software-review Capybara

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Submitting Author Name: Pacha Submitting Author Github Handle: @pachadotdev Repository: https://github.com/pachadotdev/capybara Version submitted: 0.2.5 (initially) Submission type: Stats Badge grade: silver (?) Editor: @rkillick Reviewers: TBD

Archive: TBD Version accepted: TBD Language: en

Paste the full DESCRIPTION file inside a code block below:

Package: capybara
Type: Package
Title: Fast and Memory Efficient Fitting of Linear Models With High-Dimensional
    Fixed Effects
Version: 0.5.2
Authors@R: c(
    person(
        given = "Mauricio",
        family = "Vargas Sepulveda",
        role = c("aut", "cre"),
        email = "[email protected]",
        comment = c(ORCID = "0000-0003-1017-7574"))
    )
Imports:
    dplyr,
    Formula,
    generics,
    magrittr,
    MASS,
    rlang,
    stats
Suggests: 
    knitr,
    rmarkdown,
    testthat (>= 3.0.0),
    tidyr
Depends: R(>= 3.5.0)
Description: Fast and user-friendly estimation of generalized linear models with
    multiple fixed effects and cluster the standard errors. The method to obtain
    the estimated fixed-effects coefficients is based on Stammann (2018) 
    <https://arxiv.org/abs/1707.01815> and Gaure (2013)
    <https://dx.doi.org/10.1016/j.csda.2013.03.024>.
License: Apache License (>= 2)
BugReports: https://github.com/pachadotdev/capybara/issues
URL: https://pacha.dev/capybara/, https://github.com/pachadotdev/capybara
LazyData: true
RoxygenNote: 7.3.1
Encoding: UTF-8
NeedsCompilation: yes
LinkingTo: cpp11, cpp11armadillo
VignetteBuilder: knitr
Config/testthat/edition: 3
Remotes: 
    pachadotdev/cpp11armadillo,
    ropenscilabs/srr
Roxygen: list(markdown = TRUE, roclets = c("namespace", "rd", "srr::srr_stats_roclet"))

Scope

Please indicate which of our statistical package categories this package falls under. (Please check one or more appropriate boxes below):

Statistical Packages
- [ ] Bayesian and Monte Carlo Routines
- [ ] Dimensionality Reduction, Clustering, and Unsupervised Learning
- [ ] Machine Learning
- [x] Regression and Supervised Learning
- [ ] Exploratory Data Analysis (EDA) and Summary Statistics
- [ ] Spatial Analyses
- [ ] Time Series Analyses
- [ ] Probability Distributions

Pre-submission Inquiry

[x] A pre-submission inquiry has been approved in issue#629

General Information

Who is the target audience and what are scientific applications of this package?

People (mostly) in the social sciences that need multiple controls in their models. This is especially useful in Economics and International Relations.

Paste your responses to our General Standard G1.1 here, describing whether your software is:
- An improvement on other implementations of similar algorithms in R.
Please include hyperlinked references to all other relevant software. https://github.com/amrei-stammann/alpaca/

Badging

What grade of badge are you aiming for? (silver)
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)

Have a demonstrated generality of usage beyond one single envisioned use case.
Compliance with a good number of standards beyond those identified as minimally necessary.

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.

Jun 01 '24 02:06 pachadotdev

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

Jun 01 '24 02:06 ropensci-review-bot

:rocket:

Editor check started

:wave:

Jun 01 '24 02:06 ropensci-review-bot

@pachadotdev Checks failed because of the missing comma in your DESCRIPTION file which I see you've fixed in your latest commit. Ask the bot to check package again and it should work.

Jun 03 '24 08:06 mpadge

@ropensci-review-bot check package

Jun 03 '24 19:06 pachadotdev

Thanks, about to send the query.

Jun 03 '24 19:06 ropensci-review-bot

:rocket:

Editor check started

:wave:

Jun 03 '24 19:06 ropensci-review-bot

Checks for capybara (v0.5.1)

git hash: 55b6c2d8

:heavy_check_mark: Package name is available
:heavy_multiplication_x: does not have a 'codemeta.json' file.
:heavy_multiplication_x: does not have a 'contributing' file.
:heavy_multiplication_x: The following functions have no documented return values: [fenegbin, fepoisson]
: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_multiplication_x: These functions do not have examples: [feglm_control, summary.apes, summary.feglm, summary.felm, vcov.apes, vcov.feglm, vcov.felm].
:heavy_check_mark: Package has continuous integration checks.
:heavy_multiplication_x: Package coverage is 37.5% (should be at least 75%).
:heavy_multiplication_x: This package still has TODO standards and can not be submitted
:heavy_multiplication_x: Statistical standards should be documented in most package files, yet are mostly only documented in one file.
:heavy_check_mark: R CMD check found no errors.
:heavy_check_mark: R CMD check found no warnings.
:eyes: Function names are duplicated in other packages

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

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

Package License: Apache License (>= 2)

1. rOpenSci Statistical Standards (`srr` package)

This package is in the following category:

Regression and Supervised Learning

:heavy_multiplication_x: This package still has TODO standards and can not be submitted All applicable standards [v0.2.0] have been documented in this package (68 complied with; 1 N/A standards) Statistical standards should be documented in most package files, yet are mostly only documented in one file.

