Submission: stochLAB

[grwhumphries]

Date accepted: 2023-02-03

Submitting Author Name: Grant Humphries Submitting Author Github Handle: !--author1-->@grwhumphries<!--end-author1-- Other Package Authors Github handles: (comma separated, delete if none) !--author-others-->@bcaneco<!--end-author-others-- Repository: https://github.com/HiDef-Aerial-Surveying/stochLAB Version submitted: 1.1.1 Submission type: Stats Badge grade: gold Editor: !--editor-->@stephaniehicks<!--end-editor-- Reviewers: @kstreet13, @clairemas0n

Due date for @kstreet13: 2022-11-01 Due date for @clairemas0n: 2022-11-24

Archive: TBD Version accepted: TBD Language: en

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

Type: Package
Package: stochLAB
Title: Stochastic Collision Risk Model
Version: 1.1.0
Authors@R: c(
    person("Grant", "Humphries", , "grant.humphries@hidefsurveying.co.uk", role = c("aut", "cre")),
    person("Bruno", "Caneco", , "bruno@dmpstats.com", role = "aut"),
    person("Marine Scotland", role = c("fnd", "cph")),
    person("HiDef", role = "cph"),
    person("DMPstats", role = "cph")
  )
Description: Tool for running Collision Risk Models for seabirds on
    offshore wind farms.
License: GPL (>= 3) + file LICENSE
Depends: 
    R (>= 4.0)
Imports: 
    cli,
    data.table,
    dplyr,
    foreach,
    glue,
    logr,
    magrittr,
    msm,
    pracma,
    purrr,
    rlang,
    stats,
    tibble,
    tidyr
Suggests: 
    rmarkdown,
    knitr,
    spelling,
    testthat (>= 3.0.0),
    covr
Config/testthat/edition: 3
Encoding: UTF-8
Language: en-GB
LazyData: true
LazyDataCompression: bzip2
Roxygen: list(markdown = TRUE)
URL: https://www.github.com/HiDef-Aerial-Surveying/stochLAB,
    https://hidef-aerial-surveying.github.io/stochLAB/
BugReports: https://www.github.com/HiDef-Aerial-Surveying/stochLAB/issues
RoxygenNote: 7.2.0
VignetteBuilder: knitr

Pre-submission Inquiry

• [X] A pre-submission inquiry has been approved in issue#506

General Information

• Who is the target audience and what are scientific applications of this package? This package is designed for consultants or scientists working in the offshore windfarm industry who are looking to quantify the risks of collision to seabirds

• Paste your responses to our General Standard G1.1 here, describing whether your software is:

  • The first implementation of a novel algorithm; or
  • The first implementation within R of an algorithm which has previously been implemented in other languages or contexts; or
  • An improvement on other implementations of similar algorithms in R.

Core calculations follow the work developed by Masden (2015)

Please include hyperlinked references to all other relevant software.

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

Badging

• What grade of badge are you aiming for? (bronze, silver, gold) Gold

• If aiming for silver or gold, describe which of the four aspects listed in the Guide for Authors chapter the package fulfils (at least one aspect for silver; three for gold) Compliance with a good number of standards beyond those identified as minimally necessary. This will require reviewers and authors to agree on identification of both a minimal subset of necessary standards, and a full set of potentially applicable standards. This aspect may be considered fulfilled if at least one quarter of the additional potentially applicable standards have been met, and should definitely be considered fulfilled if more than one half have been met.

Technical checks

Confirm each of the following by checking the box.

• [X] I have read the rOpenSci packaging guide.
• [X] I have read the author guide and I expect to maintain this package for at least 2 years or have another maintainer identified.
• [X] I/we have read the Statistical Software Peer Review Guide for Authors.
• [X] I/we have run autotest checks on the package, and ensured no tests fail.
• [X] The srr_stats_pre_submit() function confirms this package may be submitted.
• [X] The pkgcheck() function confirms this package may be submitted - alternatively, please explain reasons for any checks which your package is unable to pass.

This package:

• [X] does not violate the Terms of Service of any service it interacts with.
• [X] has a CRAN and OSI accepted license.
• [X] contains a README with instructions for installing the development version.

Publication options

• [X] Do you intend for this package to go on CRAN?
• [ ] Do you intend for this package to go on Bioconductor?

Code of conduct

• [X] I agree to abide by rOpenSci's Code of Conduct during the review process and in maintaining my package should it be accepted.

[ropensci-review-bot]

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

[ropensci-review-bot]

:rocket:

Editor check started

:wave:

[emilyriederer]

Hi @grwhumphries ! Thank you for making a full submission. We may experience a slight delay as @mpadge is offline next week and it appears we may need assistance with the editor check bot.

In the meantime, could you please edit your message to link your to your presubmission inquiry in #506 for record-keeping?

