`chopin`: Computation for Climate and Health research On Parallelized INfrastructure #638

sigmafelix · 2024-04-24T13:57:04Z

Date accepted: 2024-09-24

Submitting Author Name: Insang Song
Submitting Author Github Handle: @sigmafelix
Other Package Authors Github handles: (comma separated, delete if none) @kyle-messier
Repository: https://github.com/NIEHS/chopin
Version submitted: 0.6.2.20240423
Submission type: Standard
Editor: @beatrizmilz
Reviewers: @robitalec, @Aariq

Archive: TBD
Version accepted: TBD
Language: en

Paste the full DESCRIPTION file inside a code block below:

Package: chopin
Title: CHOPIN: Computation for Climate and Health research On Parallelized INfrastructure
Version: 0.6.2.20240423
Authors@R: c(
    person("Insang", "Song", , "[email protected]", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0001-8732-3256")),
    person("Kyle", "Messier", role = c("aut", "ctb"),
           comment = c(ORCID = "0000-0001-9508-9623"))
  )
Description: It enables users with basic understanding on geospatial data
    and sf and terra functions to parallelize geospatial operations for
    geospatial exposure assessment modeling and covariate computation.
    Parallelization is done by dividing large datasets into sub-regions
    with regular grids and data's own hierarchy. A computation over the
    large number of raster files can be parallelized with a chopin
    function as well.
License: MIT + file LICENSE
URL: https://github.com/NIEHS/chopin
BugReports: https://github.com/NIEHS/chopin/issues
Depends: 
    R (>= 4.1)
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
Imports: 
    anticlust,
    dplyr (>= 1.1.0),
    exactextractr (>= 0.8.2),
    future.apply,
    igraph,
    methods,
    rlang (>= 0.4.9),
    sf (>= 1.0-10),
    stars (>= 0.6-0),
    terra (>= 1.7-18)
Suggests: 
    callr,
    covr,
    DiagrammeR,
    doFuture,
    doParallel,
    future,
    future.batchtools,
    future.callr,
    knitr,
    rmarkdown,
    spatstat.random,
    testthat (>= 3.0.0),
    units,
    withr
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 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
Explain how and why the package falls under these categories (briefly, 1-2 sentences):
: chopin supports parallel processing for functions in popular spatial data manipulation packages sf and terra on a high-level parallelization framework future. This feature fits to the geospatial data category.
Who is the target audience and what are scientific applications of this package?
: Our first target audience group is spatial epidemiologists and health geographers who want to calculating spatial covariates from spatial and spatiotemporal datasets including climate, transportation, demographics, topography, hydrography, and others. We expect that users are cognizant of basic geographic information system/science. The wider audience could take advantage of the flexibility of this package for expediting spatial operations.
Are there other R packages that accomplish the same thing? If so, how does yours differ or meet our criteria for best-in-category?
: A selection of functions in terra (e.g., *app and predict) supports internal parallelization, where a single dataset is accepted. To the best of our knowledge, no packaged solution exists for parallelization of spatial operations where two datasets are involved. sprawl (GitHub-only; not maintained) partially overlaps this package's functionality in that it includes convenience functions connecting multiple basic spatial operations. Besides the R functions, a handful of teaching or demonstration materials briefly covered parallelization of spatial data applications ([1], [2], [3]).
(If applicable) Does your package comply with our guidance around Ethics, Data Privacy and Human Subjects Research?
: Not applicable
If you made a pre-submission inquiry, please paste the link to the corresponding issue, forum post, or other discussion, or @tag the editor you contacted.
: Presubmission inquiry of the previous version of this package -- Presubmission inquiry: chopin #630 commented by @ldecicco-USGS
Explain reasons for any pkgcheck items which your package is unable to pass.
: Coverage rate (99%) and installation size (25.7 MB; of which data (2.0 MB) and extdata (23.1 MB) exceeded recommended sizes) resulted in notes.

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 to find a replacement.

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

Publication options

Do you intend for this package to go on CRAN?
Do you intend for this package to go on Bioconductor?
Do you wish to submit an Applications Article about your package to Methods in Ecology and Evolution? If so:

MEE Options

The package is novel and will be of interest to the broad readership of the journal.
The manuscript describing the package is no longer than 3000 words.
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(Scope: Do consider MEE's Aims and Scope for your manuscript. We make no guarantee that your manuscript will be within MEE scope.)
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(Please do not submit your package separately to Methods in Ecology and Evolution)

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.

Thank you very much for your consideration!

