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ohun #568

Closed maRce10 closed 1 year ago

maRce10 commented 1 year ago

Date accepted: 2023-09-13

Submitting Author Name: Marcelo Araya-Salas Submitting Author Github Handle: !--author1-->@maRce10<!--end-author1-- Repository: https://github.com/maRce10/ohun Version submitted: 0.1.0 Submission type: Standard Editor: !--editor-->@jhollist<!--end-editor-- Reviewers: @sammlapp, @robitalec

Archive: TBD Version accepted: TBD Language: en

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

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

Technical checks

Confirm each of the following by checking the box.

This package:

Publication options

MEE Options - [x] The package is novel and will be of interest to the broad readership of the journal. - [x] The manuscript describing the package is no longer than 3000 words. - [x] 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](http://besjournals.onlinelibrary.wiley.com/hub/journal/10.1111/(ISSN)2041-210X/journal-resources/policy-on-publishing-code.html)) - (*Scope: Do consider MEE's [Aims and Scope](http://besjournals.onlinelibrary.wiley.com/hub/journal/10.1111/(ISSN)2041-210X/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

ropensci-review-bot commented 1 year ago

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

annakrystalli commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

@ropensci-review-bot check package

ropensci-review-bot commented 1 year ago

Thanks, about to send the query.

ropensci-review-bot commented 1 year ago

:rocket:

Editor check started

:wave:

ropensci-review-bot commented 1 year ago

Checks for ohun (v0.1.0)

git hash: c1b9be0e

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()', 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](https://docs.ropensci.org/pkgcheck/reference/checks_to_markdown.html) 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 [![R-CMD-check](https://github.com/maRce10/ohun/workflows/R-CMD-check/badge.svg)](https://github.com/maRce10/ohun/actions) **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](https://r-lib.github.io/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](https://covr.r-lib.org/) ERROR: Test Coverage Failed #### Cyclocomplexity with [cyclocomp](https://github.com/MangoTheCat/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](https://github.com/jimhester/lintr) [lintr](https://github.com/jimhester/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)

:heavy_check_mark: Package contains the following (potentially) obsolete packages: - sp See our [Recommended Scaffolding](https://devguide.ropensci.org/building.html?q=scaffol#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 :heavy_multiplication_x: have been resolved.

maRce10 commented 1 year ago

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 commented 1 year ago

Hello @maRce10

Indeed, that's odd.

Let us look into it and get back to you.

maRce10 commented 1 year ago

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

mpadge commented 1 year ago

@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.

maRce10 commented 1 year ago

OK thanks. These non-standard dependencies are not from the ohun package but from a package it relies heavily on, warbleR. These dependencies are now included in the DESCRIPTION file of warbleR on github. Should I also add them to ohun?

mpadge commented 1 year ago

No, if they're from another package then they're dependencies of that package not yours. I'll just add flac to our system and ping here when checks can be re-run.

mpadge commented 1 year ago

@maRce10 Our system has been rebuilt, and your tests all run successfully now. You may call the bot to run the checks whenever you like.

annakrystalli commented 1 year ago

@ropensci-review-bot assign @jhollist as editor

ropensci-review-bot commented 1 year ago

Assigned! @jhollist is now the editor

jhollist commented 1 year ago

@ropensci-review-bot check package

ropensci-review-bot commented 1 year ago

Thanks, about to send the query.

ropensci-review-bot commented 1 year ago

:rocket:

Editor check started

:wave:

ropensci-review-bot commented 1 year ago

Checks for ohun (v0.1.0)

git hash: 62cdc87d

(Checks marked with :eyes: may be optionally addressed.)

