quadkeyr: Tools for converting QuadKeys (Microsoft's Bing Maps Tile System) into raster images #619
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Thanks for submitting to rOpenSci, our editors and @ropensci-review-bot will reply soon. Type |
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🚀 Editor check started 👋 |
Checks for quadkeyr (v0.0.0.9000)git hash: 8f9fc6c2
Important: All failing checks above must be addressed prior to proceeding (Checks marked with 👀 may be optionally addressed.) Package License: MIT + file LICENSE 1. Package DependenciesDetails 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.
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. baselist (22), return (20), c (16), for (11), data.frame (10), nrow (5), seq_len (5), min (4), as.character (3), max (3), nchar (3), pi (3), seq (3), sign (3), abs (2), as.integer (2), as.numeric (2), by (2), file (2), floor (2), options (2), rbind (2), sum (2), unique (2), version (2), as.Date (1), atan (1), character (1), class (1), colnames (1), exp (1), is.na (1), length (1), list.files (1), log (1), ncol (1), paste (1), paste0 (1), rep (1), rev (1), rownames (1), seq_along (1), sin (1), strsplit (1), subset (1), t (1) quadkeyrmapsize (9), clip (7), pixelXY_to_latlong (4), quadkey_to_tileXY (4), create_qk_grid (3), missing_combinations (3), pixelXY_to_tileXY (3), tileXY_to_pixelXY (3), complete_grid_for_polygons (2), create_raster (2), extract_qk_coord (2), latlong_to_pixelXY (2), quadkey_to_latlong (2), apply_weekly_lag (1), extract_tile_coord (1), format_data (1), grid_to_polygon (1), ground_res (1), latlong_to_quadkey (1), mapscale (1), polygon_to_raster (1), qkmap_app (1), read_all_files (1), regular_qk_grid (1), server (1), tileXY_to_quadkey (1) utilsdata (40) sfst_as_sf (6), st_bbox (2), st_sf (2) bslibbs_theme (2), font_google (2), sidebar (2), layout_sidebar (1), page_navbar (1) dplyrmutate (5), anti_join (2), lag (1) graphicsgrid (4), title (1) starsst_as_stars (1), st_rasterize (1), write_stars (1) leafletaddMarkers (1), setView (1) shinyeventReactive (2) purrrmap_dfr (1) statsvar (1) NOTE: Some imported packages appear to have no associated function calls; please ensure with author that these 'Imports' are listed appropriately. 2. Statistical PropertiesThis 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:
Statistical properties of package structure as distributional percentiles in relation to all current CRAN packages
All parameters are explained as tooltips in the locally-rendered HTML version of this report generated by the The final measure (
2a. Network visualisationClick to see the interactive network visualisation of calls between objects in package 3.
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| id | name | conclusion | sha | run_number | date |
|---|---|---|---|---|---|
| 7105875366 | pages build and deployment | success | 22b70a | 11 | 2023-12-05 |
| 7105846578 | pkgdown | success | 65762e | 10 | 2023-12-05 |
| 7105846580 | R-CMD-check | success | 65762e | 10 | 2023-12-05 |
| 7105846581 | test-coverage | success | 65762e | 10 | 2023-12-05 |
3b. goodpractice results
R CMD check with rcmdcheck
R CMD check generated the following error:
- Error in proc$get_built_file() : Build process failed
Test coverage with covr
Package coverage: 61.94
The following files are not completely covered by tests:
| file | coverage |
|---|---|
| R/polygon_to_raster.R | 0% |
| R/qkmap_visualizer.R | 0% |
| R/read_and_format_files.R | 62.16% |
Cyclocomplexity with cyclocomp
Error : Build failed, unknown error, standard output:
- checking for file ‘quadkeyr/DESCRIPTION’ ... OK
- preparing ‘quadkeyr’:
- checking DESCRIPTION meta-information ... OK
- installing the package to build vignettes
- creating vignettes ... ERROR
--- re-building ‘create_rasters_from_grid.Rmd’ using rmarkdown
--- finished re-building ‘create_rasters_from_grid.Rmd’
--- re-building ‘get_grid_from_quadkeys.Rmd’ using rmarkdown
File figure/unnamed-chunk-2-1.png not found in resource path
Error: processing vignette 'get_grid_from_quadkeys.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘get_grid_from_quadkeys.Rmd’
--- re-building ‘quadkey_conversion.Rmd’ using rmarkdown
--- finished re-building ‘quadkey_conversion.Rmd’
SUMMARY: processing the following file failed:
‘get_grid_from_quadkeys.Rmd’
Error: Vignette re-building failed.