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	210
internal	capybara	111
internal	utils	47
internal	grDevices	13
internal	graphics	2
imports	stats	115
imports	rlang	22
imports	magrittr	6
imports	dplyr	4
imports	MASS	4
imports	Formula	1
suggests	fixest	NA
suggests	knitr	NA
suggests	rmarkdown	NA
suggests	testthat	NA
suggests	tidyr	NA
linking_to	cpp11	NA
linking_to	cpp11armadillo	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

length (13), for (11), list (11), seq.int (10), abs (9), beta (9), attr (8), drop (8), max (8), c (7), mapply (7), names (7), sum (7), nrow (6), ncol (5), matrix (4), trace (4), as.logical (3), cbind (3), class (3), diag (3), getOption (3), lapply (3), rep (3), sqrt (3), structure (3), try (3), with (3), all (2), apply (2), as.matrix (2), integer (2), is.finite (2), letters (2), levels (2), mean (2), nchar (2), numeric (2), paste0 (2), replace (2), sample (2), unlist (2), vapply (2), as.data.frame (1), as.list (1), as.vector (1), colnames (1), colSums (1), data.frame (1), inherits (1), min (1), order (1), rownames (1), summary (1), suppressWarnings (1), unname (1)

stats

family (36), formula (25), nobs (14), model.matrix (10), deviance (4), terms (4), Gamma (3), offset (3), pnorm (3), vcov (3), weights (3), coefficients (2), D (2), C (1), poisson (1), predict (1)

capybara

get_index_list_ (8), crossprod_ (5), feglm_fit_ (3), group_sums_ (3), nobs_ (3), partial_mu_eta_ (3), solve_beta_ (3), solve_y_ (3), center_variables_ (2), check_factor_ (2), feglm (2), gamma_ (2), get_alpha_ (2), getScoreMatrix (2), group_sums_cov_ (2), init_theta_ (2), inv_ (2), solve_bias_ (2), solve_eta_ (2), solve_eta2_ (2), sqrt_ (2), temp_var_ (2), apes (1), augment.feglm (1), bias_corr (1), check_control_ (1), check_data_ (1), check_family_ (1), check_formula_ (1), check_linear_dependence_ (1), check_response_ (1), check_weights_ (1), coef.apes (1), coef.feglm (1), coef.felm (1), coef.summary.apes (1), coef.summary.feglm (1), coef.summary.felm (1), drop_by_link_type_ (1), feglm_control (1), feglm_offset_ (1), felm (1), felm_fit_ (1), fenegbin (1), fepoisson (1), fitted.feglm (1), fitted.felm (1), fixed_effects (1), glance.feglm (1), glance.felm (1), group_sums_spectral_ (1), group_sums_var_ (1), model_frame_ (1), model_response_ (1), pairwise_cor_ (1), predict.feglm (1), predict.felm (1), print.apes (1), print.feglm (1), print.felm (1), print.summary.apes (1), print.summary.feglm (1), print.summary.felm (1), rank_ (1), sandwich_ (1), start_guesses_ (1), summary_estimates_ (1), summary_family_ (1), summary_fisher_ (1), summary_formula_ (1), summary.apes (1), summary.feglm (1), summary.felm (1), update_nu_ (1)

utils

data (46), combn (1)

rlang

sym (22)

grDevices

cm (13)

magrittr

%>% (6)

dplyr

all_of (2), select (2)

MASS

negative.binomial (2), theta.ml (2)

graphics

pie (2)

Formula

Formula (1)

