software-review Submission: stochLAB

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

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", , "[email protected]", role = c("aut", "cre")),
    person("Bruno", "Caneco", , "[email protected]", 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.

Jul 27 '22 20:07 grwhumphries

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

Jul 27 '22 20:07 ropensci-review-bot

:rocket:

Editor check started

:wave:

Jul 27 '22 20:07 ropensci-review-bot

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!

Jul 30 '22 02:07 emilyriederer

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

Aug 03 '22 16:08 grwhumphries

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(<path/to/repo>)', 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

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

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

R CMD check generated the following notes:

checking installed package size ... NOTE installed size is 6.8Mb sub-directories of 1Mb or more: data 6.3Mb
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘data.table’ ‘foreach’ All declared Imports should be used.
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:

cyclocomp
no_import_package_as_a_whole
rcmdcheck_imports_not_imported_from
rcmdcheck_undefined_globals
rcmdcheck_reasonable_installed_size

Test coverage with covr

Package coverage: 75.43

Cyclocomplexity with 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

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

Aug 04 '22 14:08 ropensci-review-bot

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.

Aug 04 '22 15:08 mpadge

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!

Aug 08 '22 00:08 emilyriederer

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?

Aug 08 '22 09:08 grwhumphries

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.

Aug 08 '22 10:08 emilyriederer

@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.

Aug 26 '22 15:08 grwhumphries

@ropensci-review-bot check package

Aug 26 '22 22:08 emilyriederer

Thanks, about to send the query.

Aug 26 '22 22:08 ropensci-review-bot

:rocket:

Editor check started

:wave:

Aug 26 '22 22:08 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.

Aug 26 '22 22:08 ropensci-review-bot

@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

Aug 27 '22 16:08 grwhumphries

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(<path/to/repo>)', 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

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

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

R CMD check generated the following notes:

checking installed package size ... NOTE installed size is 6.8Mb sub-directories of 1Mb or more: data 6.3Mb
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.
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:

cyclocomp
no_description_depends
no_import_package_as_a_whole
rcmdcheck_depends_not_imported_from
rcmdcheck_undefined_globals
rcmdcheck_reasonable_installed_size

Test coverage with covr

Package coverage: 75.68

Cyclocomplexity with 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

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.

Aug 29 '22 09:08 ropensci-review-bot

@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:

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.
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;
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:

Aug 29 '22 09:08 mpadge

@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

Aug 29 '22 21:08 grwhumphries

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

Aug 29 '22 23:08 emilyriederer

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

Sep 02 '22 09:09 emilyriederer

@ropensci-review-bot assign @stephaniehicks as editor

Sep 02 '22 09:09 emilyriederer

Assigned! @stephaniehicks is now the editor

Sep 02 '22 09:09 ropensci-review-bot

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

Sep 02 '22 09:09 grwhumphries

@ropensci-review-bot seeking reviewers

Oct 03 '22 01:10 stephaniehicks

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

Oct 03 '22 01:10 ropensci-review-bot

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!

Oct 03 '22 01:10 stephaniehicks

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

Oct 04 '22 08:10 mpadge

@ropensci-review-bot seeking reviewers

Oct 04 '22 20:10 stephaniehicks

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

Oct 04 '22 20:10 ropensci-review-bot

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

Oct 04 '22 20:10 stephaniehicks

software-review software-review copied to clipboard

Submission: stochLAB

Archive: TBD Version accepted: TBD Language: en

Pre-submission Inquiry

General Information

Badging

Technical checks

Publication options

Code of conduct

Checks for stochLAB (v1.1.0)

1. rOpenSci Statistical Standards (srr package)

2. Package Dependencies

3. Statistical Properties

3a. Network visualisation

4. goodpractice and other checks

3a. Continuous Integration Badges

3b. goodpractice results

R CMD check with rcmdcheck

Test coverage with covr

Cyclocomplexity with cyclocomp

Static code analyses with lintr

Editor-in-Chief Instructions:

1. rOpenSci Statistical Standards (srr package)

Checks for stochLAB (v1.1.1)

1. rOpenSci Statistical Standards (srr package)

2. Package Dependencies

3. Statistical Properties

3a. Network visualisation

4. goodpractice and other checks

3a. Continuous Integration Badges

3b. goodpractice results

R CMD check with rcmdcheck

Test coverage with covr

Cyclocomplexity with cyclocomp

Static code analyses with lintr

Editor-in-Chief Instructions:

software-review
software-review copied to clipboard

1. rOpenSci Statistical Standards (`srr` package)

4. `goodpractice` and other checks

3b. `goodpractice` results

`R CMD check` with rcmdcheck

1. rOpenSci Statistical Standards (`srr` package)

1. rOpenSci Statistical Standards (`srr` package)

4. `goodpractice` and other checks

3b. `goodpractice` results

`R CMD check` with rcmdcheck