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 | 448| |internal |warbleR | 41| |internal |ohun | 27| |internal |graphics | 12| |internal |parallel | 7| |internal |grDevices | 1| |depends |tuneR | 1| |imports |sp | 16| |imports |stats | 10| |imports |utils | 3| |imports |seewave | 3| |imports |igraph | 3| |imports |cli | 1| |imports |methods | 1| |imports |rlang | 1| |imports |fftw | NA| |suggests |knitr | NA| |suggests |rmarkdown | NA| |suggests |testthat | NA| |suggests |viridis | NA| |suggests |Sim.DiffProc | 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()', and examining the 'external_calls' table.

base

c (35), lapply (27), length (26), unique (22), vapply (17), sum (14), data.frame (13), rbind (13), unlist (13), is.na (12), do.call (11), if (11), list (11), paste0 (11), names (10), seq_len (10), drop (9), nrow (9), table (9), for (8), mean (8), strsplit (8), grep (7), numeric (7), sapply (7), as.data.frame (6), which (6), col (5), ncol (5), round (5), setdiff (5), any (4), file (4), match.call (4), min (4), seq (4), cos (3), eval (3), getOption (3), logical (3), proc.time (3), sin (3), split (3), apply (2), as.list (2), by (2), call (2), deparse (2), diff (2), expand.grid (2), matrix (2), paste (2), scale (2), abs (1), as.numeric (1), character (1), colMeans (1), colnames (1), complex (1), file.path (1), floor (1), grepl (1), ifelse (1), is.null (1), is.numeric (1), match.arg (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), colortext (1), detect_FUN (1), energy_detector (1), feature_acoustic_data (1), label_detection (1), message2 (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), text (1)

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)

cli

style_italic (1)

grDevices

cm (1)

methods

as (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 - 9 imported packages - 18 exported functions (median 65 lines of code) - 47 non-exported functions in R (median 58 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](https://docs.ropensci.org/pkgcheck/reference/checks_to_markdown.html) 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 | 2429| 87.5| | |loc_vignettes | 541| 79.9| | |loc_tests | 571| 77.3| | |num_vignettes | 1| 64.8| | |data_size_total | 385966| 90.6| | |data_size_median | 187188| 93.8| | |n_fns_r | 65| 64.8| | |n_fns_r_exported | 18| 64.2| | |n_fns_r_not_exported | 47| 65.9| | |n_fns_per_file_r | 2| 33.8| | |num_params_per_fn | 6| 79.0| | |loc_per_fn_r | 65| 93.5| | |loc_per_fn_r_exp | 66| 85.7| | |loc_per_fn_r_not_exp | 58| 92.5| | |rel_whitespace_R | 23| 90.5| | |rel_whitespace_vignettes | 45| 88.6| | |rel_whitespace_tests | 39| 86.4| | |doclines_per_fn_exp | 92| 88.7| | |doclines_per_fn_not_exp | 0| 0.0|TRUE | |fn_call_network_size | 154| 85.5| | ---

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 [![R-CMD-check](https://github.com/maRce10/ohun/workflows/R-CMD-check/badge.svg)](https://github.com/maRce10/ohun/actions) **GitHub Workflow Results** | id|name |conclusion |sha | run_number|date | |----------:|:--------------------------|:----------|:------|----------:|:----------| | 3944417614|pages build and deployment |success |62cdc8 | 103|2023-01-18 | | 3944417809|test-coverage |success |62cdc8 | 16|2023-01-18 | | 3945647101|tic |success |62cdc8 | 64|2023-01-18 | --- #### 3b. `goodpractice` results #### `R CMD check` with [rcmdcheck](https://r-lib.github.io/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](https://covr.r-lib.org/) Package coverage: 78.11 #### Cyclocomplexity with [cyclocomp](https://github.com/MangoTheCat/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](https://github.com/jimhester/lintr) [lintr](https://github.com/jimhester/lintr) found the following 512 potential issues: message | number of times --- | --- Avoid 1:nrow(...) expressions, use seq_len. | 3 Avoid library() and require() calls in packages | 3 Avoid using sapply, consider vapply instead, that's type safe | 10 Lines should not be more than 80 characters. | 495 unexpected symbol | 1

4. Other Checks

Details of other checks (click to open)

:heavy_multiplication_x: Package contains the following obsolete packages: - sp See our [Recommended Scaffolding](https://devguide.ropensci.org/building.html?q=scaffol#recommended-scaffolding) for alternatives.

Package Versions

|package |version | |:--------|:--------| |pkgstats |0.1.3 | |pkgcheck |0.1.1.11 |

Editor-in-Chief Instructions:

This package is in top shape and may be passed on to a handling editor

maRce10 commented 1 year ago

🥳

jhollist commented 1 year ago

@maRce10 just now getting a chance to take a look at this.

One question I have relates to the submission checklist. You did not check the "I have read the author guide and I expect to maintain this package for at least 2 years or to find a replacement." Was curious if that was an oversight or if you expect maintenance of this package to be short term only.

maRce10 commented 1 year ago

Oh that was an oversight. I am planning to do long term maintenance for this package.

jhollist commented 1 year ago

I think we are ready to keep moving on this. Thanks for updating the checklist, @maRce10.

Couple of things I would like to see addressed prior to review are:

As you work on these I will start to identify some possible reviewers. Any questions, just let me know.

maRce10 commented 1 year ago

Thanks!

I replaced sp with sf so sp is not longer used. I also dealt with most goodpractice results. After the first check round I fixed all possible instances in which seq_len() was a better option and replaced sapply() by vapply() when possible.

bioacoustics also has 1 method for doing automatic detection, but has no tools for diagnosing and optimizing those detections. So ohun could actually be used as a complimentary tool for bioacoustics. bioacoustics also does other things that ohun doesn't, like feature extraction and acoustic file manipulation

jhollist commented 1 year ago

@ropensci-review-bot check package

ropensci-review-bot commented 1 year ago

Thanks, about to send the query.

ropensci-review-bot commented 1 year ago

:rocket:

Editor check started

:wave:

maRce10 commented 1 year ago

🥳

ropensci-review-bot commented 1 year ago

Checks for ohun (v0.1.0)

git hash: 444576a5

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 | 430| |internal |warbleR | 41| |internal |ohun | 25| |internal |graphics | 7| |internal |parallel | 7| |internal |grDevices | 1| |depends |tuneR | 1| |imports |methods | 10| |imports |stats | 7| |imports |utils | 3| |imports |seewave | 3| |imports |sf | 3| |imports |igraph | 3| |imports |cli | 1| |imports |rlang | 1| |imports |fftw | NA| |suggests |knitr | NA| |suggests |rmarkdown | NA| |suggests |testthat | NA| |suggests |viridis | NA| |suggests |Sim.DiffProc | 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()', and examining the 'external_calls' table.

base

lapply (27), length (26), c (25), unique (22), vapply (17), data.frame (15), rbind (14), sum (14), unlist (13), do.call (11), if (11), paste0 (11), names (10), nrow (10), seq_len (10), drop (9), is.na (9), table (9), for (8), list (8), mean (8), strsplit (8), grep (7), numeric (7), sapply (7), as.data.frame (6), ncol (5), round (5), setdiff (5), any (4), file (4), match.call (4), min (4), seq (4), which (4), cos (3), eval (3), getOption (3), logical (3), proc.time (3), sin (3), split (3), apply (2), as.list (2), by (2), call (2), deparse (2), diff (2), expand.grid (2), matrix (2), paste (2), pi (2), scale (2), abs (1), as.matrix (1), as.numeric (1), character (1), colMeans (1), colnames (1), complex (1), file.path (1), floor (1), grepl (1), ifelse (1), is.null (1), is.numeric (1), match.arg (1), max (1), order (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), internal_feature_reference (2), spc_FUN (2), XC_FUN (2), detect_FUN (1), energy_detector (1), feature_acoustic_data (1), find_templates (1), label_detection (1), message2 (1), t2xy (1)

methods

is (10)

graphics

par (4), clip (1), grid (1), text (1)

parallel

makeCluster (4), makePSOCKcluster (3)

stats

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

igraph

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

seewave

env (2), duration (1)

sf

st_as_sf (1), st_intersects (1), st_polygon (1)

utils

packageVersion (2), head (1)

