Submission: stochLAB #551

grwhumphries · 2022-07-27T20:33:40Z

Date accepted: 2023-02-03

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: @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", , "[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

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.

I have read the rOpenSci packaging guide.
I have read the author guide and I expect to maintain this package for at least 2 years or have another maintainer identified.
I/we have read the Statistical Software Peer Review Guide for Authors.
I/we have run autotest checks on the package, and ensured no tests fail.
The srr_stats_pre_submit() function confirms this package may be submitted.
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:

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

Publication options

Do you intend for this package to go on CRAN?
Do you intend for this package to go on Bioconductor?

Code of conduct

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

The text was updated successfully, but these errors were encountered:

ropensci-review-bot · 2022-07-27T20:33:41Z

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

ropensci-review-bot · 2022-07-27T20:33:44Z

🚀

Editor check started

👋

emilyriederer · 2022-07-30T02:35:39Z

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 · 2022-08-03T16:24:34Z

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

ropensci-review-bot · 2022-08-04T14:19:26Z

Checks for stochLAB (v1.1.0)

git hash: e8f8f24f

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

**

✔️ 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

mpadge · 2022-08-04T15:44:58Z

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)

✖️ 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 · 2022-08-08T00:41:11Z

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 · 2022-08-08T09:57:55Z

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 · 2022-08-08T10:05:21Z

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 · 2022-08-26T15:21:38Z

@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 · 2022-08-26T22:50:19Z

@ropensci-review-bot check package

ropensci-review-bot · 2022-08-26T22:50:20Z

Thanks, about to send the query.

ropensci-review-bot · 2022-08-26T22:50:23Z

🚀

Editor check started

👋

ropensci-review-bot · 2022-08-26T22:53:11Z

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 · 2022-08-27T16:00:52Z

@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 · 2022-08-29T09:22:52Z

Checks for stochLAB (v1.1.1)

git hash: d7d7034f

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

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

Package License: GPL (>= 3)

1. rOpenSci Statistical Standards (`srr` package)

This package is in the following category:

Exploratory Data Analysis

✔️ 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 ✖️ have been resolved.

mpadge · 2022-08-29T09:33:13Z

@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! 🚀 🚄

grwhumphries · 2022-08-29T21:04:41Z

@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 · 2022-08-29T23:41:42Z

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

emilyriederer · 2022-09-02T09:17:07Z

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

emilyriederer · 2022-09-02T09:17:28Z

@ropensci-review-bot assign @stephaniehicks as editor

ropensci-review-bot · 2022-09-02T09:17:30Z

Assigned! @stephaniehicks is now the editor

grwhumphries · 2022-09-02T09:40:57Z

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

stephaniehicks · 2022-10-03T01:51:28Z

@ropensci-review-bot seeking reviewers

ropensci-review-bot · 2022-10-03T01:51:29Z

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

stephaniehicks · 2022-10-03T01:53:24Z

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!

clairemas0n · 2022-12-23T03:20:33Z

Thank you @grwhumphries for taking the time to consider my comments. The README is now very comprehensive and contextualises the package very well. I acknowledge my review has been responded to and I approve acceptance at a gold level. Congratulations @grwhumphries on all your work getting this package to this standard. Very impressive!

@clairemas0n - would you like to be listed in the DESCRIPTION as a reviewer?
Sorry missed this. I wasn't sure whether my contributions were substantial enough to be considered a reviewer. But happy to be mentioned if they contributed enough to the development of your package. Not worried either way. Thank you @grwhumphries.

@ropensci-review-bot submit review #551 (comment) time 5

grwhumphries · 2023-02-01T18:41:34Z

HI @stephaniehicks @kstreet13
just wanted to check to see if there's been any movement on the final checks for the package? Would be keen to tie this up at some point soon :)

Cheers and thanks for your efforts on this

maurolepore · 2023-02-02T10:27:12Z

Dear all,

I'm the EiC on duty and now also acting as handling editor -- thanks @stephaniehicks for your work!

@kstreet13 could you please let me know if you're happy with the author's response and either request further changes or indicate approval with the reviewer approval template?

kstreet13 · 2023-02-02T19:10:37Z

Sorry! I somehow missed this in December. I think the package is much improved and all of my concerns have been addressed.

Regarding the points for clarification:

for PD3.5, I think I was looking at get_prop_crh_fhd, which contains the comment # integration over the rotor's height bands, but I think the height bands are discrete, so this isn't actually an approximation of a continuous integral.
Model terms are sufficiently explained, I think I was just confused by the complexity and not sufficiently familiar with the original papers.

I am happy to accept this package at a gold level. I don't think the standards for testing have been met in the way that they are written, but I absolutely agree with @grwhumphries that to do so would be impractical for this package and the current implementation is more than sufficient.

Reviewer Response

Final approval (post-review)

The author has responded to my review and made changes to my satisfaction. I recommend approving this package.

Estimated hours spent reviewing: 21

maurolepore · 2023-02-03T10:06:12Z

@ropensci-review-bot approve stochLAB

ropensci-review-bot · 2023-02-03T10:06:14Z

Approved! Thanks @grwhumphries for submitting and @kstreet13, @clairemas0n for your reviews! 😁

To-dos:

Should you want to acknowledge your reviewers in your package DESCRIPTION, you can do so by making them "rev"-type contributors in the Authors@R field (with their consent).

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.

maurolepore · 2023-02-03T10:14:00Z

@grwhumphries,

Congratulations!

I believe you won't be able to check To-do's above so here they are again in plain text. You can copy-paste them in a comment of your own and check-chem as you complete them.

Let me know if you're blocked with any.

- [ ] Transfer the repo to rOpenSci's "ropensci" GitHub organization under "Settings" in your repo.  I have invited you to a team that should allow you to do so. You will need to [enable two-factor authentication](https://docs.github.com/en/authentication/securing-your-account-with-two-factor-authentication-2fa/configuring-two-factor-authentication) for your GitHub account.
**This invitation will expire after one week. If it happens write a comment `@ropensci-review-bot invite me to ropensci/<package-name>` which will re-send an invitation.**
- [ ] After transfer write a comment `@ropensci-review-bot finalize transfer of <package-name>` where `<package-name>` is the repo/package name. This will give you admin access back.
- [ ] Fix all links to the GitHub repo to point to the repo under the ropensci organization.
- [ ] Delete your current code of conduct file if you had one since rOpenSci's default one will apply, see https://devguide.ropensci.org/collaboration.html#coc-file
- [ ] If you already had a `pkgdown` website **and are ok relying only on [rOpenSci central docs building and branding](https://devguide.ropensci.org/ci.html#even-more-ci-ropensci-docs)**,
    * deactivate the automatic deployment you might have set up
    * remove styling tweaks from your pkgdown config but keep that config file
    * replace the whole current `pkgdown` website with a [redirecting page](https://devguide.ropensci.org/redirect.html)
    * replace your package docs URL with `https://docs.ropensci.org/package_name`
    * In addition, in your DESCRIPTION file, include the docs link in the `URL` field alongside the link to the GitHub repository, e.g.: `URL: https://docs.ropensci.org/foobar, https://github.com/ropensci/foobar`
- [ ] Skim the docs of the [pkgdown automatic deployment](https://devguide.ropensci.org/building.html#docsropensci), in particular if your website needs MathJax.
- [ ] Fix any links in badges for CI and coverage to point to the new repository URL. 
- [ ] Increment the package version to reflect the changes you made during review. In NEWS.md, add a heading for the new version and one bullet for each user-facing change, and each developer-facing change that you think is relevant.
- [ ] We're starting to roll out software metadata files to all rOpenSci packages via the Codemeta initiative, see https://docs.ropensci.org/codemetar/ for how to include it in your package, after installing the package - should be easy as running `codemetar::write_codemeta()` in the root of your package.
- [ ] You can add this installation method to your package README `install.packages("<package-name>", repos = "https://ropensci.r-universe.dev")` thanks to [R-universe](https://ropensci.org/blog/2021/06/22/setup-runiverse/).

maelle · 2023-02-14T06:54:44Z

@grwhumphries did you meet any difficulty? I'm asking as I'm drafting rOpenSci newsletter I'll send on Friday: if your package is transferred by then, it will be mentioned in this month's newsletter (if not, in next month's so no worries).

grwhumphries · 2023-02-23T10:13:50Z

@ropensci-review-bot finalize transfer of grwhumphries/stochLAB

ropensci-review-bot · 2023-02-23T10:13:51Z

Can't find repository ropensci/grwhumphries/stochLAB, have you forgotten to transfer it first?

grwhumphries · 2023-02-23T10:14:14Z

@ropensci-review-bot finalize transfer of ropensci/stochLAB

ropensci-review-bot · 2023-02-23T10:14:15Z

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

@ropensci-review-bot help

grwhumphries · 2023-02-23T10:15:08Z

@ropensci-review-bot finalize transfer of ropensci/stochLAB

ropensci-review-bot · 2023-02-23T10:15:11Z

Could not finalize transfer: Could not add owner rights to the ropensci/stochLAB team

grwhumphries · 2023-02-23T10:17:01Z

@ropensci-review-bot finalize transfer of ropensci/stochLAB

ropensci-review-bot · 2023-02-23T10:17:04Z

Could not finalize transfer: Could not add owner rights to the ropensci/stochLAB team

grwhumphries · 2023-02-23T10:17:52Z

@maurolepore @maelle @stephaniehicks any idea why the owner rights aren't transferring properly?

maelle · 2023-02-23T11:41:03Z

@grwhumphries you first need to transfer the repository to rOpenSci via the repository settings (I've just checked that you had accepted the invitation to the ropensci GitHub organization so you have the rights to do that).