Execution halted
Static code analyses with lintr
lintr found the following 57 potential issues:
| message | number of times |
|---|---|
| Avoid library() and require() calls in packages | 8 |
| Lines should not be more than 80 characters. | 28 |
| Use <-, not =, for assignment. | 21 |
4. Other Checks
Details of other checks (click to open)
✖️ The following 3 function names are duplicated in other packages:
-
clipfrom CUFF, ramify
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create_rasterfrom SpatialKDE
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format_datafrom GCalcium, popbayes
Package Versions
| package | version |
|---|---|
| pkgstats | 0.1.3.9 |
| pkgcheck | 0.1.2.11 |
Editor-in-Chief Instructions:
Processing may not proceed until the items marked with ✖️ have been resolved.
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@flor14 Thank you for the submission and apologies for the few days that went by prior to my response. Had a high priority thing at work that I had to focus on! I will take a closer look at your submission early next week. One thing we will need to get figured out is the R CMD Check failures that our build system is seeing. I noticed that the builds on your repo seem to be passing just fine. Stay tuned and thanks again for the submission. |
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Thank you @jhollist, don't worry. I have increased the code coverage to 84% adding tests for the Shiny app, so that is solved. About the checks, I am unsure what could be the issue, as all the tests are passing for me as you can see in the repo, but I will try to figure it out. |
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@jhollist the RMD checks are failing because there was missing this image, which now is included in the repo: https://github.com/Fernandez-Lab-WSU/quadkeyr/blob/main/figure/unnamed-chunk-2-1.png I hope that if you run the RMD Checks again, they should be ✅ without issues. |
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@ropensci-review-bot check package |
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Thanks, about to send the query. |
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🚀 Editor check started 👋 |
Checks for quadkeyr (v0.0.0.9000)git hash: 0425b02e
Important: All failing checks above must be addressed prior to proceeding (Checks marked with 👀 may be optionally addressed.) Package License: MIT + file LICENSE 1. Package DependenciesDetails 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.
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. NOTE: No imported packages appear to have associated function calls; please ensure with author that these 'Imports' are listed appropriately. 2. Statistical PropertiesThis 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:
Statistical properties of package structure as distributional percentiles in relation to all current CRAN packages
All parameters are explained as tooltips in the locally-rendered HTML version of this report generated by the The final measure (
2a. Network visualisationClick to see the interactive network visualisation of calls between objects in package 3.
|
| id | name | conclusion | sha | run_number | date |
|---|---|---|---|---|---|
| 7161851741 | pages build and deployment | success | 7fb7aa | 20 | 2023-12-11 |
| 7161834160 | pkgdown | success | 0425b0 | 19 | 2023-12-11 |
| 7161834165 | R-CMD-check | success | 0425b0 | 19 | 2023-12-11 |
| 7161834161 | test-coverage | success | 0425b0 | 19 | 2023-12-11 |
3b. goodpractice results
R CMD check with rcmdcheck
R CMD check generated the following notes:
- checking installed package size ... NOTE
installed size is 6.0Mb
sub-directories of 1Mb or more:
app 1.5Mb
data 2.3Mb
doc 1.8Mb - checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘bslib’ ‘DT’ ‘ggplot2’ ‘leaflet’ ‘rnaturalearth’ ‘tidyr’ ‘viridis’
All declared Imports should be used. - checking R code for possible problems ... NOTE
apply_weekly_lag: no visible binding for global variable ‘.data’
create_qk_grid: no visible binding for global variable ‘.data’
grid_to_polygon: no visible binding for global variable ‘.data’
missing_combinations: no visible binding for global variable ‘.data’
polygon_to_raster: no visible binding for global variable ‘.data’
Undefined global functions or variables:
.data
R CMD check generated the following check_fails:
- rcmdcheck_imports_not_imported_from
- rcmdcheck_undefined_globals
- rcmdcheck_reasonable_installed_size
Test coverage with covr
Package coverage: 83.77
Cyclocomplexity with cyclocomp
The following function have cyclocomplexity >= 15:
| function | cyclocomplexity |
|---|---|
| create_qk_grid | 18 |
Static code analyses with lintr
lintr found the following 73 potential issues:
| message | number of times |
|---|---|
| Avoid library() and require() calls in packages | 15 |
| Lines should not be more than 80 characters. | 29 |
| Use <-, not =, for assignment. | 29 |
4. Other Checks
Details of other checks (click to open)
✖️ The following 3 function names are duplicated in other packages:
-
clipfrom CUFF, ramify
-
create_rasterfrom SpatialKDE
-
format_datafrom GCalcium, popbayes
Package Versions
| package | version |
|---|---|
| pkgstats | 0.1.3.9 |
| pkgcheck | 0.1.2.11 |
Editor-in-Chief Instructions:
Processing may not proceed until the items marked with ✖️ have been resolved.
