Prepare package for rOpenSci onboarding

[peterdesmet]

Guide: https://ropensci.github.io/dev_guide/index.html. Things I noticed that might not be covered yet:

• [x] Add codemeta.json using codemetar::write_codemeta(): 5683c0d
• [ ] Use message() and warning() to communicate with the user
• [x] Code style, run styler::style_pkg(filetype = c("R", "Rmd")): dc9dff6
• [x] README: #155
• [x] Add links for authors: e1f117a
• [ ] All packages should have a test suite that covers major functionality of the package. The tests should also cover the behavior of the package in case of errors. See also issue #97
• [ ] For http requests we strongly recommend using httr over RCurl.
• [x] Try goodpractice::gp(): getting

[adokter]

You might want to check whether it is not a problem that our package uses an external Docker image that contains an important part of the code and functionality

[peterdesmet]

Below is the full template for submitting an rOpenSci package for review. @adokter I suggest we edit this comment in preparation for submission. We should tackle all TODOs

---

Submitting Author Name: Adriaan Dokter Submitting Author Github Handle: @adokter Other Package Authors Github handles: (comma separated, delete if none) @peterdesmet, @github_handle2, TODO Repository: https://github.com/adokter/bioRad/ Version submitted: TODO Submission type: Standard Editor: TBD Reviewers: TBD

Archive: TBD Version accepted: TBD Language: en

---

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

TODO

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.):

  • [x] data retrieval
  • [x] data extraction
  • [x] data munging
  • [ ] data deposition
  • [ ] data validation and testing
  • [ ] workflow automation
  • [ ] version control
  • [ ] citation management and bibliometrics
  • [ ] scientific software wrappers
  • [x] field and lab reproducibility tools
  • [ ] database software bindings
  • [x] geospatial data
  • [ ] text analysis

• Explain how and why the package falls under these categories (briefly, 1-2 sentences):

TODO

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

TODO

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

TODO

• (If applicable) Does your package comply with our guidance around Ethics, Data Privacy and Human Subjects Research?

Not applicable

• If you made a pre-submission inquiry, please paste the link to the corresponding issue, forum post, or other discussion, or @tag the editor you contacted.

Not applicable

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

TODO

Technical checks

Confirm each of the following by checking the box.

TODO

• [ ] I have read the rOpenSci packaging guide.
• [ ] I have read the author guide and I expect to maintain this package for at least 2 years or to find a replacement.

This package:

TODO

• [x] does not violate the Terms of Service of any service it interacts with.
• [x] has a CRAN and OSI accepted license.
• [ ] contains a README with instructions for installing the development version.
• [ ] includes documentation with examples for all functions, created with roxygen2.
• [ ] contains a vignette with examples of its essential functions and uses.
• [ ] has a test suite.
• [ ] has continuous integration, including reporting of test coverage.

Publication options

• [x] Do you intend for this package to go on CRAN?

• [ ] Do you intend for this package to go on Bioconductor?

• [ ] Do you wish to submit an Applications Article about your package to Methods in Ecology and Evolution? If so:

MEE Options

• [ ] The package is novel and will be of interest to the broad readership of the journal.
• [ ] The manuscript describing the package is no longer than 3000 words.
• [ ] 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

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

[PietrH]

We could consider using the rOpenSci github action for pkgcheck to check on our current status: https://docs.ropensci.org/pkgcheck/

I've generated a report locally and I'll include it below:

Checks for bioRad (v0.7.0.9579)

git hash: 52616411

• :heavy_check_mark: Package is already on CRAN.
• :heavy_check_mark: has a 'codemeta.json' file.
• :heavy_check_mark: has a 'contributing' file.
• :heavy_multiplication_x: The following functions have no documented return values: [attribute_table, download_basemap, download_pvolfiles, download_vpfiles, doy_noy, plot.ppi, plot.scan, plot.vp, plot.vpi, plot.vpts, rcs<-, sd_vvp_threshold<-]
• :heavy_check_mark: uses 'roxygen2'.
• :heavy_check_mark: 'DESCRIPTION' has a URL field.
• :heavy_check_mark: 'DESCRIPTION' has a BugReports field.
• :heavy_check_mark: Package has at least one HTML vignette
• :heavy_multiplication_x: These functions do not have examples: [c.vp, get_iris_raw_task, read_cajun].
• :heavy_multiplication_x: Package uses global assignment operator ('<<-').
• :heavy_multiplication_x: Package has no continuous integration checks.
• :heavy_multiplication_x: Package coverage is 68.3% (should be at least 75%).
• :heavy_multiplication_x: R CMD check found 1 error.
• :heavy_multiplication_x: R CMD check found 1 warning.
• :eyes: Package depends on the following obsolete packages: [sp]
• :eyes: Function names are duplicated in other packages

