized. 
  Reference: Hossin & Sulaiman (2015) <doi:10.5121/ijdkp.2015.5201>.
License: GPL (>= 2)
Encoding: UTF-8
URL: https://marce10.github.io/ohun/
BugReports: https://github.com/maRce10/ohun/issues/
VignetteBuilder: knitr, rmarkdown
RoxygenNote: 7.2.1
Repository: CRAN
Language: en-US
Authors@R: c(person("Marcelo", "Araya-Salas", role = c("aut", "cre"), email = "marcelo.araya@ucr.ac.cr", comment = c(ORCID = "0000-0003-3594-619X")))
Date/Publication: 2016-04-19 08:12:11
Imports: pbapply, viridis, crayon, methods, stats, utils, seewave (>= 2.0.1), RCurl, fftw, knitr, rjson, rlang, sp, igraph, Sim.DiffProc
Depends: R (>= 3.2.1), tuneR, warbleR (>= 1.1.28)
Suggests: rmarkdown, testthat (>= 3.0.0), formatR
Config/testthat/edition: 3

Scope

• Please indicate which category or categories from our package fit policies 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
  • text analysis

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

The packages allows to get data from animal acoustic signal recordings in an automated manner

• Who is the target audience and what are scientific applications of this package?
  Scientific community working with bioacoustic data. Useful to automate analysis of animal acoustic signals for a variety of research questions (e.g. behavior, ecology, evolution, conservation)

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

• the warbleR package has similar functions for detecting but the implementation is not as friendly (I am also the maintainer) and has no tools for detection diagnose/optimization. monitoR also implements one of the detection approaches in ohun but no diagnosing/optimization tools are supplied.

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

• 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.

• Explain reasons for any pkgcheck items which your package is unable to 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 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.
• includes documentation with examples for all functions, created with roxygen2.
• contains a vignette with examples of its essential functions and uses.
• has a test suite.
• has continuous integration, 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?

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[ropensci-review-bot]

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

[annakrystalli]

Dear @maRce10 ,

Many thanks for your submission and apologies for the delay.

The editorial team was taking a break for the holidays and are now catching up. We'll respond with a decision on whether to accept for review shortly.

[annakrystalli]

Hello again @maRce10 ,

I can confirm we are happy to accept the package for review!

I will shortly assign a handling editor.

In the meantime, I'll run our automated checks. If any issues are flagged, feel free to start addressing them.

[annakrystalli]

@ropensci-review-bot check package

[ropensci-review-bot]

Thanks, about to send the query.

[ropensci-review-bot]

🚀

Editor check started

👋

[ropensci-review-bot]

Checks for ohun (v0.1.0)

git hash: c1b9be0e

• ✔️ 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 continuous integration checks.
• ✖️ Package coverage failed
• ✔️ R CMD check found no errors.
• ✔️ R CMD check found no warnings.

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

Package License: GPL (>= 2)

---

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	417
internal	warbleR	41
internal	ohun	25
internal	graphics	11
internal	parallel	7
internal	grDevices	1
depends	tuneR	1
imports	sp	16
imports	methods	10
imports	stats	10
imports	utils	3
imports	seewave	3
imports	igraph	3
imports	crayon	2
imports	rlang	1
imports	pbapply	NA
imports	viridis	NA
imports	fftw	NA
imports	knitr	NA
imports	Sim.DiffProc	NA
suggests	rmarkdown	NA
suggests	testthat	NA
suggests	formatR	NA
suggests	covr	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

c (33), lapply (27), length (25), sapply (24), unique (22), data.frame (13), rbind (13), is.na (12), unlist (12), do.call (11), if (11), list (11), paste0 (11), sum (11), names (10), drop (9), nrow (9), table (9), for (8), grep (7), strsplit (7), as.data.frame (6), mean (6), which (6), col (5), file (5), ncol (5), round (5), setdiff (5), match.call (4), min (4), seq (4), cos (3), eval (3), getOption (3), paste (3), proc.time (3), sin (3), split (3), any (2), apply (2), as.list (2), by (2), call (2), deparse (2), diff (2), expand.grid (2), matrix (2), scale (2), abs (1), as.numeric (1), cat (1), colMeans (1), colnames (1), complex (1), file.path (1), floor (1), grepl (1), ifelse (1), is.null (1), is.numeric (1), max (1), order (1), pi (1), plot (1), regexpr (1), rep (1), rownames (1), seq.int (1), substring (1), summary (1), t (1), try (1), vector (1), which.min (1)

warbleR

pblapply_wrblr_int (17), read_sound_file (8), sound_pressure_level (4), info_sound_files (3), duration_sound_ (2), duration_sound_files (2), gaps (2), duration_wavs (1), envelope (1), stft_wrblr_int (1)

ohun

FUN (10), diagnose_detection (2), find_templates (2), internal_feature_reference (2), spc_FUN (2), XC_FUN (2), detect_FUN (1), energy_detector (1), feature_acoustic_data (1), label_detection (1), t2xy (1)

sp

over (3), Polygon (3), Polygons (3), Spatia (3), SpatialPoints (3), SpatialPolygons (1)

graphics

lines (5), par (4), clip (1), grid (1)

methods

is (10)

stats

poly (4), prcomp (2), smooth (2), na.omit (1), step (1)

parallel

makeCluster (4), makePSOCKcluster (3)

igraph

as_data_frame (1), graph_from_incidence_matrix (1), max_bipartite_match (1)

seewave

env (2), duration (1)

utils

packageVersion (2), head (1)

crayon

italic (1), silver (1)

grDevices

cm (1)

rlang

call_args (1)

tuneR

writeWave (1)

NOTE: Some imported packages appear to have no associated function calls; please ensure with author that these 'Imports' are listed appropriately.