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

ropensci-review-bot · 2024-04-24T13:57:07Z

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

ropensci-review-bot · 2024-04-24T13:57:10Z

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Editor check started

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ropensci-review-bot · 2024-04-24T14:24:25Z

Checks for chopin (v0.6.2.20240423)

git hash: 26153abb

✔️ Package name is available
✔️ has a 'codemeta.json' file.
✖️ does not have a 'contributing' file.
✖️ The following function has no documented return value: [clip_ras_ext]
✔️ 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 99.6%.
✔️ R CMD check found no errors.
✔️ R CMD check found no warnings.

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

Package License: 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	123
internal	chopin	33
internal	graphics	8
internal	stats	6
internal	utils	2
imports	terra	38
imports	sf	20
imports	dplyr	5
imports	methods	5
imports	exactextractr	3
imports	future.apply	3
imports	rlang	3
imports	igraph	2
imports	anticlust	1
imports	stars	1
suggests	callr	NA
suggests	covr	NA
suggests	DiagrammeR	NA
suggests	doFuture	NA
suggests	doParallel	NA
suggests	future	NA
suggests	future.batchtools	NA
suggests	future.callr	NA
suggests	knitr	NA
suggests	rmarkdown	NA
suggests	spatstat.random	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.

base

list (9), switch (9), lapply (7), c (6), unlist (6), split (5), which (5), names (4), grepl (3), if (3), mapply (3), nrow (3), abs (2), any (2), as.integer (2), ceiling (2), class (2), data.frame (2), expand.grid (2), log10 (2), mode (2), paste (2), round (2), rownames (2), seq (2), seq_len (2), sum (2), t (2), tryCatch (2), unique (2), args (1), as.data.frame (1), as.logical (1), as.numeric (1), as.vector (1), by (1), exp (1), for (1), formals (1), ifelse (1), intersect (1), lengths (1), pi (1), rbind (1), Reduce (1), search (1), seq_along (1), sort (1), sprintf (1), strsplit (1), suppressWarnings (1), table (1), try (1), vector (1)

terra

buffer (9), crop (8), ext (4), rast (4), distance (3), crs (2), nearby (2), project (2), crds (1), intersect (1), is.lonlat (1), nlyr (1)

chopin

dep_check (15), any_class_args (4), dep_switch (4), datamod (2), get_clip_ext (2), clip_ras_ext (1), clip_vec_ext (1), crs_check (1), ext2poly (1), extract_at_buffer_kernel (1), par_group_balanced (1)

sf

st_crs (3), st_relate (3), st_as_sf (2), st_area (1), st_as_sfc (1), st_bbox (1), st_centroid (1), st_coordinates (1), st_covered_by (1), st_geometry_type (1), st_intersection (1), st_intersects (1), st_make_grid (1), st_transform (1), st_within (1)

graphics

points (8)

stats

dist (3), quantile (3)

dplyr

n (2), left_join (1), mutate (1), summarize (1)

methods

is (3), el (2)

exactextractr

exact_extract (3)

future.apply

future_lapply (3)

rlang

inject (3)

igraph

graph_from_edgelist (2)

utils

combn (2)

anticlust

balanced_clustering (1)

stars

st_as_stars (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 7 files) and
2 authors
3 vignettes
2 internal data files
10 imported packages
33 exported functions (median 17 lines of code)
34 non-exported functions in R (median 29 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	7	45.7
files_vignettes	3	92.4
files_tests	9	89.6
loc_R	1163	72.0
loc_vignettes	652	83.8
loc_tests	1193	89.2
num_vignettes	3	94.2
data_size_total	2100956	97.8	TRUE
data_size_median	1050478	98.5	TRUE
n_fns_r	67	65.5
n_fns_r_exported	33	80.4
n_fns_r_not_exported	34	56.6
n_fns_per_file_r	7	77.9
num_params_per_fn	3	33.6
loc_per_fn_r	21	62.0
loc_per_fn_r_exp	17	40.3
loc_per_fn_r_not_exp	29	77.1
rel_whitespace_R	12	61.7
rel_whitespace_vignettes	32	85.6
rel_whitespace_tests	17	85.6
doclines_per_fn_exp	37	45.3
doclines_per_fn_not_exp	0	0.0	TRUE
fn_call_network_size	59	69.7

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

GitHub Workflow Results

id	name	conclusion	sha	run_number	date
8817187321	pages build and deployment	success	a8aaed	33	2024-04-24
8817133786	pkgdown	success	26153a	69	2024-04-24
8817133742	R-CMD-check	success	26153a	149	2024-04-24
8817133730	test-coverage-local	success	26153a	17	2024-04-24