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

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

Package License: MIT + file LICENSE

---

1. Package Dependencies

Details of Package Dependency Usage (click to open)

The table below tallies all function calls to all packages ('ncalls'), both internal (r-base + recommended, along with the package itself), and external (imported and suggested packages). 'NA' values indicate packages to which no identified calls to R functions could be found. Note that these results are generated by an automated code-tagging system which may not be entirely accurate.

type	package	ncalls
internal	base	1036
internal	bioRad	240
internal	grDevices	11
imports	stats	78
imports	methods	29
imports	raster	28
imports	dplyr	25
imports	glue	7
imports	graphics	6
imports	lubridate	5
imports	utils	4
imports	rlang	3
imports	lutz	2
imports	maptools	2
imports	viridis	2
imports	curl	1
imports	readr	1
imports	tidyr	1
imports	viridisLite	1
imports	assertthat	NA
imports	fields	NA
imports	ggplot2	NA
imports	rgdal	NA
imports	rhdf5	NA
imports	sp	NA
suggests	vol2birdR	7
suggests	aws.s3	4
suggests	ggmap	2
suggests	tidyselect	2
suggests	knitr	NA
suggests	rmarkdown	NA
suggests	testthat	NA
suggests	vdiffr	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

c (89), data.frame (77), sapply (58), list (49), file (42), length (42), lapply (33), max (33), attributes (31), min (29), paste (23), unique (22), dim (18), do.call (18), range (18), for (17), seq (17), names (15), seq_along (14), by (12), ifelse (12), pi (12), scan (12), is.null (11), as.numeric (10), as.POSIXct (10), colSums (10), row (10), which (10), format (9), nrow (9), F (8), t (8), col (7), if (7), rep (7), as.Date (6), date (6), dir (6), getOption (6), pmin (6), T (6), as.data.frame (5), attr (5), basename (5), cbind (5), gsub (5), ncol (5), source (5), suppressWarnings (5), tryCatch (5), units (5), apply (4), cos (4), cumsum (4), eval (4), matrix (4), sin (4), sum (4), tempfile (4), abs (3), all (3), atan2 (3), difftime (3), expand.grid (3), labels (3), mapply (3), paste0 (3), rbind (3), rowSums (3), substring (3), unlist (3), url (3), withCallingHandlers (3), as.integer (2), as.list (2), findInterval (2), floor (2), is.na (2), levels (2), mean (2), pmax (2), row.names (2), setdiff (2), sort (2), sprintf (2), stopifnot (2), strsplit (2), substitute (2), substr (2), vapply (2), which.min (2), all.equal (1), args (1), as.character (1), as.difftime (1), as.double (1), as.vector (1), ceiling (1), character (1), colnames (1), diff (1), dirname (1), drop (1), file.path (1), integer (1), is.finite (1), is.nan (1), load (1), match (1), months (1), nchar (1), normalizePath (1), order (1), q (1), seq_len (1), sqrt (1), startsWith (1), suppressMessages (1), Sys.info (1), table (1), UseMethod (1), warning (1)