|
@flor14 Thanks for tracking down that issue! That was really helpful. Couple of thoughts for you. 1.) I re-ran the checks and the only thing that comes up now is related to the new function you added, In the meantime I will look closer at the package and vignettes. |
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Thank you @jhollist
Thank you |
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@flor14 Sounds good. Just ping me again here once everything is working again. I have taken a closer look and I think quadkeyr is ready to be passed on to a handling editor. I will do that as soon as you get the changes pushed. Cheers, |
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@jhollist |
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@ropensci-review-bot check package |
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Thanks, about to send the query. |
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🚀 Editor check started 👋 |
Checks for quadkeyr (v0.0.0.9000)git hash: 10376c70
(Checks marked with 👀 may be optionally addressed.) Package License: MIT + file LICENSE 1. Package DependenciesDetails 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.
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. baselist (18), return (18), c (16), for (11), data.frame (9), nrow (5), seq_len (5), min (3), nchar (3), pi (3), seq (3), sign (3), abs (2), as.integer (2), by (2), file (2), floor (2), max (2), rbind (2), sum (2), unique (2), as.character (1), as.Date (1), as.numeric (1), atan (1), character (1), colnames (1), exp (1), is.na (1), length (1), list.files (1), log (1), paste0 (1), rev (1), seq_along (1), sin (1), strsplit (1), subset (1), system.file (1) quadkeyrclip (7), mapsize (6), missing_combinations (3), pixelXY_to_latlong (3), pixelXY_to_tileXY (3), quadkey_to_tileXY (3), complete_grid_for_polygons (2), create_qk_grid (2), create_raster (2), latlong_to_pixelXY (2), quadkey_to_latlong (2), tileXY_to_pixelXY (2), apply_weekly_lag (1), extract_qk_coord (1), extract_tile_coord (1), format_data (1), grid_to_polygon (1), ground_res (1), latlong_to_quadkey (1), mapscale (1), polygon_to_raster (1), qkmap_app (1), tileXY_to_quadkey (1) utilsdata (35) sfst_as_sf (6), st_bbox (2), st_sf (2) dplyrmutate (5), anti_join (2), all_of (1), lag (1) graphicsgrid (3) starsst_as_stars (1), st_rasterize (1), write_stars (1) purrrmap_dfr (1) statsvar (1) NOTE: Some imported packages appear to have no associated function calls; please ensure with author that these 'Imports' are listed appropriately. 2. Statistical PropertiesThis 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:
Statistical properties of package structure as distributional percentiles in relation to all current CRAN packages
All parameters are explained as tooltips in the locally-rendered HTML version of this report generated by the The final measure (
2a. Network visualisationClick to see the interactive network visualisation of calls between objects in package 3.
