gigs: Assess Fetal, Newborn, and Child Growth with International Standards #626

simpar1471 · 2024-02-07T13:26:27Z

Date accepted: 2024-12-10

Submitting Author Name: Simon Parker
Submitting Author Github Handle: @simpar1471
Repository: https://github.com/lshtm-gigs/gigs/
Version submitted: 0.4.1
Submission type: Stats
Badge grade: gold
Editor: @rkillick
Reviewers: @chitrams, @BroVic

Due date for @chitrams: 2024-09-20

Due date for @BroVic: 2024-09-24
Archive: TBD
Version accepted: TBD
Language: en

Paste the full DESCRIPTION file inside a code block below:

Type: Package
Package: gigs
Title: Assess Fetal, Newborn, and Child Growth with International Standards
Version: 0.4.1
Authors@R: c(
    person(given = "Simon", family = "Parker",
           email = "[email protected]",
           role = c("aut", "cre"), comment = c(ORCID = "0009-0003-8214-4496")),
    person(given = "Linda", family = "Vesel", role = c("dtc"),
           comment = c(ORCID = "0000-0003-3753-4172")),
    person(given = "Eric", family = "Ohuma", role = c("dtc"),
           comment = c(ORCID = "0000-0002-3116-2593")),
    person(given = "Bill & Melinda Gates Foundation", role = c("fnd", "cph"))
    )
Description: Convert between anthropometric measures and z-scores/centiles in
    multiple growth standards, and classify fetal, newborn, and child growth
    accordingly. With a simple interface to growth standards from the World
    Health Organisation and International Fetal and Newborn Growth Consortium
    for the 21st Century, gigs makes growth assessment easy and reproducible for
    clinicians, researchers and policy-makers.
License: GPL (>= 3)
URL: https://github.com/lshtm-gigs/gigs/,
    https://lshtm-gigs.github.io/gigs/
BugReports: https://github.com/lshtm-gigs/gigs/issues
Depends: 
    R (>= 4.1.0)
Imports:
    stats,
    gamlss.dist,
    checkmate,
    vctrs
Suggests:
    knitr,
    rmarkdown,
    testthat (>= 3.0.0),
    units,
    withr
VignetteBuilder: knitr
Config/testthat/edition: 3
Config/testthat/parallel: true
Config/testthat/start-first: who_gs, ig_nbs, ig_fet, ig_png
Encoding: UTF-8
Language: en-GB
LazyData: true
RoxygenNote: 7.3.0
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 appropriate box below):

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

Pre-submission Inquiry

A pre-submission inquiry has been approved in issue#616

General Information

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

The target audience for this package is researchers, clinicians, and policy-makers interested in nutrition and fetal/newborn/child health. The package itself is used to convert measurements, for example a baby's weight at a given age, into summary statistics such as z-scores (i.e. number of standard deviations away from mean) and percentiles (i.e. number of percentage points above/below the median, expressed as a decimal). It can also be used to classify these z-scores and percentiles into specific categories for specific facets of growth. Scientific applications of this package would therefore include using our functions to generate statistical measures of growth in individuals or populations across time or pre/post a healthcare intervention. These could then be used in further downstream analyses.

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

Several R packages which implement child growth charts already exist, but they differ in the range of growth charts offered, their flexibility in conversion, and in what data they make available to users.

anthro converts measurements into z-scores in the WHO Child Growth Standards, but lacks any INTERGROWTH-21^st standards and outputs tabular data. We provide an interface which takes vectors in and gives vectors out, so is more flexible (e.g. with dplyr pipelines). This package is available on CRAN.
childsds can convert measurements to z-scores or percentiles, but cannot convert z-scores/percentiles to expected measurements. Additionally, childsds does not contain the newborn/postnatal INTERGROWTH-21^st growth standards, which we implement. Though childsds does include more growth references, growth references are not within the scope of the GIGS project. We can discuss the reasons for this if necessary. This package is available on CRAN.
growthstandards contains functions for converting between values and z-scores/percentiles, as in gigs. It includes the INTERGROWTH-21^st fetal standards, but not the newborn or postnatal standards we implement. This package makes coefficients available to end-users, but not reference growth curves. This package is not available on CRAN. It was last updated in January 2024.
intergrowth provides more fetal growth standards than gigs, but cannot convert between z-scores/percentiles in the lacks the INTERGROWTH-21^st newborn or postnatal growth standards, which we have implemented in gigs. This package also does not make coefficients for the growth standards available to end-users, though it it does provide growth curve data to end-users. This package is not available on CRAN, and was last updated in January 2023.
gigs provides a simple interface for working with the growth standards it implements, which can be easily included in dplyr-like data wrangling pipelines. It implements all available WHO 2006/2007 and INTERGROWTH-21^st growth standards, and makes published growth curves and model coefficients are available wherever possible. In our own testing, we found that it also warns end users about bad input data more comprehensively.