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 C++ (26% in 6 files) and R (74% in 23 files)
1 authors
1 vignette
1 internal data file
7 imported packages
14 exported functions (median 22 lines of code)
163 non-exported functions in R (median 6 lines of code)
45 R functions (median 5 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	23	84.5
files_src	6	90.2
files_vignettes	2	85.7
files_tests	6	84.4
loc_R	1554	78.9
loc_src	549	48.8
loc_vignettes	81	19.3
loc_tests	228	58.3
num_vignettes	1	64.8
data_size_total	285103	89.1
data_size_median	285103	95.3	TRUE
n_fns_r	177	88.0
n_fns_r_exported	14	56.3
n_fns_r_not_exported	163	91.1
n_fns_src	45	64.7
n_fns_per_file_r	4	63.6
n_fns_per_file_src	7	66.4
num_params_per_fn	3	33.6
loc_per_fn_r	7	16.0
loc_per_fn_r_exp	22	52.1
loc_per_fn_r_not_exp	6	13.8
loc_per_fn_src	5	5.0	TRUE
rel_whitespace_R	20	80.6
rel_whitespace_src	24	55.8
rel_whitespace_vignettes	23	12.6
rel_whitespace_tests	22	56.4
doclines_per_fn_exp	34	41.6
doclines_per_fn_not_exp	0	0.0	TRUE
fn_call_network_size	145	84.8

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
9340075153	format_check	failure	55b6c2	35	2024-06-02
9340075080	pages build and deployment	success	55b6c2	57	2024-06-02
9340075152	R-CMD-check	success	55b6c2	55	2024-06-02
9340075157	test-coverage	success	55b6c2	34	2024-06-02

3b. `goodpractice` results

`R CMD check` with rcmdcheck

R CMD check generated the following note:

checking installed package size ... NOTE installed size is 9.0Mb sub-directories of 1Mb or more: libs 8.2Mb

R CMD check generated the following check_fail:

rcmdcheck_reasonable_installed_size

Test coverage with covr

Package coverage: 37.48

The following files are not completely covered by tests:

file	coverage
R/apes.R	24.26%
R/bias_corr.R	0%
R/felm.R	0%
R/fenegbin.R	0%
R/fixed_effects.R	0%
R/generics_augment.R	0%
R/generics_coef.R	0%
R/generics_fitted.R	0%
R/generics_glance.R	0%
R/generics_print.R	0%
R/generics_summary.R	39.66%
R/generics_tidy.R	0%
R/generics_vcov.R	52.63%
R/helpers.R	63.19%
R/internals.R	54.82%
src/02_get_alpha.cpp	0%
src/03_group_sums.cpp	0%

Cyclocomplexity with cyclocomp

The following functions have cyclocomplexity >= 15:

function	cyclocomplexity
apes	38
feglm_fit_	26
feglm_offset_	21
bias_corr	19
vcov.feglm	18
fenegbin	15

Static code analyses with lintr

lintr found the following 124 potential issues:

message	number of times
Avoid 1:ncol(...) expressions, use seq_len.	2
Avoid library() and require() calls in packages	1
Lines should not be more than 80 characters. This line is 103 characters.	1
Lines should not be more than 80 characters. This line is 104 characters.	1
Lines should not be more than 80 characters. This line is 105 characters.	1
Lines should not be more than 80 characters. This line is 106 characters.	2
Lines should not be more than 80 characters. This line is 108 characters.	1
Lines should not be more than 80 characters. This line is 110 characters.	2
Lines should not be more than 80 characters. This line is 113 characters.	1
Lines should not be more than 80 characters. This line is 114 characters.	2
Lines should not be more than 80 characters. This line is 115 characters.	1
Lines should not be more than 80 characters. This line is 116 characters.	1
Lines should not be more than 80 characters. This line is 117 characters.	2
Lines should not be more than 80 characters. This line is 121 characters.	1
Lines should not be more than 80 characters. This line is 122 characters.	2
Lines should not be more than 80 characters. This line is 126 characters.	1
Lines should not be more than 80 characters. This line is 128 characters.	1
Lines should not be more than 80 characters. This line is 129 characters.	1
Lines should not be more than 80 characters. This line is 131 characters.	2
Lines should not be more than 80 characters. This line is 132 characters.	1
Lines should not be more than 80 characters. This line is 133 characters.	1
Lines should not be more than 80 characters. This line is 134 characters.	1
Lines should not be more than 80 characters. This line is 136 characters.	1
Lines should not be more than 80 characters. This line is 141 characters.	1
Lines should not be more than 80 characters. This line is 142 characters.	1
Lines should not be more than 80 characters. This line is 144 characters.	1
Lines should not be more than 80 characters. This line is 145 characters.	1
Lines should not be more than 80 characters. This line is 147 characters.	1
Lines should not be more than 80 characters. This line is 151 characters.	1
Lines should not be more than 80 characters. This line is 154 characters.	1
Lines should not be more than 80 characters. This line is 155 characters.	1
Lines should not be more than 80 characters. This line is 156 characters.	1
Lines should not be more than 80 characters. This line is 161 characters.	2
Lines should not be more than 80 characters. This line is 163 characters.	1
Lines should not be more than 80 characters. This line is 165 characters.	2
Lines should not be more than 80 characters. This line is 166 characters.	1
Lines should not be more than 80 characters. This line is 169 characters.	1
Lines should not be more than 80 characters. This line is 170 characters.	1
Lines should not be more than 80 characters. This line is 174 characters.	3
Lines should not be more than 80 characters. This line is 176 characters.	1
Lines should not be more than 80 characters. This line is 178 characters.	1
Lines should not be more than 80 characters. This line is 184 characters.	4
Lines should not be more than 80 characters. This line is 185 characters.	1
Lines should not be more than 80 characters. This line is 193 characters.	1
Lines should not be more than 80 characters. This line is 195 characters.	2
Lines should not be more than 80 characters. This line is 199 characters.	1
Lines should not be more than 80 characters. This line is 214 characters.	1
Lines should not be more than 80 characters. This line is 217 characters.	1
Lines should not be more than 80 characters. This line is 219 characters.	1
Lines should not be more than 80 characters. This line is 220 characters.	1
Lines should not be more than 80 characters. This line is 223 characters.	1
Lines should not be more than 80 characters. This line is 225 characters.	1
Lines should not be more than 80 characters. This line is 229 characters.	1
Lines should not be more than 80 characters. This line is 230 characters.	1
Lines should not be more than 80 characters. This line is 232 characters.	1
Lines should not be more than 80 characters. This line is 244 characters.	1
Lines should not be more than 80 characters. This line is 247 characters.	1
Lines should not be more than 80 characters. This line is 250 characters.	1
Lines should not be more than 80 characters. This line is 257 characters.	1
Lines should not be more than 80 characters. This line is 261 characters.	1
Lines should not be more than 80 characters. This line is 269 characters.	2
Lines should not be more than 80 characters. This line is 277 characters.	2
Lines should not be more than 80 characters. This line is 279 characters.	1
Lines should not be more than 80 characters. This line is 282 characters.	1
Lines should not be more than 80 characters. This line is 287 characters.	1
Lines should not be more than 80 characters. This line is 288 characters.	1
Lines should not be more than 80 characters. This line is 291 characters.	1
Lines should not be more than 80 characters. This line is 293 characters.	1
Lines should not be more than 80 characters. This line is 305 characters.	1
Lines should not be more than 80 characters. This line is 318 characters.	1
Lines should not be more than 80 characters. This line is 320 characters.	2
Lines should not be more than 80 characters. This line is 333 characters.	1
Lines should not be more than 80 characters. This line is 334 characters.	1
Lines should not be more than 80 characters. This line is 339 characters.	1
Lines should not be more than 80 characters. This line is 341 characters.	1
Lines should not be more than 80 characters. This line is 360 characters.	1
Lines should not be more than 80 characters. This line is 363 characters.	1
Lines should not be more than 80 characters. This line is 385 characters.	1
Lines should not be more than 80 characters. This line is 389 characters.	1
Lines should not be more than 80 characters. This line is 396 characters.	1
Lines should not be more than 80 characters. This line is 441 characters.	1
Lines should not be more than 80 characters. This line is 81 characters.	2
Lines should not be more than 80 characters. This line is 82 characters.	3
Lines should not be more than 80 characters. This line is 83 characters.	1
Lines should not be more than 80 characters. This line is 84 characters.	1
Lines should not be more than 80 characters. This line is 85 characters.	1
Lines should not be more than 80 characters. This line is 86 characters.	2
Lines should not be more than 80 characters. This line is 87 characters.	1
Lines should not be more than 80 characters. This line is 88 characters.	1
Lines should not be more than 80 characters. This line is 90 characters.	1
Lines should not be more than 80 characters. This line is 91 characters.	1
Lines should not be more than 80 characters. This line is 92 characters.	5
Lines should not be more than 80 characters. This line is 94 characters.	2
Lines should not be more than 80 characters. This line is 95 characters.	2
Lines should not be more than 80 characters. This line is 96 characters.	1
Lines should not be more than 80 characters. This line is 98 characters.	1

5. Other Checks

Details of other checks (click to open)

:heavy_multiplication_x: The following 4 function names are duplicated in other packages:

- bias_corr from bife
- feglm from alpaca
- felm from lfe
- fixed_effects from baggr, gratia, gravity

Package Versions

package	version
pkgstats	0.1.5.2
pkgcheck	0.1.2.42
srr	0.1.3.2

Editor-in-Chief Instructions:

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

Jun 03 '24 19:06 ropensci-review-bot

Dear @pachadotdev , Thank you for your submission.

