baRulho #609
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Thanks for submitting to rOpenSci, our editors and @ropensci-review-bot will reply soon. Type |
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🚀 Editor check started 👋 |
Checks for baRulho (v2.1.0)git hash: 128b6ca3
Important: All failing checks above must be addressed prior to proceeding (Checks marked with 👀 may be optionally addressed.) Package License: GPL (>= 2) 1. Package DependenciesDetails 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.
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. basec (80), names (36), nrow (30), for (26), if (25), unique (25), vapply (25), seq_len (24), length (22), args (21), match.call (21), as.list (20), which (19), lapply (18), getOption (15), is.na (14), list (13), options (13), plot (13), paste (12), rep (12), seq (12), as.character (10), ncol (9), numeric (9), sum (9), do.call (8), rbind (8), data.frame (7), on.exit (7), paste0 (7), seq_along (7), abs (6), min (6), nchar (6), pretty (6), return (5), t (5), as.data.frame (4), cbind (4), character (4), drop (4), labels (4), log10 (4), matrix (4), sort (4), unlist (4), any (3), diff (3), exp (3), file.path (3), max (3), sub (3), units (3), which.min (3), expand.grid (2), rev (2), sqrt (2), suppressWarnings (2), tempdir (2), all (1), call (1), factor (1), file (1), grepl (1), levels (1), list.files (1), match.arg (1), mean (1), range (1), rank (1), setdiff (1), split (1), sprintf (1), strwrap (1), Sys.info (1), tapply (1), tempfile (1), try (1), vector (1), which.max (1) warbleRpblapply_wrblr_int (27), read_sound_file (26), envelope (5), cross_correlation (3), freq_range_detec (3), read_wave (3), image_to_wave (2), lessdB (2), check_sels (1), info_sound_files (1), rename_est_waves (1), selection_table (1), simulate_songs (1) baRulhocheck_arguments (21), FUN (12), check_unique_sels (3), check_unique_sound.id (3), check_deprecated (2), check_several_distances (2), attenuation (1), find_peaks_bRlh_int (1), rbind2 (1) graphicspar (23), grconvertX (9), lines (5), grid (3), grconvertY (2), split.screen (2), close.screen (1) seewaveenv (7), rms (7), pastew (5), duration (3), fpeaks (2), cutw (1), spec (1) statsfrequency (8), dist (5), approx (1), ave (1), end (1), spectrum (1), start (1), time (1) methodsnew (16) parallelmakePSOCKcluster (15) grDevicespalette (4), colors (3), dev.off (1), recordPlot (1), X11 (1) tuneRsilence (5), normalize (1), writeWave (1) checkmatemakeAssertionFunction (5), makeAssertCollection (1) climake_ansi_style (1), num_ansi_colors (1) ohuntemplate_correlator (1) toolsfind_gs_cmd (1) utilsstr (1) NOTE: Some imported packages appear to have no associated function calls; please ensure with author that these 'Imports' are listed appropriately. 2. Statistical PropertiesThis 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:
Statistical properties of package structure as distributional percentiles in relation to all current CRAN packages
All parameters are explained as tooltips in the locally-rendered HTML version of this report generated by the The final measure (
2a. Network visualisationClick to see the interactive network visualisation of calls between objects in package 3.
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| function | cyclocomplexity |
|---|---|
| check_arguments | 74 |
| manual_realign | 64 |
| plot_degradation | 48 |
| plot_blur_FUN | 26 |
| signal_to_noise_ratio | 26 |
| synth_sounds | 23 |
| noise_profile | 22 |
| master_sound_file | 18 |
| set_reference_sounds | 17 |
| detection_distance | 15 |
Static code analyses with lintr
lintr found the following 664 potential issues:
| message | number of times |
|---|---|
| Avoid 1:nrow(...) expressions, use seq_len. | 2 |
| Avoid library() and require() calls in packages | 12 |
| Avoid using sapply, consider vapply instead, that's type safe | 1 |
| Lines should not be more than 80 characters. | 649 |
4. Other Checks
Details of other checks (click to open)
✖️ The following 2 function names are duplicated in other packages:
-
attenuationfrom seewave
-
find_markersfrom dtangle
Package Versions
| package | version |
|---|---|
| pkgstats | 0.1.3.9 |
| pkgcheck | 0.1.2.3 |
Editor-in-Chief Instructions:
Processing may not proceed until the items marked with ✖️ have been resolved.