The Other packages section of the repository README also contains links to each of these packages, and a table describing features present in gigs compared to other growth standards packages.

We have a benchmarking vignette which shows the scaling of these packages when analysing datasets containing 1 to 100,000 cases. In summary: anthro scales the worst (29 ms to 2.24 seconds). The other packages are then clustered together: growthstandards is the fastest for 100,000 cases (4.62 ms to 125 ms); childsds is next (2.40 ms to 126 ms); then gigs (1.32 ms to 128 ms).

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

Not applicable.

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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)

Demonstrating excellence in compliance with multiple standards from at least two broad sub-categories. I feel this package has a comprehensive test suite and good error/warning behaviours in response to undesired input.

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.

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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 · 2024-02-07T13:26:29Z

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

ropensci-review-bot · 2024-02-07T13:26:32Z

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Editor check started

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ropensci-review-bot · 2024-02-07T13:31:07Z

Checks for gigs (v0.4.1)

git hash: a9d9654a

✔️ 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 100%.
✔️ R CMD check found no errors.
✔️ R CMD check found no warnings.

Package License: GPL (>= 3)

1. rOpenSci Statistical Standards (`srr` package)

This package is in the following category:

Exploratory Data Analysis

✔️ All applicable standards [v0.2.0] have been documented in this package (632 complied with; 0 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	gigs	401
internal	base	271
imports	stats	36
imports	checkmate	13
imports	gamlss.dist	1
imports	vctrs	1
suggests	knitr	NA
suggests	rmarkdown	NA
suggests	testthat	NA
suggests	units	NA
suggests	withr	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.