Thanks!

[grwhumphries]

Hi @emilyriederer - thanks for that and no worries - just updated with the link to issue #506

[ropensci-review-bot]

Checks for stochLAB (v1.1.0)

git hash: e8f8f24f

• :heavy_check_mark: Package name is available
• :heavy_check_mark: has a 'codemeta.json' file.
• :heavy_check_mark: has a 'contributing' file.
• :heavy_check_mark: uses 'roxygen2'.
• :heavy_check_mark: 'DESCRIPTION' has a URL field.
• :heavy_check_mark: 'DESCRIPTION' has a BugReports field.
• :heavy_check_mark: Package has at least one HTML vignette
• :heavy_check_mark: All functions have examples.
• :heavy_check_mark: Package has continuous integration checks.
• :heavy_check_mark: Package coverage is 75.4%.
• :heavy_check_mark: R CMD check found no errors.
• :heavy_check_mark: R CMD check found no warnings.

Package License: GPL (>= 3) + file LICENSE

---

1. rOpenSci Statistical Standards (srr package)

This package is in the following categories:

• **

:heavy_check_mark: All applicable standards [v0.1.0] have been documented in this package (47 complied with; 21 N/A standards)

Click to see the report of author-reported standards compliance of the package with links to associated lines of code, which can be re-generated locally by running the srr_report() function from within a local clone of the repository.

---

2. 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 | 285| |internal |stochLAB | 56| |internal |methods | 2| |internal |utils | 2| |imports |magrittr | 41| |imports |stats | 37| |imports |tidyr | 12| |imports |rlang | 11| |imports |dplyr | 8| |imports |purrr | 7| |imports |glue | 5| |imports |tibble | 5| |imports |logr | 4| |imports |pracma | 3| |imports |cli | NA| |imports |data.table | NA| |imports |foreach | NA| |imports |msm | NA| |suggests |rmarkdown | NA| |suggests |knitr | NA| |suggests |spelling | NA| |suggests |testthat | 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), mean (25), list (21), message (18), paste0 (16), for (15), pi (10), nrow (7), length (6), month.abb (6), rep (6), replace (6), deparse (5), if (5), round (5), seq (5), substitute (5), apply (4), beta (4), eval (4), names (4), sum (4), which (4), by (3), cos (3), data.frame (3), missing (3), return (3), sqrt (3), abs (2), colnames (2), data.matrix (2), dim (2), dirname (2), ifelse (2), intersect (2), match (2), matrix (2), min (2), months (2), ncol (2), numeric (2), pmin (2), sample (2), sapply (2), sin (2), array (1), as.integer (1), atan (1), ceiling (1), diff (1), findInterval (1), floor (1), is.null (1), max (1), mode (1), order (1), Reduce (1), switch (1), sys.call (1), t (1)

stochLAB

format_months (6), Day_Length (4), collide_length (3), generate_rotor_grids (3), get_avg_prob_collision (3), get_fhd_rotor (3), get_lac_factor (3), get_pcoll_grid (3), sampler_hd (3), band_crm (2), get_flux_factor (2), get_mig_flux_factor (2), get_phi_grid (2), get_prop_crh_fhd (2), get_x_grid (2), seq_months (2), check_fhd_vs_maxtip (1), crm_opt1 (1), crm_opt2 (1), crm_opt3 (1), crm_opt4 (1), get_collisions_basic (1), get_collisions_extended (1), get_risk_y (1), get_y_grid (1), sample_parameters (1), sample_turbine_mCRM (1)

magrittr

%>% (41)

stats

median (18), quantile (9), df (5), dt (2), rbeta (2), runif (1)

tidyr

pivot_wider (4), separate (4), pivot_longer (2), replace_na (2)

rlang

expr (4), sym (4), format_error_bullets (2), fn_fmls_names (1)

dplyr

filter (2), rename_with (2), slice_sample (2), mutate (1), select (1)

purrr

map (4), imap (1), iwalk (1), pmap (1)

glue

glue_collapse (5)

tibble

add_column (4), tribble (1)

logr

log_open (4)

pracma

interp1 (3)

methods

is (2)

utils

data (2)

