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Submission of naijR 0.6.1 for review under the rOpenSci Champions Program #600

Closed BroVic closed 7 months ago

BroVic commented 10 months ago

Date accepted: 2023-12-02

Submitting Author Name: Victor Ordu Submitting Author Github Handle: !--author1-->@BroVic<!--end-author1--

Other Package Authors Github handles: (comma separated, delete if none) Repository: https://github.com/BroVic/naijR

Version submitted: 0.6.1

Submission type: Standard

Editor: !--editor-->@emilyriederer<!--end-editor--

Reviewers: @mcsiple, @cagrigokcek

Archive: TBD Version accepted: TBD Language: en

Package: naijR
Type: Package
Title: Operations to Ease Data Analyses Specific to Nigeria
Version: 0.6.1
Depends: R (>= 3.6)
Imports:
    RColorBrewer (>= 1.1.2),
    cli (>= 3.6.0),
    lifecycle (>= 0.2.0),
    grDevices,
    graphics,
    mapdata (>= 2.3.0),
    maps (>= 3.3.0),
    rlang (>= 0.4.0),
    sf (>= 1.0.13),
    stats,
    stringi (>= 1.7.6),
    utils
Suggests: 
    ISOcodes,
    covr,
    here,
    knitr,
    purrr,
    readxl,
    rmarkdown,
    testthat (>= 3.0.0),
    usethis
Authors@R: person("Victor", "Ordu", 
              email = "victorordu@outlook.com",
              role = c("aut", "cre"),
              comment = c(ORCID = "0000-0003-3716-0668"))
Description: A set of convenience functions as well as geographical/political
  data about Nigeria, aimed at simplifying work with data and information that
  are specific to the country.
License: GPL-3
LazyData: TRUE
Encoding: UTF-8
RoxygenNote: 7.2.3
VignetteBuilder: knitr
RdMacros: lifecycle
URL: https://brovic.github.io/naijR/
BugReports: https://github.com/BroVic/naijR/issues
Config/testthat/edition: 3

Scope

Technical checks

Confirm each of the following by checking the box.

This package:

Publication options

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](http://besjournals.onlinelibrary.wiley.com/hub/journal/10.1111/(ISSN)2041-210X/journal-resources/policy-on-publishing-code.html)) - (*Scope: Do consider MEE's [Aims and Scope](http://besjournals.onlinelibrary.wiley.com/hub/journal/10.1111/(ISSN)2041-210X/aims-and-scope/read-full-aims-and-scope.html) 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

ropensci-review-bot commented 10 months ago

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

ropensci-review-bot commented 10 months ago

:rocket:

Editor check started

:wave:

ropensci-review-bot commented 10 months ago

Checks for naijR (v0.6.1)

git hash: ec9bffb5

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

(Checks marked with :eyes: may be optionally addressed.)

Package License: GPL-3

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 | 217| |internal |naijR | 52| |internal |methods | 6| |imports |cli | 71| |imports |graphics | 16| |imports |utils | 16| |imports |stats | 11| |imports |grDevices | 10| |imports |lifecycle | 9| |imports |rlang | 6| |imports |maps | 3| |imports |sf | 3| |imports |RColorBrewer | NA| |imports |mapdata | NA| |imports |stringi | NA| |suggests |ISOcodes | NA| |suggests |covr | NA| |suggests |here | NA| |suggests |knitr | NA| |suggests |purrr | NA| |suggests |readxl | NA| |suggests |rmarkdown | NA| |suggests |testthat | NA| |suggests |usethis | NA| |linking_to |NA | NA| Click below for tallies of functions used in each package. Locations of each call within this package may be generated locally by running 's <- pkgstats::pkgstats()', and examining the 'external_calls' table.

base

paste (17), list (16), c (11), attr (9), if (9), length (9), unlist (7), character (6), plot (6), sub (6), vapply (6), which (6), col (5), grep (5), names (5), for (4), grepl (4), paste0 (4), data.frame (3), ls (3), match (3), sprintf (3), sum (3), any (2), as.character (2), as.data.frame (2), attributes (2), class (2), duplicated (2), integer (2), interactive (2), lapply (2), logical (2), mapply (2), nchar (2), sapply (2), sort (2), sQuote (2), strrep (2), substitute (2), try (2), agrep (1), as.list (1), as.vector (1), charToRaw (1), deparse (1), eval (1), get (1), getOption (1), identical (1), inherits (1), is.character (1), is.data.frame (1), is.factor (1), is.null (1), is.numeric (1), labels (1), levels (1), match.arg (1), mode (1), ngettext (1), quit (1), range (1), seq_along (1), setdiff (1), stop (1), switch (1), sys.calls (1), typeof (1), unclass (1), unique (1), unname (1)