3b. `goodpractice` results

`R CMD check` with rcmdcheck

R CMD check generated the following notes:

checking installed package size ... NOTE
installed size is 25.6Mb
sub-directories of 1Mb or more:
data 2.0Mb
extdata 23.1Mb
checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
...
--- re-building ‘v00_good_practice_parallelization.Rmd’ using rmarkdown
--- finished re-building ‘v00_good_practice_parallelization.Rmd’

--- re-building ‘v01_par_make_gridset.Rmd’ using rmarkdown
File figures/nc-load-1.png not found in resource path
Error: processing vignette 'v01_par_make_gridset.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘v01_par_make_gridset.Rmd’

--- re-building ‘v02_climate_examples.Rmd’ using rmarkdown
File figures/climate-se-states.png not found in resource path
Error: processing vignette 'v02_climate_examples.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘v02_climate_examples.Rmd’

SUMMARY: processing the following files failed:
‘v01_par_make_gridset.Rmd’ ‘v02_climate_examples.Rmd’

Error: Vignette re-building failed.
Execution halted

R CMD check generated the following check_fail:

rcmdcheck_reasonable_installed_size

Test coverage with covr

Package coverage: 99.65

Cyclocomplexity with cyclocomp

No functions have cyclocomplexity >= 15

Static code analyses with lintr

lintr found the following 1 potential issues:

message	number of times
Lines should not be more than 80 characters.	1

Package Versions

package	version
pkgstats	0.1.3.13
pkgcheck	0.1.2.21

Editor-in-Chief Instructions:

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

sigmafelix · 2024-04-24T15:51:34Z

@ropensci-review-bot check package

ropensci-review-bot · 2024-04-24T15:51:37Z

Thanks, about to send the query.

ropensci-review-bot · 2024-04-24T15:51:39Z

🚀

Editor check started

👋

ropensci-review-bot · 2024-04-24T16:01:46Z

Checks for chopin (v0.6.2.20240423)

git hash: c0e53b6e

✔️ 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 99.6%.
✔️ R CMD check found no errors.
✔️ R CMD check found no warnings.

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	123
internal	chopin	33
internal	graphics	8
internal	stats	6
internal	utils	2
imports	terra	38
imports	sf	20
imports	dplyr	5
imports	methods	5
imports	exactextractr	3
imports	future.apply	3
imports	rlang	3
imports	igraph	2
imports	anticlust	1
imports	stars	1
suggests	callr	NA
suggests	covr	NA
suggests	DiagrammeR	NA
suggests	doFuture	NA
suggests	doParallel	NA
suggests	future	NA
suggests	future.batchtools	NA
suggests	future.callr	NA
suggests	knitr	NA
suggests	rmarkdown	NA
suggests	spatstat.random	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.

base

list (9), switch (9), lapply (7), c (6), unlist (6), split (5), which (5), names (4), grepl (3), if (3), mapply (3), nrow (3), abs (2), any (2), as.integer (2), ceiling (2), class (2), data.frame (2), expand.grid (2), log10 (2), mode (2), paste (2), round (2), rownames (2), seq (2), seq_len (2), sum (2), t (2), tryCatch (2), unique (2), args (1), as.data.frame (1), as.logical (1), as.numeric (1), as.vector (1), by (1), exp (1), for (1), formals (1), ifelse (1), intersect (1), lengths (1), pi (1), rbind (1), Reduce (1), search (1), seq_along (1), sort (1), sprintf (1), strsplit (1), suppressWarnings (1), table (1), try (1), vector (1)

terra

buffer (9), crop (8), ext (4), rast (4), distance (3), crs (2), nearby (2), project (2), crds (1), intersect (1), is.lonlat (1), nlyr (1)

chopin

dep_check (15), any_class_args (4), dep_switch (4), datamod (2), get_clip_ext (2), clip_ras_ext (1), clip_vec_ext (1), crs_check (1), ext2poly (1), extract_at_buffer_kernel (1), par_group_balanced (1)

sf

st_crs (3), st_relate (3), st_as_sf (2), st_area (1), st_as_sfc (1), st_bbox (1), st_centroid (1), st_coordinates (1), st_covered_by (1), st_geometry_type (1), st_intersection (1), st_intersects (1), st_make_grid (1), st_transform (1), st_within (1)

graphics

points (8)

stats

dist (3), quantile (3)

dplyr

n (2), left_join (1), mutate (1), summarize (1)

methods

is (3), el (2)

exactextractr

exact_extract (3)

future.apply

future_lapply (3)

rlang

inject (3)

igraph

graph_from_edgelist (2)

utils

combn (2)