You have checked "Regression and Supervised Learning" which would entail a "Statistical software review" (a different issue template to be opened, but that is ok). Would you be willing to go through the statistical software review as described here and implementing the standards:https://stats-devguide.ropensci.org/pkgdev.html

Thanks, Julia

Jun 05 '24 18:06 jooolia

Dear @pachadotdev , Thank you for your submission.

You have checked "Regression and Supervised Learning" which would entail a "Statistical software review" (a different issue template to be opened, but that is ok). Would you be willing to go through the statistical software review as described here and implementing the standards:https://stats-devguide.ropensci.org/pkgdev.html

Thanks, Julia

thanks a lot !

indeed, when I opened the issue that was the only available template on my end

I already implemented https://stats-devguide.ropensci.org/pkgdev.html#pkgdev-srr

Jun 06 '24 15:06 pachadotdev

@ropensci-review-bot check package

Jun 18 '24 18:06 pachadotdev

Thanks, about to send the query.

Jun 18 '24 18:06 ropensci-review-bot

:rocket:

Editor check started

:wave:

Jun 18 '24 18:06 ropensci-review-bot

Checks for capybara (v0.5.1)

git hash: f277de6d

: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_multiplication_x: These functions do not have examples: [feglm_control].
:heavy_check_mark: Package has continuous integration checks.
:heavy_multiplication_x: Package coverage is 74.9% (should be at least 75%).
:heavy_multiplication_x: This package still has TODO standards and can not be submitted
:heavy_multiplication_x: Statistical standards should be documented in most package files, yet are mostly only documented in one file.
:heavy_check_mark: R CMD check found no errors.
:heavy_check_mark: R CMD check found no warnings.
:eyes: Function names are duplicated in other packages

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

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

Package License: Apache License (>= 2)

1. rOpenSci Statistical Standards (`srr` package)

This package is in the following category:

Regression and Supervised Learning

:heavy_multiplication_x: This package still has TODO standards and can not be submitted All applicable standards [v0.2.0] have been documented in this package (68 complied with; 1 N/A standards) Statistical standards should be documented in most package files, yet are mostly only documented in one file.

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	209
internal	capybara	109
internal	utils	47
internal	grDevices	13
internal	graphics	2
imports	stats	114
imports	rlang	22
imports	magrittr	6
imports	dplyr	4
imports	MASS	4
imports	Formula	1
suggests	fixest	NA
suggests	knitr	NA
suggests	rmarkdown	NA
suggests	testthat	NA
suggests	tidyr	NA
linking_to	cpp11	NA
linking_to	cpp11armadillo	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

length (13), for (11), list (11), seq.int (10), abs (9), beta (9), attr (8), drop (8), max (8), c (7), mapply (7), names (7), sum (7), nrow (6), ncol (5), matrix (4), trace (4), as.logical (3), cbind (3), class (3), diag (3), getOption (3), lapply (3), rep (3), sqrt (3), structure (3), try (3), with (3), all (2), apply (2), as.matrix (2), integer (2), is.finite (2), letters (2), levels (2), mean (2), nchar (2), numeric (2), paste0 (2), replace (2), sample (2), vapply (2), as.data.frame (1), as.list (1), as.vector (1), colnames (1), colSums (1), data.frame (1), inherits (1), min (1), order (1), rownames (1), summary (1), suppressWarnings (1), unlist (1), unname (1)

stats

family (36), formula (25), nobs (14), model.matrix (10), deviance (4), terms (4), Gamma (3), offset (3), pnorm (3), vcov (3), weights (3), coefficients (2), D (2), C (1), poisson (1)

capybara

get_index_list_ (8), crossprod_ (5), feglm_fit_ (3), group_sums_ (3), nobs_ (3), partial_mu_eta_ (3), solve_beta_ (3), solve_y_ (3), center_variables_ (2), check_factor_ (2), feglm (2), gamma_ (2), get_alpha_ (2), getScoreMatrix (2), group_sums_cov_ (2), init_theta_ (2), inv_ (2), solve_bias_ (2), solve_eta_ (2), solve_eta2_ (2), sqrt_ (2), temp_var_ (2), apes (1), augment.feglm (1), bias_corr (1), check_control_ (1), check_data_ (1), check_family_ (1), check_formula_ (1), check_linear_dependence_ (1), check_response_ (1), check_weights_ (1), coef.apes (1), coef.feglm (1), coef.felm (1), coef.summary.apes (1), coef.summary.feglm (1), coef.summary.felm (1), drop_by_link_type_ (1), feglm_control (1), feglm_offset_ (1), felm (1), felm_fit_ (1), fenegbin (1), fepoisson (1), fitted.feglm (1), fitted.felm (1), fixed_effects (1), glance.feglm (1), glance.felm (1), group_sums_spectral_ (1), group_sums_var_ (1), model_frame_ (1), model_response_ (1), predict.feglm (1), predict.felm (1), print.apes (1), print.feglm (1), print.felm (1), print.summary.apes (1), print.summary.feglm (1), print.summary.felm (1), rank_ (1), sandwich_ (1), start_guesses_ (1), summary_estimates_ (1), summary_family_ (1), summary_fisher_ (1), summary.apes (1), summary.feglm (1), summary.felm (1), update_nu_ (1)