cli

cli_abort (53), cli_warn (18)

naijR

lgas (12), states (5), lgas_like_states (4), f (3), get_all_states (3), is_state (3), check_nesting_func (2), country_name (2), is_lga (2), stateList (2), as_lga (1), as_state (1), c.regions (1), disambiguate_lga (1), doOneMap (1), findStates (1), fix_mobile (1), fix_region (1), fix_region_manual (1), fix_region.default (1), fix_region.states (1), get_proper_value (1), head.regions (1), map_ng (1)

graphics

title (8), text (7), legend (1)

utils

data (6), str (6), menu (2), packageVersion (1), prompt (1)

stats

df (3), dt (3), stl (3), na.exclude (2)

grDevices

colors (9), palette (1)

lifecycle

deprecate_warn (3), deprecated (3), is_present (3)

methods

show (6)

rlang

is_null (3), expr (1), is_symbol (1), warn (1)

maps

map (3)

sf

st_as_text (1), st_bbox (1), st_centroid (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 - 2 vignettes - 2 internal data files - 12 imported packages - 18 exported functions (median 20 lines of code) - 172 non-exported functions in R (median 7 lines of code) --- Statistical properties of package structure as distributional percentiles in relation to all current CRAN packages The following terminology is used: - `loc` = "Lines of Code" - `fn` = "function" - `exp`/`not_exp` = exported / not exported All parameters are explained as tooltips in the locally-rendered HTML version of this report generated by [the `checks_to_markdown()` function](https://docs.ropensci.org/pkgcheck/reference/checks_to_markdown.html) The final measure (`fn_call_network_size`) is the total number of calls between functions (in R), or more abstract relationships between code objects in other languages. Values are flagged as "noteworthy" when they lie in the upper or lower 5th percentile. |measure | value| percentile|noteworthy | |:------------------------|-----:|----------:|:----------| |files_R | 13| 68.2| | |files_vignettes | 2| 85.7| | |files_tests | 7| 86.4| | |loc_R | 1330| 75.4| | |loc_vignettes | 177| 45.0| | |loc_tests | 922| 85.8| | |num_vignettes | 2| 89.2| | |data_size_total | 4821| 67.1| | |data_size_median | 2410| 69.8| | |n_fns_r | 190| 89.0| | |n_fns_r_exported | 18| 64.2| | |n_fns_r_not_exported | 172| 91.8| | |n_fns_per_file_r | 9| 85.5| | |num_params_per_fn | 2| 11.9| | |loc_per_fn_r | 8| 20.0| | |loc_per_fn_r_exp | 20| 48.3| | |loc_per_fn_r_not_exp | 8| 22.0| | |rel_whitespace_R | 48| 91.7| | |rel_whitespace_vignettes | 39| 50.4| | |rel_whitespace_tests | 21| 84.8| | |doclines_per_fn_exp | 46| 57.9| | |doclines_per_fn_not_exp | 0| 0.0|TRUE | |fn_call_network_size | 162| 86.1| | ---

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 [![R-CMD-check](https://github.com/BroVic/naijR/workflows/R-CMD-check/badge.svg)](https://github.com/BroVic/naijR/actions) **GitHub Workflow Results** | id|name |conclusion |sha | run_number|date | |----------:|:--------------------------|:----------|:------|----------:|:----------| | 5848527475|pages build and deployment |success |ec9bff | 16|2023-08-13 | | 5848527510|R-CMD-check |success |ec9bff | 150|2023-08-13 | --- #### 3b. `goodpractice` results #### `R CMD check` with [rcmdcheck](https://r-lib.github.io/rcmdcheck/) R CMD check generated the following note: 1. checking R/sysdata.rda ... NOTE Note: significantly better compression could be obtained by using R CMD build --resave-data old_size new_size compress sysdata.rda 1.2Mb 780Kb xz R CMD check generated the following check_fails: 1. no_import_package_as_a_whole 2. rcmdcheck_uncompressed_sysdata #### Test coverage with [covr](https://covr.r-lib.org/) Package coverage: 70.12 #### Cyclocomplexity with [cyclocomp](https://github.com/MangoTheCat/cyclocomp) The following functions have cyclocomplexity >= 15: function | cyclocomplexity --- | --- map_ng | 43 lgas | 22 states | 21 #### Static code analyses with [lintr](https://github.com/jimhester/lintr) [lintr](https://github.com/jimhester/lintr) found the following 9 potential issues: message | number of times --- | --- Avoid library() and require() calls in packages | 5 Avoid using sapply, consider vapply instead, that's type safe | 3 Lines should not be more than 80 characters. | 1