gigs

validate_ig_fet (22), validate_ig_nbs (17), fn_on_subset (13), validate_who_gs (11), who_gs_lms2value (9), validate_ig_png (6), gigs_xaz_lgls (5), validate_yzp (5), ig_fet_doppler_gms (3), ig_fet_efw_lms (3), ig_fet_gwg_mu_sigma (3), ig_fet_mu_sigma (3), ig_nbs_bodycomp_mu_sigma (3), ig_nbs_msnt (3), ig_nbs_wlr_mu_sigma (3), ig_png_equations (3), ig_vpns_equations (3), mu_sigma_z2y (3), validate_parameter_lengths (3), who_gs_lms (3), classify_sfga (2), gigs_laz (2), gigs_option_get (2), gigs_waz (2), gigs_wlz (2), ig_nbs_hcfga_value2zscore (2), ig_nbs_lfga_value2zscore (2), ig_nbs_wfga_value2centile (2), ig_nbs_wfga_value2zscore (2), ig_png_hcfa_value2zscore (2), ig_png_lfa_value2zscore (2), ig_png_wfa_value2zscore (2), ig_png_wfl_value2zscore (2), inrange (2), validate_hcaz_params (2), validate_laz_params (2), validate_waz_params (2), validate_wlz_params (2), who_gs_hcfa_value2zscore (2), who_gs_lhfa_value2zscore (2), who_gs_wfa_value2zscore (2), classify_stunting (1), classify_svn (1), classify_wasting (1), classify_wfa (1), drop_null_elements (1), exponent (1), gigs_hcaz (1), gigs_option_set (1), handle_invalid_chr_options (1), handle_missing_data (1), handle_oob_centiles (1), handle_oob_xvar (1), handle_undefined_data (1), handle_var (1), hcfa_mu (1), hcfa_sigma (1), hcfga_mu (1), ig_fet_acfga_centile2value (1), ig_fet_acfga_value2centile (1), ig_fet_acfga_value2zscore (1), ig_fet_acfga_zscore2value (1), ig_fet_avfga_centile2value (1), ig_fet_avfga_value2centile (1), ig_fet_avfga_value2zscore (1), ig_fet_avfga_zscore2value (1), ig_fet_bpdfga_centile2value (1), ig_fet_bpdfga_value2centile (1), ig_fet_bpdfga_value2zscore (1), ig_fet_bpdfga_zscore2value (1), ig_fet_centile2value (1), ig_fet_cmfga_centile2value (1), ig_fet_cmfga_value2centile (1), ig_fet_cmfga_value2zscore (1), ig_fet_cmfga_zscore2value (1), ig_fet_crlfga_centile2value (1), ig_fet_crlfga_value2centile (1), ig_fet_crlfga_value2zscore (1), ig_fet_crlfga_zscore2value (1), ig_fet_doppler_y2z (1), ig_fet_doppler_z2y (1), ig_fet_efw_y2z (1), ig_fet_efw_z2y (1), ig_fet_efwfga_centile2value (1), ig_fet_efwfga_value2centile (1), ig_fet_efwfga_value2zscore (1), ig_fet_efwfga_zscore2value (1), ig_fet_estimate_fetal_weight (1), ig_fet_estimate_ga (1), ig_fet_estimate_ga_crl (1), ig_fet_estimate_ga_hc (1), ig_fet_estimate_ga_hcfl (1), ig_fet_flfga_centile2value (1), ig_fet_flfga_value2centile (1), ig_fet_flfga_value2zscore (1), ig_fet_flfga_zscore2value (1), ig_fet_gafcrl_centile2value (1), ig_fet_gafcrl_value2centile (1), ig_fet_gafcrl_value2zscore (1), ig_fet_gafcrl_zscore2value (1), ig_fet_gaftcd_centile2value (1), ig_fet_gaftcd_value2centile (1), ig_fet_gaftcd_value2zscore (1), ig_fet_gaftcd_zscore2value (1), ig_fet_gwg_y2z (1), ig_fet_gwg_z2y (1), ig_fet_gwgfga_centile2value (1), ig_fet_gwgfga_value2centile (1), ig_fet_gwgfga_value2zscore (1), ig_fet_gwgfga_zscore2value (1), ig_fet_hcfga_centile2value (1), ig_fet_hcfga_value2centile (1), ig_fet_hcfga_value2zscore (1), ig_fet_hcfga_zscore2value (1), ig_fet_mu_sigma_y2z (1), ig_fet_mu_sigma_z2y (1), ig_fet_ofdfga_centile2value (1), ig_fet_ofdfga_value2centile (1), ig_fet_ofdfga_value2zscore (1), ig_fet_ofdfga_zscore2value (1), ig_fet_pifga_centile2value (1), ig_fet_pifga_value2centile (1), ig_fet_pifga_value2zscore (1), ig_fet_pifga_zscore2value (1), ig_fet_poffga_centile2value (1), ig_fet_poffga_value2centile (1), ig_fet_poffga_value2zscore (1), ig_fet_poffga_zscore2value (1), ig_fet_pvfga_centile2value (1), ig_fet_pvfga_value2centile (1), ig_fet_pvfga_value2zscore (1), ig_fet_pvfga_zscore2value (1), ig_fet_rifga_centile2value (1), ig_fet_rifga_value2centile (1), ig_fet_rifga_value2zscore (1), ig_fet_rifga_zscore2value (1), ig_fet_sdrfga_centile2value (1), ig_fet_sdrfga_value2centile (1), ig_fet_sdrfga_value2zscore (1), ig_fet_sdrfga_zscore2value (1), ig_fet_sffga_centile2value (1), ig_fet_sffga_value2centile (1), ig_fet_sffga_value2zscore (1), ig_fet_sffga_zscore2value (1), ig_fet_sfhfga_centile2value (1), ig_fet_sfhfga_value2centile (1), ig_fet_sfhfga_value2zscore (1), ig_fet_sfhfga_zscore2value (1), ig_fet_tcdfga_centile2value (1), ig_fet_tcdfga_value2centile (1), ig_fet_tcdfga_value2zscore (1), ig_fet_tcdfga_zscore2value (1), ig_fet_v2z_internal (1), ig_fet_value2centile (1), ig_fet_value2zscore (1), ig_fet_z2v_internal (1), ig_fet_zscore2value (1), ig_nbs_bfpfga_centile2value (1), ig_nbs_bfpfga_value2centile (1), ig_nbs_bfpfga_value2zscore (1), ig_nbs_bfpfga_zscore2value (1), ig_nbs_bodycomp_p2v (1), ig_nbs_bodycomp_v2p (1), ig_nbs_c2v_internal (1), ig_nbs_centile2value (1), ig_nbs_ffmfga_centile2value (1), ig_nbs_ffmfga_value2centile (1), ig_nbs_ffmfga_value2zscore (1), ig_nbs_ffmfga_zscore2value (1), ig_nbs_fmfga_centile2value (1), ig_nbs_fmfga_value2centile (1), ig_nbs_fmfga_value2zscore (1), ig_nbs_fmfga_zscore2value (1), ig_nbs_hcfga_centile2value (1), ig_nbs_hcfga_value2centile (1), ig_nbs_hcfga_zscore2value (1), ig_nbs_lfga_centile2value (1), ig_nbs_lfga_value2centile (1), ig_nbs_lfga_zscore2value (1), ig_nbs_msnt_p2v (1), ig_nbs_msnt_v2p (1), ig_nbs_v2c_internal (1), ig_nbs_value2centile (1), ig_nbs_value2zscore (1), ig_nbs_wfga_centile2value (1), ig_nbs_wfga_zscore2value (1), ig_nbs_wlrfga_centile2value (1), ig_nbs_wlrfga_p2v (1), ig_nbs_wlrfga_v2p (1), ig_nbs_wlrfga_value2centile (1), ig_nbs_wlrfga_value2zscore (1), ig_nbs_wlrfga_zscore2value (1), ig_nbs_zscore2value (1), ig_png_centile2value (1), ig_png_hcfa_centile2value (1), ig_png_hcfa_value2centile (1), ig_png_hcfa_zscore2value (1), ig_png_lfa_centile2value (1), ig_png_lfa_value2centile (1), ig_png_lfa_zscore2value (1), ig_png_v2z_internal (1), ig_png_value2centile (1), ig_png_value2zscore (1), ig_png_wfa_centile2value (1), ig_png_wfa_value2centile (1), ig_png_wfa_zscore2value (1), ig_png_wfl_centile2value (1), ig_png_wfl_value2centile (1), ig_png_wfl_zscore2value (1), ig_png_z2v_internal (1), ig_png_zscore2value (1), ig_vpns_value2zscore (1), ig_vpns_zscore2value (1), lfa_log_mu (1), lfa_sigma (1), lfga_mu (1), msg_invalid_sex_acronym (1), msg_missing_data (1), msg_oob_centiles (1), msg_oob_xvar (1), msg_undefined_data (1), mu_sigma_y2z (1), remove_attributes (1), retrieve_coefficients (1), validate_acronym (1), validate_chr (1), validate_ig_fet_estimation_param (1), validate_ig_fet_weight_estimation_param (1), validate_numeric (1), validate_sex (1), validate_xvar (1), wfa_log_mu (1), wfa_sigma (1), wfga_logmu (1), wfl_mu (1), wfl_sigma (1), who_gs_acfa_centile2value (1), who_gs_acfa_value2centile (1), who_gs_acfa_value2zscore (1), who_gs_acfa_zscore2value (1), who_gs_bfa_centile2value (1), who_gs_bfa_value2centile (1), who_gs_bfa_value2zscore (1), who_gs_bfa_zscore2value (1), who_gs_centile2value (1), who_gs_hcfa_centile2value (1), who_gs_hcfa_value2centile (1), who_gs_hcfa_zscore2value (1), who_gs_lhfa_centile2value (1), who_gs_lhfa_value2centile (1), who_gs_lhfa_zscore2value (1), who_gs_lms_v2z (1), who_gs_lms_v2z_constrained (1), who_gs_lms_v2z_over_three (1), who_gs_lms_v2z_under_minus_three (1), who_gs_lms_z2v (1), who_gs_lms_z2v_over_three (1), who_gs_lms_z2v_under_minus_three (1), who_gs_ssfa_centile2value (1), who_gs_ssfa_value2centile (1), who_gs_ssfa_value2zscore (1), who_gs_ssfa_zscore2value (1), who_gs_tsfa_centile2value (1), who_gs_tsfa_value2centile (1), who_gs_tsfa_value2zscore (1), who_gs_tsfa_zscore2value (1), who_gs_v2z_internal (1), who_gs_value2centile (1), who_gs_value2zscore (1), who_gs_wfa_centile2value (1), who_gs_wfa_value2centile (1), who_gs_wfa_zscore2value (1), who_gs_wfh_centile2value (1), who_gs_wfh_value2centile (1), who_gs_wfh_value2zscore (1), who_gs_wfl_value2zscore (1)