utils

data (46), combn (1)

rlang

sym (22)

grDevices

cm (13)

magrittr

%>% (6)

dplyr

all_of (2), select (2)

MASS

negative.binomial (2), theta.ml (2)

graphics

pie (2)

Formula

Formula (1)

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 C++ (24% in 5 files) and R (76% in 23 files)
1 authors
1 vignette
1 internal data file
7 imported packages
10 exported functions (median 39 lines of code)
163 non-exported functions in R (median 7 lines of code)
39 R functions (median 5 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	23	84.5
files_src	5	88.8
files_vignettes	2	85.7
files_tests	9	89.6
loc_R	1537	78.7
loc_src	496	46.6
loc_vignettes	81	19.3
loc_tests	289	63.3
num_vignettes	1	64.8
data_size_total	285103	89.1
data_size_median	285103	95.3	TRUE
n_fns_r	173	87.5
n_fns_r_exported	10	45.3
n_fns_r_not_exported	163	91.1
n_fns_src	39	61.4
n_fns_per_file_r	4	62.9
n_fns_per_file_src	8	68.5
num_params_per_fn	4	54.6
loc_per_fn_r	7	16.0
loc_per_fn_r_exp	40	72.6
loc_per_fn_r_not_exp	7	18.0
loc_per_fn_src	5	5.0	TRUE
rel_whitespace_R	20	80.5
rel_whitespace_src	24	53.5
rel_whitespace_vignettes	23	12.6
rel_whitespace_tests	24	63.8
doclines_per_fn_exp	44	55.5
doclines_per_fn_not_exp	0	0.0	TRUE
fn_call_network_size	137	84.0

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
9557026802	format_check	failure	f277de	37	2024-06-18
9557026743	pages build and deployment	success	f277de	59	2024-06-18
9557026803	R-CMD-check	failure	f277de	57	2024-06-18
9557026804	test-coverage	success	f277de	36	2024-06-18

3b. `goodpractice` results

`R CMD check` with rcmdcheck

R CMD check generated the following note:

checking installed package size ... NOTE installed size is 8.1Mb sub-directories of 1Mb or more: libs 7.4Mb

R CMD check generated the following check_fail:

rcmdcheck_reasonable_installed_size

Test coverage with covr

Package coverage: 74.89

Cyclocomplexity with cyclocomp

The following functions have cyclocomplexity >= 15:

function	cyclocomplexity
apes	38
feglm_fit_	26
feglm_offset_	21
bias_corr	19
vcov.feglm	18
fenegbin	15

Static code analyses with lintr

lintr found the following 125 potential issues:

message	number of times
Avoid 1:ncol(...) expressions, use seq_len.	2
Avoid library() and require() calls in packages	1
Lines should not be more than 80 characters. This line is 103 characters.	2
Lines should not be more than 80 characters. This line is 104 characters.	1
Lines should not be more than 80 characters. This line is 105 characters.	1
Lines should not be more than 80 characters. This line is 106 characters.	2
Lines should not be more than 80 characters. This line is 108 characters.	1
Lines should not be more than 80 characters. This line is 110 characters.	2
Lines should not be more than 80 characters. This line is 113 characters.	1
Lines should not be more than 80 characters. This line is 114 characters.	2
Lines should not be more than 80 characters. This line is 115 characters.	1
Lines should not be more than 80 characters. This line is 116 characters.	1
Lines should not be more than 80 characters. This line is 117 characters.	2
Lines should not be more than 80 characters. This line is 121 characters.	1
Lines should not be more than 80 characters. This line is 122 characters.	2
Lines should not be more than 80 characters. This line is 126 characters.	1
Lines should not be more than 80 characters. This line is 128 characters.	1
Lines should not be more than 80 characters. This line is 129 characters.	1
Lines should not be more than 80 characters. This line is 131 characters.	2
Lines should not be more than 80 characters. This line is 132 characters.	1
Lines should not be more than 80 characters. This line is 133 characters.	1
Lines should not be more than 80 characters. This line is 134 characters.	1
Lines should not be more than 80 characters. This line is 136 characters.	1
Lines should not be more than 80 characters. This line is 141 characters.	1
Lines should not be more than 80 characters. This line is 142 characters.	1
Lines should not be more than 80 characters. This line is 144 characters.	1
Lines should not be more than 80 characters. This line is 145 characters.	1
Lines should not be more than 80 characters. This line is 147 characters.	1
Lines should not be more than 80 characters. This line is 151 characters.	1
Lines should not be more than 80 characters. This line is 154 characters.	1
Lines should not be more than 80 characters. This line is 155 characters.	1
Lines should not be more than 80 characters. This line is 156 characters.	1
Lines should not be more than 80 characters. This line is 161 characters.	2
Lines should not be more than 80 characters. This line is 163 characters.	1
Lines should not be more than 80 characters. This line is 165 characters.	2
Lines should not be more than 80 characters. This line is 166 characters.	1
Lines should not be more than 80 characters. This line is 169 characters.	1
Lines should not be more than 80 characters. This line is 170 characters.	1
Lines should not be more than 80 characters. This line is 174 characters.	3
Lines should not be more than 80 characters. This line is 176 characters.	1
Lines should not be more than 80 characters. This line is 178 characters.	1
Lines should not be more than 80 characters. This line is 184 characters.	4
Lines should not be more than 80 characters. This line is 185 characters.	1
Lines should not be more than 80 characters. This line is 193 characters.	1
Lines should not be more than 80 characters. This line is 195 characters.	2
Lines should not be more than 80 characters. This line is 199 characters.	1
Lines should not be more than 80 characters. This line is 214 characters.	1
Lines should not be more than 80 characters. This line is 217 characters.	1
Lines should not be more than 80 characters. This line is 219 characters.	1
Lines should not be more than 80 characters. This line is 220 characters.	1
Lines should not be more than 80 characters. This line is 223 characters.	1
Lines should not be more than 80 characters. This line is 225 characters.	1
Lines should not be more than 80 characters. This line is 229 characters.	1
Lines should not be more than 80 characters. This line is 230 characters.	1
Lines should not be more than 80 characters. This line is 232 characters.	1
Lines should not be more than 80 characters. This line is 244 characters.	1
Lines should not be more than 80 characters. This line is 247 characters.	1
Lines should not be more than 80 characters. This line is 250 characters.	1
Lines should not be more than 80 characters. This line is 257 characters.	1
Lines should not be more than 80 characters. This line is 261 characters.	1
Lines should not be more than 80 characters. This line is 269 characters.	2
Lines should not be more than 80 characters. This line is 277 characters.	2
Lines should not be more than 80 characters. This line is 279 characters.	1
Lines should not be more than 80 characters. This line is 282 characters.	1
Lines should not be more than 80 characters. This line is 287 characters.	1
Lines should not be more than 80 characters. This line is 288 characters.	1
Lines should not be more than 80 characters. This line is 291 characters.	1
Lines should not be more than 80 characters. This line is 293 characters.	1
Lines should not be more than 80 characters. This line is 305 characters.	1
Lines should not be more than 80 characters. This line is 318 characters.	1
Lines should not be more than 80 characters. This line is 320 characters.	2
Lines should not be more than 80 characters. This line is 333 characters.	1
Lines should not be more than 80 characters. This line is 334 characters.	1
Lines should not be more than 80 characters. This line is 339 characters.	1
Lines should not be more than 80 characters. This line is 341 characters.	1
Lines should not be more than 80 characters. This line is 360 characters.	1
Lines should not be more than 80 characters. This line is 363 characters.	1
Lines should not be more than 80 characters. This line is 385 characters.	1
Lines should not be more than 80 characters. This line is 389 characters.	1
Lines should not be more than 80 characters. This line is 396 characters.	1
Lines should not be more than 80 characters. This line is 441 characters.	1
Lines should not be more than 80 characters. This line is 81 characters.	2
Lines should not be more than 80 characters. This line is 82 characters.	3
Lines should not be more than 80 characters. This line is 83 characters.	1
Lines should not be more than 80 characters. This line is 84 characters.	1
Lines should not be more than 80 characters. This line is 85 characters.	1
Lines should not be more than 80 characters. This line is 86 characters.	2
Lines should not be more than 80 characters. This line is 87 characters.	1
Lines should not be more than 80 characters. This line is 88 characters.	1
Lines should not be more than 80 characters. This line is 90 characters.	1
Lines should not be more than 80 characters. This line is 91 characters.	1
Lines should not be more than 80 characters. This line is 92 characters.	5
Lines should not be more than 80 characters. This line is 94 characters.	2
Lines should not be more than 80 characters. This line is 95 characters.	2
Lines should not be more than 80 characters. This line is 96 characters.	1
Lines should not be more than 80 characters. This line is 98 characters.	1