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

---

3. 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 31 files) and - 2 authors - 1 vignette - 10 internal data files - 14 imported packages - 31 exported functions (median 22 lines of code) - 56 non-exported functions in R (median 26 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 | 31| 89.9| | |files_vignettes | 1| 68.4| | |files_tests | 32| 98.2| | |loc_R | 2175| 85.7| | |loc_vignettes | 326| 66.5| | |loc_tests | 880| 85.1| | |num_vignettes | 1| 64.8| | |data_size_total | 4622918| 99.7|TRUE | |data_size_median | 2018| 68.7| | |n_fns_r | 87| 72.8| | |n_fns_r_exported | 31| 79.2| | |n_fns_r_not_exported | 56| 70.6| | |n_fns_per_file_r | 2| 30.6| | |num_params_per_fn | 6| 79.0| | |loc_per_fn_r | 24| 67.9| | |loc_per_fn_r_exp | 22| 50.8| | |loc_per_fn_r_not_exp | 26| 73.5| | |rel_whitespace_R | 27| 90.8| | |rel_whitespace_vignettes | 21| 49.2| | |rel_whitespace_tests | 15| 77.5| | |doclines_per_fn_exp | 51| 64.2| | |doclines_per_fn_not_exp | 0| 0.0|TRUE | |fn_call_network_size | 156| 85.6| | ---

3a. Network visualisation

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

---

4. goodpractice and other checks

Details of goodpractice checks (click to open)

#### 3a. Continuous Integration Badges [](https://github.com/HiDef-Aerial-Surveying/stochLAB/actions) [](https://github.com/HiDef-Aerial-Surveying/stochLAB/actions) [](https://github.com/HiDef-Aerial-Surveying/stochLAB/actions) [](https://github.com/HiDef-Aerial-Surveying/stochLAB/actions) **GitHub Workflow Results** | id|name |conclusion |sha | run_number|date | |----------:|:--------------------------|:----------|:------|----------:|:----------| | 2749423525|pages build and deployment |success |409934 | 50|2022-07-27 | | 2749399803|pkgcheck |success |e8f8f2 | 11|2022-07-27 | | 2749399805|pkgdown |success |e8f8f2 | 22|2022-07-27 | | 2749399804|R-CMD-check |success |e8f8f2 | 26|2022-07-27 | | 2749399802|test-coverage |success |e8f8f2 | 25|2022-07-27 | --- #### 3b. `goodpractice` results #### `R CMD check` with [rcmdcheck](https://r-lib.github.io/rcmdcheck/) R CMD check generated the following notes: 1. checking installed package size ... NOTE installed size is 6.8Mb sub-directories of 1Mb or more: data 6.3Mb 2. checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘data.table’ ‘foreach’ All declared Imports should be used. 3. checking R code for possible problems ... NOTE band_crm: no visible binding for global variable ‘Month’ band_crm: no visible binding for global variable ‘month’ mig_stoch_crm: no visible binding for global variable ‘RotorRadius’ mig_stoch_crm: no visible binding for global variable ‘BladeWidth’ mig_stoch_crm: no visible binding for global variable ‘RotorSpeed’ mig_stoch_crm: no visible binding for global variable ‘Pitch’ mig_stoch_crm: no visible global function definition for ‘contains’ sample_parameters: no visible binding for global variable ‘.’ sample_parameters: no visible binding for global variable ‘month’ sample_parameters: no visible binding for global variable ‘p’ sample_turbine_mCRM: no visible binding for global variable ‘month’ stoch_crm: no visible global function definition for ‘!<-’ stoch_crm: no visible binding for global variable ‘Month’ stoch_crm : : no visible global function definition for ‘everything’ stoch_crm : : no visible binding for global variable ‘name’ stoch_crm : : no visible binding for global variable ‘period’ stoch_crm : : no visible binding for global variable ‘stat’ Undefined global functions or variables: !<- . BladeWidth contains everything month Month name p period Pitch RotorRadius RotorSpeed stat R CMD check generated the following check_fails: 1. cyclocomp 2. no_import_package_as_a_whole 3. rcmdcheck_imports_not_imported_from 4. rcmdcheck_undefined_globals 5. rcmdcheck_reasonable_installed_size #### Test coverage with [covr](https://covr.r-lib.org/) Package coverage: 75.43 #### Cyclocomplexity with [cyclocomp](https://github.com/MangoTheCat/cyclocomp) The following functions have cyclocomplexity >= 15: function | cyclocomplexity --- | --- validate_inputs | 99 stoch_crm | 51 band_crm | 33 sample_parameters | 26 mig_stoch_crm | 24 val_df_columns | 23 val_pars_df | 17 #### Static code analyses with [lintr](https://github.com/jimhester/lintr) [lintr](https://github.com/jimhester/lintr) found the following 364 potential issues: message | number of times --- | --- Avoid 1:length(...) expressions, use seq_len. | 1 Avoid 1:nrow(...) expressions, use seq_len. | 4 Avoid length(...):1 expressions, use seq_len. | 1 Avoid library() and require() calls in packages | 1 Avoid using sapply, consider vapply instead, that's type safe | 2 Lines should not be more than 80 characters. | 355

---

Package Versions

|package |version | |:--------|:---------| |pkgstats |0.1.1.4 | |pkgcheck |0.0.3.77 | |srr |0.0.1.167 |

---

Editor-in-Chief Instructions:

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

[mpadge]

Thanks for the submission @grwhumphries, and for bearing with us while we use submissions to refine our system. In your case, the above "srr" section reveals a bug which we didn't anticipate. I can now appreciate that our Guide for Authors of statistical packages isn't clear enough, and needs a sentence at the outset along the lines of:

All packages submitted for software peer review must document compliance with both General Standards, and at least one set of our category-specific standards.