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Thank you for this submission @maRce10! Two quick notes before I start the process:
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@ropensci-review-bot assign @jhollist as editor |
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Assigned! @jhollist is now the editor |
Hi @noamross! I just removed those weird files ropensci/baRulho@e6f1b4d |
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Hey @maRce10. Long time no see (ha!) I will get started on this early next week. Just wanted to let you know that the impending US Gov shutdown may impact my ability to work on this. I am good to work all next week, but if we do shutdown and it is not resolved, I will have to stop all work activities (my serving as an editor counts as one) after the 7th and I can't resume until the shutdown has been lifted. Hopefully this all for naught and I am able to keep on working on this. But I will do what I can to make progress next week. |
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@noamross @maRce10 The failing "no continuous integration" check is because it actually just checks for an |
Thanks! I added the
Thanks for letting me know! |
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@ropensci-review-bot check baRulho |
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I'm sorry human, I don't understand that. You can see what commands I support by typing:
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@ropensci-review-bot check package |
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Thanks, about to send the query. |
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🚀 Editor check started 👋 |
Checks for baRulho (v2.1.0)git hash: 46763a23
Important: All failing checks above must be addressed prior to proceeding (Checks marked with 👀 may be optionally addressed.) Package License: GPL (>= 2) 1. Package DependenciesDetails 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.
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. basec (83), names (36), nrow (33), seq_len (28), for (27), if (27), unique (25), vapply (25), length (23), match.call (22), args (21), as.list (21), lapply (19), which (19), getOption (18), is.na (14), list (13), options (13), paste (12), rep (12), seq (12), plot (11), as.character (10), ncol (9), numeric (9), sum (9), do.call (8), rbind (8), attributes (7), data.frame (7), on.exit (7), paste0 (7), seq_along (7), abs (6), min (6), nchar (6), pretty (6), return (5), t (5), as.data.frame (4), cbind (4), character (4), drop (4), labels (4), log10 (4), matrix (4), sort (4), unlist (4), any (3), diff (3), exp (3), file.path (3), max (3), sub (3), units (3), which.min (3), expand.grid (2), is.null (2), mean (2), rev (2), sqrt (2), suppressWarnings (2), tempdir (2), all (1), call (1), factor (1), file (1), grepl (1), levels (1), list.files (1), match.arg (1), q (1), range (1), rank (1), setdiff (1), split (1), sprintf (1), strwrap (1), Sys.info (1), tapply (1), tempfile (1), try (1), vector (1), which.max (1) warbleRpblapply_wrblr_int (30), read_sound_file (27), envelope (8), cross_correlation (3), freq_range_detec (3), read_wave (3), image_to_wave (2), lessdB (2), check_sels (1), info_sound_files (1), rename_est_waves (1), selection_table (1), simulate_songs (1) baRulhocheck_arguments (21), FUN (12), check_unique_sels (3), by_element_est (2), check_deprecated (2), check_extended_selection_table (2), check_several_distances (2), attenuation (1), check_unique_sound.id (1), find_peaks_bRlh_int (1), rbind2 (1) graphicspar (23), grconvertX (9), lines (5), grid (3), grconvertY (2), split.screen (2), close.screen (1) seewaverms (6), env (5), pastew (5), duration (3), fpeaks (2), cutw (1), spec (1) statsfrequency (8), dist (5), approx (2), ave (1), end (1), spectrum (1), start (1), time (1) methodsnew (16), formalArgs (1) parallelmakePSOCKcluster (16) grDevicespalette (4), colors (3), dev.off (1), recordPlot (1), X11 (1) checkmatemakeAssertionFunction (6), makeAssertCollection (1) tuneRsilence (5), normalize (1), writeWave (1) climake_ansi_style (1), num_ansi_colors (1) ohuntemplate_correlator (1) toolsfind_gs_cmd (1) utilsstr (1) NOTE: Some imported packages appear to have no associated function calls; please ensure with author that these 'Imports' are listed appropriately. 2. Statistical PropertiesThis 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:
Statistical properties of package structure as distributional percentiles in relation to all current CRAN packages
All parameters are explained as tooltips in the locally-rendered HTML version of this report generated by the The final measure (
2a. Network visualisationClick to see the interactive network visualisation of calls between objects in package 3.