4. Other Checks

Details of other checks (click to open)

:heavy_multiplication_x: The following function name is duplicated in other packages: - - `states` from aphylo, clickstream, datafsm, markovchain, pop, rEMM, segclust2d, tigris

Package Versions

|package |version | |:--------|:-------| |pkgstats |0.1.3.4 | |pkgcheck |0.1.2.1 |

Editor-in-Chief Instructions:

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

BroVic commented 10 months ago

@ropensci-review-bot check package

ropensci-review-bot commented 10 months ago

Thanks, about to send the query.

ropensci-review-bot commented 10 months ago

:rocket:

Editor check started

:wave:

ropensci-review-bot commented 10 months ago

Checks for naijR (v0.6.1)

git hash: 8ccaf792

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

(Checks marked with :eyes: may be optionally addressed.)

Package License: GPL-3

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 | 219| |internal |naijR | 54| |internal |methods | 6| |imports |cli | 71| |imports |graphics | 15| |imports |utils | 15| |imports |grDevices | 10| |imports |lifecycle | 9| |imports |stats | 7| |imports |rlang | 6| |imports |maps | 3| |imports |sf | 3| |imports |RColorBrewer | NA| |imports |mapdata | NA| |imports |stringi | NA| |suggests |ISOcodes | NA| |suggests |covr | NA| |suggests |here | NA| |suggests |knitr | NA| |suggests |purrr | NA| |suggests |readxl | NA| |suggests |rmarkdown | NA| |suggests |testthat | NA| |suggests |usethis | NA| |linking_to |NA | NA| Click below for tallies of functions used in each package. Locations of each call within this package may be generated locally by running 's <- pkgstats::pkgstats()', and examining the 'external_calls' table.

base

list (16), paste (16), c (11), length (10), attr (9), if (9), unlist (7), which (7), character (6), sub (6), vapply (6), col (5), grep (5), names (5), plot (5), for (4), grepl (4), paste0 (4), data.frame (3), interactive (3), ls (3), sprintf (3), substitute (3), sum (3), any (2), as.character (2), as.data.frame (2), attributes (2), class (2), deparse (2), duplicated (2), integer (2), lapply (2), logical (2), mapply (2), match (2), nchar (2), sapply (2), sQuote (2), strrep (2), try (2), agrep (1), as.list (1), as.vector (1), charToRaw (1), eval (1), get (1), getOption (1), identical (1), inherits (1), is.character (1), is.data.frame (1), is.factor (1), is.null (1), is.numeric (1), labels (1), levels (1), match.arg (1), mode (1), ngettext (1), quit (1), range (1), seq_along (1), setdiff (1), sort (1), split (1), stop (1), switch (1), sys.calls (1), typeof (1), unclass (1), unique (1), unname (1)

cli

cli_abort (52), cli_warn (19)

naijR

lgas (11), states (5), get_all_states (4), lgas_like_states (4), f (3), is_state (3), arg_str (2), check_nesting_func (2), country_name (2), is_lga (2), as_lga (1), as_state (1), assert.lgl.arg (1), c.regions (1), disambiguate_lga (1), doOneMap (1), findStates (1), first_elem_warn (1), fix_mobile (1), fix_region (1), fix_region_manual (1), fix_region.default (1), fix_region.states (1), get_proper_value (1), head.regions (1), lgas_ng (1)

graphics

text (7), title (7), legend (1)

utils

data (6), str (6), menu (2), packageVersion (1)

grDevices

colors (9), palette (1)

lifecycle

deprecate_warn (3), deprecated (3), is_present (3)

stats

df (3), dt (2), na.exclude (2)

methods

show (6)

rlang

is_null (3), expr (1), is_symbol (1), warn (1)

maps

map (3)

sf

st_as_text (1), st_bbox (1), st_centroid (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 17 files) and - 1 authors - 2 vignettes - 2 internal data files - 12 imported packages - 18 exported functions (median 20 lines of code) - 172 non-exported functions in R (median 7 lines of code) --- Statistical properties of package structure as distributional percentiles in relation to all current CRAN packages The following terminology is used: - `loc` = "Lines of Code" - `fn` = "function" - `exp`/`not_exp` = exported / not exported All parameters are explained as tooltips in the locally-rendered HTML version of this report generated by [the `checks_to_markdown()` function](https://docs.ropensci.org/pkgcheck/reference/checks_to_markdown.html) The final measure (`fn_call_network_size`) is the total number of calls between functions (in R), or more abstract relationships between code objects in other languages. Values are flagged as "noteworthy" when they lie in the upper or lower 5th percentile. |measure | value| percentile|noteworthy | |:------------------------|-----:|----------:|:----------| |files_R | 17| 76.7| | |files_vignettes | 2| 85.7| | |files_tests | 7| 86.4| | |loc_R | 1331| 75.4| | |loc_vignettes | 177| 45.0| | |loc_tests | 948| 86.1| | |num_vignettes | 2| 89.2| | |data_size_total | 4821| 67.1| | |data_size_median | 2410| 69.8| | |n_fns_r | 190| 89.0| | |n_fns_r_exported | 18| 64.2| | |n_fns_r_not_exported | 172| 91.8| | |n_fns_per_file_r | 7| 77.7| | |num_params_per_fn | 2| 11.9| | |loc_per_fn_r | 8| 20.0| | |loc_per_fn_r_exp | 20| 46.7| | |loc_per_fn_r_not_exp | 7| 18.0| | |rel_whitespace_R | 46| 91.3| | |rel_whitespace_vignettes | 39| 50.4| | |rel_whitespace_tests | 22| 85.6| | |doclines_per_fn_exp | 46| 57.9| | |doclines_per_fn_not_exp | 0| 0.0|TRUE | |fn_call_network_size | 163| 86.2| | ---

2a. Network visualisation

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

3. goodpractice and other checks

Details of goodpractice checks (click to open)

#### 3a. Continuous Integration Badges [![R-CMD-check](https://github.com/BroVic/naijR/workflows/R-CMD-check/badge.svg)](https://github.com/BroVic/naijR/actions) **GitHub Workflow Results** | id|name |conclusion |sha | run_number|date | |----------:|:--------------------------|:----------|:------|----------:|:----------| | 5890683643|pages build and deployment |success |8ccaf7 | 17|2023-08-17 | | 5890683746|R-CMD-check |success |8ccaf7 | 159|2023-08-17 | --- #### 3b. `goodpractice` results #### `R CMD check` with [rcmdcheck](https://r-lib.github.io/rcmdcheck/) R CMD check generated the following check_fail: 1. no_import_package_as_a_whole #### Test coverage with [covr](https://covr.r-lib.org/) Package coverage: 71.96 #### Cyclocomplexity with [cyclocomp](https://github.com/MangoTheCat/cyclocomp) The following functions have cyclocomplexity >= 15: function | cyclocomplexity --- | --- map_ng | 43 lgas | 22 states | 19 fix_region.lgas | 15 #### Static code analyses with [lintr](https://github.com/jimhester/lintr) [lintr](https://github.com/jimhester/lintr) found the following 8 potential issues: message | number of times --- | --- Avoid library() and require() calls in packages | 5 Avoid using sapply, consider vapply instead, that's type safe | 3

4. Other Checks

Details of other checks (click to open)

:heavy_multiplication_x: The following function name is duplicated in other packages: - - `states` from aphylo, clickstream, datafsm, markovchain, pop, rEMM, segclust2d, tigris

Package Versions

|package |version | |:--------|:-------| |pkgstats |0.1.3.4 | |pkgcheck |0.1.2.1 |

Editor-in-Chief Instructions:

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

BroVic commented 10 months ago

@ropensci-review-bot check package

ropensci-review-bot commented 10 months ago

Thanks, about to send the query.

ropensci-review-bot commented 10 months ago

:rocket:

Editor check started

:wave:

ropensci-review-bot commented 10 months ago

Checks for naijR (v0.6.1)

git hash: 5d70cafd

(Checks marked with :eyes: may be optionally addressed.)

Package License: GPL-3

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 | 219| |internal |naijR | 53| |internal |methods | 6| |imports |cli | 72| |imports |graphics | 15| |imports |utils | 15| |imports |grDevices | 10| |imports |stats | 7| |imports |rlang | 6| |imports |maps | 3| |imports |sf | 3| |imports |RColorBrewer | NA| |imports |lifecycle | NA| |imports |mapdata | NA| |imports |stringi | NA| |suggests |ISOcodes | NA| |suggests |covr | NA| |suggests |here | NA| |suggests |knitr | NA| |suggests |purrr | NA| |suggests |readxl | NA| |suggests |rmarkdown | NA| |suggests |testthat | NA| |suggests |usethis | NA| |linking_to |NA | NA| Click below for tallies of functions used in each package. Locations of each call within this package may be generated locally by running 's <- pkgstats::pkgstats()', and examining the 'external_calls' table.