Your package only documents compliance with the general standards, and needs to include statements of compliance with at least one specific category of standards. Updates to our checking system in response to your submission would now generate the following message:

---

1. rOpenSci Statistical Standards (srr package)

:heavy_multiplication_x: Error: Package documents compliance only with general standards. Statistical packages must document compliance with at least one set of category-specific standards as well.

---

I'll leave you to discuss with @emilyriederer whether you might need to put a "Holding" label on this submission while you address the missing standards. Please accept our apologies for any confusion.

[emilyriederer]

Thanks, @mpadge

Hi @grwhumphries - per Mark's comment, please let us know what sort of timeline you prefer for addressing the standards. I can put a holding label in this issue in the meantime if you don't expect it to be a short-term priority. Whatever works best for you!

[grwhumphries]

Hi @emilyriederer and @mpadge - sorry about the delay. I think I can address this within the week - I just need to get my head back into it. Hope that's okay?

[emilyriederer]

Sounds great @grwhumphries ! No timeline pressure on our side. Only wanted to know about the tag for repo / issue-log hygiene but not a big deal either way.

[grwhumphries]

@mpadge and @emilyriederer okay the latest version of stochLAB (v1.1.1) has just been pushed and I think that covers out the standards for EDA and PD.

[emilyriederer]

@ropensci-review-bot check package

[ropensci-review-bot]

Thanks, about to send the query.

[ropensci-review-bot]

:rocket:

Editor check started

:wave:

[ropensci-review-bot]

Oops, something went wrong with our automatic package checks. Our developers have been notified and package checks will appear here as soon as we've resolved the issue. Sorry for any inconvenience.

[grwhumphries]

@emilyriederer @mpadge - I just realized that the package check failed because the PD standards aren't merged into the package check yet. How do you want me to handle that?

Cheers G

[ropensci-review-bot]

Checks for stochLAB (v1.1.1)

git hash: d7d7034f

• :heavy_check_mark: Package name is available
• :heavy_check_mark: has a 'codemeta.json' file.
• :heavy_check_mark: has a 'contributing' file.
• :heavy_multiplication_x: The following functions have no documented return values: [format_months, get_pcoll_grid, seq_months, validate_inputs]
• :heavy_check_mark: uses 'roxygen2'.
• :heavy_check_mark: 'DESCRIPTION' has a URL field.
• :heavy_check_mark: 'DESCRIPTION' has a BugReports field.
• :heavy_check_mark: Package has at least one HTML vignette
• :heavy_check_mark: All functions have examples.
• :heavy_check_mark: Package has continuous integration checks.
• :heavy_check_mark: Package coverage is 75.7%.
• :heavy_check_mark: R CMD check found no errors.
• :heavy_check_mark: R CMD check found no warnings.

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

Package License: GPL (>= 3)

---

1. rOpenSci Statistical Standards (srr package)

This package is in the following category:

• Exploratory Data Analysis

:heavy_check_mark: All applicable standards [v0.1.0] have been documented in this package (78 complied with; 38 N/A standards)

Click to see the report of author-reported standards compliance of the package with links to associated lines of code, which can be re-generated locally by running the srr_report() function from within a local clone of the repository.

---

2. 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 | 285| |internal |stochLAB | 56| |internal |methods | 2| |internal |utils | 2| |depends |tidyverse | NA| |imports |magrittr | 41| |imports |stats | 37| |imports |tidyr | 12| |imports |dplyr | 11| |imports |rlang | 11| |imports |purrr | 7| |imports |glue | 5| |imports |tibble | 5| |imports |logr | 4| |imports |pracma | 3| |imports |cli | NA| |imports |msm | NA| |suggests |rmarkdown | NA| |suggests |knitr | NA| |suggests |spelling | NA| |suggests |testthat | 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), mean (25), list (21), message (18), paste0 (16), for (15), pi (10), nrow (7), length (6), month.abb (6), rep (6), replace (6), deparse (5), if (5), round (5), seq (5), substitute (5), apply (4), beta (4), eval (4), names (4), sum (4), which (4), by (3), cos (3), data.frame (3), missing (3), return (3), sqrt (3), abs (2), colnames (2), data.matrix (2), dim (2), dirname (2), ifelse (2), intersect (2), match (2), matrix (2), min (2), months (2), ncol (2), numeric (2), pmin (2), sample (2), sapply (2), sin (2), array (1), as.integer (1), atan (1), ceiling (1), diff (1), findInterval (1), floor (1), is.null (1), max (1), mode (1), order (1), Reduce (1), switch (1), sys.call (1), t (1)