anticlust

balanced_clustering (1)

stars

st_as_stars (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 7 files) and
2 authors
3 vignettes
2 internal data files
10 imported packages
33 exported functions (median 17 lines of code)
34 non-exported functions in R (median 29 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	7	45.7
files_vignettes	3	92.4
files_tests	9	89.6
loc_R	1163	72.0
loc_vignettes	652	83.8
loc_tests	1193	89.2
num_vignettes	3	94.2
data_size_total	2100956	97.8	TRUE
data_size_median	1050478	98.5	TRUE
n_fns_r	67	65.5
n_fns_r_exported	33	80.4
n_fns_r_not_exported	34	56.6
n_fns_per_file_r	7	77.9
num_params_per_fn	3	33.6
loc_per_fn_r	21	62.0
loc_per_fn_r_exp	17	40.3
loc_per_fn_r_not_exp	29	77.1
rel_whitespace_R	12	61.7
rel_whitespace_vignettes	32	85.6
rel_whitespace_tests	17	85.6
doclines_per_fn_exp	37	45.3
doclines_per_fn_not_exp	0	0.0	TRUE
fn_call_network_size	59	69.7

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

GitHub Workflow Results

id	name	conclusion	sha	run_number	date
8818976584	pages build and deployment	success	1b88a2	36	2024-04-24
8818927586	pkgdown	success	f8c659	71	2024-04-24
8818927598	R-CMD-check	success	f8c659	151	2024-04-24
8818927585	test-coverage-local	success	f8c659	19	2024-04-24

3b. `goodpractice` results

`R CMD check` with rcmdcheck

R CMD check generated the following notes:

checking installed package size ... NOTE
installed size is 25.6Mb
sub-directories of 1Mb or more:
data 2.0Mb
extdata 23.1Mb
checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
...
--- re-building ‘v00_good_practice_parallelization.Rmd’ using rmarkdown
--- finished re-building ‘v00_good_practice_parallelization.Rmd’

--- re-building ‘v01_par_make_gridset.Rmd’ using rmarkdown
File figures/nc-load-1.png not found in resource path
Error: processing vignette 'v01_par_make_gridset.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘v01_par_make_gridset.Rmd’

--- re-building ‘v02_climate_examples.Rmd’ using rmarkdown
File figures/climate-se-states.png not found in resource path
Error: processing vignette 'v02_climate_examples.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘v02_climate_examples.Rmd’

SUMMARY: processing the following files failed:
‘v01_par_make_gridset.Rmd’ ‘v02_climate_examples.Rmd’

Error: Vignette re-building failed.
Execution halted

R CMD check generated the following check_fail:

rcmdcheck_reasonable_installed_size

Test coverage with covr

Package coverage: 99.65

Cyclocomplexity with cyclocomp

No functions have cyclocomplexity >= 15

Static code analyses with lintr

lintr found the following 1 potential issues:

message	number of times
Lines should not be more than 80 characters.	1

Package Versions

package	version
pkgstats	0.1.3.13
pkgcheck	0.1.2.21

Editor-in-Chief Instructions:

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

sigmafelix · 2024-04-25T17:24:06Z

@ropensci-review-bot help

ropensci-review-bot · 2024-04-25T17:24:09Z

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


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sigmafelix · 2024-04-25T17:25:25Z

@ropensci-review-bot submit response #638 (comment)

ropensci-review-bot · 2024-04-25T17:25:30Z

Couldn't find entry for chopin in the packages log

ldecicco-USGS · 2024-04-30T14:19:56Z

@ropensci-review-bot assign @beatrizmilz as editor

ropensci-review-bot · 2024-04-30T14:19:59Z

Assigned! @beatrizmilz is now the editor

beatrizmilz · 2024-05-06T01:59:38Z

Hello @sigmafelix !
Thank you for your submission. I am the editor who will be working with you on this package.

Editor checks:

Editor comments

1. Seems like the package was created in the organization called Spatiotemporal-Exposures-and-Toxicology and then was transfered to NIEHS, and some of the links in the documentation are still pointing to the old organization. Can you update them to point to the new organization, please? This might help: https://github.com/search?q=repo%3ANIEHS%2Fchopin%20Spatiotemporal-Exposures-and-Toxicology&type=code
1. The vignette Extracting Weather/Climate Geospatial Data with chopin is well detailed and informative. However, the vignette Generate computational grids can be more detailed. It would be great if you could improve that vignette with more text explaining the code and the steps.
1. I ran devtools::test() and all the tests passed. However, I noticed that there is a lot of messages from dplyr joins, because aparently there are some joins that are being done without declaring which are the key columns. This is not a problem, but it would be nice if you could add the by argument to the dplyr::**_join() functions in the code. Here is part of the messages that I got:

✔ |         41 | processing [8.1s]                                             
⠏ |          0 | tests                                                         Joining with `by = join_by(from_id)`
Joining with `by = join_by(to_id)`
Joining with `by = join_by(from_id, to_id)`
⠴ |          6 | tests                                                         Joining with `by = join_by(from_id)`
Joining with `by = join_by(to_id)`
Joining with `by = join_by(from_id, to_id)`
Joining with `by = join_by(from_id)`
Joining with `by = join_by(to_id)`
Joining with `by = join_by(from_id, to_id)`
⠙ |         12 | tests                                                         Joining with `by = join_by(from_id)`
Joining with `by = join_by(to_id, FIPS)`
Joining with `by = join_by(from_id, to_id)`
✔ |         13 | tests

1. The package has >99% of code covered by tests. 🎉

Can you please address these comments?
Thank you!

sigmafelix · 2024-05-06T17:57:30Z

@beatrizmilz I appreciate your time to review our package. I will address all your points in the revision on top of fixing some bugs we identified in the meantime and respond to you soon. Thank you.

sigmafelix · 2024-05-16T17:45:49Z

@beatrizmilz Thank you for your patience. I think I addressed all comments in the current version available in main. Please let me know if you have additional comments.

beatrizmilz · 2024-05-22T18:16:55Z

Thank you @sigmafelix !

beatrizmilz · 2024-05-22T18:17:46Z

@ropensci-review-bot seeking reviewers

ropensci-review-bot · 2024-05-22T18:17:48Z

Please add this badge to the README of your package repository:

[![Status at rOpenSci Software Peer Review](https://badges.ropensci.org/638_status.svg)](https://github.com/ropensci/software-review/issues/638)

Furthermore, if your package does not have a NEWS.md file yet, please create one to capture the changes made during the review process. See https://devguide.ropensci.org/releasing.html#news

beatrizmilz · 2024-05-22T20:16:43Z

@ropensci-review-bot check package

ropensci-review-bot · 2024-05-22T20:16:44Z

Thanks, about to send the query.

ropensci-review-bot · 2024-05-22T20:16:47Z

🚀

Editor check started

👋

ropensci-review-bot · 2024-05-22T20:46:43Z

Checks for chopin (v0.6.3.20240515)

git hash: 094a6460

✔️ 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 99.7%.
✖️ R CMD check found 1 error.
✔️ R CMD check found no warnings.

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

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	133
internal	chopin	33
internal	graphics	8
internal	stats	6
internal	utils	2
imports	terra	38
imports	sf	20
imports	dplyr	10
imports	methods	5
imports	exactextractr	3
imports	future.apply	3
imports	rlang	3
imports	igraph	2
imports	anticlust	1
imports	stars	1
suggests	callr	NA
suggests	covr	NA
suggests	DiagrammeR	NA
suggests	doFuture	NA
suggests	doParallel	NA
suggests	future	NA
suggests	future.batchtools	NA
suggests	future.callr	NA
suggests	knitr	NA
suggests	rmarkdown	NA
suggests	spatstat.random	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.

base

list (9), switch (9), c (7), lapply (7), by (6), data.frame (6), unlist (6), split (5), which (5), names (4), grepl (3), if (3), mapply (3), nrow (3), abs (2), any (2), as.integer (2), ceiling (2), class (2), expand.grid (2), log10 (2), mode (2), paste (2), round (2), rownames (2), seq (2), seq_len (2), sum (2), t (2), tryCatch (2), unique (2), args (1), as.data.frame (1), as.logical (1), as.numeric (1), as.vector (1), exp (1), for (1), formals (1), ifelse (1), intersect (1), lengths (1), pi (1), rbind (1), Reduce (1), search (1), seq_along (1), sort (1), sprintf (1), strsplit (1), suppressWarnings (1), table (1), try (1), vector (1)

terra

buffer (9), crop (8), ext (4), rast (4), distance (3), crs (2), nearby (2), project (2), crds (1), intersect (1), is.lonlat (1), nlyr (1)

chopin

dep_check (15), any_class_args (4), dep_switch (4), datamod (2), get_clip_ext (2), clip_ras_ext (1), clip_vec_ext (1), crs_check (1), ext2poly (1), extract_at_buffer_kernel (1), par_group_balanced (1)