base

list (16), paste (16), c (11), length (10), attr (9), if (9), unlist (7), which (7), character (6), sub (6), vapply (6), col (5), grep (5), names (5), plot (5), for (4), grepl (4), paste0 (4), data.frame (3), interactive (3), ls (3), sprintf (3), substitute (3), sum (3), any (2), as.character (2), as.data.frame (2), attributes (2), class (2), deparse (2), duplicated (2), integer (2), lapply (2), logical (2), mapply (2), match (2), nchar (2), sapply (2), sQuote (2), strrep (2), try (2), agrep (1), as.list (1), as.vector (1), charToRaw (1), eval (1), get (1), getOption (1), identical (1), inherits (1), is.character (1), is.data.frame (1), is.factor (1), is.null (1), is.numeric (1), labels (1), levels (1), match.arg (1), mode (1), ngettext (1), quit (1), range (1), seq_along (1), setdiff (1), sort (1), split (1), stop (1), switch (1), sys.calls (1), typeof (1), unclass (1), unique (1), unname (1)

cli

cli_abort (53), cli_warn (19)

naijR

lgas (11), states (5), get_all_states (4), lgas_like_states (4), f (3), is_state (3), arg_str (2), check_nesting_func (2), country_name (2), is_lga (2), as_lga (1), as_state (1), assert.lgl.arg (1), c.regions (1), disambiguate_lga (1), doOneMap (1), findStates (1), first_elem_warn (1), fix_mobile (1), fix_region (1), fix_region_manual (1), fix_region.default (1), fix_region.states (1), get_proper_value (1), head.regions (1)

graphics

text (7), title (7), legend (1)

utils

data (6), str (6), menu (2), packageVersion (1)

grDevices

colors (9), palette (1)

stats

df (3), dt (2), na.exclude (2)

methods

show (6)

rlang

is_null (3), expr (1), is_symbol (1), warn (1)

maps

map (3)

sf

st_as_text (1), st_bbox (1), st_centroid (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 17 files) and - 1 authors - 2 vignettes - 2 internal data files - 12 imported packages - 17 exported functions (median 20 lines of code) - 171 non-exported functions in R (median 7 lines of code) --- Statistical properties of package structure as distributional percentiles in relation to all current CRAN packages The following terminology is used: - `loc` = "Lines of Code" - `fn` = "function" - `exp`/`not_exp` = exported / not exported All parameters are explained as tooltips in the locally-rendered HTML version of this report generated by [the `checks_to_markdown()` function](https://docs.ropensci.org/pkgcheck/reference/checks_to_markdown.html) The final measure (`fn_call_network_size`) is the total number of calls between functions (in R), or more abstract relationships between code objects in other languages. Values are flagged as "noteworthy" when they lie in the upper or lower 5th percentile. |measure | value| percentile|noteworthy | |:------------------------|-----:|----------:|:----------| |files_R | 17| 76.7| | |files_vignettes | 2| 85.7| | |files_tests | 7| 86.4| | |loc_R | 1321| 75.2| | |loc_vignettes | 177| 45.0| | |loc_tests | 962| 86.3| | |num_vignettes | 2| 89.2| | |data_size_total | 4821| 67.1| | |data_size_median | 2410| 69.8| | |n_fns_r | 188| 88.8| | |n_fns_r_exported | 17| 62.4| | |n_fns_r_not_exported | 171| 91.7| | |n_fns_per_file_r | 7| 77.4| | |num_params_per_fn | 2| 11.9| | |loc_per_fn_r | 8| 20.0| | |loc_per_fn_r_exp | 20| 46.7| | |loc_per_fn_r_not_exp | 7| 18.0| | |rel_whitespace_R | 45| 91.1| | |rel_whitespace_vignettes | 39| 50.4| | |rel_whitespace_tests | 21| 85.3| | |doclines_per_fn_exp | 46| 58.1| | |doclines_per_fn_not_exp | 0| 0.0|TRUE | |fn_call_network_size | 156| 85.6| | ---

2a. Network visualisation

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

3. goodpractice and other checks

Details of goodpractice checks (click to open)

#### 3a. Continuous Integration Badges [![R-CMD-check](https://github.com/BroVic/naijR/workflows/R-CMD-check/badge.svg)](https://github.com/BroVic/naijR/actions) **GitHub Workflow Results** | id|name |conclusion |sha | run_number|date | |----------:|:--------------------------|:----------|:------|----------:|:----------| | 5905586565|pages build and deployment |success |5d70ca | 18|2023-08-18 | | 5905586586|R-CMD-check |success |5d70ca | 163|2023-08-18 | --- #### 3b. `goodpractice` results #### `R CMD check` with [rcmdcheck](https://r-lib.github.io/rcmdcheck/) R CMD check generated the following check_fail: 1. no_import_package_as_a_whole #### Test coverage with [covr](https://covr.r-lib.org/) Package coverage: 79.29 #### Cyclocomplexity with [cyclocomp](https://github.com/MangoTheCat/cyclocomp) The following functions have cyclocomplexity >= 15: function | cyclocomplexity --- | --- map_ng | 40 lgas | 22 states | 19 fix_region.lgas | 15 #### Static code analyses with [lintr](https://github.com/jimhester/lintr) [lintr](https://github.com/jimhester/lintr) found the following 5 potential issues: message | number of times --- | --- Avoid library() and require() calls in packages | 2 Avoid using sapply, consider vapply instead, that's type safe | 3