stochLAB

format_months (6), Day_Length (4), collide_length (3), generate_rotor_grids (3), get_avg_prob_collision (3), get_fhd_rotor (3), get_lac_factor (3), get_pcoll_grid (3), sampler_hd (3), band_crm (2), get_flux_factor (2), get_mig_flux_factor (2), get_phi_grid (2), get_prop_crh_fhd (2), get_x_grid (2), seq_months (2), check_fhd_vs_maxtip (1), crm_opt1 (1), crm_opt2 (1), crm_opt3 (1), crm_opt4 (1), get_collisions_basic (1), get_collisions_extended (1), get_risk_y (1), get_y_grid (1), sample_parameters (1), sample_turbine_mCRM (1)

magrittr

%>% (41)

stats

median (18), quantile (9), df (5), dt (2), rbeta (2), runif (1)

tidyr

pivot_wider (4), separate (4), pivot_longer (2), replace_na (2)

dplyr

everything (2), filter (2), rename_with (2), slice_sample (2), (1), mutate (1), select (1)

rlang

expr (4), sym (4), format_error_bullets (2), fn_fmls_names (1)

purrr

map (4), imap (1), iwalk (1), pmap (1)

glue

glue_collapse (5)

tibble

add_column (4), tribble (1)

logr

log_open (4)

pracma

interp1 (3)

methods

is (2)

utils

data (2)

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

---

3. 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 31 files) and - 2 authors - 1 vignette - 10 internal data files - 12 imported packages - 31 exported functions (median 22 lines of code) - 56 non-exported functions in R (median 26 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 | 31| 89.9| | |files_vignettes | 1| 68.4| | |files_tests | 32| 98.2| | |loc_R | 2184| 85.8| | |loc_vignettes | 326| 66.5| | |loc_tests | 948| 86.1| | |num_vignettes | 1| 64.8| | |data_size_total | 4622918| 99.7|TRUE | |data_size_median | 2018| 68.7| | |n_fns_r | 87| 72.8| | |n_fns_r_exported | 31| 79.2| | |n_fns_r_not_exported | 56| 70.6| | |n_fns_per_file_r | 2| 30.6| | |num_params_per_fn | 6| 79.0| | |loc_per_fn_r | 24| 67.9| | |loc_per_fn_r_exp | 22| 50.8| | |loc_per_fn_r_not_exp | 26| 73.5| | |rel_whitespace_R | 27| 90.9| | |rel_whitespace_vignettes | 21| 49.2| | |rel_whitespace_tests | 15| 79.3| | |doclines_per_fn_exp | 51| 64.2| | |doclines_per_fn_not_exp | 0| 0.0|TRUE | |fn_call_network_size | 156| 85.6| | ---

3a. Network visualisation

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

---

4. goodpractice and other checks

Details of goodpractice checks (click to open)

#### 3a. Continuous Integration Badges [](https://github.com/HiDef-Aerial-Surveying/stochLAB/actions) [](https://github.com/HiDef-Aerial-Surveying/stochLAB/actions) [](https://github.com/HiDef-Aerial-Surveying/stochLAB/actions) [](https://github.com/HiDef-Aerial-Surveying/stochLAB/actions) **GitHub Workflow Results** | id|name |conclusion |sha | run_number|date | |----------:|:--------------------------|:----------|:------|----------:|:----------| | 2934839587|pages build and deployment |success |43af2a | 56|2022-08-26 | | 2934816348|pkgcheck |failure |d7d703 | 16|2022-08-26 | | 2934816354|pkgdown |success |d7d703 | 28|2022-08-26 | | 2934816353|R-CMD-check |success |d7d703 | 31|2022-08-26 | | 2934816352|test-coverage |success |d7d703 | 30|2022-08-26 | --- #### 3b. `goodpractice` results #### `R CMD check` with [rcmdcheck](https://r-lib.github.io/rcmdcheck/) R CMD check generated the following notes: 1. checking installed package size ... NOTE installed size is 6.8Mb sub-directories of 1Mb or more: data 6.3Mb 2. checking dependencies in R code ... NOTE Package in Depends field not imported from: ‘tidyverse’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. 3. checking R code for possible problems ... NOTE mig_stoch_crm: no visible global function definition for ‘as_tibble’ Undefined global functions or variables: as_tibble R CMD check generated the following check_fails: 1. cyclocomp 2. no_description_depends 3. no_import_package_as_a_whole 4. rcmdcheck_depends_not_imported_from 5. rcmdcheck_undefined_globals 6. rcmdcheck_reasonable_installed_size #### Test coverage with [covr](https://covr.r-lib.org/) Package coverage: 75.68 #### Cyclocomplexity with [cyclocomp](https://github.com/MangoTheCat/cyclocomp) The following functions have cyclocomplexity >= 15: function | cyclocomplexity --- | --- validate_inputs | 99 stoch_crm | 51 band_crm | 33 sample_parameters | 26 mig_stoch_crm | 24 val_df_columns | 23 val_pars_df | 17 #### Static code analyses with [lintr](https://github.com/jimhester/lintr) [lintr](https://github.com/jimhester/lintr) found the following 414 potential issues: message | number of times --- | --- Avoid 1:length(...) expressions, use seq_len. | 1 Avoid 1:nrow(...) expressions, use seq_len. | 4 Avoid length(...):1 expressions, use seq_len. | 1 Avoid library() and require() calls in packages | 1 Avoid using sapply, consider vapply instead, that's type safe | 2 Lines should not be more than 80 characters. | 405