sf

st_crs (3), st_relate (3), st_as_sf (2), st_area (1), st_as_sfc (1), st_bbox (1), st_centroid (1), st_coordinates (1), st_covered_by (1), st_geometry_type (1), st_intersection (1), st_intersects (1), st_make_grid (1), st_transform (1), st_within (1)

dplyr

left_join (6), n (2), mutate (1), summarize (1)

graphics

points (8)

stats

dist (3), quantile (3)

methods

is (3), el (2)

exactextractr

exact_extract (3)

future.apply

future_lapply (3)

rlang

inject (3)

igraph

graph_from_edgelist (2)

utils

combn (2)

anticlust

balanced_clustering (1)

stars

st_as_stars (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 7 files) and
2 authors
3 vignettes
2 internal data files
10 imported packages
33 exported functions (median 17 lines of code)
34 non-exported functions in R (median 29 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	7	45.7
files_vignettes	3	92.4
files_tests	9	89.6
loc_R	1176	72.3
loc_vignettes	831	88.0
loc_tests	1289	90.2
num_vignettes	3	94.2
data_size_total	2100956	97.8	TRUE
data_size_median	1050478	98.5	TRUE
n_fns_r	67	65.5
n_fns_r_exported	33	80.4
n_fns_r_not_exported	34	56.6
n_fns_per_file_r	7	77.9
num_params_per_fn	3	33.6
loc_per_fn_r	21	62.0
loc_per_fn_r_exp	17	40.3
loc_per_fn_r_not_exp	29	77.1
rel_whitespace_R	12	61.7
rel_whitespace_vignettes	33	90.4
rel_whitespace_tests	16	85.6
doclines_per_fn_exp	37	45.3
doclines_per_fn_not_exp	0	0.0	TRUE
fn_call_network_size	61	70.3

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

GitHub Workflow Results

id	name	conclusion	sha	run_number	date
9116757038	pages build and deployment	success	9e3af8	43	2024-05-16
9116716549	pkgdown	success	094a64	77	2024-05-16
9116716555	R-CMD-check	success	094a64	157	2024-05-16
9116716552	test-coverage-local	success	094a64	25	2024-05-16

3b. `goodpractice` results

`R CMD check` with rcmdcheck

R CMD check generated the following error:

checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘v00_good_practice_parallelization.Rmd’ using rmarkdown
--- finished re-building ‘v00_good_practice_parallelization.Rmd’

--- re-building ‘v01_par_make_gridset.Rmd’ using rmarkdown
File figures/nc-gen-points-1.png not found in resource path
Error: processing vignette 'v01_par_make_gridset.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘v01_par_make_gridset.Rmd’

--- re-building ‘v02_climate_examples.Rmd’ using rmarkdown
File figures/climate-se-states.png not found in resource path
Error: processing vignette 'v02_climate_examples.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘v02_climate_examples.Rmd’

SUMMARY: processing the following files failed:
‘v01_par_make_gridset.Rmd’ ‘v02_climate_examples.Rmd’

Error: Vignette re-building failed.
Execution halted

R CMD check generated the following note:

checking installed package size ... NOTE
installed size is 25.8Mb
sub-directories of 1Mb or more:
data 2.0Mb
extdata 23.1Mb

R CMD check generated the following check_fail:

rcmdcheck_reasonable_installed_size

Test coverage with covr

Package coverage: 99.65

Cyclocomplexity with cyclocomp

No functions have cyclocomplexity >= 15

Static code analyses with lintr

lintr found the following 2 potential issues:

message	number of times
Avoid using sapply, consider vapply instead, that's type safe	1
Lines should not be more than 80 characters. This line is 81 characters.	1

Package Versions

package	version
pkgstats	0.1.5.2
pkgcheck	0.1.2.34

Editor-in-Chief Instructions:

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

beatrizmilz · 2024-05-27T18:08:04Z

Hi @sigmafelix !
There was one error on the R CMD check: #638 (comment) .
Could you please verify that, before we proceed to add the reviewers?

Thank you!

beatrizmilz · 2024-09-23T16:53:34Z

Thank you both @robitalec and @Aariq for the second review and suggestions.

@sigmafelix Congratulations on the package approval! @robitalec and @Aariq gave more suggestions, and I would like to know if you plan to address those, and if yes, if you prefer to do it before or after transferring the repository to the account of rOpenSci.

The following comment from @Aariq seems really important to be addressed:

When I install or load_all() the package, I get the following message printed: in method for ‘[’ with signature ‘x="SpatVector",i="bbox",j="missing"’: no definition for class “bbox”. Something might be wrong with how this method is implemented.

