ILSM: Analyze Interconnection Structure of Multilayer Interaction Networks

WeichengSun commented 2 months ago

Submitting Author Name: SunWeicheng Submitting Author Github Handle: !--author1-->@WeichengSun<!--end-author1-- Repository: https://github.com/WeichengSun/ILSM Version submitted: 1.0.3.2 Submission type: Stats Editor: TBD Reviewers: TBD

Archive: TBD Version accepted: TBD Language: en

Paste the full DESCRIPTION file inside a code block below:

Package: ILSM
Title: Analyze Interconnection Structure of Multilayer Interaction Networks
Version: 1.0.3.2
Authors@R: c(
    person("WeiCheng", "Sun", , "sunwch2023@lzu.edu.cn", role = c("aut", "cre")),
    person("Chuan", "Yan", , "yanchuan@lzu.edu.cn", role = c("aut")),
    person("Yangyang", "Zhao", , "120220907711@lzu.edu.cn", role = c("aut")))
Description: 
    In view of the analysis of the structural characteristics of the multilayer network has been complete, however, there is still a lack of a unified operation that can quickly obtain the corresponding characteristics of the multilayer network. 
    To solve this insufficiency, 'ILSM' was designed for supporting calculating such metrics of multilayer networks by functions of this R package.
License: MIT + file LICENSE
URL: https://github.com/WeichengSun/ILSM
BugReports: https://github.com/WeichengSun/ILSM/issues
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
Depends: R (>= 3.5.0)
Imports: 
    stats,
    Matrix,
    igraph
Suggests: 
    knitr,
    rmarkdown,
    testthat (>= 3.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3

Scope

Please indicate which category or categories from our package fit policies this package falls under: (Please check an appropriate box below. If you are unsure, we suggest you make a pre-submission inquiry.):
Data Packages
- [ ] data retrieval
- [ ] data extraction
- [ ] data munging
- [ ] data deposition
- [ ] data validation and testing
- [ ] workflow automation
- [ ] version control
- [ ] citation management and bibliometrics
- [ ] scientific software wrappers
- [ ] field and lab reproducibility tools
- [ ] database software bindings
- [ ] geospatial data
- [ ] text analysis
Statistical Packages
- [ ] bayesian and monte carlo routines
- [ ] dimensionality reduction, clustering, and unsupervised learning
- [ ] machine learning
- [x] ecological network analysis
- [ ] regression and supervised learning
- [x] exploratory data analysis (EDA) and summary statistics
- [ ] spatial analysis
- [ ] time series analysis
Explain how and why the package falls under these categories (briefly, 1-2 sentences):

This package was designed for supporting calculating such metrics of multilayer networks.

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

Reseachers who work for ecological interaction effects.

Are there other R packages that accomplish the same thing? If so, how does yours differ or meet our criteria for best-in-category?
(If applicable) Does your package comply with our guidance around Ethics, Data Privacy and Human Subjects Research?

Yes!

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Explain reasons for any pkgcheck items which your package is unable to pass.

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Confirm each of the following by checking the box.

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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.
[x] includes documentation with examples for all functions, created with roxygen2.
[x] contains a vignette with examples of its essential functions and uses.
[x] has a test suite.
[x] has continuous integration, including reporting of test coverage.

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

ropensci-review-bot commented 2 months ago

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

ropensci-review-bot commented 2 months ago

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The following problem was found in your submission template:

'author1' variable must be GitHub handle only ('@myhandle') Editors: Please ensure these problems with the submission template are rectified. Package checks have been started regardless.

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ropensci-review-bot commented 2 months ago

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

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WeichengSun commented 2 months ago

@ropensci-review-bot check package

ropensci-review-bot commented 2 months ago

I'm sorry @WeichengSun, I'm afraid I can't do that. That's something only editors, author1, author-others and reviewers-list are allowed to do.

WeichengSun commented 2 months ago

@ropensci-review-bot check package

ropensci-review-bot commented 2 months ago

I'm sorry @WeichengSun, I'm afraid I can't do that. That's something only editors, author1, author-others and reviewers-list are allowed to do.

WeichengSun commented 2 months ago

@ropensci-review-bot help

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Hello @WeichengSun, here are the things you can ask me to do:


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WeichengSun commented 2 months ago

@ropensci-review-bot check package

ropensci-review-bot commented 2 months ago

Thanks, about to send the query.

ropensci-review-bot commented 2 months ago

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Editor check started

:wave:

WeichengSun commented 2 months ago

@ropensci-review-bot check package

ropensci-review-bot commented 2 months ago

Thanks, about to send the query.

ropensci-review-bot commented 2 months ago

:rocket:

Editor check started

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adamhsparks commented 2 months ago

Hi @WeichengSun, it seems that the bot is having some issues, I'll see what we can do about that. Do you still wish to proceed with the review?

