Open osorensen opened 1 year ago
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Package License: GPL (>= 3)
srr
package):heavy_check_mark: All applicable standards [v0.2.0] have been documented in this package (217 complied with; 0 N/A standards)
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 | 439|
|internal |galamm | 76|
|internal |utils | 30|
|internal |graphics | 6|
|imports |stats | 79|
|imports |lme4 | 11|
|imports |Matrix | 11|
|imports |mgcv | 8|
|imports |methods | 3|
|imports |nlme | 3|
|imports |memoise | 1|
|imports |Rcpp | NA|
|imports |Rdpack | NA|
|suggests |covr | NA|
|suggests |gamm4 | NA|
|suggests |knitr | NA|
|suggests |PLmixed | NA|
|suggests |rmarkdown | NA|
|suggests |testthat | NA|
|linking_to |Rcpp | NA|
|linking_to |RcppEigen | 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(
list (31), seq_along (22), for (19), lapply (19), length (18), c (17), names (15), ncol (15), attr (14), seq_len (14), vapply (14), if (13), drop (11), rep (11), as.numeric (10), is.null (9), nrow (9), integer (8), unlist (8), factor (7), paste (7), qr (7), diff (6), max (6), seq (6), all.vars (5), any (5), matrix (5), numeric (5), cbind (4), colnames (4), logical (4), sqrt (4), beta (3), eval (3), grepl (3), levels (3), Map (3), match.call (3), Reduce (3), return (3), row.names (3), scale (3), unique (3), by (2), col (2), data.frame (2), diag (2), do.call (2), ifelse (2), lengths (2), order (2), parent.frame (2), qr.R (2), rank (2), rbind (2), abs (1), array (1), as.character (1), as.integer (1), as.logical (1), as.matrix (1), assign (1), backsolve (1), deparse (1), deparse1 (1), dim (1), environment (1), getOption (1), inherits (1), intersect (1), is.infinite (1), is.nan (1), min (1), parse (1), pmax (1), qr.qty (1), regexpr (1), rep.int (1), rowSums (1), setdiff (1), split (1), sum (1), t (1), tabulate (1), which (1)
deviance (9), pf (8), formula (6), as.formula (4), BIC (4), family (4), logLik (4), model.matrix (4), weights (4), quantile (3), terms (3), AIC (2), nobs (2), rf (2), terms.formula (2), contrasts (1), D (1), delete.response (1), df (1), gaussian (1), getCall (1), model.frame (1), model.response (1), na.action (1), optim (1), pchisq (1), pnorm (1), qnorm (1), reformulate (1), smooth (1), start (1), update (1), vcov (1)
extractor (3), factor_finder (3), find_parm_inds (3), fn (3), gr (3), mlwrapper (3), define_factor_mappings (2), extend_lambda (2), extract_name (2), find_k (2), gam.setup (2), gamm4 (2), gamm4.setup (2), interpret.gam0 (2), set_initial_values (2), setup_factor (2), anova.galamm (1), coef.galamm (1), confint.galamm (1), deviance.galamm (1), extract_optim_parameters (1), extract_optim_parameters.galamm (1), factor_loadings (1), factor_loadings.galamm (1), family.galamm (1), fitted.galamm (1), fixef.galamm (1), formula.galamm (1), galamm (1), galamm_control (1), gam.side (1), gamm4.wrapup (1), llikAIC (1), logLik.galamm (1), mappingunwrapping (1), marginal_likelihood (1), new_galamm_control (1), nobs.galamm (1), plot_smooth (1), plot_smooth.galamm (1), plot.galamm (1), predict.galamm (1), print.summary.galamm (1), print.VarCorr.galamm (1), ranef.galamm (1), release_questions (1), residuals.galamm (1), setup_family (1), setup_response_object (1), sl (1), squeeze_mappings (1), t2l (1), VarCorr.galamm (1), variable.summary (1)
data (30)
findbars (3), nobars (3), lFormula (2), mkReTrms (2), .prt.VC (1)
t (4), chol (2), Matrix (2), solve (2), Diagonal (1)
new.name (2), smooth2random (2), Rrank (1), s (1), smoothCon (1), t2 (1)
par (3), abline (2), text (1)
as (3)
fixef (1), ranef (1), VarCorr (1)
memoise (1)
base
stats
galamm
utils
lme4
Matrix
mgcv
graphics
methods
nlme
memoise
This package features some noteworthy statistical properties which may need to be clarified by a handling editor prior to progressing.
The package has: - code in C++ (4% in 2 files), C/C++ Header (66% in 18 files) and R (29% in 30 files) - 1 authors - 9 vignettes - 8 internal data files - 9 imported packages - 31 exported functions (median 6 lines of code) - 81 non-exported functions in R (median 16 lines of code) - 618 C/C++ functions (median 4 lines of code) --- Statistical properties of package structure as distributional percentiles in relation to all current CRAN packages The following terminology is used: - `loc` = "Lines of Code" - `fn` = "function" - `exp`/`not_exp` = exported / not exported All parameters are explained as tooltips in the locally-rendered HTML version of this report generated by [the `checks_to_markdown()` function](https://docs.ropensci.org/pkgcheck/reference/checks_to_markdown.html) The final measure (`fn_call_network_size`) is the total number of calls between functions (in R), or more abstract relationships between code objects in other languages. Values are flagged as "noteworthy" when they lie in the upper or lower 5th percentile. |measure | value| percentile|noteworthy | |:------------------------|------:|----------:|:----------| |files_R | 30| 89.3| | |files_src | 2| 79.1| | |files_inst | 18| 99.6| | |files_vignettes | 9| 99.2| | |files_tests | 10| 90.7| | |loc_R | 1777| 81.8| | |loc_src | 252| 31.9| | |loc_inst | 4014| 86.1| | |loc_vignettes | 1732| 96.3|TRUE | |loc_tests | 2479| 95.4|TRUE | |num_vignettes | 9| 99.6|TRUE | |data_size_total | 265405| 88.8| | |data_size_median | 13688| 80.9| | |n_fns_r | 112| 79.1| | |n_fns_r_exported | 31| 79.2| | |n_fns_r_not_exported | 81| 79.5| | |n_fns_src | 618| 96.1|TRUE | |n_fns_per_file_r | 2| 39.7| | |n_fns_per_file_src | 24| 95.1|TRUE | |num_params_per_fn | 2| 11.9| | |loc_per_fn_r | 12| 36.1| | |loc_per_fn_r_exp | 6| 10.5| | |loc_per_fn_r_not_exp | 16| 52.7| | |loc_per_fn_src | 4| 2.0|TRUE | |rel_whitespace_R | 18| 80.9| | |rel_whitespace_src | 14| 29.1| | |rel_whitespace_inst | 24| 85.7| | |rel_whitespace_vignettes | 51| 99.2|TRUE | |rel_whitespace_tests | 11| 88.9| | |doclines_per_fn_exp | 42| 52.8| | |doclines_per_fn_not_exp | 0| 0.0|TRUE | |fn_call_network_size | 1302| 98.5|TRUE | ---
Click to see the interactive network visualisation of calls between objects in package
goodpractice
and other checks#### 3a. Continuous Integration Badges [![R-CMD-check.yaml](https://github.com/LCBC-UiO/galamm/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/LCBC-UiO/galamm/actions) **GitHub Workflow Results** | id|name |conclusion |sha | run_number|date | |----------:|:--------------------------|:----------|:------|----------:|:----------| | 6584930507|lint |success |26cfad | 495|2023-10-20 | | 6584967181|pages build and deployment |success |2fba91 | 144|2023-10-20 | | 6584930514|pkgdown |success |26cfad | 350|2023-10-20 | | 6584930510|R-CMD-check |success |26cfad | 558|2023-10-20 | | 6584930523|test-coverage |success |26cfad | 248|2023-10-20 | --- #### 3b. `goodpractice` results #### `R CMD check` with [rcmdcheck](https://r-lib.github.io/rcmdcheck/) R CMD check generated the following note: 1. checking installed package size ... NOTE installed size is 34.0Mb sub-directories of 1Mb or more: doc 2.0Mb libs 30.7Mb R CMD check generated the following check_fail: 1. rcmdcheck_reasonable_installed_size #### Test coverage with [covr](https://covr.r-lib.org/) Package coverage: 98.35 #### Cyclocomplexity with [cyclocomp](https://github.com/MangoTheCat/cyclocomp) The following functions have cyclocomplexity >= 15: function | cyclocomplexity --- | --- galamm | 45 gam.setup | 44 gamm4.wrapup | 44 interpret.gam0 | 29 define_factor_mappings | 17 galamm_control | 17 #### Static code analyses with [lintr](https://github.com/jimhester/lintr) [lintr](https://github.com/jimhester/lintr) found the following 296 potential issues: message | number of times --- | --- Avoid library() and require() calls in packages | 10 Lines should not be more than 80 characters. | 286
:heavy_multiplication_x: The following 2 function names are duplicated in other packages: - - `plot_smooth` from itsadug - - `sl` from reinsureR
|package |version | |:--------|:---------| |pkgstats |0.1.3.9 | |pkgcheck |0.1.2.10 | |srr |0.0.1.194 |
This package is in top shape and may be passed on to a handling editor
👋 @noamross, I just wanted to ask: what's the status of this submission? Is rOpenSci interested in reviewing it?
@osorensen, thanks for following up. My apologies, I think this package fell between cracks in our editor hand-off. I'll follow up later today.
@osorensen Apologies once again, with recent organisational changes this once again fell through the cracks. We are now finally on it. How are you positioned if we finally get the process started now?
@mpadge, a paper describing the package is currently under review for a journal, so I think my best option now is the withdraw the submission to ropensci. I can maybe just to that by closing this issue?
@osorensen We'd still like to work with you to get this through our review process. How about one of the following options:
Note that if your submission is to Journal of Statistical Software, then our system has been developed in collaboration with their processes, and they would likely welcome you using the results of a review here to support their own process.
Thanks @mpadge, I go for option 1 then, and will ping you here once I've got a final decision on the paper.
@osorensen We'd still like to work with you to get this through our review process. How about one of the following options:
- We put the submission on hold here, until you let us know when your paper has passed through review. We'll then re-start the official review process straight after then. Or,
- We start the review process anyway. Our reviews are generally completed within just a few months at most. Especially given our slow response thus far, we'd ensure that our process would be completed well before a typical manuscript review. (Some good examples for recent stats submissions are Submission - melt: Multiple Empirical Likelihood Tests #550 and waywiser: Ergonomic Methods for Assessing Spatial Models #571, both done in around 2 months.) All changes and software improvements during our review could be used to support your responses to manuscript reviews.
Note that if your submission is to Journal of Statistical Software, then our system has been developed in collaboration with their processes, and they would likely welcome you using the results of a review here to support their own process.
@mpadge, I just stumbled upon this notification. Thank you for mentioning my package review case. The peer review process has significantly enhanced the package's quality in a very short period of time, and I also believe this has expedited its review for publication in the Journal of Statistical Software.
@mpadge, the software paper is now published in Multivariate Behavioral Research, https://doi.org/10.1080/00273171.2024.2385336. We can therefore start this review now.
@ropensci-review-bot check srr
@ropensci-review-bot check srr
@ropensci-review-bot check srr
@ropensci-review-bot check srr
@adamhsparks @osorensen Sorry for any inconvenience. The non-responsive bot was a bug on our side that has now been fixed. It should all work now when you call check srr
again.
@ropensci-review-bot check srr
:heavy_multiplication_x: Error: Package documents compliance only with general standards. Statistical packages must document compliance with at least one set of category-specific standards as well.
The following standards are missing:
General standards:
G5.2, G5.2a, G5.2b, G5.3, G5.4a, G5.4b, G5.5, G5.6
All standards must be documented prior to submission
@maelle, the above seems to be a false positive. The mentioned standards are documented here:
@osorensen, unfortunately, that's not a false positive. They are not properly documented so that the bot can find the standards.
The documentation for ROxygen2 needs to be in /R, not /tests for it to be valid, e.g., https://github.com/giovsaraceno/QuadratiK-package/blob/master/R/srr-stats-standards.R
If you just move it, and redocument it should be fine.
@ropensci-review-bot check srr
@osorensen Sorry, bot's not quite ready for your case. Yours is the first package we've had with standards in tests/testthat.R
. That is of course perfectly okay, but we simply hadn't encountered it, and so didn't realise that it caused a failure on our side. I'll ping here when our system has been rebuilt with the fix.
(And FYI @adamhsparks, "srrstats" tags can go pretty much anywhere at all, including README, tests, src, and R code.)
:heavy_multiplication_x: Error: Package documents compliance only with general standards. Statistical packages must document compliance with at least one set of category-specific standards as well.
:heavy_check_mark: This package complies with > 50% of all standads and may be submitted.
@mpadge, I moved the documentation to R/
, so hope it's fine now.
@osorensen Sorry, bot's not quite ready for your case. Yours is the first package we've had with standards in
tests/testthat.R
. That is of course perfectly okay, but we simply hadn't encountered it, and so didn't realise that it caused a failure on our side. I'll ping here when our system has been rebuilt with the fix.(And FYI @adamhsparks, "srrstats" tags can go pretty much anywhere at all, including README, tests, src, and R code.)
Sorry, my bad. I was just trying to help based on previous cases.
@adamhsparks and @osorensen The system has now been rebuilt, and the bot comment above that "This package ... may be submitted" would no longer appear. The first "Error:" would first have to be addressed.
@adamhsparks and @osorensen The system has now been rebuilt, and the bot comment above that "This package ... may be submitted" would no longer appear. The first "Error:" would first have to be addressed.
@mpadge, this seemed to be fine when I submitted the package, see the srr
check in this comment. Have the standards changed since October 2023?
@osorensen The standards haven't changed, but since that time we've added additional checks to identify packages which only document general standards, with no category-specific ones. The general package checks also now generate and link to the full report on stats standards compliance, like in this example here, so we'd explicitly see there also that compliance statements with regression standards were missing.
So before proceeding, we'd need you to comply with our Regression Standards. Previous experience suggests that'll require around one day's work or so. As always, please let us know if you've got any questions, and in particular, feel free to comment in any way you like regarding the standards, ideally in the stats-devguide repo, linked directly from the book. Thanks!
@ropensci-review-bot check srr
@mpadge @adamhsparks, I'm not sure if I'm allowed to run check srr
myself, but I've added tags which confirm that the package complies with the regression standards now. They are all in the main branch of my repository. Could you please check if this is sufficient?
@osorensen Sorry, that was a wee :bug: on our side. Should work now, but note that result will currently indicate that RE4.15 is missing, so maybe add that standard first before calling?
@ropensci-review-bot check srr
Thanks @mpadge, there was a typo in there, which should be fixed now. I tried running check srr
above but not sure if anything happens.
@ropensci-review-bot check srr
@ropensci-review-bot check srr
:heavy_check_mark: This package complies with > 50% of all standards and may be submitted.
@osorensen @adamhsparks The previous calls seem to have issued during our weekly system rebuild. Just rotten timing, but all should work fine from here on. And nice work @osorensen - 100% compliance!!
@ropensci-review-bot assign @noamross as editor
Assigned! @noamross is now the editor
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@ropensci-review-bot assign @nicholasjclark as reviewer
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Review due date for @nicholasjclark is now 10-November-2024
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@ropensci-review-bot set due date for @eric-pedersen to 2024-11-23
Review due date for @eric-pedersen is now 23-November-2024
Submitting Author Name: Øystein Sørensen Submitting Author Github Handle: !--author1-->@osorensen<!--end-author1-- Repository: https://github.com/LCBC-UiO/galamm Version submitted: 0.1.1.9000 Submission type: Stats Badge grade: gold Editor: !--editor-->@noamross<!--end-editor-- Reviewers: @nicholasjclark, @eric-pedersen
Due date for @nicholasjclark: 2024-11-10 Due date for @eric-pedersen: 2024-11-23Archive: TBD Version accepted: TBD Language: en
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Who is the target audience and what are scientific applications of this package? The target audience is applied statisticians and quantitative scientists, particularly those working on the social sciences. The package is motivated by longitudinal studies in cognitive neuroscience, but it is applicable wherever a measurement model (of factor analysis type) needs to be combined with hierarchical modeling.
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