@ropensci-review-bot approve chopin

beatrizmilz · 2024-09-24T12:27:08Z

@ropensci-review-bot approve chopin

ropensci-review-bot · 2024-09-24T12:27:11Z

Approved! Thanks @sigmafelix for submitting and @robitalec, @Aariq for your reviews! 😁

To-dos:

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

Welcome aboard! We'd love to host a post about your package - either a short introduction to it with an example for a technical audience or a longer post with some narrative about its development or something you learned, and an example of its use for a broader readership. If you are interested, consult the blog guide, and tag @ropensci/blog-editors in your reply. They will get in touch about timing and can answer any questions.

We maintain an online book with our best practice and tips, this chapter starts the 3d section that's about guidance for after onboarding (with advice on releases, package marketing, GitHub grooming); the guide also feature CRAN gotchas. Please tell us what could be improved.

Last but not least, you can volunteer as a reviewer via filling a short form.

sigmafelix · 2024-09-25T03:41:20Z

@beatrizmilz Thank you very much for approving our package! We are excited to see that chopin is included in ROpenSci packages. We sincerely appreciate the reviewers @Aariq and @robitalec for extremely helpful comments for improving chopin.

For the recent comment, we are aware of the bbox class detection error in S4 context as being pointed out by @Aariq. I speculate that this error might come from different mechanisms of setting a class to an object between S3 and S4. I think I will consult sf maintainers about this issue further before I make changes.

library(sf)
dd <- st_bbox(c(xmin = 16.1, xmax = 16.6, ymax = 48.6, ymin = 47.9), crs = st_crs(4326))
class(dd)
[1] "bbox"

setGeneric("detect_bbox", function(x){})
[1] "detect_bbox"
setMethod("detect_bbox", signature = c(x = "bbox"), function(x){class(x)})
# in method for ‘detect_bbox’ with signature ‘x="bbox"’: no definition for class “bbox”

kyle-messier · 2024-10-03T00:57:19Z

@ropensci-review-bot invite me to ropensci/chopin

ropensci-review-bot · 2024-10-03T00:57:20Z

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

@ropensci-review-bot help

kyle-messier · 2024-10-03T00:58:45Z

@ropensci-review-bot invite me to ropensci/chopin

ropensci-review-bot · 2024-10-03T00:58:46Z

Could not invite, you are not the author of the package

sigmafelix · 2024-10-03T01:07:29Z

@beatrizmilz Could you invite @kyle-messier as the co-author of the package? He has the administrator privilege of the repository to finalize the transfer of the repository to ropensci. Thank you!

kyle-messier · 2024-10-03T15:13:41Z

@ropensci-review-bot invite me to ropensci/chopin

ropensci-review-bot · 2024-10-03T15:13:44Z

Could not invite, you are not the author of the package

beatrizmilz · 2024-10-03T16:09:04Z

@beatrizmilz Could you invite @kyle-messier as the co-author of the package? He has the administrator privilege of the repository to finalize the transfer of the repository to ropensci. Thank you!

Hi @sigmafelix ! I saw your message this morning but was not sure how to proceed. I asked other editors and I'll write back soon, ok?

sigmafelix · 2024-10-04T01:19:55Z

@ropensci-review-bot invite @kyle-messier to ropensci/chopin

ropensci-review-bot · 2024-10-04T01:19:56Z

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

@ropensci-review-bot help

maelle · 2024-10-10T08:01:53Z

@sigmafelix I've now invited @kyle-messier.

Sorry for the lack of automation, it's tracked (ropensci/dev_guide#466)

sigmafelix · 2024-10-10T09:48:24Z

@maelle Thank you for figuring it out for us. I'm glad to hear that the automated invitation will be available in the future.

kyle-messier · 2024-10-10T13:23:35Z

@ropensci-review-bot invite me to ropensci/chopin

ropensci-review-bot · 2024-10-10T13:23:38Z

Could not invite, you are not the author of the package

sigmafelix · 2024-10-10T13:29:16Z

@maelle Could you check if the invitation was sent or processed? I couldn't find @kyle-messier on the member list of ropensci/chopin team.

kyle-messier · 2024-10-10T13:30:03Z

@maelle @beatrizmilz I am still not able to transfer the repository. It could be due to setting on our NIEHS GitHub enterprise. Before I ping our enterprise managers, could you confirm whether I should be able to see github.com/ropensci/chopin ? It is currently 404 not found for me.

maelle · 2024-10-10T14:03:01Z

@kyle-messier you should have received an invitation to https://github.com/orgs/ropensci/teams/chopin, I still see you as pending member. Can you check your email inbox?