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| id | name | conclusion | sha | run_number | date |
|---|---|---|---|---|---|
| 6384082445 | .github/workflows/deploy_ghpages.yaml | failure | d5364f | 4 | 2023-10-02 |
| 6385163073 | Continuous Deployment | failure | 1b0f43 | 6 | 2023-10-02 |
| 6385275826 | pages build and deployment | success | 995476 | 75 | 2023-10-02 |
| 6396499245 | R-CMD-check | failure | c488df | 16 | 2023-10-03 |
| 6393038656 | Render README | success | 833ca7 | 17 | 2023-10-03 |
| 6397662241 | tic | failure | 46763a | 100 | 2023-10-03 |
| 6396505549 | Update CITATION.cff | success | 0925c7 | 1 | 2023-10-03 |
3b. goodpractice results
R CMD check with rcmdcheck
R CMD check generated the following error:
- Error in proc$get_built_file() : Build process failed
R CMD check generated the following check_fails:
- no_description_depends
- no_import_package_as_a_whole
Test coverage with covr
ERROR: Test Coverage Failed
Cyclocomplexity with cyclocomp
Error : Build failed, unknown error, standard output:
- checking for file ‘baRulho/DESCRIPTION’ ... OK
- preparing ‘baRulho’:
- checking DESCRIPTION meta-information ... OK
- installing the package to build vignettes
----------------------------------- - installing source package ‘baRulho’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘baRulho’ in namespaceExport(ns, exports):
undefined exports: add_noise
Error: loading failed
Execution halted
ERROR: loading failed - removing ‘/tmp/RtmpaoozZw/Rinst16cd73656348/baRulho’
-----------------------------------
ERROR: package installation failed
Static code analyses with lintr
lintr found the following 680 potential issues:
| message | number of times |
|---|---|
| Avoid 1:nrow(...) expressions, use seq_len. | 2 |
| Avoid library() and require() calls in packages | 12 |
| Avoid using sapply, consider vapply instead, that's type safe | 1 |
| Lines should not be more than 80 characters. | 665 |
4. Other Checks
Details of other checks (click to open)
✖️ The following 3 function names are duplicated in other packages:
-
add_noisefrom errorlocate, pauwels2014, spant, tdaunif, TestFunctions, vpc
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attenuationfrom seewave
-
find_markersfrom dtangle
Package Versions
| package | version |
|---|---|
| pkgstats | 0.1.3.9 |
| pkgcheck | 0.1.2.9 |
Editor-in-Chief Instructions:
Processing may not proceed until the items marked with ✖️ have been resolved.
Editor checks:
Editor comments@maRce10 See checks in previous comment. R CMD Check is now failing. I did see that you recently merged some new work and that is triggering this failure. I assume you are still doing a bit of work on this. Let me know when you have that completed and your checks pass. I will check again and then move forward with finding reviewers. I also noted a few others things. Data is a bit large, not sure if you can reduce that.
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OK I solved and closed the issues and now R CMD check is working again. The size of data is probably due to having sounds as examples. I shrank it as much as I could. |
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@ropensci-review-bot check package |
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Thanks, about to send the query. |
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🚀 Editor check started 👋 |
Checks for baRulho (v2.1.0)git hash: 36f90248
(Checks marked with 👀 may be optionally addressed.) Package License: GPL (>= 2) 1. Package DependenciesDetails 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.
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. basec (83), names (38), nrow (34), seq_len (29), for (28), if (26), unique (26), vapply (25), match.call (24), args (23), as.list (23), length (23), which (20), lapply (19), getOption (18), is.na (14), list (14), options (13), paste (12), plot (12), rep (12), seq (12), as.character (10), sum (10), ncol (9), numeric (9), attributes (8), do.call (8), rbind (8), on.exit (7), paste0 (7), seq_along (7), abs (6), data.frame (6), min (6), nchar (6), pretty (6), return (6), t (5), as.data.frame (4), cbind (4), character (4), drop (4), file.path (4), labels (4), log10 (4), matrix (4), sort (4), unlist (4), any (3), diff (3), exp (3), max (3), sub (3), units (3), vector (3), which.min (3), expand.grid (2), is.null (2), mean (2), rev (2), sqrt (2), suppressWarnings (2), tempdir (2), all (1), call (1), factor (1), file (1), grepl (1), levels (1), list.files (1), match.arg (1), q (1), range (1), sapply (1), setdiff (1), split (1), sprintf (1), strwrap (1), Sys.info (1), tapply (1), tempfile (1), try (1), which.max (1) warbleRpblapply_wrblr_int (31), read_sound_file (27), envelope (6), cross_correlation (3), freq_range_detec (3), read_wave (3), image_to_wave (2), lessdB (2), check_sels (1), info_sound_files (1), rename_est_waves (1), simulate_songs (1) baRulhocheck_arguments (23), FUN (13), by_element_est (2), check_deprecated (2), check_extended_selection_table (2), check_several_distances (2), check_sound_files_found (2), check_unique_sels (2), attenuation (1), check_unique_sound.id (1), colortext (1), find_peaks_bRlh_int (1), rbind2 (1), signal_to_noise_ratio (1) graphicspar (23), grconvertX (9), lines (5), grid (3), grconvertY (2), split.screen (2), close.screen (1) seewaverms (6), env (5), pastew (5), duration (3), fpeaks (2), cutw (1), spec (1) statsfrequency (8), dist (5), approx (2), end (1), runif (1), start (1), time (1) methodsnew (16), formalArgs (1) parallelmakePSOCKcluster (16) grDevicespalette (4), colors (3), dev.off (1), recordPlot (1), X11 (1) checkmatemakeAssertionFunction (7), makeAssertCollection (1) tuneRsilence (5), normalize (1), writeWave (1) climake_ansi_style (1), num_ansi_colors (1) ohuntemplate_correlator (1) toolsfind_gs_cmd (1) utilsstr (1) NOTE: Some imported packages appear to have no associated function calls; please ensure with author that these 'Imports' are listed appropriately. 2. Statistical PropertiesThis 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:
Statistical properties of package structure as distributional percentiles in relation to all current CRAN packages
All parameters are explained as tooltips in the locally-rendered HTML version of this report generated by the The final measure (
2a. Network visualisationClick to see the interactive network visualisation of calls between objects in package 3.
|
| id | name | conclusion | sha | run_number | date |
|---|---|---|---|---|---|
| 6414603275 | pages build and deployment | success | 09b477 | 80 | 2023-10-05 |
| 6411731627 | R-CMD-check | success | 36f902 | 20 | 2023-10-04 |
| 6419119914 | Render README | success | 36f902 | 20 | 2023-10-05 |
| 6414533822 | tic | success | 36f902 | 111 | 2023-10-05 |
| 6396505549 | Update CITATION.cff | success | 0925c7 | 1 | 2023-10-03 |
3b. goodpractice results
R CMD check with rcmdcheck
R CMD check generated the following note:
- checking installed package size ... NOTE
installed size is 12.2Mb
sub-directories of 1Mb or more:
data 1.6Mb
doc 8.8Mb
help 1.5Mb
R CMD check generated the following check_fails:
- cyclocomp
- no_description_depends
- no_import_package_as_a_whole
- rcmdcheck_reasonable_installed_size
Test coverage with covr
Package coverage: 79.91
Cyclocomplexity with cyclocomp
The following functions have cyclocomplexity >= 15:
| function | cyclocomplexity |
|---|---|
| check_arguments | 84 |
| manual_realign | 64 |
| plot_degradation | 48 |
| signal_to_noise_ratio | 29 |
| plot_blur_FUN | 26 |
| synth_sounds | 25 |
| noise_profile | 22 |
| master_sound_file | 18 |
| set_reference_sounds | 17 |
| detection_distance | 15 |
Static code analyses with lintr
lintr found the following 703 potential issues:
| message | number of times |
|---|---|
| Avoid 1:nrow(...) expressions, use seq_len. | 2 |
| Avoid library() and require() calls in packages | 12 |
| Avoid using sapply, consider vapply instead, that's type safe | 3 |
| Lines should not be more than 80 characters. | 686 |
4. Other Checks
Details of other checks (click to open)
✖️ The following 3 function names are duplicated in other packages:
-
add_noisefrom errorlocate, pauwels2014, spant, tdaunif, TestFunctions, vpc
-
attenuationfrom seewave
-
find_markersfrom dtangle
Package Versions
| package | version |
|---|---|
| pkgstats | 0.1.3.9 |
| pkgcheck | 0.1.2.9 |
Editor-in-Chief Instructions:
This package is in top shape and may be passed on to a handling editor
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@maRce10 I think we are good to move on to review. Couple of things to think about in the lintr results, in particular the 1:nrow and sapply ones. The library calls you can ignore since those are in Rmd and tests. Look through those results for other ideas as well. For instance, your lines of code are on the high side, but so is cyclomatic complexity. If you can simplify some of these functions you could probably reduce both and make future maintenance a little easier. That being said, we are good to go for reviewers. I'll start pinging on a few folks today. |
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@ropensci-review-bot seeking reviewers |
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Please add this badge to the README of your package repository: [](https://github.com/ropensci/software-review/issues/609)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 |
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@ropensci-review-bot assign @mikemahoney218 as reviewer |
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I'm sorry human, I don't understand that. You can see what commands I support by typing:
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@maRce10 Thanks for submitting your response to @mikemahoney218 feedback. As a side note, I think the review bot commands need to be submitted in a comment without anything else in that comment. Try that again and see if it works. @DenaJGibbon could you take a look at the response to your review in #609 (comment) and let us know if there any outstanding concerns? |
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Opened ropensci/baRulho#18 to hopefully fix the website, but otherwise all my concerns have been addressed and I'm comfortable recommending acceptance 😄 |
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@ropensci-review-bot submit response #609 (comment) |
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Logged author response! |
yes it fixed the website. Thanks a lot! |
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@maRce10 quick update. @DenaJGibbon is away doing field work and will respond towards the end of next week. If you have any questions or concerns, let me know. |
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Hello @maRce10 . I have had an enjoyable afternoon working through "baRulho" using my own data. I am at the 'excess attenuation' function, and in the vignette it says: "Two methods for calculating excess attenuation are provided (see ‘method’ argument)." However, the function returns an error when I try to specify a method and there is nothing about the method in the function documentation. Could you please clarify? Does this mean based on the two reference methods, or are there two ways to calculate EA with the package? Below is the output from the 'plot_degradation' function on my own data (gibbons from Borneo). It looks great!
I am still working through all the functions and will probably not be able to submit the full review until next week. Thanks for your patience! |
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Thanks @DenaJGibbon ! There was an argument in excess_attenuation() to select the type of EA to calculate. However I removed that option as one method was not very reliable. However I forgot to update the vignette. I Just did that in this commit: ropensci/baRulho@69fafb8 |
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First, I want to say you have done a great job getting all these functions together in a relatively easy to digest format. This will be a highly useful tool for folks working in bioacoustics. I worked through all of the example using my own data, and have some specific comments based on that experience below. I also apologize for the delay - I have been playing catch up since I got back from the field. I should be able to respond sooner in the future. Getting set upI spent much of the time I allotted to do this review getting my data in the correct format. As I suggested in my previous review, I really think that to lower the barrier to entry for folks you should include step-by-step instructions on how to get the data into the correct format. I referred to the 'warbleR' documentation on the extended selection tables, but it was not clear (from reading the documentation) how to get the information about distance, sound.id, etc. into the table. After lots of trial and error I was able to get it working, but for folks that don't have a ton of coding experience this will be hard for them. Plot degradationIt would be great if you could include bit more information in the description for envelope and spectrum - I dug into the code to see how they were calculated but it should be easier to see. Also if there is some way to include the axis labels or units of the two in the plot (or maybe default printed somewhere) that would be good. Excess attenuationI am a bit confused about the example in the EA section, as a proportion of the values are negative (which would indicate amplification of the sound). Could you please double check and let me know what is going on here? I also think that including the equation in the documentation would be helpful here. Noise profilesI think there is some missing info: "The function uses internally to calculate frequency spectra. " |
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@maRce10 Just pinging to make sure you saw @DenaJGibbon response. Once you deal with those we can get reviewer concurrence and should have baRulho ready to go! |
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Thanks a lot @DenaJGibbon for your very useful comments! Here are the responses: comment: I spent much of the time I allotted to do this review getting my data in the correct format. As I suggested in my previous review, I really think that to lower the barrier to entry for folks you should include step-by-step instructions on how to get the data into the correct format. I referred to the 'warbleR' documentation on the extended selection tables, but it was not clear (from reading the documentation) how to get the information about distance, sound.id, etc. into the table. After lots of trial and error I was able to get it working, but for folks that don't have a ton of coding experience this will be hard for them. response: You are totally right, this is an issue I have had in mine for a while, mostly related to the package warbleR which is where these different input data formats are defined. baRulho basically take all 3 data formats used by the package warbleR, which I also maintain. So I added a new vignette to warbleR, called "annotation data format" (https://marce10.github.io/warbleR/articles/annotation_data_format.html), to have a more detailed explanation of the structure of these objects. I have added a link to this vignette to the section "Require data structure" in the vignette "Quantify degradation" in baRulho. I have also added definitions for all the required columns in the input data description in "Quantify degradation". ropensci/baRulho@626e999 comment: Excess attenuation I am a bit confused about the example in the EA section, as a proportion of the values are negative (which would indicate amplification of the sound). Could you please double check and let me know what is going on here? I also think that including the equation in the documentation would be helpful here. response: I have revised the code (thanks to input from users) and the EA calculation is now more accurate. Now only 2 measures are negative in the example ropensci/baRulho@176266b. comment: Plot degradation It would be great if you could include bit more information in the description for envelope and spectrum I dug into the code to see how they were calculated but it should be easier to see. Also if there is some way to include the axis labels or units of the two in the plot (or maybe default printed somewhere) that would be good. response: I have added to the function description that "Amplitude envelopes and power spectra are computed using the functions \code{\link[seewave]{envelope}} (warbleR package) and \code{\link[seewave]{spec}} (seewave package) respectively. This two visualizations show the power distribution in time and frequency between the minimum and maximum power values for each sound. Therefore scales are not necessarily comparable across panels." ropensci/baRulho@e6e4412 _ Adding scales would be tricky as plots are already pretty busy. I also think this scales are not extremely informative if sound files are not calibrated as in most cases. _ comment: Noise profiles I think there is some missing info: "The function uses internally to calculate frequency spectra. " response: fixed! (The function uses \code{\link[seewave]{meanspec}} internally to calculate frequency spectra) ropensci/baRulho@e6e4412 thanks! |
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@ropensci-review-bot submit response #609 (comment) |
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Logged author response! |
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@jhollist just wondering if the response to the reviews was noticed 😄 |
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Thanks for the heads up @maRce10. Not sure why these keep slipping by! @DenaJGibbon everything look good to you in #609 (comment) |
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A few more comments - the package is in pretty good shape! Nice job! Vignette
Package
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Thank you for these last few comments, @DenaJGibbon. Really great review! @maRce10 Once these are done, we are good to go and can move on the accept! Let me know if you have questions, and I will make sure to keep my eye on the notifications this time, but also feel free to ping me so I don't let it slip (again...) |
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Thanks again @DenaJGibbon for your useful comments! Here are the responses: comment: The printout of class(est) appears to have distances in it, but there is not an explanation in the text about where they came from in this vignette (https://marce10.github.io/warbleR/articles/annotation_data_format.html) response: There was an issue with the ANSI format of the selection table printing method. But it is already fixed maRce10/warbleR@3f3efc3 comment: I find the printout sections in the vignette page hard to follow/understand. Perhaps another call like head or colnames would provide the info needed and be cleaner? response: I think this was also fixed with the changes made when dealing with the previous comment comment: In the 'add_noise' function description it would be helpful to describe what kind of noise (e.g, white noise?) response: It adds white noise. But I just added a new argument "kind" that can be used for using different (white, pink, brown, red, and power). ropensci/baRulho@e413199 comment: The 'detection_distance' function is in the package, but I couldn't find anything in the vignette about it (unless am I missing something?). This is a cool feature, but I couldn't find much info on it. And when I run the example the output is not intuitive. response: I added this to the function description: "The function computes the maximum distance at which a sound would be detected, which is calculated as the distance in which the sound pressure level (SPL) goes below the specified SPL cutoff ('spl.cutoff')). This is returned as an additional column 'detection.distance' (in m). " ropensci/baRulho@e6b07b1 comment: I ran through all the (~22) function examples, and they all worked - nice job! _response: sweeet! thanks! |
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@maRce10, @DenaJGibbon, and @mikemahoney218 I think we are there! Thank you all for you efforts on this. |
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@ropensci-review-bot approve baRulho |
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Approved! Thanks @maRce10 for submitting and @mikemahoney218, @DenaJGibbon for your reviews! 😁 To-dos:
Should you want to acknowledge your reviewers in your package DESCRIPTION, you can do so by making them Welcome aboard! We'd love to host a post about your package - either a short introduction to it with an example for a technical audience or a longer post with some narrative about its development or something you learned, and an example of its use for a broader readership. If you are interested, consult the blog guide, and tag @ropensci/blog-editors in your reply. They will get in touch about timing and can answer any questions. We maintain an online book with our best practice and tips, this chapter starts the 3d section that's about guidance for after onboarding (with advice on releases, package marketing, GitHub grooming); the guide also feature CRAN gotchas. Please tell us what could be improved. Last but not least, you can volunteer as a reviewer via filling a short form. |
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@ropensci-review-bot finalize transfer of baRulho |
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Transfer completed. |
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@DenaJGibbon @mikemahoney218 would you like to be included in the package as contributors? |
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If you see fit, I'd happy to be included as |
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Sure, thanks! Nice job on getting this out there! |
Date accepted: 2024-03-28
Submitting Author Name: Marcelo Araya-Salas
Submitting Author Github Handle: @maRce10
Repository: https://github.com/maRce10/baRulho/
Version submitted: 2.1.0
Submission type: Standard
Editor: @jhollist
Reviewers: @mikemahoney218, @DenaJGibbon
Archive: TBD
Version accepted: TBD
Language: en
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.):
Explain how and why the package falls under these categories (briefly, 1-2 sentences):
It estimates degradation measures from sounds that have been re-recorded in standard playback experiments. It also helps to prepare acoustic data for playback experiments.
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?
To the best of my knowledge the only other similar tools is the warbleR package, which has similar functions for measuring features from annotation tables but not specifically related to sound degradation (I am also the maintainer) except for sig2noise.
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pkgcheckitems which your package is unable to pass.Somehow continuous integration is not detected when running
pkgcheck::pkgcheck(), but it is fully implemented https://app.codecov.io/gh/maRce10/baRulho?branch=masterTechnical checks
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