|
| id | name | conclusion | sha | run_number | date |
|---|---|---|---|---|---|
| 7183862151 | pages build and deployment | success | a8f312 | 25 | 2023-12-12 |
| 7183832573 | pkgcheck | success | 10376c | 4 | 2023-12-12 |
| 7183832572 | pkgdown | success | 10376c | 24 | 2023-12-12 |
| 7183832584 | R-CMD-check | success | 10376c | 24 | 2023-12-12 |
| 7183832577 | test-coverage | success | 10376c | 24 | 2023-12-12 |
3b. goodpractice results
R CMD check with rcmdcheck
R CMD check generated the following notes:
- checking installed package size ... NOTE
installed size is 6.0Mb
sub-directories of 1Mb or more:
app 1.5Mb
data 2.3Mb
doc 1.8Mb - checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘bslib’ ‘DT’ ‘ggplot2’ ‘leaflet’ ‘rnaturalearth’ ‘tidyr’ ‘viridis’
All declared Imports should be used. - checking R code for possible problems ... NOTE
apply_weekly_lag: no visible binding for global variable ‘.data’
create_qk_grid: no visible binding for global variable ‘.data’
grid_to_polygon: no visible binding for global variable ‘.data’
missing_combinations: no visible binding for global variable ‘.data’
polygon_to_raster: no visible binding for global variable ‘.data’
Undefined global functions or variables:
.data
R CMD check generated the following check_fails:
- rcmdcheck_imports_not_imported_from
- rcmdcheck_undefined_globals
- rcmdcheck_reasonable_installed_size
Test coverage with covr
Package coverage: 83.9
Cyclocomplexity with cyclocomp
The following function have cyclocomplexity >= 15:
| function | cyclocomplexity |
|---|---|
| create_qk_grid | 18 |
Static code analyses with lintr
lintr found the following 48 potential issues:
| message | number of times |
|---|---|
| Avoid library() and require() calls in packages | 15 |
| Lines should not be more than 80 characters. | 12 |
| Use <-, not =, for assignment. | 21 |
4. Other Checks
Details of other checks (click to open)
✖️ The following 3 function names are duplicated in other packages:
-
clipfrom CUFF, ramify
-
create_rasterfrom SpatialKDE
-
format_datafrom GCalcium, popbayes
Package Versions
| package | version |
|---|---|
| pkgstats | 0.1.3.9 |
| pkgcheck | 0.1.2.11 |
Editor-in-Chief Instructions:
This package is in top shape and may be passed on to a handling editor
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@flor14, looks like we are all set. Are you ready to have me pass this on the a handling editor or do you anticipate a few more changes? |
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Yes, I think it is ready. The issue was that my changes were passing the |
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Fantastic! I'll work on getting the handling editor lined up.
…On Wed, Dec 13, 2023 at 2:19 PM flor14 ***@***.***> wrote:
Yes, I think it is ready. The issue was that my changes were passing the R
CMD checks, so I didn't anticipate issues before the review started. Now
I learned that pkgcheck works differently and seems to be more strict.
If there is any new change (even if it is small) I will retain it to make
all of them together after the review, to avoid any potential issue.
Thank you @jhollist <https://github.com/jhollist>
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You are receiving this because you were mentioned.Message ID:
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@flor14 I have found a handling editor (thanks @emilyriederer!). There may be a delay of a week or two before she is able to get started in earnest on this because of a hectic end of year schedule. |
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@ropensci-review-bot assign @emilyriederer as editor |
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Assigned! @emilyriederer is now the editor |
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Thank you @jhollist and happy holidays |
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Happy holidays to you as well! |
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Hi @flor14 ! It's great to meet you. Thanks for your submission. As @jhollist mentioned, I may not be able to engage more fully until next week, but I thought I'd send over a few preliminary observations. I think this is a compelling project and is close to being ready for reviewers. On a cursory review of the automated outputs, I just had a few small requests to touch up before we hand this off:
Thank you! |
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Hello, @emilyriederer, nice to meet you as well. Including more high-level documentation is a good idea, I have been paying attention mostly to the function documentation so far. |
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Thank you @flor14 ! Your dedication to this ambitious project is very impressive and its great to see all these updates. I know we are actively reviewing packages now in multiple languages, so I will check in with the editorial team regarding best practices for maintaing versions of both. @mpaulacaldas and @vincentvanhees - can you please take a pass through all these wonderful updates and confirm your approval with this template? |
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Hi there @mpaulacaldas and @vincentvanhees - just a reminder, at your convenience, could you please review @flor14 's updates and confirm your approval with this template? Per our reviewer guide, the goal of this stage is to ensure you feel your comments have been sufficiently addressed |
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Sorry, I have been crazily occupied, it is on my to do list for the weekend. |
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For the past few days, I have been using
I will not merge these changes because I believe the review has already been addressed, and I don't want to create confusion. However, if after reading the review you still have concerns about these specific functions, you can check that branch. Thank you. |
Reviewer ResponseGreat job @flor14! My comments have been addressed satisfactory. A few remarks for your consideration:
Final approval (post-review)
Estimated hours spent reviewing: 1 |
Reviewer ResponseThank you @flor14 for all of the detailed and careful changes you made in this last round. With these, I believe you have addressed my key comments in a satisfactory way, and I am happy for to recommend approval. Like Vincent, I leave here a couple of remarks for future consideration:
Final approval (post-review)
Estimated hours spent reviewing: 1 |
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Thank you @mpaulacaldas and @vincentvanhees I will change what you are saying @mpaulacaldas tomorrow morning. The |
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Thank you, @mpaulacaldas and @vincentvanhees for your continued, thoughtful engagement! We really appreciate your support @flor14 - please give me a tag after you've made the last tweaks based on @mpaulacaldas 's feedback, and I think we will be ready to approve |
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I am on hold with this because the researcher I am working with is asking the university about the copyright. Also, I will ask a question in ROpenSci Slack regarding how to specify the authorship, in case you have an opinion about it. |
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My understanding is that if you work for an institute then usually they are the copyright holder and not the external funder that funded the research.