On another hand it might be the case that you have to first transfer the repo to your personal account then to ropensci. Repo transfers are sometimes clunky in this way. In any case, official docs https://docs.github.com/en/repositories/creating-and-managing-repositories/transferring-a-repository#transferring-a-repository-owned-by-your-organization

kyle-messier · 2024-10-10T14:40:09Z

I apologize @maelle but I do not see an invitation email nor anything on my github account

maelle · 2024-10-11T04:53:32Z

I've just deleted the invitation and regenerated it, did it help at all?

kyle-messier · 2024-10-11T12:02:52Z

Yes, I received that invitation, thank you! It appears the repo transfer is now in process!

maelle · 2024-10-11T12:06:42Z

Yay, thanks for your patience 🎉

ldecicco-USGS added the 0/editorial-team-prep label Apr 25, 2024

ropensci-review-bot assigned beatrizmilz Apr 30, 2024

ropensci-review-bot added 1/editor-checks and removed 0/editorial-team-prep labels Apr 30, 2024

ropensci-review-bot added 2/seeking-reviewer(s) and removed 1/editor-checks labels May 22, 2024

ropensci-review-bot added 6/approved and removed 5/awaiting-reviewer(s)-response labels Sep 24, 2024

ropensci-review-bot closed this as completed Sep 24, 2024

sigmafelix mentioned this issue Sep 28, 2024

0.8.0 development roadmap: addressing ROpenSci review ropensci/chopin#85

Closed

49 tasks

sigmafelix mentioned this issue Oct 12, 2024

0.8.3 ropensci/chopin#104

Merged

chopin: Computation for Climate and Health research On Parallelized INfrastructure #638

chopin: Computation for Climate and Health research On Parallelized INfrastructure #638

Comments

sigmafelix commented Apr 24, 2024 • edited by ropensci-review-bot Loading

Scope

Technical checks

Publication options

Code of conduct

ropensci-review-bot commented Apr 24, 2024

ropensci-review-bot commented Apr 24, 2024

ropensci-review-bot commented Apr 24, 2024

Checks for chopin (v0.6.2.20240423)

1. Package Dependencies

2. Statistical Properties

2a. Network visualisation

3. 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:

sigmafelix commented Apr 24, 2024

ropensci-review-bot commented Apr 24, 2024

ropensci-review-bot commented Apr 24, 2024

ropensci-review-bot commented Apr 24, 2024

Checks for chopin (v0.6.2.20240423)

1. Package Dependencies

2. Statistical Properties

2a. Network visualisation

3. 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:

sigmafelix commented Apr 25, 2024

ropensci-review-bot commented Apr 25, 2024

sigmafelix commented Apr 25, 2024

ropensci-review-bot commented Apr 25, 2024

ldecicco-USGS commented Apr 30, 2024

ropensci-review-bot commented Apr 30, 2024

beatrizmilz commented May 6, 2024

Editor checks:

Editor comments

sigmafelix commented May 6, 2024

sigmafelix commented May 16, 2024

beatrizmilz commented May 22, 2024

beatrizmilz commented May 22, 2024

ropensci-review-bot commented May 22, 2024

beatrizmilz commented May 22, 2024

ropensci-review-bot commented May 22, 2024

ropensci-review-bot commented May 22, 2024

ropensci-review-bot commented May 22, 2024

Checks for chopin (v0.6.3.20240515)

1. Package Dependencies

2. Statistical Properties

2a. Network visualisation

3. 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:

beatrizmilz commented May 27, 2024

beatrizmilz commented Sep 23, 2024

beatrizmilz commented Sep 24, 2024

ropensci-review-bot commented Sep 24, 2024

sigmafelix commented Sep 25, 2024

kyle-messier commented Oct 3, 2024 • edited Loading

ropensci-review-bot commented Oct 3, 2024

kyle-messier commented Oct 3, 2024

ropensci-review-bot commented Oct 3, 2024

sigmafelix commented Oct 3, 2024

kyle-messier commented Oct 3, 2024

`chopin`: Computation for Climate and Health research On Parallelized INfrastructure #638

`chopin`: Computation for Climate and Health research On Parallelized INfrastructure #638

sigmafelix commented Apr 24, 2024 •

edited by ropensci-review-bot

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3. `goodpractice` and other checks

3b. `goodpractice` results

`R CMD check` with rcmdcheck

3. `goodpractice` and other checks

3b. `goodpractice` results

`R CMD check` with rcmdcheck

3. `goodpractice` and other checks

3b. `goodpractice` results

`R CMD check` with rcmdcheck

kyle-messier commented Oct 3, 2024 •

edited

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