base

list (63), length (32), is.null (18), c (15), rep (12), log (9), is.na (8), names (8), for (7), ifelse (6), gamma (5), lengths (5), sqrt (5), data.frame (4), logical (4), matrix (4), paste0 (4), unique (4), abs (3), character (3), get (3), if (3), lapply (3), ncol (3), nrow (3), numeric (3), vapply (3), as.data.frame (2), levels (2), options (2), parent.frame (2), rep_len (2), sum (2), with (2), deparse (1), emptyenv (1), exp (1), inherits (1), max (1), mode (1), new.env (1), paste (1), q (1), range (1), rep.int (1), replace (1), seq_along (1), sign (1), substitute (1), unlist (1), vector (1)

stats

sigma (28), complete.cases (4), var (2), approx (1), qnorm (1)

checkmate

qassert (8), assert_numeric (2), assert_subset (2), assert_character (1)

gamlss.dist

pST3C (1)

vctrs

vec_recycle_common (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 R (100% in 15 files) and
1 authors
3 vignettes
7 internal data files
4 imported packages
185 exported functions (median 6 lines of code)
376 non-exported functions in R (median 8 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	15	73.0
files_vignettes	3	92.4
files_tests	10	90.7
loc_R	2689	89.0
loc_vignettes	877	89.0
loc_tests	4157	97.6	TRUE
num_vignettes	3	94.2
data_size_total	1093128	95.5	TRUE
data_size_median	11317	79.8
n_fns_r	561	98.0	TRUE
n_fns_r_exported	185	98.3	TRUE
n_fns_r_not_exported	376	97.5	TRUE
n_fns_per_file_r	21	95.9	TRUE
num_params_per_fn	3	33.6
loc_per_fn_r	6	12.1
loc_per_fn_r_exp	6	10.5
loc_per_fn_r_not_exp	8	22.6
rel_whitespace_R	13	82.6
rel_whitespace_vignettes	13	67.8
rel_whitespace_tests	12	94.8
doclines_per_fn_exp	163	97.4	TRUE
doclines_per_fn_not_exp	0	0.0	TRUE
fn_call_network_size	408	94.2

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
7815041175	pages build and deployment	success	ea59a9	20	2024-02-07
7815003364	pkgcheck	success	a9d965	5	2024-02-07
7815003368	pkgdown	success	a9d965	45	2024-02-07
7814822521	R-CMD-check	success	a9d965	51	2024-02-07
7814822525	test-coverage	success	a9d965	51	2024-02-07
7815003373	Update CITATION.cff	success	a9d965	2	2024-02-07

3b. `goodpractice` results

`R CMD check` with rcmdcheck

rcmdcheck found no errors, warnings, or notes

Test coverage with covr

Package coverage: 100

Cyclocomplexity with cyclocomp

No functions have cyclocomplexity >= 15

Static code analyses with lintr

lintr found the following 69 potential issues:

message	number of times
Avoid library() and require() calls in packages	2
Lines should not be more than 80 characters.	67

Package Versions

package	version
pkgstats	0.1.3.9
pkgcheck	0.1.2.14
srr	0.0.1.194

Editor-in-Chief Instructions:

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

ldecicco-USGS · 2024-02-22T20:10:00Z

@ropensci-review-bot check srr

ropensci-review-bot · 2024-02-22T20:12:26Z

'srr' standards compliance:

Complied with: 53 / 102 = 52% (eda: 8 / 34; general: 45 / 68)
Not complied with: 49 / 102 = 48% (eda: 26 / 34; general: 23 / 68)