This will transfer the repo but lock you out. To get admin access back, you will then write a comment like #551 (comment)

Please tell me how it goes + if anything is unclear.

grwhumphries · 2023-02-23T14:12:29Z

@ropensci-review-bot finalize transfer of ropensci/stochLAB

ropensci-review-bot · 2023-02-23T14:12:31Z

Could not finalize transfer: Could not add owner rights to the ropensci/stochLAB team

grwhumphries · 2023-02-23T14:14:04Z

Hi @maelle - I've already transferred the repo over to rOpenSci (check out ropensci/stochLAB). Then I wrote @ropensci-review-bot finalize transfer of ropensci/stochLAB - but still getting: Could not finalize transfer: Could not add owner rights to the ropensci/stochLAB team

grwhumphries · 2023-02-23T14:14:37Z

@ropensci-review-bot finalize transfer of stochLAB

ropensci-review-bot · 2023-02-23T14:14:40Z

Transfer completed.
The stochLAB team is now owner of the repository and the author has been invited to the team

grwhumphries · 2023-02-23T14:15:22Z

AH! This needs to be in the format: @ropensci-review-bot finalize transfer of stochLAB -> the instructions suggested this had to be ropensci/stochLAB

maelle · 2023-02-24T13:13:13Z

@grwhumphries this is due to a confusion with the "invite me" command, correct? or which instructions do you mean? (I agree the two different syntaxes are confusing)

mpadge mentioned this issue Aug 4, 2022

Clarify need to document at least one category ropensci/statistical-software-review-book#69

Closed

ropensci-review-bot assigned stephaniehicks Sep 2, 2022

ropensci-review-bot added the 1/editor-checks label Sep 2, 2022

mpadge added the stats label Sep 20, 2022

maelle removed the 4/review(s)-in-awaiting-changes label Jan 10, 2023

ropensci-review-bot added 6/approved-gold-v0.2 Statistical software grade 6/approved and removed 5/awaiting-reviewer(s)-response labels Feb 3, 2023

ropensci-review-bot closed this as completed Feb 3, 2023

Submission: stochLAB #551

Submission: stochLAB #551

Comments

grwhumphries commented Jul 27, 2022 • edited by ropensci-review-bot Loading

Due date for @clairemas0n: 2022-11-24 Archive: TBD Version accepted: TBD Language: en

Pre-submission Inquiry

General Information

Badging

Technical checks

Publication options

Code of conduct

ropensci-review-bot commented Jul 27, 2022

ropensci-review-bot commented Jul 27, 2022

emilyriederer commented Jul 30, 2022

grwhumphries commented Aug 3, 2022

ropensci-review-bot commented Aug 4, 2022

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:

mpadge commented Aug 4, 2022

1. rOpenSci Statistical Standards (srr package)

emilyriederer commented Aug 8, 2022

grwhumphries commented Aug 8, 2022

emilyriederer commented Aug 8, 2022

grwhumphries commented Aug 26, 2022

emilyriederer commented Aug 26, 2022

ropensci-review-bot commented Aug 26, 2022

ropensci-review-bot commented Aug 26, 2022

ropensci-review-bot commented Aug 26, 2022

grwhumphries commented Aug 27, 2022

ropensci-review-bot commented Aug 29, 2022

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:

mpadge commented Aug 29, 2022

grwhumphries commented Aug 29, 2022

emilyriederer commented Aug 29, 2022

emilyriederer commented Sep 2, 2022

emilyriederer commented Sep 2, 2022

ropensci-review-bot commented Sep 2, 2022

grwhumphries commented Sep 2, 2022

stephaniehicks commented Oct 3, 2022

ropensci-review-bot commented Oct 3, 2022

stephaniehicks commented Oct 3, 2022

clairemas0n commented Dec 23, 2022

grwhumphries commented Feb 1, 2023

maurolepore commented Feb 2, 2023

kstreet13 commented Feb 2, 2023

Reviewer Response

Final approval (post-review)

maurolepore commented Feb 3, 2023

ropensci-review-bot commented Feb 3, 2023

maurolepore commented Feb 3, 2023

maelle commented Feb 14, 2023

grwhumphries commented Feb 23, 2023

ropensci-review-bot commented Feb 23, 2023

grwhumphries commented Feb 23, 2023

ropensci-review-bot commented Feb 23, 2023

grwhumphries commented Feb 23, 2023

ropensci-review-bot commented Feb 23, 2023

grwhumphries commented Jul 27, 2022 •

edited by ropensci-review-bot

Loading

Due date for @clairemas0n: 2022-11-24
Archive: TBD
Version accepted: TBD
Language: en

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