4. Other Checks

Details of other checks (click to open)

:heavy_multiplication_x: The following function name is duplicated in other packages: - - `states` from aphylo, clickstream, datafsm, markovchain, pop, rEMM, segclust2d, tigris

Package Versions

|package |version | |:--------|:-------| |pkgstats |0.1.3.4 | |pkgcheck |0.1.2.1 |

Editor-in-Chief Instructions:

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

noamross commented 10 months ago

@ropensci-review-bot assign @emilyriederer as editor

ropensci-review-bot commented 10 months ago

Assigned! @emilyriederer is now the editor

emilyriederer commented 10 months ago

Editor checks:

Editor comments

This package is in good shape and seems like it could be a powerful accelerant to a data science workflow. Before preceding with the review, I just notice a few changes to be made:

Additionally, the following dimensions could be improved. However, these are not critical to move forward:

emilyriederer commented 10 months ago

Hi @BroVic ! It's great to meet you and I'm looking forward to working as your editor on this package. I left some comments above. I think we are close to looking for reviewers, but I'd love to discuss the "Fit" question with you first. Could you please review our categories and let me know if you think this package fits the "Data munging" category more than "geospatial"?

BroVic commented 10 months ago

Hello @emilyriederer, indeed the original intent for the package was not to draw maps but help with data validation and/or transformation. The mapping was really a child of necessity due to the absence of elements for drawing subnational maps in existing packages. Future versions will delve into ward level maps, but the focus is to provide objects that can be consumed by actual geospatial packages. So I agree—we could recategorize it as you've suggested.

emilyriederer commented 10 months ago

Hi @BroVic - thanks for the reply. I think it makes sense to chose the category the best represents the current scope of the package. If you're aligned, please change the category in your initial post at the top.

After that, I'm comfortable moving to identify reviewers. However, I'd encourage you to check out a few of the other notes in my "Editor comments" above in the meantime.

Thanks!

emilyriederer commented 10 months ago

@ropensci-review-bot seeking reviewers

ropensci-review-bot commented 10 months ago

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

[![Status at rOpenSci Software Peer Review](https://badges.ropensci.org/600_status.svg)](https://github.com/ropensci/software-review/issues/600)

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

BroVic commented 10 months ago

Hello @emilyriederer

I've made some changes to address your comments. Thank you very much!

emilyriederer commented 10 months ago

@ropensci-review-bot add @mcsiple to reviewers

ropensci-review-bot commented 10 months ago

@mcsiple added to the reviewers list. Review due date is 2023-09-23. Thanks @mcsiple for accepting to review! Please refer to our reviewer guide.

rOpenSci’s community is our best asset. We aim for reviews to be open, non-adversarial, and focused on improving software quality. Be respectful and kind! See our reviewers guide and code of conduct for more.

ropensci-review-bot commented 10 months ago

@mcsiple: If you haven't done so, please fill this form for us to update our reviewers records.

emilyriederer commented 10 months ago

Hi @BroVic - I'm thrilled to introduce @mcsiple as the first reviewer for your package! Her expertise is in both text and spatial data so she seemed like a great fit for this package. I should have an update on the second reviewer soon.

BroVic commented 10 months ago

Thank you @emilyriederer. I really appreciate your efforts and I can't wait to learn from you guys. Cheers!

emilyriederer commented 10 months ago

@ropensci-review-bot add @cagrigokcek to reviewers

ropensci-review-bot commented 10 months ago

@cagrigokcek added to the reviewers list. Review due date is 2023-09-24. Thanks @cagrigokcek for accepting to review! Please refer to our reviewer guide.

rOpenSci’s community is our best asset. We aim for reviews to be open, non-adversarial, and focused on improving software quality. Be respectful and kind! See our reviewers guide and code of conduct for more.

ropensci-review-bot commented 10 months ago

@cagrigokcek: If you haven't done so, please fill this form for us to update our reviewers records.

emilyriederer commented 10 months ago

Hi @BroVic ! I'm delighted to introduce the @cagrigokcek as the second reviewer. His domain expertise is in political science, so I'm sure that will help him empathize with potential users of this package. Earlier this summer, he was featured in this rOpenSci blog post

BroVic commented 10 months ago

Hello @emilyriederer, noted with thanks 👍🏽

ropensci-review-bot commented 9 months ago

:calendar: @mcsiple you have 2 days left before the due date for your review (2023-09-23).

ropensci-review-bot commented 9 months ago

:calendar: @cagrigokcek you have 2 days left before the due date for your review (2023-09-24).

mcsiple commented 9 months ago

naijR Package Review

Good work on this package @BroVic et al. I used the rOpenSci review template to set up my checks. My limited comments/suggestions can be found at the bottom of this review. Please let me know if you have any questions about anything I wrote.