---

Package Versions

|package |version | |:--------|:---------| |pkgstats |0.1.1.20 | |pkgcheck |0.1.0.21 | |srr |0.0.1.180 |

---

Editor-in-Chief Instructions:

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

[mpadge]

@emilyriederer One of the statistical categories this package complies with is "Probability Distributions", which is currently in draft-mode only. I've implemented a corresponding "dev" branch of the srr package which the above checks use. These dev branches should be merged by mid-September 2022. Until then please note the following:

1. Automated checks will fail, because there is no way to trigger "dev" branch checks here, but we'll always see that fail and be able to ping the dev checks ourselves to dump results here.
2. Anybody wanting to check the package locally can easily do so by first running:

   remotes::install_github("ropensci-review-tools/srr@dev")

   All checks will then be re-directed to current "dev" branch of standards including the new categories;

3. We'll strive to get these new standards incorporated before reviews of this package commence. If we don't notify here, both @grwhumphries and reviewers will need to be warned that the Probability Distributions Standards may change during the review process, and so reviews may require iteration. (We will of course strive to avoid this!).

Thanks both, and great to have submissions really pushing our system along! :rocket: :bullettrain_side:

[grwhumphries]

@emilyriederer and @mpadge I've just re-run the package check with the srr dev branch and that seems to have passed. I also fixed the issue above (no returns documented) - which I guess is a new check as that wasn't picked up in previous checks? It should be ready to go again now

[emilyriederer]

Thanks @grwhumphries ! This is all great news. We will begin looking for an editor and hope to connect you shortly

[emilyriederer]

Hi @grwhumphries - I'm delighted to introduce @stephaniehicks as the handling editor for this submission. Thank you both for your work on this!

[emilyriederer]

@ropensci-review-bot assign @stephaniehicks as editor

[ropensci-review-bot]

Assigned! @stephaniehicks is now the editor

[grwhumphries]

@stephaniehicks - nice to meet you and looking forward to working with you

[stephaniehicks]

@ropensci-review-bot seeking reviewers

[ropensci-review-bot]

I'm sorry @stephaniehicks, I'm afraid I can't do that. That's something only editors are allowed to do.

[stephaniehicks]

Hi @grwhumphries, great to meet you too. I apologize for my slow response on this. I'm working on identifying reviewers.

@mpadge can you confirm that I have access to @ropensci-review-bot seeking reviewers. At the moment, it looks like I don't have access to it and will need you or another editor's help here to initiate the bot. Thanks!

[mpadge]

@stephaniehicks Sorry about that, an oversight on our part. You should now be able to access all bot commands.

[stephaniehicks]

@ropensci-review-bot seeking reviewers

[ropensci-review-bot]

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

[![Status at rOpenSci Software Peer Review](https://badges.ropensci.org/551_status.svg)](https://github.com/ropensci/software-review/issues/551)

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

[stephaniehicks]

@mpadge Thanks! It looks like it is working now. Appreciate the help.

[stephaniehicks]

@grwhumphries, feel free to add the badge to the README of your package 👆

[stephaniehicks]

@ropensci-review-bot add @kstreet13

[ropensci-review-bot]

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

@ropensci-review-bot help

[stephaniehicks]

@ropensci-review-bot assign @kstreet13 as reviewer

[ropensci-review-bot]

@kstreet13 added to the reviewers list. Review due date is 2022-11-01. Thanks @kstreet13 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]

@kstreet13: If you haven't done so, please fill this form for us to update our reviewers records.