✔️ This package complies with > 50% of all standads and may be submitted.

rkillick · 2024-02-23T18:33:26Z

@ropensci-review-bot assign @rkillick as editor

ropensci-review-bot · 2024-02-23T18:33:29Z

Assigned! @rkillick is now the editor

simpar1471 · 2024-03-19T16:06:56Z

Hi @rkillick, have you had any chance to look at this? Not meaning to be pushy if you're rained in with other things at the moment!

ldecicco-USGS · 2024-08-30T13:21:05Z

Sorry about this! I think I missed an internal discussion about reassigning editors. I'll take over and get some reviewers assigned!

ldecicco-USGS · 2024-08-30T13:21:37Z

@ropensci-review-bot assign @ldecicco-USGS as editor

ropensci-review-bot · 2024-08-30T13:21:40Z

Assigned! @ldecicco-USGS is now the editor

ldecicco-USGS · 2024-08-30T17:08:10Z

@ropensci-review-bot add @chitrams to reviewers

ropensci-review-bot · 2024-08-30T17:08:13Z

@chitrams added to the reviewers list. Review due date is 2024-09-20. Thanks @chitrams for accepting to review! Please refer to our reviewer guide.

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ropensci-review-bot · 2024-08-30T17:08:19Z

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

ldecicco-USGS · 2024-09-03T22:46:27Z

@ropensci-review-bot add @BroVic to reviewers

ropensci-review-bot · 2024-09-03T22:46:30Z

@BroVic added to the reviewers list. Review due date is 2024-09-24. Thanks @BroVic for accepting to review! Please refer to our reviewer guide.

rOpenSci’s community is our best asset. We aim for reviews to be open, non-adversarial, and focused on improving software quality. Be respectful and kind! See our reviewers guide and code of conduct for more.

ropensci-review-bot · 2024-09-03T22:46:35Z

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

ldecicco-USGS · 2024-09-05T19:59:36Z

@ropensci-review-bot assign @rkillick as editor

ropensci-review-bot · 2024-09-05T19:59:39Z

Assigned! @rkillick is now the editor

chitrams · 2024-11-19T03:35:16Z

Hi all,

I've reviewed the changes and think they look great!

@simpar1471 the package documentation is excellent! I liked that in each help file, the limits for each combination for x values are provided. I also really like the report_units function.

Well done on refactoring the code to use zscore2value, value2zscore, value2centile etc functions instead of the growth standard name. I appreciate this would have taken a lot of work, but I do believe that this would really help make the package user-friendly.

@rkillick I would like to recommend this software to be awarded a gold badge. This package:

Complies with a good number (more than one half) of standards beyond those identified as minimally necessary
Demonstrates excellence in compliance with multiple standards. Generally, I think this package is excellently documented and has a fantastic test suite. Specifically, these sub-categories were fulfilled: G1.1, G1.3, G1.4-G1.6, G2.7, G5.2a, G5.2b, G5.3; EA1.0-1.3, EA4.0, EA6.0
- @simpar1471 if you cite the growth standards (WHO and INTERGROWTH) you will be able to fulfil an additional standard, G1.0: Statistical Software should list at least one primary reference from published academic literature. I think doing this will be useful for users anyway.
Excellent design choices for the internal aspects of package structure and design. I especially appreciate the refactoring for generalisability of the conversions (using the conversions instead of the growth standards as the function names).

@BroVic let me know your thoughts on the points above!

Thank you,
Chitra

simpar1471 · 2024-11-19T10:37:32Z

Hello again folks!

@chitrams Thanks for the thorough look-over and gold(!) badge recommendation. In terms of references to primary literature, we have listed relevant articles for the data objects that have previously published z-score/centile data, e.g. for gigs::who_gs (pkgdown page).

I assume you'd want references in value2zscore() and friends, so I was thinking adding something which users can use to click through to the set of references they want:

#' ...
#' @references
#' * For the INTERGROWTH-21<sup>st</sup> Fetal standards see the
#'   [`gigs::ig_fet`][ig_fet] documentation
#' * For the INTERGROWTH-21<sup>st</sup> Newborn Size standards see the
#'   [`gigs::ig_nbs`][ig_nbs] documentation
#' * For the INTERGROWTH-21<sup>st</sup> Postnatal Growth standards see the
#'   [`gigs::ig_png`][ig_png] documentation
#' * For the WHO Growth standards see the [`gigs::who_gs`][who_gs] documentation
#' ...

I think this would be less unwieldy than listing >10 references on the value2zscore() and zscore2value() pages, but I'm happy to prioritise accessibility of the information if you think that's best. Also, do you want the references added elsewhere?

Also @chitrams and @BroVic, I've added another feature in the last week. It's an extended version of the INTERGROWTH-21^st Newborn Size standards, which can take gestational age (GA) values in a wider range than the normal Newborn Size Standards. Eric, the co-PI for this project, has done these extrapolations before for other research groups but has needed to re-compute them at times where the underlying code/data has gone missing. Our hope is to situate them in gigs as an easy place to direct folks to. Users can apply the extended standards by specifying family = "ig_nbs_ext" in any of the conversion functions, and using an acronym out of c("wfga", "lfga", "hcfga"). This all in extra ./R code, unit tests, and an article describing the extrapolation process, all added in ropensci/gigs@69caa7f and passing CI checks.

chitrams · 2024-11-19T11:53:51Z

Oh, awesome! I was only thinking at the bottom of the README under a "References" heading, but that (the former) sounds good too :) Whichever is easiest for you should be fine @simpar1471.

Ooh thank you for the update. I'll have a look at that new feature.

Small aside: I realise I've actually met Eric briefly last year, at a talk he gave at the RSS Conference in Harrogate. I vaguely remember him mentioning working on these child growth standards :) So it's super cool that it's come back full circle and I'm now reviewing gigs!

simpar1471 · 2024-11-19T13:23:56Z

@chitrams I've added both sets of extra references in ropensci/gigs@5615503. As for you having met Eric IRL, looks like it's a small world after all!

simpar1471 · 2024-11-26T18:25:49Z

Sorry for pestering you both @chitrams and @BroVic - if you're happy to go ahead, would @rkillick be able to progress this review to its next stage?

rkillick · 2024-11-26T18:48:56Z

Just to make sure everyone is in agreement. @BroVic are you happy with a gold award as recommended by chitrams?

BroVic · 2024-11-27T11:36:44Z

@rkillick I agree one hundred percent.

simpar1471 · 2024-12-10T15:02:59Z

Hiya @rkillick! Given Victor's agreement would it be possible to progress to another pkgcheck run here, or perform whatever the other next steps are?

rkillick · 2024-12-10T15:18:30Z

@simpar1471 thanks for prodding. This is the first one I've completed so I was trying to make sure I do the next bit correctly!

rkillick · 2024-12-10T15:18:34Z

@ropensci-review-bot stats grade

ropensci-review-bot · 2024-12-10T15:18:36Z

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

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rkillick · 2024-12-10T15:18:56Z

@ropensci-review-bot help

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rkillick · 2024-12-10T15:20:19Z

@ropensci-review-bot check readme

ropensci-review-bot · 2024-12-10T15:20:23Z

{}

rkillick · 2024-12-10T15:23:03Z

@ropensci-review-bot approve

ropensci-review-bot · 2024-12-10T15:23:06Z

Could not approve. Please, specify the name of the package.

rkillick · 2024-12-10T15:23:29Z

@ropensci-review-bot approve gigs

ropensci-review-bot · 2024-12-10T15:23:33Z

Approved! Thanks @simpar1471 for submitting and @chitrams, @BroVic for your reviews! 😁

To-dos:

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simpar1471 · 2024-12-10T16:12:28Z

@ropensci-review-bot finalize transfer of gigs

ropensci-review-bot · 2024-12-10T16:12:33Z

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

rkillick · 2024-12-16T13:03:25Z

@simpar1471 can you please use the checklist from last week to make sure all tasks have been done. I've ticked off the two I can see.

simpar1471 · 2024-12-16T14:12:44Z

Hiya @rkillick, I’m checking the items but they take a long time to update?

rkillick · 2024-12-16T14:15:45Z

@simpar1471 hmmmmm, it should be instant, it was for me. I checked without being logged in and I can see my check marks but no more. I'm not sure why it isn't registering any from you, if you want you can let me know and I'll tick them off.

simpar1471 · 2024-12-18T08:19:43Z

Thanks @rkillick. I've done all of the items on the checklist, including setting up the old GH pages website redirect (try here: https://lshtm-gigs.github.io/gigs/).

Do you know much about the process of submitting to JOSS afer rOpenSci review?

rkillick · 2024-12-18T11:09:25Z

Great, I've checked everything off. I haven't submitted to JOSS myself but would assume that you would link to this thread in the covering letter. @mpadge do you know any specifics around this?

mpadge · 2024-12-23T23:46:29Z

@simpar1471 @rkillick JOSS submission should proceed fairlly automatically from this point on. The rOpenSci review is generally considered sufficient for JOSS, and only main decision made on that side is scope and fit. A recent example of the process in action is openjournals/joss-reviews#6163. In short: @simpar1471 please go ahead and submit directly to JOSS

simpar1471 changed the title ~~gigs:~~ gigs: Assess Fetal, Newborn, and Child Growth with International Standards Feb 7, 2024

ldecicco-USGS added the stats label Feb 9, 2024

rkillick self-assigned this Feb 23, 2024

ropensci-review-bot added the 1/editor-checks label Feb 23, 2024

ropensci deleted a comment from ropensci-review-bot Feb 23, 2024

ropensci-review-bot assigned ldecicco-USGS and unassigned rkillick Aug 30, 2024

ropensci-review-bot added the 3/reviewer(s)-assigned label Sep 3, 2024

ldecicco-USGS removed the 1/editor-checks label Sep 3, 2024

ropensci-review-bot unassigned ldecicco-USGS Sep 5, 2024

ropensci-review-bot assigned rkillick Sep 5, 2024

ropensci-review-bot added 6/approved-gold-v0.2 Statistical software grade 6/approved labels Dec 10, 2024

ropensci-review-bot closed this as completed Dec 10, 2024

gigs: Assess Fetal, Newborn, and Child Growth with International Standards #626

gigs: Assess Fetal, Newborn, and Child Growth with International Standards #626

Comments

simpar1471 commented Feb 7, 2024 • edited by ropensci-review-bot Loading

Due date for @BroVic: 2024-09-24 Archive: TBD Version accepted: TBD Language: en

Scope

Pre-submission Inquiry

General Information

Badging

Technical checks

Publication options

Code of conduct

ropensci-review-bot commented Feb 7, 2024

ropensci-review-bot commented Feb 7, 2024

ropensci-review-bot commented Feb 7, 2024

Checks for gigs (v0.4.1)

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:

ldecicco-USGS commented Feb 22, 2024

ropensci-review-bot commented Feb 22, 2024

'srr' standards compliance:

rkillick commented Feb 23, 2024

ropensci-review-bot commented Feb 23, 2024

simpar1471 commented Mar 19, 2024

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chitrams commented Nov 19, 2024 • edited Loading

simpar1471 commented Nov 19, 2024

chitrams commented Nov 19, 2024 • edited Loading

simpar1471 commented Nov 19, 2024

simpar1471 commented Nov 26, 2024

rkillick commented Nov 26, 2024

BroVic commented Nov 27, 2024

simpar1471 commented Dec 10, 2024

rkillick commented Dec 10, 2024

rkillick commented Dec 10, 2024

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rkillick commented Dec 10, 2024

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rkillick commented Dec 10, 2024

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ropensci-review-bot commented Dec 10, 2024 • edited by rkillick Loading

simpar1471 commented Dec 10, 2024

ropensci-review-bot commented Dec 10, 2024

rkillick commented Dec 16, 2024

simpar1471 commented Dec 16, 2024

rkillick commented Dec 16, 2024

simpar1471 commented Dec 18, 2024

rkillick commented Dec 18, 2024

mpadge commented Dec 23, 2024

simpar1471 commented Feb 7, 2024 •

edited by ropensci-review-bot

Loading

Due date for @BroVic: 2024-09-24
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

chitrams commented Nov 19, 2024 •

edited

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chitrams commented Nov 19, 2024 •

edited

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ropensci-review-bot commented Dec 10, 2024 •

edited by rkillick

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