Documentation

The package includes all the following forms of documentation:

Functionality

Estimated hours spent reviewing: 5

Review Comments

Great work putting together the package so comprehensively. It made it easier to review and will be easier for users, too. I have just a couple of comments.

emilyriederer commented 9 months ago

Thanks for the review, @mcsiple ! I really appreciate the thorough suggestions here.

@cagrigokcek , do you have an update from your side of when you will have your review completed?

cagrigokcek commented 9 months ago

Hi Emily,

Is it ok if I submit my review by the end of Sunday night? I know that I already demanded a few days extra. But, this will be the last and final request from me. Please let me know.

Best.

Cagri

From: Emily Riederer @.> Sent: Thursday, September 28, 2023 2:38 AM To: ropensci/software-review @.> Cc: A. Cagri gokcek @.>; Mention @.> Subject: Re: [ropensci/software-review] Submission of naijR 0.6.1 for review under the rOpenSci Champions Program (Issue #600)

Thanks for the review, @mcsiple https://github.com/mcsiple ! I really appreciate the thorough suggestions here.

@cagrigokcek https://github.com/cagrigokcek , do you have an update from your side of when you will have your review completed?

— Reply to this email directly, view it on GitHub https://github.com/ropensci/software-review/issues/600#issuecomment-1738815530 , or unsubscribe https://github.com/notifications/unsubscribe-auth/A3LYXAC6WWAYXWRBOBJCEC3X4VAQ7ANCNFSM6AAAAAA3OYM35U . You are receiving this because you were mentioned.Message ID: @.***>

emilyriederer commented 9 months ago

Thanks for the update, @cagrigokcek ! Yes, that should work just fine. I appreciate your taking the time to do a thorough review!

On Thu, Sep 28, 2023 at 3:43 PM A. Cagri gokcek @.***> wrote:

Hi Emily,

Is it ok if I submit my review by the end of Sunday night? I know that I already demanded a few days extra. But, this will be the last and final request from me. Please let me know.

Best.

Cagri

From: Emily Riederer @.> Sent: Thursday, September 28, 2023 2:38 AM To: ropensci/software-review @.> Cc: A. Cagri gokcek @.>; Mention @.> Subject: Re: [ropensci/software-review] Submission of naijR 0.6.1 for review under the rOpenSci Champions Program (Issue #600)

Thanks for the review, @mcsiple https://github.com/mcsiple ! I really appreciate the thorough suggestions here.

@cagrigokcek https://github.com/cagrigokcek , do you have an update from your side of when you will have your review completed?

— Reply to this email directly, view it on GitHub < https://github.com/ropensci/software-review/issues/600#issuecomment-1738815530> , or unsubscribe < https://github.com/notifications/unsubscribe-auth/A3LYXAC6WWAYXWRBOBJCEC3X4VAQ7ANCNFSM6AAAAAA3OYM35U> . You are receiving this because you were mentioned.Message ID: @.***>

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cagrigokcek commented 9 months ago

Hello @Brovic, I am very happy to give you feedback. As you know, this is my first chance of getting involved in a peer-review process. That said, please forgive me if I miss any crucial point in this review, and don't hesitate to forward me any type of accessibility-related questions. In this review, I majorly focused on your map_ng() function. My main goal was checking the level of accessibility of maps created by your package. Thus, I skipped some items in the check list due to the lack of enough knowledge to test them. Drawing insights from this review process, I also offer an extra bullet point under the heading of functionality to @emilyriederer on behalf of @rOpenSci. I added a new bullet point below, and left my feedback there. I hope that it will help @BroVic to make naijR more inclusive and accessible for everyone.:

Please check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide

Documentation

The package includes all the following forms of documentation:

Functionality

I will recommend to benefit from BrailleR packages' functions for discovering maps in the package. the pertinant information about BrailleR in regards to making data visualization more accessible for the blind can be obtained via this vignette: https://cran.r-project.org/web/packages/BrailleR/vignettes/ExploringGraphs.html When I created two objects by map_ng(), I was not able to use BraileR's relevant commends for graphs. At this moment, I should also admit that I am not sure whether BrailleR's commands work for maps. I know that BrailleR works smoothly with ggplot2 and tidyverse in general. I am sharing my codes and the message received in R for @BroVic's consideration.

library(naijR)
library(BrailleR)
map1=map_ng("Nigeria")

Describe(map1)
#> No description of this type of object has been written at this time.
#> 
#> General Description:
#> none yet
#> 
#> R hints:
#> none yet

map2=map_ng()

Describe(map2) 
#> No description of this type of object has been written at this time.
#> 
#> General Description:
#> none yet
#> 
#> R hints:
#> none yet

Describe function, if it worked, could allow a screen reader user to understand basic features of the maps such as the state names displayed in the map, their geographic position in the map, the color of states, if any, in the map, and any other features considered fundamentally important by the author of the package. Here, I only demonstrated Describe() function. Other functions of BrailleR (e.g. VI()) can be integrated in naijR package to increase the inclusivity of naijR package. Overall, as it is seen, a development task for naijR can be making naijR package compatible with BrailleR package's commands related to data visualization.

Estimated hours spent reviewing:

Review Comments

I am very excited to see what kind of changes can ebedone for improving the accessibility of maps in this package. Please don't hesitate to keep in touch with me anytime if you need me to test your new features.

BroVic commented 9 months ago

Thank you, @mcsiple and @cagrigokcek for your detailed reviews. I will proceed to incorporate your input and will revert when I'm done or if I run into any issues.

emilyriederer commented 8 months ago

Thank you so much for the reviews @mcsiple and @cagrigokcek ! Could you please both share an estimated time spent reviewing? This is a metric we track internally and I need it so I can trigger the bot to formally "submit" the reviews

mcsiple commented 8 months ago

Sorry about that! I missed it the first time. I just edited my comment in the thread above with the estimated hours spent reviewing.

emilyriederer commented 8 months ago

@ropensci-review-bot submit review https://github.com/ropensci/software-review/issues/600#issuecomment-1732091598 time 5

ropensci-review-bot commented 8 months ago

Logged review for mcsiple (hours: 5)

emilyriederer commented 8 months ago

Thanks @mcsiple ! Not a problem at all -- I know there's a lot of information to fill out on those!

cagrigokcek commented 8 months ago

Hi Emily,

I didn’t actually count my hours while reviewing the package. I spent few hours in two days to complete the review. I should say that I didn’t spend more than 5 hours in two days.

Thanks.

Cagri

From: Emily Riederer @.> Sent: Thursday, October 5, 2023 5:03 PM To: ropensci/software-review @.> Cc: A. Cagri gokcek @.>; Mention @.> Subject: Re: [ropensci/software-review] Submission of naijR 0.6.1 for review under the rOpenSci Champions Program (Issue #600)

Thank you so much for the reviews @mcsiple https://github.com/mcsiple and @cagrigokcek https://github.com/cagrigokcek ! Could you please both share an estimated time spent reviewing? This is a metric we track internally and I need it so I can trigger the bot to formally "submit" the reviews

— Reply to this email directly, view it on GitHub https://github.com/ropensci/software-review/issues/600#issuecomment-1749812113 , or unsubscribe https://github.com/notifications/unsubscribe-auth/A3LYXAHN3OKELAPT3QP7YU3X55DCDAVCNFSM6AAAAAA3OYM35WVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONBZHAYTEMJRGM . You are receiving this because you were mentioned.Message ID: @.***>

emilyriederer commented 8 months ago

@ropensci-review-bot submit review https://github.com/ropensci/software-review/issues/600#issuecomment-1742267778 time 5

ropensci-review-bot commented 8 months ago

Logged review for cagrigokcek (hours: 5)

emilyriederer commented 8 months ago

Hi @BroVic ! I hope you are well. I thought I'd drop a line and see how you are feeling about any changes inspired by the review comments? It would be great if we can give our reviewers a heads-up on when to expect a final version to review for approval. Thanks!

BroVic commented 8 months ago

Dear @emilyriederer I thought I would have finished applying the requested updates by now, but I had a little battle with malaria last weekend. I'm fine now and recuperating, so you will definitely hear from me in this regard very soon. Thanks. ❤️‍🩹

emilyriederer commented 8 months ago

@BroVic - very sorry to hear that! Please don't stress about this or feel any pressure on the turnaround. Feel better soon!

ropensci-review-bot commented 8 months ago

@BroVic: please post your response with @ropensci-review-bot submit response <url to issue comment> if you haven't done so already (this is an automatic reminder).

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