bioRad

get_quantity (26), add_expected_eta_to_scan (7), rcs (7), scan_to_raster (6), sunrise (6), sunset (6), map (5), sd_vvp_threshold (5), check_night (4), error (4), errorf (4), polar_to_index (4), beam_profile_overlap_help (3), cartesian_to_polar (3), color_scale_fill (3), combined_heights (3), earth_radius (3), get_odim_object_type (3), add_color_transparency (2), beam_distance (2), beam_height (2), beam_profile (2), beam_profile_overlap (2), beam_range (2), calculate_vp (2), extract_string (2), get_elevation_angles (2), integrate_profile.vp (2), is.vp (2), is.vpts (2), match_filenames (2), proj_to_wgs (2), sample_polar (2), scan_to_spatial (2), add_heights_vp (1), add_heights_vpts (1), apply_mistnet (1), apply_mistnet_body (1), as.data.frame.vp (1), as.data.frame.vpts (1), beam_height_internal (1), beam_width (1), beam_width_internal (1), bind_into_vpts (1), bind_into_vpts.list (1), bind_into_vpts.vp (1), bind_into_vpts.vpts (1), c.vp (1), calculate_param (1), calculate_param.ppi (1), calculate_param.pvol (1), calculate_param.scan (1), check_date_format (1), check_docker (1), check_night.default (1), check_night.list (1), check_night.pvol (1), check_night.vp (1), check_night.vpi (1), check_night.vpts (1), check_radar_codes (1), col_func (1), color_palette (1), color_palette_to_scale_colour (1), color_scale (1), convert_legacy (1), convert_legacy.vp (1), convert_legacy.vpts (1), dbz_to_eta (1), dim.ppi (1), dim.pvol (1), dim.scan (1), dim.vp (1), dim.vpts (1), download_basemap (1), download_pvolfiles (1), download_vpfiles (1), doy (1), doy.default (1), doy.pvol (1), doy.vp (1), doy.vpi (1), doy.vpts (1), eta_expected (1), eta_to_dbz (1), filter_vpts (1), format_reason_vol2bird (1), gaussian_beam_profile (1), gaussian_beam_profile_internal (1), get_elevation_angles.param (1), get_elevation_angles.pvol (1), get_elevation_angles.scan (1), get_iris_raw_task (1), get_param (1), get_quantity.list (1), get_quantity.vp (1), get_quantity.vpts (1), get_scan (1), get_zlim (1), integrate_profile (1), integrate_profile.list (1), integrate_profile.vpts (1), integrate_to_ppi (1), is.na2 (1), is.nan.data.frame (1), is.odimfile (1), is.param (1), is.ppi (1), is.pvol (1), is.pvolfile (1), is.scan (1), is.vpfile (1), is.vpi (1), list_vpts_aloft (1), map.ppi (1), nexrad_to_odim (1), noy (1), noy.default (1), noy.pvol (1), noy.vp (1), noy.vpi (1), noy.vpts (1), nyquist_velocity (1), plot_wind_barbs (1), plot.ppi (1), plot.scan (1), plot.vp (1), plot.vpi (1), plot.vpts (1), print.param (1), print.ppi (1), print.pvol (1), print.scan (1), print.vp (1), print.vpts (1), project_as_ppi (1), read_pvolfile (1), read_vp (1), read_vpfiles (1), wgs_to_proj (1)

stats

rt (26), offset (18), ts (12), dt (6), profile (4), weighted.mean (4), df (3), median (2), approx (1), cov (1), step (1)

methods

is (18), as (11)

raster

raster (9), brick (5), extent (4), as.data.frame (3), flip (2), crs (1), projection (1), rasterToPoints (1), setValues (1), weighted.mean (1)

dplyr

join (9), left_join (9), bind_rows (4), distinct (1), if_else (1), pull (1)

grDevices

colors (4), palette (3), colours (2), col2rgb (1), rgb (1)

glue

glue (3), glue_collapse (3), backtick (1)

vol2birdR

vol2bird_config (4), rsl2odim (3)

graphics

grid (5), par (1)

lubridate

ym (2), ceiling_date (1), floor_date (1), make_difftime (1)

aws.s3

get_bucket_df (3), bucket_exists (1)

utils

read.table (2), read.csv (1), txtProgressBar (1)

rlang

check_installed (2), expr (1)

ggmap

calc_zoom (1), get_map (1)

lutz

tz_lookup_coords (2)

maptools

crepuscule (2)

tidyselect

eval_select (2)

viridis

scale_colour_viridis (1), scale_fill_viridis (1)

curl

curl_fetch_disk (1)

readr

read_lines (1)

tidyr

fill (1)

viridisLite

viridis (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 61 files) and
• 3 authors
• 3 vignettes
• 3 internal data files
• 22 imported packages
• 151 exported functions (median 7 lines of code)
• 254 non-exported functions in R (median 9 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	61	97.3
files_vignettes	3	92.4
files_tests	58	99.4
loc_R	4970	95.3	TRUE
loc_vignettes	438	74.8
loc_tests	1937	93.9
num_vignettes	3	94.2
data_size_total	1451194	96.5	TRUE
data_size_median	544736	97.2	TRUE
n_fns_r	405	96.2	TRUE
n_fns_r_exported	151	97.6	TRUE
n_fns_r_not_exported	254	95.2	TRUE
n_fns_per_file_r	4	58.9
num_params_per_fn	2	11.9
loc_per_fn_r	8	20.0
loc_per_fn_r_exp	7	13.5
loc_per_fn_r_not_exp	9	27.1
rel_whitespace_R	10	88.5
rel_whitespace_vignettes	48	85.6
rel_whitespace_tests	15	89.8
doclines_per_fn_exp	52	65.3
doclines_per_fn_not_exp	0	0.0	TRUE
fn_call_network_size	228	89.9

---

2a. Network visualisation

Github doesn't allow uploading html files!

---

3. goodpractice and other checks

Details of goodpractice checks (click to open)

---

3b. goodpractice results

R CMD check with rcmdcheck

R CMD check generated the following error:

1. checking PDF version of manual without index ... ERROR Re-running with no redirection of stdout/stderr. Hmm ... looks like a package Converting parsed Rd's to LaTeX ........ Creating pdf output from LaTeX ... Warning in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : texi2dvi script/program not available, using emulation Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : pdflatex is not available Warning in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : texi2dvi script/program not available, using emulation Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : pdflatex is not available Error in running tools::texi2pdf() You may want to clean up by 'rm -Rf /tmp/RtmpD2FFw2/Rd2pdf829f681852ef'

R CMD check generated the following warning:

1. checking PDF version of manual ... WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems.

R CMD check generated the following check_fails:

1. cyclocomp
2. no_import_package_as_a_whole
3. rcmdcheck_can_convert_rd_to_pdf_2

Test coverage with covr

Package coverage: 68.28

The following files are not completely covered by tests:

file	coverage
R/apply_mistnet.R	0%
R/bioRad-deprecated.R	0%
R/color_scale.R	29.31%
R/composite_ppi.R	0%
R/download_basemap.R	0%
R/download_vpfiles.R	43.1%
R/filter_vpts.R	66.67%
R/iris.R	0%
R/map.R	0%
R/nexrad_odim.R	0%
R/nyquist_velocity.R	0%
R/plot.vpi.R	61.33%
R/plot.vpts.R	69.01%
R/read_cajun.R	0%
R/read_vpts.R	0%
R/select_vpfiles.R	0%

Cyclocomplexity with cyclocomp

The following functions have cyclocomplexity >= 15:

function	cyclocomplexity
composite_ppi	54
read_pvolfile_body	46
integrate_to_ppi	45
plot.vpts	45
scan_to_raster	44
plot_wind_barbs	43
read_vpts	41
plot.vpi	37
get_zlim	31
calculate_vp	24
filter_vpts	22
map.ppi	21
scan_to_spdf	20
add_expected_eta_to_scan	19
download_basemap	17
beam_profile_overlap	16
regularize_vpts	16

Static code analyses with lintr

lintr found the following 714 potential issues:

message	number of times
Avoid 1:length(...) expressions, use seq_len.	9
Avoid 1:nrow(...) expressions, use seq_len.	1
Avoid changing the working directory, or restore it in on.exit	1
Avoid library() and require() calls in packages	4
Avoid trailing semicolons, they are not needed.	1
Avoid using sapply, consider vapply instead, that's type safe	50
Lines should not be more than 80 characters.	612
Use <-, not ->, for assignment.	2
Use <-, not =, for assignment.	34

---

4. Other Checks

Details of other checks (click to open)

:heavy_multiplication_x: Package contains the following (potentially) obsolete packages:

• sp
• maptools
• rgdal

See our Recommended Scaffolding for alternatives.

:heavy_multiplication_x: The following 5 function names are duplicated in other packages:

• • doy from solaR
• • get_param from EpiModel, gplite, ldamatch, mapbayr, phenofit
• • map from aphid, arakno, BGData, BGGM, bgmm, bReeze, gapmap, html5, jqr, kohonen, listenv, mapfit, maps, mclust, missSOM, mlr3misc, modchart, narray, neuroim, onemap, OpenRepGrid, pomp, purrr, Qtools, SpatialExtremes, spidR, tipsae, Z10
• • rcs from dplR, rms
• • sunrise from reactablefmtr

---

Package Versions

package	version
pkgstats	0.1.1
pkgcheck	0.1.1.20