cli

style_italic (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 - 9 imported packages - 18 exported functions (median 65 lines of code) - 47 non-exported functions in R (median 58 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](https://docs.ropensci.org/pkgcheck/reference/checks_to_markdown.html) 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 | 2497| 88.0| | |loc_vignettes | 541| 79.9| | |loc_tests | 571| 77.3| | |num_vignettes | 1| 64.8| | |data_size_total | 385966| 90.6| | |data_size_median | 187188| 93.8| | |n_fns_r | 65| 64.8| | |n_fns_r_exported | 18| 64.2| | |n_fns_r_not_exported | 47| 65.9| | |n_fns_per_file_r | 2| 33.8| | |num_params_per_fn | 6| 79.0| | |loc_per_fn_r | 65| 93.5| | |loc_per_fn_r_exp | 66| 85.7| | |loc_per_fn_r_not_exp | 58| 92.5| | |rel_whitespace_R | 23| 90.4| | |rel_whitespace_vignettes | 45| 88.6| | |rel_whitespace_tests | 39| 86.4| | |doclines_per_fn_exp | 92| 88.7| | |doclines_per_fn_not_exp | 0| 0.0|TRUE | |fn_call_network_size | 154| 85.5| | ---

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 [![R-CMD-check](https://github.com/maRce10/ohun/workflows/R-CMD-check/badge.svg)](https://github.com/maRce10/ohun/actions) **GitHub Workflow Results** | id|name |conclusion |sha | run_number|date | |----------:|:--------------------------|:----------|:------|----------:|:----------| | 3988367740|pages build and deployment |success |444576 | 104|2023-01-23 | | 3988367842|test-coverage |success |444576 | 17|2023-01-23 | | 3992954250|tic |success |444576 | 71|2023-01-24 | --- #### 3b. `goodpractice` results #### `R CMD check` with [rcmdcheck](https://r-lib.github.io/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](https://covr.r-lib.org/) Package coverage: 78.3 #### Cyclocomplexity with [cyclocomp](https://github.com/MangoTheCat/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](https://github.com/jimhester/lintr) [lintr](https://github.com/jimhester/lintr) found the following 503 potential issues: message | number of times --- | --- Avoid 1:nrow(...) expressions, use seq_len. | 3 Avoid library() and require() calls in packages | 3 Avoid using sapply, consider vapply instead, that's type safe | 10 Lines should not be more than 80 characters. | 486 unexpected symbol | 1

Package Versions

|package |version | |:--------|:--------| |pkgstats |0.1.3 | |pkgcheck |0.1.1.11 |

Editor-in-Chief Instructions:

This package is in top shape and may be passed on to a handling editor

jhollist commented 1 year ago

I think this is ready for reviewers! I have a few that I am going to start reaching out to. If you have a few suggested reviewers, I am happy to take a look at those as well.

jhollist commented 1 year ago

@ropensci-review-bot seeking reviewers

ropensci-review-bot commented 1 year ago

Please add this badge to the README of your package repository:

[![Status at rOpenSci Software Peer Review](https://badges.ropensci.org/568_status.svg)](https://github.com/ropensci/software-review/issues/568)

Furthermore, if your package does not have a NEWS.md file yet, please create one to capture the changes made during the review process. See https://devguide.ropensci.org/releasing.html#news

maRce10 commented 1 year ago

OK, I added NEWS.md and the rOpenSci status badge (although doesn't seem to show up properly)

jhollist commented 1 year ago

Thanks, @maRce10. I looked over at your README and the badge looks good to me.

I have two requests out for reviewers. Now we wait!

jhollist commented 1 year ago

@ropensci-review-bot assign @sammlapp

ropensci-review-bot commented 1 year ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@ropensci-review-bot help

jhollist commented 1 year ago

@ropensci-review-bot assign @sammlapp as reviewer

ropensci-review-bot commented 1 year ago

@sammlapp added to the reviewers list. Review due date is 2023-02-24. Thanks @sammlapp for accepting to review! Please refer to our reviewer guide.

rOpenSci’s community is our best asset. We aim for reviews to be open, non-adversarial, and focused on improving software quality. Be respectful and kind! See our reviewers guide and code of conduct for more.

ropensci-review-bot commented 1 year ago

@sammlapp: If you haven't done so, please fill this form for us to update our reviewers records.

sammlapp commented 1 year ago

@maRce10 I'm working on my review, but would like to check in on devtools::check('ohun'). I've never run devtools in R, so forgive me if I'm doing something wrong here. Running devtools::test('ohun') in R Studio completes without errors, showing all tests passed. However, running devtools::check('ohun') in R Studio results in an error. I have a MackBook Pro running Mac OS 12.6 with R Studio 2022.07.1 Build 554 and the following version info

platform       aarch64-apple-darwin20      
arch           aarch64                     
os             darwin20                    
system         aarch64, darwin20           
status                                     
major          4                           
minor          2.1                         
year           2022                        
month          06                          
day            23                          
svn rev        82513                       
language       R                           
version.string R version 4.2.1 (2022-06-23)
nickname       Funny-Looking Kid

Full traceback of devtools::check('ohun') :


Documenting ════════════════════════════════════════════════════════════════════════════════════════
ℹ Updating ohun documentation
ℹ Loading ohun

══ Building ═══════════════════════════════════════════════════════════════════════════════════════════
Setting env vars:
• CFLAGS    : -Wall -pedantic -fdiagnostics-color=always
• CXXFLAGS  : -Wall -pedantic -fdiagnostics-color=always
• CXX11FLAGS: -Wall -pedantic -fdiagnostics-color=always
• CXX14FLAGS: -Wall -pedantic -fdiagnostics-color=always
• CXX17FLAGS: -Wall -pedantic -fdiagnostics-color=always
• CXX20FLAGS: -Wall -pedantic -fdiagnostics-color=always
── R CMD build ────────────────────────────────────────────────────────────────────────────────────────
✔  checking for file ‘/Users/SML161/ohun/DESCRIPTION’ (351ms)
─  preparing ‘ohun’:
✔  checking DESCRIPTION meta-information ...
─  installing the package to build vignettes
E  creating vignettes (16s)
   --- re-building ‘ohun.Rmd’ using rmarkdown
   Loading required package: tuneR
   Loading required package: warbleR
   Loading required package: seewave
   Loading required package: NatureSounds
   Loading required package: knitr
   Quitting from lines 326-353 (ohun.Rmd) 
   Error: processing vignette 'ohun.Rmd' failed with diagnostics:
   must install 'Sim.DiffProc' to use this function
   --- failed re-building ‘ohun.Rmd’

   SUMMARY: processing the following file failed:
     ‘ohun.Rmd’

   Error: Vignette re-building failed.
   Execution halted
Error in `(function (command = NULL, args = character(), error_on_status = TRUE, …`:
! System command 'R' failed
---
Exit status: 1
stdout & stderr: <printed>
---
Type .Last.error to see the more details.

.Last.error #outputs 

Backtrace:
 1. devtools::check("ohun")
 2. withr::with_envvar(pkgbuild::compiler_flags(FALSE), action = "prefix", …
 3. base::force(code)
 4. pkgbuild::build(pkg$path, tempdir(), args = build_args, quiet = quiet, …
 5. withr::with_temp_libpaths(rcmd_build_tools(options$cmd, c(options$path, …
 6. base::force(code)
 7. pkgbuild::rcmd_build_tools(options$cmd, c(options$path, options$args), …
 8. pkgbuild::with_build_tools({ …
 9. base::withCallingHandlers(callr::rcmd_safe(..., env = env, spinner = FALSE, …
10. callr::rcmd_safe(..., env = env, spinner = FALSE, show = FALSE, …
11. callr:::run_r(options)
12. base::with(options, with_envvar(env, do.call(processx::run, c(list(bin, …
13. base::with.default(options, with_envvar(env, do.call(processx::run, …
14. base::eval(substitute(expr), data, enclos = parent.frame())
15. base::eval(substitute(expr), data, enclos = parent.frame())
16. callr:::with_envvar(env, do.call(processx::run, c(list(bin, args = real_cmdargs, …
17. base::force(code)
18. base::do.call(processx::run, c(list(bin, args = real_cmdargs, stdout_line_callback = real_callback(stdo…
19. (function (command = NULL, args = character(), error_on_status = TRUE, …
20. base::throw(new_process_error(res, call = sys.call(), echo = echo, …
21. | base::signalCondition(cond)
22. (function (e) …
23. asNamespace("callr")$err$throw(e)
sammlapp commented 1 year ago

Package Review

Please check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide

Documentation

The package includes all the following forms of documentation:

Functionality

Estimated hours spent reviewing: 10

Review Comments

General notes

I don't typically use R, so some things are not obvious to me. Where can I find the full API documentation? I opened the /docs/index.html to view the docs by rendering the HTML locally, but presumably they are online somewhere. I would recommend linking to the documentation near the top of the README.

The use of the word "reference" to mean "audio annotations" or "labels" is unfamiliar to me, I'm not sure if this word is typically used in the related warbleR package.

The package should give the user some expectation for under what circumstances the detection methods are likely to be effective. Although it mentions that high SNR is required for amplitude thresholding and stereotyped sounds are necessary for template matching, there are other requirements of the data for these approaches to be effective.

In this review, I have not delved into the creation of warbleR selection tables and the interaction of the package with such tables. It seems that this package is aimed towards users who already create and use warbleR selection tables, and because that package is established I consider it "legacy" in the sense that I don't want to review or critique it here. In my experiments with the package, I created a dataframe of "selections" using the split_acoustic_data function on dry mode (only.sels=TRUE), renamed columns, and added random values for annotation bounds just to have a fake set of annotations on local audio files to play with.

Overall, functions generally worked as described in the documentation. However, in my experiments the get_templates function gave an error that I coudn't figure out how to avoid. The primary recommendations of this review are

(1) to improve documentation and function/variable/argument names to better match the action that is actually taken by a function;

(2) to consider a moderate refactor of code to increase modularity, reduce redundancy, and aim to follow the Single Responsibility Principle;

(3) increase code readability by breaking complex logical lines into separate lines with additional comments, plus comments describing the general purpose of large blocks of code.

devtools::test('ohun')runs without error, but as posted above devtools::check('ohun') raises an error for me.

Redundancy of functionality:

Template-based cross correlation is implemented in monitoR, while energy-based detection is implemented in bioacoustics (the implementation seems more generic and featured than the one in ohun).

I wonder if the proposed value of Ohun is mostly in its specific ability to interact with the formats of annotations produced by warbleR. If so, the top-level documentation and README could clarify this purpose.

Specifically, when I started using the program without having any experience with warbleR, it was not clear to me how to create annotation tables or generally what the utility of most of the package functions are. Writing a description of the characteristics of data that this package expects as input would be helpful. For instance, "This package provides utilities for comparing detection and annotations of audio events described by frequency and time boxes. Creating annotations containing such frequency-time boxes [is possible in the warbleR package?]."

Notes on the package design

The package is very 'flat' in the sense that functions rarely call other functions, but instead take a bunch of arguments to do a bunch of things in one go. One result of this is that many functions take a long list of parameters, and parameters are redundant across many functions. For example, several functions take the same set of spectrogram parameters. To me, this raises the concern of accidental inconsistency in a user's script (eg, by passing different spectrogram parameters to two different functions).

In the language of rOpenSci software recommendations, this is a sign that the functions are not "modular". In other places it might be seen as a violation of the Single Responsibility Principle (SRP). For example, the label_specto function violates SRP because it doesn't just label a spectrogram: it computes a spectrogram, plots it, then overlays labels, and might additionally comput and plot an amplitude signal. As another example, I get_envelopes.R and energy_detector.R seem to both implement the process of getting an amplitude envelope, rather than using shared modular functionality specific to this purpose.

Though it would take a significant refactoring effort, I believe creating a more modular code base that aims to achieve the SRP could improve the package and user experience overall.

Notes on the source code

split_acoustic_data.R:

summarize_diagnostic.R:

          summ_diagnostic$mean.duration.true.positives <-
            if (any(!is.na(Y$mean.duration.true.positives)))
              round(
                stats::weighted.mean(
                  x = Y$mean.duration.true.positives,
                  w = Y$true.positives,
                  na.rm = TRUE
                ),
                0
              ) else
            NA

In general I'm not reading this code base to check for logical errors, but I think that the code style will make it difficult for others (or the authors) to debug, extend, understand or modify the code. In this example, separating the logical operation into a few separate and sequential lines of code could make it easier to digest, and would provide opportunities to add comments for any individual steps whose purposes are not obvious. (For example in this code, a comment could explain why we would want a weighted mean of true positive durations.)

Notes on the Getting Started tutorial page

The "main features" description is jargon-y and could be written in broader language. For example, "The use of signal detection theory indices to evaluate detection performance" -> "Evaluate detection accuracy with precision, recall, and other metrics". As is, I feel like it obscures the functionality of the package. As another example, I wasn't sure what "Optimize detection routines based on reference annotations" meant - after reading further, I think it basically means "Adjust detection parameters to optimize accuracy on a labeled set of recordings"

"Template-based detection" It's not true that template-based detection "doesn’t depend on the signal-to-noise ratio" - high background noise or low signal level will decrease the accuracy of this approach

outputs (eg, tables) in the Getting Started tutorial are very hard to interpret in the current form, could they be rendered as human-readable tables?

"Detections from other software can also be explored and optimized." I don't see how detections from another platform could be "optimized" in ohun unless you just mean changing a score threshold and measuring the resulting precision and recall.

An example of how to analyze a large set of files, for instance all files in a folder-subfolder structure, would be helpful. I had to do some googling to figure out how to do "globbing" ie find all paths mathing a pattern.

Notes on API documentation and variable/function names

Throughout the codebase, I recommend more informative variable and argument names: for example, in the function merge_overlaps, to a new user, pb is not interpreted as "progress bar"

Throughout the documentation: why are arguments that are numbers/strings called "numeric vectors of length 1" and "character vectors of length 1"? This makes me thing I should pass c(0) or [0] instead of 0, for instance, as an argument.

get_envelopes :

energy_detector: again, I don't think making files optional and defaulting to all audio in the working directory is a good idea.

label_spectro: can you provide an example of how to use this function with an audio file? If I want to run it on anything other than a simulated array of numbers or the two built-in audio files, I need some prior line of code to load the audio file, for example:

library(tuneR)
w <- readWave("~/sample_audio/birds_10s.wav")

bp argument (in several functions): how is the signal bandpassed? Should state specifically, for example, a 9th order Butterworth bandpass filter

feature_reference: "Extract quantitative features of references" - from the function name and short description, I expected this to extract acoustic features of the annotated audio events themselves, rather than summary statistics of the annotations per se. Perhaps the description could be "Summarize temporal and frequency dimensions of annotations and gaps" or something similar. Ideally, the function's name would reflect its functionality, something like summarize_annotation_boxes.

Similarly, feature_acoustic_data sounds like it would measure some acoustic feature. Since the function returns information about the file types, I would call it something like summarize_audio_file_characteristics

filter_detection I'm confused as to what this function is doing. The documentation says it "removes ambiguous detections (split and merged detections)", but the detailed documentation should explain what is meant by split and merged detections. I'm also confused whether this is meant to be applied to human-created annotations, automatically-generated detections, or can be used for either purpose.

optimize_template_detector: this function compares performance across parameter values, it does not itself optimize the algorithm, so its name is a bit misleading. Perhaps template_parameter_sweep is closer. I'm not sure what paramter values it sweeps over after reading the documentation, since it requires the user to have already run template_correlator. Also, I think the part of the documentation that says "Those parameters can be later used for performing a more efficient detection using optimize_template_detector." must be a typo, perhaps it means "using template_correlator" instead?

label_spectro(): this is a plotting function, so it would be better named something like plot_spec_and_labels

get_templates: can you explain what features are being used to create this principle component analysis of template similarity? Also, after understanding what this function does, it seems like it would be better named something like select_representative_templates or select_representative_annotations since it chooses representative templates from a set of annotations.

split_acoustic_data: it should be possible, if not required, to list the audio files to split. It seems like I must split every file within a folder in the current implementation.

label_detection function name does not match what it does. It seems this function evaluates detections against a set of annotations/labels/"references" so perhaps it should be called evaluate_detections or compare_annotations_and_detections

template_correlator it's unclear to me how to use the files argument. I don't know what 'X' is as referred to in the documentation, and I would expect to simply be able to pass a vector of file paths.

full_spectrograms: it was surprising to me that this function automatically saved image files to the current working directory, rather than asking for a save dir or displaying them in the console. This doesn't seem like a good practice, because I might not want to save the results and if I do, I'd like to choose where they go.

Other note: I would be very surprised if template matching is faster than amplitude-based detection, as claimed in the "Improving detection speed" section. Amplitude-based detection is about the lightest task you can perform on a time signal while 2d cross correlation is relatively heavy.

Errors during usage

When I try to run get_templates on my own file set, I get this error: 

Error in prcomp.default(spectral_parameters[, 2:27], scale. = TRUE) : 
  cannot rescale a constant/zero column to unit variance

I tried to run get_templates on a set of local files, but it seems somehow one of the features has no variance and this is causing the PCA to fail. I wasn't able to resolve this.

Running template_correlator then template_detector on the results produced a table containing NA values for many rows in the start, end, and scores columns. I did not expect this, and it caused errors when I tried to run other analyses on these detections.

Once I ran template_correlator and template_detector, I wasn't sure how to inspect my detections although it seemed like I should be able to use full_spectrograms or some other package function.

When I first ran label_spectro, I got the message "Error in loadNamespace(x) : there is no package called ‘viridis’". I'm not sure if this suggests a missing dependency. I resolved the issue by running install.packages("viridis")

When I run label_spectro with env = TRUE, I get an error message: 

w <- readWave("~/sample_audio/birds_10s.wav")

label_spectro(wave = w@left,
              f=w@samp.rate,
              env = TRUE)

Error in label_spectro(wave = w@left, f = w@samp.rate, env = TRUE, fastdisp = TRUE) : 
  trying to get slot "samp.rate" from an object of a basic class ("integer") with no slots

Add a more helpful error message for accidental use of Hz instead of kHz: If my detection table has Hz instead of kHz and I run get_templates, the error message says "Caution! This is a null spectrum. The spectral entropy is null!"

maRce10 commented 1 year ago

Thanks for the review. Is there a specific format to respond to these concerns?

jhollist commented 1 year ago

@maRce10 Typically it is best to provide an itemized response in this issue for each of the comments in the review. Also make sure you address any of the relevant, unchecked items in the checklist at the top of the review. For some more detailed info please see https://devguide.ropensci.org/authors-guide.html#the-review-process for some more informatoin.

Also, I am still working on finding a second reviewer. You can either wait until the 2nd review is complete or you can make updates now and then the 2nd reviewer can address the updated version. In either case I will keep forging ahead with trying to find reviewers.

ropensci-review-bot commented 1 year ago

:calendar: @sammlapp you have 2 days left before the due date for your review (2023-02-24).

jhollist commented 1 year ago

@maRce10 Just wanted to update you. I am still looking for a second reviewer. I have a few more on my list to try. If you have anymore questions or concerns, please let me know.

jhollist commented 1 year ago

@maRce10 And the search for a 2nd reviewer continues... Was curious if you had worked on the edits that @sammlapp suggested in his review or if you were waiting until both reviews are in? Sorry for the delay in moving this along!

jhollist commented 1 year ago

@ropensci-review-bot assign @robitalec as reviewer

ropensci-review-bot commented 1 year ago

@robitalec added to the reviewers list. Review due date is 2023-05-11. Thanks @robitalec for accepting to review! Please refer to our reviewer guide.

rOpenSci’s community is our best asset. We aim for reviews to be open, non-adversarial, and focused on improving software quality. Be respectful and kind! See our reviewers guide and code of conduct for more.

ropensci-review-bot commented 1 year ago

@robitalec: If you haven't done so, please fill this form for us to update our reviewers records.