[stephaniehicks]

@mpadge just a small note about the stats dev guide:

The Handling Editor Checklist (https://stats-devguide.ropensci.org/pkgsubmission.html#handling-editor-checklist) says to use @ropensci-review-bot add <@GITHUB_USERNAME> to reviewers to add a reviewer, but following @ropensci-review-bot help, I noticed it is @ropensci-review-bot assign xxxxx as reviewer (i.e. need to replace add with assign).

[stephaniehicks]

Hi everyone, I'd like to introduce Kelly Street (@kstreet13) (https://kellystreet.org) who is an Assistant Professor at UCS. He has kindly agreed to be a reviewer here. However, I wanted to mention that he will need some time to review the guide to go through the content there first. Just a heads up! Thank you again @kstreet13 and let me know if you have any questions!

[mpadge]

Sorry for confusion @stephaniehicks! The bot should recognise any one of "add to reviewers" "add as reviewer", "assign as reviewer", or "assign to reviewers". I think the preceding glitch was because of missing "to reviewers". Happy that all now seems good :smile:

[stephaniehicks]

Ah! that makes sense. Thanks for the clarification!

[ropensci-review-bot]

:calendar: @kstreet13 you have 2 days left before the due date for your review (2022-11-01).

[kstreet13]

Apologies for the delay, everybody. I was unclear on the expectations for reviewers and ended up wasting some effort checking various standards in great detail. I will have a review for you as soon as I can!

[stephaniehicks]

Thank you @kstreet13! Please let me know if there's anything I can do to help support you in the review process. We greatly appreciate your time and effort on this.

[stephaniehicks]

@ropensci-review-bot assign @clairemas0n as reviewer

[ropensci-review-bot]

@clairemas0n added to the reviewers list. Review due date is 2022-11-24. Thanks @clairemas0n 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]

@clairemas0n: If you haven't done so, please fill this form for us to update our reviewers records.

[stephaniehicks]

Hi everyone, I'd like to welcome Claire Mason (@clairemas0n) to the thread! She has kindly agreed to be a reviewer here. Thank you again @clairemas0n and let me know if you have any questions!

[kstreet13]

Sorry again for the delay! As I said, this was my first time reviewing for ROpenSci and I was a little unclear on the expectations.

---

Package Review

• [x] As the reviewer I confirm that there are no conflicts of interest for me to review this work (If you are unsure whether you are in conflict, please speak to your editor before starting your review).

---

Compliance with Standards

• [x] This package complies with a sufficient number of standards for a silver badge
• [ ] This grade of badge is the same as what the authors wanted to achieve

The following standards currently deemed non-applicable (through tags of @srrstatsNA) could potentially be applied to future versions of this software:

• EA2.4 and EA2.5 concern the use of multitabular input, which is relevant to both stoch_crm and band_crm.
• G5.2, G5.2a, and G5.2b. The authors are correct that inputs are checked by the validate_inputs scripts, but this is not explicitly tested, as far as I can tell (ie. by having unit tests that give invalid inupts and checking for the correct error message).
• G1.5 is not directly applicable, but the authors do claim in the documentation that their implementation of the extended model is "over 30x faster than Masden's code", which is not demonstrated.
• PD3.5 seems to concern integration generally, which is a part of the model.

Please also comment on any standards which you consider either particularly well, or insufficiently, documented.

• G1.3 Details of the models including statistical terminology are not always explained, but users are directed to appropriate sources, such as Masden (2015) and Band (2012).
• G1.4a Internal functions are not all documented (esp. in validate_inputs)

For packages aiming for silver or gold badges:

• [x] This package extends beyond minimal compliance with standards in the following ways: Function documentation is quite extensive, which may be consequence of how complicated the core methods are, but is nonetheless impressive.

---

General Review

Documentation

The package includes all the following forms of documentation:

• [ ] A statement of need clearly stating problems the software is designed to solve and its target audience in README The first sentence lays out what the package does, but I'm a little unclear on who the target audience is. I'm guessing it's some combination of people who own wind farms and ornithologists?
• [x] Installation instructions: for the development version of package and any non-standard dependencies in README
• [x] Community guidelines including contribution guidelines in the README or CONTRIBUTING
• [x] The documentation is sufficient to enable general use of the package beyond one specific use case

Algorithms

• How well are algorithms encoded? The overall structure looks good to me, though some of the details (both of the method and the implementation) are lost on me. I'm guessing the big for loop that runs the model a bunch of times with different parameters is the most time-consuming part, so one potential future improvement would be to run those in parallel rather than sequentially.

• Is the choice of computer language appropriate for that algorithm, and/or envisioned use of package? Definitely. This is a stats-heavy model, so R seems like a natural choice.

• Are aspects of algorithmic scaling sufficiently documented and tested? I'm not sure this question is relevant. It (presumably) scales linearly with the number of iterations, but most functions parameters (that may or may not be inferred from data) rather than directly using any data.