5. Other Checks

Details of other checks (click to open)

:heavy_multiplication_x: The following 4 function names are duplicated in other packages:

- bias_corr from bife
- feglm from alpaca
- felm from lfe
- fixed_effects from baggr, gratia, gravity

Package Versions

package	version
pkgstats	0.1.5.2
pkgcheck	0.1.2.42
srr	0.1.3.2

Editor-in-Chief Instructions:

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

Jun 18 '24 18:06 ropensci-review-bot

@jooolia Hi, I cannot find the statistical review template.

Jun 18 '24 18:06 pachadotdev

Hi @pachadotdev , sorry for the delayed response. You have the option of several different types of templates when you open an issue the statistical one is the last choice (the template is viewable here: https://github.com/ropensci/software-review/blob/main/.github/ISSUE_TEMPLATE/F-submit-statistical-software-for-review.md). Does this help? Thanks, Julia

Jun 29 '24 15:06 jooolia

hi @jooolia I think the software is ready for review as is

Jul 25 '24 10:07 pachadotdev

Dear @pachadotdev , thanks for your patience. We are discussing with the statistical editors and will get back to you shortly. Thanks, Julia

Jul 26 '24 08:07 jooolia

Dear @pachadotdev , thanks for your patience. We are discussing with the statistical editors and will get back to you shortly. Thanks, Julia

thanks! I uploaded some changes yesterday

Jul 26 '24 15:07 pachadotdev

Dear @pachadotdev, thanks for updating to address the statistical aspects of the package. Currently there are some srrstatsTODO tags in your srr-stats-standards.R file and we note that "software to be submitted for review must contain no @srrstatsTODO tags" (https://stats-devguide.ropensci.org/pkgdev.html#pkgdev-srr).

Could you also edit your first comment in this issue so that it contains the comment here https://github.com/ropensci/software-review/issues/645#issuecomment-2209395422 (e.g. replace the content with the statistical issue content? )

Thanks, Julia

Jul 29 '24 23:07 jooolia

Dear @pachadotdev, thanks for updating to address the statistical aspects of the package. Currently there are some srrstatsTODO tags in your srr-stats-standards.R file and we note that "software to be submitted for review must contain no @srrstatsTODO tags" (https://stats-devguide.ropensci.org/pkgdev.html#pkgdev-srr).

Could you also edit your first comment in this issue so that it contains the comment here #645 (comment) (e.g. replace the content with the statistical issue content? )

Thanks, Julia

thanks!

I updated the comment. I will need 3-4 weeks to finish all the srrstatsTODO

Jul 30 '24 14:07 pachadotdev

Ok thanks @pachadotdev for the update. Another editor will take over from me in few days to continue helping with the process. Cheers, Julia

Jul 30 '24 16:07 jooolia

Hi, @pachadotdev, I'm taking over where @jooolia is leaving off as EIC. Please let me know what assistance you may need from me.

Aug 02 '24 06:08 adamhsparks

hi @adamhsparks I think the pkg is ready for review

Sep 06 '24 00:09 pachadotdev

@ropensci-review-bot check package

Sep 06 '24 01:09 adamhsparks

Thanks, about to send the query.

Sep 06 '24 01:09 ropensci-review-bot

:rocket:

Error: Issue template has no 'repourl'

:wave:

Sep 06 '24 01:09 ropensci-review-bot

@ropensci-review-bot check package

Sep 06 '24 05:09 maelle

@pachadotdev thanks for your submission! I'm fixing the content of your issue as you deleted HTML comments. Please do not delete them, they help the bot find the necessary metadata.

Sep 06 '24 05:09 maelle

@ropensci-review-bot check package

Sep 06 '24 05:09 maelle

Thanks, about to send the query.

Sep 06 '24 05:09 ropensci-review-bot

software-review software-review copied to clipboard

Capybara

Archive: TBD Version accepted: TBD Language: en

Scope

Pre-submission Inquiry

General Information

Badging

Technical checks

Publication options

Code of conduct

Checks for capybara (v0.5.1)

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

5. Other Checks

Editor-in-Chief Instructions:

Checks for capybara (v0.5.1)

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

5. Other Checks

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)

4. `goodpractice` and other checks

3b. `goodpractice` results

`R CMD check` with rcmdcheck