You can just do: EDIT: I now saw the question you posted which is a of a different nature. Agree with Noam that minor contributors do not need to be code contributions, and auth should be reserved for those who made significant contributions. |
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Thank you @vincentvanhees, you are always ready to answer. |
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The review is finished, I have updated the authors, the Remaining questions:
Thank you |
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thanks, there is a typo in my name, it is "van Hees" not "Van Hess". |
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Oh, I will fix it before the end of the day.
…On Thu, Mar 14, 2024 at 12:06 AM Vincent van Hees ***@***.***> wrote:
thanks, there is a typo in my name is "van Hees" not "Van Hess".
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You are receiving this because you were mentioned.Message ID:
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Done! I modified the release so there is not a version with your name incorrect. |
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Congratulations @flor14 ! Thank you so much for your dedication to this package |
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@ropensci-review-bot approve quadkeyr |
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Approved! Thanks @flor14 for submitting and @mpaulacaldas, @vincentvanhees for your reviews! 😁 To-dos:
Should you want to acknowledge your reviewers in your package DESCRIPTION, you can do so by making them 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. |
ropensci-review-bot
added
6/approved
and removed
5/awaiting-reviewer(s)-response
labels
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A few additional notes @flor14 :
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I will jump here to add that we are discussing multilingual documentation and publishing and sharing projects, ideas, and progress in the #multilingual channel in our Slack. 😃 |
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@ropensci-review-bot finalize transfer of quadkeyr |
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Transfer completed. |
Date accepted: 2024-03-14
Submitting Author Name: Florencia D'Andrea
Submitting Author Github Handle: @flor14
Repository: https://github.com/Fernandez-Lab-WSU/quadkeyr
Version submitted:
Submission type: Standard
Editor: @emilyriederer
Reviewers: @mpaulacaldas, @vincentvanhees
Archive: TBD
Version accepted: TBD
Language: en
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.):
Explain how and why the package falls under these categories (briefly, 1-2 sentences):
🗺️ The package offers tools to analyze data reported by QuadKey and convert it to raster images. QuadKeys are strings that encode information about map coordinates and the level of detail of the Bing Maps Tile System.
Anyone trying to analyze data reported in this format. Facebook mobility data, for example, can be reported by QuadKey. This package could help this StackOverflow user or this other one.
The closer R package dealing with this type of data is
slippymathwhich has a more general objective.quadkeyris only based on Microsoft Bing Maps Tile System documentation and it is focused on raster creation.You can read a list of packages with similar functions in the README references section.
✅
✖️
pkgcheckitems which your package is unable to pass.👍🏼 I have fixed all the
pkgcheckcomments.Technical checks
Confirm each of the following by checking the box.
1. The package coverage is less than 75% but I think that the main reason for that is that the Shiny app included doesn't have tests yet. The backend of that app is all the functions that are tested.
2. There are also missing 2 notes that still appear after running
check. The functionspolygon_to_rasterandformat_datadon't have valid roxygen2 examples, andpolygon_to_rasterdon't have tests. At least a warning is missing increate_rasterand some functions could be potentially improved in efficiency and documentation (I would like to improve the technical terminology). Despite this, I think it is a good moment to get some feedback as I will be using the package in the next weeks and I will be available to update it.This package:
📔 There are 3 vignettes, one for each major goal of the package. There are links on the
READMEto each of them, not only in thepkgdownsite. They grow in complexity from goals 1 to 3. I think reading them in order should give a good idea about the package's core functionalities and logic.Publication options
❓ Probably yes? After all the packages that were deleted from CRAN, I would appreciate comments about this. I was careful to use as dependencies only
starsandsf, which are packages that will continue to be active.MEE Options
Code of conduct
Thank you!
The text was updated successfully, but these errors were encountered: