quadkeyr: Tools for converting QuadKeys (Microsoft's Bing Maps Tile System) into raster images

[flor14]

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

---

• Paste the full DESCRIPTION file inside a code block below:

Package: quadkeyr
Title: Tools for converting QuadKeys used in Microsoft's Bing Maps Tile System into raster images
Version: 0.0.0.9000
Authors@R: 
    person(given = "Florencia",
           family = "D'Andrea", 
           email = "florencia.dandrea@gmail.com", 
           role = c("aut", "cre"),
           comment = c(ORCID = "0000-0002-0041-097X"))
Description: quadkeyr enables the generation of raster images based on QuadKeys, facilitating efficient integration of Bing Maps data into R workflows. In particular, quadkeyr provides support to process and analyze Facebook mobility datasets within the R environment.
License: MIT + file LICENSE
URL: https://fernandez-lab-wsu.github.io/quadkeyr/, https://github.com/Fernandez-Lab-WSU/quadkeyr
BugReports: https://github.com/Fernandez-Lab-WSU/quadkeyr/issues
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.1
Suggests: 
    knitr,
    rmarkdown,
    shinytest2,
    testthat (>= 3.1.10)
VignetteBuilder: knitr
Depends: 
    R (>= 2.10)
LazyData: true
Imports: 
    bslib (>= 0.5.1),
    dplyr (>= 1.1.2),
    DT (>= 0.27),
    ggplot2 (>= 3.4.3),
    leaflet (>= 2.2.0),
    lubridate (>= 1.9.2),
    purrr (>= 1.0.1),
    readr (>= 2.1.4),
    rnaturalearth (>= 0.3.2),
    sf (>= 1.0.14),
    shiny (>= 1.7.4),
    stars (>= 0.6.2),
    tidyr (>= 1.3.0),
    viridis (>= 0.6.4)

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):

🗺️ 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.

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

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.

• Are there other R packages that accomplish the same thing? If so, how does yours differ or meet our criteria for best-in-category?

The closer R package dealing with this type of data is slippymath which has a more general objective. quadkeyr is 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.

• (If applicable) Does your package comply with our guidance around Ethics, Data Privacy and Human Subjects Research?
  ✅
• 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.
  ✖️
• Explain reasons for any pkgcheck items which your package is unable to pass.
  👍🏼 I have fixed all the pkgcheck comments.

Technical checks

Confirm each of the following by checking the box.

• I have read the rOpenSci packaging guide.
  ⚠️ Yes, and I have to mention:
  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 functions polygon_to_raster and format_data don't have valid roxygen2 examples, and polygon_to_raster don't have tests. At least a warning is missing in create_raster and 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.
• 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.
  📔 There are 3 vignettes, one for each major goal of the package. There are links on the README to each of them, not only in the pkgdown site. 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.
• has a test suite.
• has continuous integration, including reporting of test coverage.

Publication options

• Do you intend for this package to go on CRAN?
  ❓ 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 stars and sf, which are packages that will continue to be active.
• 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.
• You intend to archive the code for the package in a long-term repository which meets the requirements of the journal (see MEE's Policy on Publishing Code)
• (Scope: Do consider MEE's Aims and Scope for your manuscript. We make no guarantee that your manuscript will be within MEE scope.)
• (Although not required, we strongly recommend having a full manuscript prepared when you submit here.)
• (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!

[ropensci-review-bot]

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

[ropensci-review-bot]

🚀

Editor check started

👋

[ropensci-review-bot]

Checks for quadkeyr (v0.0.0.9000)

git hash: 8f9fc6c2

• ✔️ 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 61.9% (should be at least 75%).
• ✖️ R CMD check process failed with message: 'Build process failed'.
• 👀 Function names are duplicated in other packages

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 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	154
internal	quadkeyr	59
internal	utils	40
internal	graphics	5
internal	stats	1
imports	sf	10
imports	bslib	8
imports	dplyr	8
imports	stars	3
imports	leaflet	2
imports	shiny	2
imports	purrr	1
imports	DT	NA
imports	ggplot2	NA
imports	lubridate	NA
imports	readr	NA
imports	rnaturalearth	NA
imports	tidyr	NA
imports	viridis	NA
suggests	knitr	NA
suggests	rmarkdown	NA
suggests	shinytest2	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(<path/to/repo>)', and examining the 'external_calls' table.

base

list (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)

quadkeyr

mapsize (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)

utils

data (40)

sf

st_as_sf (6), st_bbox (2), st_sf (2)

bslib

bs_theme (2), font_google (2), sidebar (2), layout_sidebar (1), page_navbar (1)

dplyr

mutate (5), anti_join (2), lag (1)

graphics

grid (4), title (1)

stars

st_as_stars (1), st_rasterize (1), write_stars (1)

leaflet

addMarkers (1), setView (1)

shiny

eventReactive (2)

purrr

map_dfr (1)

stats

var (1)

NOTE: Some imported packages appear to have no associated function calls; please ensure with author that these 'Imports' are listed appropriately.

---

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 13 files) and
• 1 authors
• 3 vignettes
• 2 internal data files
• 14 imported packages
• 24 exported functions (median 13 lines of code)
• 27 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	13	68.2
files_vignettes	3	92.4
files_tests	13	93.3
loc_R	556	50.8
loc_vignettes	349	68.4
loc_tests	419	71.4
num_vignettes	3	94.2
data_size_total	2037768	97.7	TRUE
data_size_median	1018884	98.5	TRUE
n_fns_r	51	57.3
n_fns_r_exported	24	72.5
n_fns_r_not_exported	27	49.7
n_fns_per_file_r	2	39.8
num_params_per_fn	2	11.9
loc_per_fn_r	19	57.3
loc_per_fn_r_exp	13	30.5
loc_per_fn_r_not_exp	29	77.1
rel_whitespace_R	48	77.5
rel_whitespace_vignettes	45	78.5
rel_whitespace_tests	28	75.7
doclines_per_fn_exp	21	15.7
doclines_per_fn_not_exp	0	0.0	TRUE
fn_call_network_size	52	67.1

---

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
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:

1. 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:

• • clip from CUFF, ramify
• • create_raster from SpatialKDE
• • format_data from 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.

[jhollist]

@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.

[flor14]

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.

[flor14]

@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
This is the error that the bot reported:

    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

I hope that if you run the RMD Checks again, they should be ✅ without issues.
Also, I will continue using the package these days and probably improve things, let me know if you want me to do a first release for the review.

[jhollist]

@ropensci-review-bot check package

[ropensci-review-bot]

Thanks, about to send the query.

[ropensci-review-bot]

🚀

Editor check started

👋

[ropensci-review-bot]

Checks for quadkeyr (v0.0.0.9000)

git hash: 0425b02e

• ✔️ Package name is available
• ✔️ has a 'codemeta.json' file.
• ✔️ has a 'contributing' file.
• ✖️ The following function has no documented return value: [qkmap_app]
• ✔️ uses 'roxygen2'.
• ✔️ 'DESCRIPTION' has a URL field.
• ✔️ 'DESCRIPTION' has a BugReports field.
• ✔️ Package has at least one HTML vignette
• ✖️ These functions do not have examples: [qkmap_app].
• ✔️ Package has continuous integration checks.
• ✔️ Package coverage is 83.8%.
• ✔️ R CMD check found no errors.
• ✔️ R CMD check found no warnings.
• 👀 Function names are duplicated in other packages

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 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
imports	bslib	NA
imports	dplyr	NA
imports	DT	NA
imports	ggplot2	NA
imports	leaflet	NA
imports	lubridate	NA
imports	purrr	NA
imports	readr	NA
imports	rnaturalearth	NA
imports	sf	NA
imports	shiny	NA
imports	stars	NA
imports	tidyr	NA
imports	viridis	NA
suggests	knitr	NA
suggests	rmarkdown	NA
suggests	shinytest2	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(<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 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 13 files) and
• 1 authors
• 3 vignettes
• 2 internal data files
• 14 imported packages
• 25 exported functions (median 12 lines of code)
• no non-exported function in R (median 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	13	68.2
files_vignettes	3	92.4
files_tests	14	93.8
loc_R	439	43.4
loc_vignettes	450	75.5
loc_tests	424	71.6
num_vignettes	3	94.2
data_size_total	2037768	97.7	TRUE
data_size_median	1018884	98.5	TRUE
n_fns_r	25	34.7
n_fns_r_exported	25	73.6
n_fns_r_not_exported	0	0.0	TRUE
n_fns_per_file_r	2	38.7
num_params_per_fn	2	11.9
loc_per_fn_r	12	36.1
loc_per_fn_r_exp	12	27.7
rel_whitespace_R	52	74.2
rel_whitespace_vignettes	37	80.0
rel_whitespace_tests	29	76.2
doclines_per_fn_exp	21	15.7
fn_call_network_size	0	0.0	TRUE

---

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
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:

1. 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
2. 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.
3. 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:

1. rcmdcheck_imports_not_imported_from
2. rcmdcheck_undefined_globals
3. 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:

• • clip from CUFF, ramify
• • create_raster from SpatialKDE
• • format_data from 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.

[jhollist]

@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, qkmap_app. I am guessing you are still in progress on that.
2.) If you are going to be working on the package in the next few days I would prefer to see you reach a somewhat stable release that we can use as the basis for the review.
3.) If you want to run the checks on your own, you can use the action at https://github.com/ropensci-review-tools/pkgcheck-action.

In the meantime I will look closer at the package and vignettes.

[flor14]

Thank you @jhollist

1. qkmap_app is a simple function that calls the app from inst/ and it has examples, so I will try to see what that error means in the following days.
2. I won't be working on the package, but I will be heavily using it. And I would probably like to make changes. Let's do this: after I fix the problem with qkmap_app I will not push more changes.
3. Will do it and let you know when everything is working again.

Thank you

[jhollist]

@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,
Jeff

[flor14]

@jhollist pkgcheck is passing now, I have added the GitHub action to the repository.

[jhollist]

@ropensci-review-bot check package