If so, you'll need to set up CI with test coverage reporting and ensure all of your exported functions have examples in your ROxygen code as you've not indicated that these criteria are met.

WeichengSun commented 2 months ago

Hey, @adamhsparks, thanks for your suggestion, I have revised part of it. Since this is the first submission, there may be many questions. Please give us more suggestions on the future progress.

adamhsparks commented 2 months ago

@ropensci-review-bot check package

ropensci-review-bot commented 2 months ago

Thanks, about to send the query.

ropensci-review-bot commented 2 months ago

:rocket:

Editor check started

:wave:

ropensci-review-bot commented 2 months ago

Checks for ILSM (v1.0.3.2)

git hash: 47a1d48c

:heavy_multiplication_x: Package name is not available (on CRAN).
:heavy_check_mark: has a 'codemeta.json' file.
:heavy_check_mark: has a 'contributing' file.
:heavy_check_mark: uses 'roxygen2'.
:heavy_check_mark: 'DESCRIPTION' has a URL field.
:heavy_check_mark: 'DESCRIPTION' has a BugReports field.
:heavy_check_mark: Package has at least one HTML vignette
:heavy_check_mark: All functions have examples.
:heavy_check_mark: Package has continuous integration checks.
:heavy_multiplication_x: Package coverage is 69.2% (should be at least 75%).
: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: MIT + file LICENSE

1. 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 | 704| |internal |ILSM | 167| |imports |igraph | 66| |imports |Matrix | 13| |imports |stats | 3| |suggests |knitr | NA| |suggests |rmarkdown | NA| |suggests |testthat | 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()', and examining the 'external_calls' table.

base

c (109), matrix (72), sum (63), return (40), rownames (37), data.frame (34), rowSums (32), t (32), ncol (30), length (27), colSums (24), for (18), apply (17), message (16), as.matrix (15), list (15), nrow (14), paste (12), rep (12), unique (12), as.numeric (11), lapply (9), colnames (5), paste0 (4), T (4), which (4), rbind (3), abs (2), drop (2), if (2), mean (2), round (2), sample (2), seq (2), tcrossprod (2), unlist (2), eigen (1), F (1), Im (1), is.na (1), kronecker (1), max (1), min (1), mode (1), names (1), order (1), Re (1), replace (1), solve (1), sqrt (1), which.max (1)

ILSM

Two (42), Three (15), mEdges (10), Kendall_cor (9), Four (7), adject_net (6), GetLargestEigenv_r (6), sumR_r (6), GetMultiClosenessCentrality_r (5), GetMultiEigenvectorCentrality_r (5), GetMultiHubCentrality_r (5), GetMultiKatzCentrality_r (5), GetMultiPageRankCentrality_r (5), GetMultiAuthCentrality_r (4), emptyR (3), me_interlayer (3), vaznullR (3), BuildSupraAdjacencyMatrixFromExtendedEdgelist_r (2), BuildSupraTransitionMatrixFromSupraAdjacencyMatrix_r (2), edgelist_from_matrices (2), GetMultiPathStatistics_r (2), role_sim (2), SupraAdjacencyToBlockTensor_r (2), build_net (1), coid (1), cois (1), diagR_r (1), GetMultiRWCentrality_r (1), hc (1), icmotif_count (1), icmotif_role (1), igraph_from_matrices (1), Multi_motif (1), node_cv (1), null_model (1), pc (1), poc (1), savue.fastc (1), SavueR (1)

igraph

V (53), graph_from_adjacency_matrix (8), distances (2), layout_with_sugiyama (2), get.edgelist (1)

Matrix

t (5), Matrix (3), sparseMatrix (3), Diagonal (2)

stats

C (1), lm (1), offset (1)

2. 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 22 files) and - 3 authors - 1 vignette - 1 internal data file - 3 imported packages - 14 exported functions (median 67 lines of code) - 66 non-exported functions in R (median 19 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 | 22| 82.4| | |files_vignettes | 1| 62.0| | |files_tests | 8| 84.2| | |loc_R | 2388| 85.4| | |loc_vignettes | 40| 6.0| | |loc_tests | 273| 58.6| | |num_vignettes | 1| 59.0| | |data_size_total | 5642| 66.4| | |data_size_median | 5642| 74.6| | |n_fns_r | 80| 68.9| | |n_fns_r_exported | 14| 56.1| | |n_fns_r_not_exported | 66| 72.8| | |n_fns_per_file_r | 2| 35.0| | |num_params_per_fn | 2| 26.7| | |loc_per_fn_r | 26| 71.4| | |loc_per_fn_r_exp | 68| 86.3| | |loc_per_fn_r_not_exp | 20| 63.0| | |rel_whitespace_R | 8| 66.8| | |rel_whitespace_vignettes | 22| 5.5| | |rel_whitespace_tests | 10| 42.0| | |doclines_per_fn_exp | 82| 85.2| | |doclines_per_fn_not_exp | 0| 0.0|TRUE | |fn_call_network_size | 120| 80.9| | ---

2a. Network visualisation

Click to see the interactive network visualisation of calls between objects in package

3. `goodpractice` and other checks

Details of goodpractice checks (click to open)

#### 3a. Continuous Integration Badges [![R-CMD-check.yaml](https://github.com/WeichengSun/ILSM/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/WeichengSun/ILSM/actions) **GitHub Workflow Results** | id|name |conclusion |sha | run_number|date | |-----------:|:------------------|:----------|:------|----------:|:----------| | 10732233292|pkgdown.yaml |success |47a1d4 | 3|2024-09-06 | | 10732195886|R-CMD-check.yaml |success |47a1d4 | 2|2024-09-06 | | 10732195887|test-coverage.yaml |failure |47a1d4 | 2|2024-09-06 | --- #### 3b. `goodpractice` results #### `R CMD check` with [rcmdcheck](https://r-lib.github.io/rcmdcheck/) R CMD check generated the following check_fails: 1. cyclocomp 2. no_import_package_as_a_whole #### Test coverage with [covr](https://covr.r-lib.org/) Package coverage: 69.23 The following files are not completely covered by tests: file | coverage --- | --- R/coid.R | 0% R/cois.R | 0% R/hc.R | 0% R/Kendall_cor.R | 0% R/mEdges.R | 0% R/node_cv.R | 62.5% R/null_model.R | 0% R/pc.R | 0% R/poc.R | 0% R/role_sim.R | 0% R/SavueR.R | 0% R/subnet_cor.R | 0% R/vaznullR.R | 0% #### Cyclocomplexity with [cyclocomp](https://github.com/MangoTheCat/cyclocomp) The following functions have cyclocomplexity >= 15: function | cyclocomplexity --- | --- Multi_motif | 99 icmotif_role | 59 subnet_cor | 27 cois | 25 node_cv | 21 Kendall_cor | 18 coid | 17 icmotif_count | 17 #### Static code analyses with [lintr](https://github.com/jimhester/lintr) [lintr](https://github.com/jimhester/lintr) found the following 531 potential issues: message | number of times --- | --- Avoid 1:length(...) expressions, use seq_len. | 2 Avoid 1:ncol(...) expressions, use seq_len. | 5 Avoid 1:NCOL(...) expressions, use seq_len. | 2 Avoid 1:nrow(...) expressions, use seq_len. | 26 Avoid 1:NROW(...) expressions, use seq_len. | 2 Avoid library() and require() calls in packages | 2 Lines should not be more than 80 characters. This line is 100 characters. | 7 Lines should not be more than 80 characters. This line is 102 characters. | 12 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. | 11 Lines should not be more than 80 characters. This line is 105 characters. | 4 Lines should not be more than 80 characters. This line is 106 characters. | 1 Lines should not be more than 80 characters. This line is 107 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 109 characters. | 6 Lines should not be more than 80 characters. This line is 110 characters. | 10 Lines should not be more than 80 characters. This line is 111 characters. | 6 Lines should not be more than 80 characters. This line is 112 characters. | 1 Lines should not be more than 80 characters. 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4. Other Checks

Details of other checks (click to open)

:heavy_multiplication_x: The following 3 function names are duplicated in other packages: - - `hc` from adana, bnlearn, mclust, multigraph - - `null_model` from fabletools, insight, parsnip, qtlpoly - - `pc` from bReeze, FaultTree, gamlss.foreach, kader, lessR, pcalg, SEAsic, tabr, yasp

Package Versions

|package |version | |:--------|:--------| |pkgstats |0.1.6.17 | |pkgcheck |0.1.2.58 |

Editor-in-Chief Instructions:

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

adamhsparks commented 2 months ago

@WeichengSun, the package checks indicate that the test coverage needs to be improved before we can start the review but everything else checks out.

Would you like to proceed? If so, just ping me in this Issue when you've got the package's test coverage up to 75% and I'll take it from there. Also, feel free to ask me if you have any other questions.

WeichengSun commented 2 months ago

Hi @adamhsparks, I've added some tests to address the test coverage issue, but I wonder why the report shows package name is not available. If so, you can continue. Thank you.

adamhsparks commented 2 months ago

You have it on CRAN, already, so it shows unavailable.

adamhsparks commented 2 months ago

@ropensci-review-bot check package

ropensci-review-bot commented 2 months ago

Thanks, about to send the query.

ropensci-review-bot commented 2 months ago

:rocket:

Editor check started

:wave:

ropensci-review-bot commented 2 months ago

Checks for ILSM (v1.0.3.2)

git hash: 0af56b16

:heavy_multiplication_x: Package name is not available (on CRAN).
:heavy_check_mark: has a 'codemeta.json' file.
:heavy_check_mark: has a 'contributing' file.
:heavy_check_mark: uses 'roxygen2'.
:heavy_check_mark: 'DESCRIPTION' has a URL field.
:heavy_check_mark: 'DESCRIPTION' has a BugReports field.
:heavy_check_mark: Package has at least one HTML vignette
:heavy_check_mark: All functions have examples.
:heavy_check_mark: Package has continuous integration checks.
:heavy_check_mark: Package coverage is 78.8%.
: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: MIT + file LICENSE

1. 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 | 704| |internal |ILSM | 167| |imports |igraph | 66| |imports |Matrix | 13| |imports |stats | 3| |suggests |knitr | NA| |suggests |rmarkdown | NA| |suggests |testthat | 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()', and examining the 'external_calls' table.

base

c (109), matrix (72), sum (63), return (40), rownames (37), data.frame (34), rowSums (32), t (32), ncol (30), length (27), colSums (24), for (18), apply (17), message (16), as.matrix (15), list (15), nrow (14), paste (12), rep (12), unique (12), as.numeric (11), lapply (9), colnames (5), paste0 (4), T (4), which (4), rbind (3), abs (2), drop (2), if (2), mean (2), round (2), sample (2), seq (2), tcrossprod (2), unlist (2), eigen (1), F (1), Im (1), is.na (1), kronecker (1), max (1), min (1), mode (1), names (1), order (1), Re (1), replace (1), solve (1), sqrt (1), which.max (1)

ILSM

Two (42), Three (15), mEdges (10), Kendall_cor (9), Four (7), adject_net (6), GetLargestEigenv_r (6), sumR_r (6), GetMultiClosenessCentrality_r (5), GetMultiEigenvectorCentrality_r (5), GetMultiHubCentrality_r (5), GetMultiKatzCentrality_r (5), GetMultiPageRankCentrality_r (5), GetMultiAuthCentrality_r (4), emptyR (3), me_interlayer (3), vaznullR (3), BuildSupraAdjacencyMatrixFromExtendedEdgelist_r (2), BuildSupraTransitionMatrixFromSupraAdjacencyMatrix_r (2), edgelist_from_matrices (2), GetMultiPathStatistics_r (2), role_sim (2), SupraAdjacencyToBlockTensor_r (2), build_net (1), coid (1), cois (1), diagR_r (1), GetMultiRWCentrality_r (1), hc (1), icmotif_count (1), icmotif_role (1), igraph_from_matrices (1), Multi_motif (1), node_cv (1), null_model (1), pc (1), poc (1), savue.fastc (1), SavueR (1)

igraph

V (53), graph_from_adjacency_matrix (8), distances (2), layout_with_sugiyama (2), get.edgelist (1)

Matrix

t (5), Matrix (3), sparseMatrix (3), Diagonal (2)

stats

C (1), lm (1), offset (1)

2. 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 22 files) and - 3 authors - 1 vignette - 1 internal data file - 3 imported packages - 14 exported functions (median 67 lines of code) - 66 non-exported functions in R (median 19 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 | 22| 82.4| | |files_vignettes | 1| 62.0| | |files_tests | 12| 90.0| | |loc_R | 2388| 85.4| | |loc_vignettes | 40| 6.0| | |loc_tests | 431| 68.3| | |num_vignettes | 1| 59.0| | |data_size_total | 5642| 66.4| | |data_size_median | 5642| 74.6| | |n_fns_r | 80| 68.9| | |n_fns_r_exported | 14| 56.1| | |n_fns_r_not_exported | 66| 72.8| | |n_fns_per_file_r | 2| 35.0| | |num_params_per_fn | 2| 26.7| | |loc_per_fn_r | 26| 71.4| | |loc_per_fn_r_exp | 68| 86.3| | |loc_per_fn_r_not_exp | 20| 63.0| | |rel_whitespace_R | 8| 66.8| | |rel_whitespace_vignettes | 22| 5.5| | |rel_whitespace_tests | 12| 55.0| | |doclines_per_fn_exp | 82| 85.2| | |doclines_per_fn_not_exp | 0| 0.0|TRUE | |fn_call_network_size | 120| 80.9| | ---

2a. Network visualisation

Click to see the interactive network visualisation of calls between objects in package

3. `goodpractice` and other checks

Details of goodpractice checks (click to open)

#### 3a. Continuous Integration Badges [![R-CMD-check.yaml](https://github.com/WeichengSun/ILSM/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/WeichengSun/ILSM/actions) **GitHub Workflow Results** | id|name |conclusion |sha | run_number|date | |-----------:|:------------------|:----------|:------|----------:|:----------| | 10752142571|pkgdown.yaml |success |0af56b | 4|2024-09-07 | | 10752142569|R-CMD-check.yaml |success |0af56b | 3|2024-09-07 | | 10752142570|test-coverage.yaml |failure |0af56b | 3|2024-09-07 | --- #### 3b. `goodpractice` results #### `R CMD check` with [rcmdcheck](https://r-lib.github.io/rcmdcheck/) R CMD check generated the following check_fails: 1. cyclocomp 2. no_import_package_as_a_whole #### Test coverage with [covr](https://covr.r-lib.org/) Package coverage: 78.75 #### Cyclocomplexity with [cyclocomp](https://github.com/MangoTheCat/cyclocomp) The following functions have cyclocomplexity >= 15: function | cyclocomplexity --- | --- Multi_motif | 99 icmotif_role | 59 subnet_cor | 27 cois | 25 node_cv | 21 Kendall_cor | 18 coid | 17 icmotif_count | 17 #### Static code analyses with [lintr](https://github.com/jimhester/lintr) [lintr](https://github.com/jimhester/lintr) found the following 550 potential issues: message | number of times --- | --- Avoid 1:length(...) expressions, use seq_len. | 2 Avoid 1:ncol(...) expressions, use seq_len. | 5 Avoid 1:NCOL(...) expressions, use seq_len. | 2 Avoid 1:nrow(...) expressions, use seq_len. | 26 Avoid 1:NROW(...) expressions, use seq_len. | 2 Avoid library() and require() calls in packages | 2 Lines should not be more than 80 characters. 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4. Other Checks

Details of other checks (click to open)

:heavy_multiplication_x: The following 3 function names are duplicated in other packages: - - `hc` from adana, bnlearn, mclust, multigraph - - `null_model` from fabletools, insight, parsnip, qtlpoly - - `pc` from bReeze, FaultTree, gamlss.foreach, kader, lessR, pcalg, SEAsic, tabr, yasp

Package Versions

|package |version | |:--------|:--------| |pkgstats |0.1.6.17 | |pkgcheck |0.1.2.58 |

Editor-in-Chief Instructions:

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

adamhsparks commented 2 months ago

@WeichengSun, could you please set up or fix the test coverage for GitHub Actions and add a badge for it? This indicates that it's not passing, https://github.com/WeichengSun/ILSM/actions/runs/10752142570

WeichengSun commented 2 months ago

Hi @adamhsparks, it's passing now.

WeichengSun commented 2 months ago

Hi @adamhsparks, I want to submit an Applications Article about my package to Methods in Ecology and Evolution, but I don't know how my package can pass the review of ropensci. Please give me some suggestions. Thank you.

adamhsparks commented 2 months ago

Hi @WeichengSun, I'm currently seeking a handling editor for your package but haven't found anyone yet. I'll get someone assigned as soon as I can.

adamhsparks commented 2 months ago

Hi @WeichengSun, after checking with the editorial board, I was alerted that you seemingly have mashed together our pre-submission and regular stats templates with your submission.

Could I ask you to please close this and open a regular stats submission so that the bot picks up this as a stats submission?

You will need to add our stats standard annotations to the package as well. The bot will pick that up and the process won't proceed until you've done that, so I suggest doing that before opening a new issue and using the proper stats template.

WeichengSun commented 2 months ago

Hi @adamhsparks, what can I refer to for 'stats standard annotations' you mentioned? I am very confused about this.

adamhsparks commented 2 months ago

Hi @WeichengSun, I'd start with our rOpenSci Statistical Software Peer Review guide, specifically Chapter3 for these details.

ropensci / software-review