---

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 21 files) and
• 1 authors
• 1 vignette
• 3 internal data files
• 13 imported packages
• 18 exported functions (median 65 lines of code)
• 39 non-exported functions in R (median 75 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	21	82.3
files_vignettes	1	68.4
files_tests	17	95.3
loc_R	2404	87.4
loc_vignettes	541	79.9
loc_tests	564	77.1
num_vignettes	1	64.8
data_size_total	385966	90.6
data_size_median	187188	93.8
n_fns_r	57	60.6
n_fns_r_exported	18	64.2
n_fns_r_not_exported	39	60.5
n_fns_per_file_r	2	29.4
num_params_per_fn	6	79.0
loc_per_fn_r	66	93.6
loc_per_fn_r_exp	66	85.7
loc_per_fn_r_not_exp	75	95.2	TRUE
rel_whitespace_R	23	90.3
rel_whitespace_vignettes	45	88.6
rel_whitespace_tests	39	86.3
doclines_per_fn_exp	92	88.7
doclines_per_fn_not_exp	0	0.0	TRUE
fn_call_network_size	120	82.1

---

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
3864222159	pages build and deployment	success	c1b9be	94	2023-01-07
3864222174	test-coverage	success	c1b9be	7	2023-01-07
3899091232	tic	success	c1b9be	49	2023-01-12

---

3b. goodpractice results

R CMD check with rcmdcheck

R CMD check generated the following note:

1. checking installed package size ... NOTE
   installed size is 5.9Mb
   sub-directories of 1Mb or more:
   doc 5.2Mb

R CMD check generated the following check_fails:

1. cyclocomp
2. no_description_depends
3. no_import_package_as_a_whole
4. rcmdcheck_reasonable_installed_size

Test coverage with covr

ERROR: Test Coverage Failed

Cyclocomplexity with cyclocomp

The following functions have cyclocomplexity >= 15:

function	cyclocomplexity
energy_detector	52
label_detection	35
template_correlator	34
split_acoustic_data	26
feature_reference	25
get_envelopes	21
optimize_energy_detector	20
summarize_diagnostic	20
diagnose_detection	19
label_spectro	18

Static code analyses with lintr

lintr found the following 558 potential issues:

message	number of times
Avoid 1:length(...) expressions, use seq_len.	2
Avoid 1:ncol(...) expressions, use seq_len.	3
Avoid 1:nrow(...) expressions, use seq_len.	34
Avoid library() and require() calls in packages	3
Avoid using sapply, consider vapply instead, that's type safe	27
Lines should not be more than 80 characters.	488
unexpected symbol	1

---

4. Other Checks

Details of other checks (click to open)

✔️ Package contains the following (potentially) obsolete packages:

• sp

See our Recommended Scaffolding for alternatives.

---

Package Versions

package	version
pkgstats	0.1.3
pkgcheck	0.1.0.32

---

Editor-in-Chief Instructions:

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

[maRce10]

Hi

thanks for reviewing my package. Not sure why you got problems with coverage. It shows 78% coverage in codecov:

https://app.codecov.io/github/maRce10/ohun

as well as in the coverage status badge

https://github.com/maRce10/ohun

So I am not sure how to proceed now.

Cheers

Marcelo

[annakrystalli]

Hello @maRce10

Indeed, that's odd.

Let us look into it and get back to you.

[maRce10]

I replaced with seq_len() and vapply() when possible, replace cat() with message() and removed unused dependencies/suggests: 6ea380d

[mpadge]

@maRce10 It took a bit of digging, but the test failures are because flac is not installed. I see you're doing explicit installs in your own GitHub action file. It's common to put these kind of "non-standard" system dependencies in the "SystemRequirements" field of your DESCRIPTION file. Our system would then pick that up and install it, but without that has no way of knowing which libraries your package might need. That said, most systems only match entries given there to the "rules" directory of rstudio/r-system-requirements. Any libraries not listed there, including "flac", are simply ignored. What you should at least do is:

1. List all libraries which do appear there, and which your package requires, in your DESCRIPTION file.
2. Let us know of any libraries on which your package depends are which are not listed there , and we'll add them to our build system. (Or you couuld submit a PR to this Dockerfile.)

Many of the libraries given in your actions file will automatically pull in several of the others, so you should reduce this set to the minimal possible length, either through checking disribution listings (at least for Debian or Ubuntu), or iterating in a docker container.

Please ping here when your DESCRIPTION has been updated, and let us know what else we might need to install. Thanks.