• Are there any aspects of algorithmic implementation which could be improved? The parallelization mentioned above could help in cases where users want to run more iterations or try more models. But overall, the examples run pretty quickly, so it seems to be pretty well optimized (and I'm not qualified to comment on the correctness of the implementation, but that seems to checked by the tests).

Testing

• Regardless of actual coverage of tests, are there any fundamental software operations which are not sufficiently expressed in tests? I might be missing something, but I don't see any code coverage statistics. That said, tests seem to focus on assessing the correctness of the implementation. This is very important, but misses some of the more granular stuff like making sure every error/warning message works (as in G5.8). test-validate_inputs.R has some of this (and then some more, commented out), but given that there are SO MANY inputs to the main functions in this package, it definitely seems like these tests should be more extensive.

• Is there a need for extended tests, or if extended tests exists, have they been implemented in an appropriate way, and are they appropriately documented? I think there need to be more tests, but not an explicit set of "extended tests". The additional checks for appropriate warnings/errors, while numerous, should be relatively quick to run.

Visualisation (where appropriate)

• Do visualisations aid the primary purposes of statistical interpretation of results? N/A

• Are there any aspects of visualisations which could risk statistical misinterpretation? N/A

Package Design

• Is the package well designed for its intended purpose? Mostly. It enables the usage of a few different models for a common purpose and while there are a lot of exported functions, most users will probably only interact with a few. The main issue is the complexity of those functions.

• In relation to External Design: Do exported functions and the relationships between them enable general usage of the package? The functions listed on the main documentation page (stoch_crm and band_crm) are extrememly complex and I think this makes them difficult to use. stoch_crm has 31 arguments, which actually hides the number of parameters in the model, as many of these arguments expect data frames containing multiple parameters. I recognize that this isn't the authors' fault (it's a complex model and they have worked to make it more accessible), but the resulting code is still fairly intimidating. I don't know how familiar users will be with some of these specific arguments, but if it is at all possible to provide more reasonable default values, I think that would help.

• In relation to External Design: Do exported functions best serve inter-operability with other packages? I'm not familiar with any other packages that handle similar questions.

• In relation to Internal Design: Are algorithms implemented appropriately in terms of aspects such as efficiency, flexibility, generality, and accuracy? I think so.

• In relation to Internal Design: Could ranges of admissible input structures, or form(s) of output structures, be expanded to enhance inter-operability with other packages? A little bit, yes. All of the `_parsarguments expect a one-row data frame with column names"mean"and"sd", but I think these could accept numeric vectors, as well. You could require names (as inc(mean = 0, sd = 1)`), or just make it clear in the documentation of these arguments that the first element is assumed to be the mean and the second is the SD.*

---

• [x] Packaging guidelines: The package conforms to the rOpenSci packaging guidelines

Estimated hours spent reviewing: 20

• [x] Should the author(s) deem it appropriate, I agree to be acknowledged as a package reviewer ("rev" role) in the package DESCRIPTION file.

---

Review Comments

The guidelines don't seem too concerned about this, but my biggest concern with the package is the vignette. This is usually where I start when I want to use a new package, but it's very sparse and doesn't explain much. I would like for the vignette to provide more background and explanation, like the main package documentation. Also, none of the code is actually executed and some of it doesn't even run (there's a stray "messages" that should have been commented out in the Multiscenario Example. This is also present in the README).

I also want to reiterate that if there's anything the authors can do to reduce the number of arguments, provide more suggested default values, or in any way simplify the user experience, that would be greatly appreciated and make the package more approachable.

Some other minor notes:

• In the main package documentation, there seems to be some filler text that needs to be replaced ("...fill with migration functions..")
• There are a lot of checks that look like this:

  if(missing(bird_dens_opt)){
  bird_dens_opt <- "tnorm"
  }

  but should probably look like this:

  bird_dens_opt <- match.arg(bird_dens_opt)

  and match.arg will automatically treat the first possible value as the default.

• In those same checks, stoch_crm has two checks for out_period, but I'm guessing the second one was supposed to be out_format.
• I don't know if this is intentional, but in the vignette and README, you provide the argument log_file = paste0(getwd(), "scrm_example.log"). Since this doesn't include a separator it's creating something with the name [currentdirectory]scrm_example.log in the parent of the current directory. If that's not the intended behavior, it might be safer to replace this with file.path(getwd(), "scrm_example.log").
• There are a few commented out functions at the end of validate_inputs.R that could probably be removed

[grwhumphries]

@kstreet13 - thank you very much for the extensive review of our package! All of your comments are greatly appreciated and we owe you one.

@stephaniehicks @mpadge - what are the next steps for us?

[ropensci-review-bot]

:calendar: @clairemas0n you have 2 days left before the due date for your review (2022-11-24).