Pre-submission Inquiry: GeoPressureR

[Rafnuss]

Submitting Author Name: Raphaël Nussbaumer
Submitting Author Github Handle: @Rafnuss
Other Package Authors Github handles:
Repository: https://github.com/Rafnuss/GeoPressureR
Version submitted: v3.5.1
Submission type: Standard
Editor: TBD
Reviewers: TBD

Archive: TBD
Version accepted: TBD
Language: en

---

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

Package: GeoPressureR
Title: Global Positioning by Atmospheric Pressure
Version: 3.5.1
Authors@R: c(
    person("Raphaël", "Nussbaumer", , "rafnuss@gmail.com", role = c("aut", "cre", "cph"),
           comment = c(ORCID = "0000-0002-8185-1020")),
    person("Mathieu", "Gravey", , "mathieu@mgravey.com", role = "aut",
           comment = c(ORCID = "0000-0002-0871-1507"))
  )
Description: R package to determine the position and trajectory of a bird based on light-weight data-logger measuring at lease atmospheric pressure.
License: GPL (>= 3)
URL: https://github.com/Rafnuss/GeoPressureR,
    https://raphaelnussbaumer.com/GeoPressureR/
BugReports: https://github.com/Rafnuss/GeoPressureR/issues
Depends: 
    R (>= 4.1.0)
Imports: 
    cli,
    config,
    EBImage,
    future,
    future.apply,
    ggplot2,
    glue,
    httr2 (>= 1.0.0),
    jsonlite,
    leaflet (>= 2.2.0),
    lifecycle,
    Matrix,
    methods,
    plotly,
    pracma,
    progressr,
    RColorBrewer,
    stats,
    suntools,
    terra,
    utils
Suggests: 
    callr,
    assertthat,
    BiocManager,
    covr,
    ecmwfr (>= 2.0.0),
    knitr,
    leaflet.providers,
    maps,
    rnaturalearth,
    rnaturalearthdata,
    ncdf4,
    readxl,
    shiny,
    shinyjs,
    shinyWidgets,
    testthat (>= 3.0.0),
    withr
biocViews:
Config/testthat/edition: 3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Language: en-GB

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
  • translation

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

GeoPressureR ingests geolocator/tag data and labelled CSVs, retrieves external environmental data via the GeoPressure API/ERA5 and related services, and munges these into geospatial likelihood maps and reconstructed trajectories. It also supports exporting/producing analysis-ready outputs (e.g., label files/pressurepaths) and provides template-style functions to run the full workflow.

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

Researchers and practitioners in movement ecology and ornithology (and more broadly bio-logging/animal tracking) who work with geolocator tag data, especially pressure and light loggers, and need to reconstruct migration routes and stationary periods.

Reconstructing animal trajectories and stopover locations from pressure/light data; generating spatial likelihood maps from atmospheric reanalysis (ERA5) and twilight information; integrating wind fields to model movement; supporting reproducible migration analyses and quality control of tag-derived tracks.

See for more details:

Nussbaumer, R., Gravey, M., Briedis, M., & Liechti, F. (2023). Global positioning with animal-borne pressure sensors. Methods in Ecology and Evolution, 14(4), 1104–1117. https://doi.org/10.1111/2041-210X.14043

Nussbaumer, R., Gravey, M., Briedis, M., Liechti, F., & Sheldon, D. (2023). Reconstructing bird trajectories from pressure and wind data using a highly optimised hidden Markov model. Methods in Ecology and Evolution, 14(4), 1–32. https://doi.org/10.1111/2041-210X.14082

Nussbaumer, R., & Nussbaumer, A. (2024). GeoPressureManual: Learn how to use GeoPressureR with examples. Zenodo. https://doi.org/10.5281/zenodo.10799355. Available at: https://github.com/Rafnuss/GeoPressureManual

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

No other R pacakge.

• (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.

✖ avoid long code lines, it is bad for readability. Also, many people
prefer editor windows that are about 80 characters wide. Try make your lines
shorter than 80 characters
We are using Air, and define a max line of 100 characters.

✖ Package has no HTML vignettes
We are using a quatro book for more complete examples and details information: https://raphaelnussbaumer.com/GeoPressureManual/

Note that the package does not comply with https://devguide.ropensci.org/pkg_building.html#packages-wrapping-web-resources-api-clients. We have several function calling internal API (https://github.com/Rafnuss/GeoPressureAPI). I'm not sure what would be the best practice for this. As a starting point here is what Codex 5.2 is suggesting me: GeoPressure/GeoPressureR#152

Technical checks

Confirm each of the following by checking the box.

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

This package:

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

Publication options

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

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

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

MEE Options

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

[ropensci-review-bot]

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

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Editor check started

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[ropensci-review-bot]

Checks for GeoPressureR (v3.5.0)

git hash: 92ba93ba

• ✔️ Package name is available
• ✔️ has a 'contributing' file.
• ✔️ uses 'roxygen2'.
• ✔️ 'DESCRIPTION' has a URL field.
• ✔️ 'DESCRIPTION' has a BugReports field.
• ✖️ Package has no HTML vignettes
• ✔️ All functions have examples.
• ✔️ Package has continuous integration checks.
• ✖️ Package coverage is 65.5% (should be at least 75%).
• ✖️ Default GitHub branch of 'master' is not acceptable.
• ✔️ R CMD check found no errors.
• ✔️ R CMD check found no warnings.
• 👀 Some goodpractice linters failed.
• 👀 Package has unusually large number of 21 Imports (> 98% of all packages)
• 👀 Examples should not use \dontrun{} unless really necessary.

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

(Checks marked with 👀 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	1911
internal	GeoPressureR	317
internal	grDevices	54
internal	datasets	18
internal	graphics	13
internal	tools	2
imports	cli	196
imports	stats	113
imports	utils	75
imports	ggplot2	66
imports	methods	23
imports	httr2	20
imports	glue	11
imports	lifecycle	9
imports	Matrix	9
imports	terra	9
imports	jsonlite	8
imports	leaflet	6
imports	plotly	5
imports	RColorBrewer	3
imports	progressr	2
imports	EBImage	1
imports	future	1
imports	future.apply	1
imports	config	NA
imports	pracma	NA
imports	suntools	NA
suggests	ncdf4	8
suggests	readxl	2
suggests	callr	1
suggests	ecmwfr	1
suggests	rnaturalearth	1
suggests	assertthat	NA
suggests	BiocManager	NA
suggests	covr	NA
suggests	knitr	NA
suggests	leaflet.providers	NA
suggests	maps	NA
suggests	rnaturalearthdata	NA
suggests	shiny	NA
suggests	shinyjs	NA
suggests	shinyWidgets	NA
suggests	testthat	NA
suggests	withr	NA
linking_to	NA	NA

Click below for tallies of functions used in each package. Locations of each call within this package may be generated locally by running 's <- pkgstats::pkgstats(<path/to/repo>)', and examining the 'external_calls' table.

base

c (302), list (239), length (61), for (57), formals (56), nrow (50), file (44), names (43), data.frame (37), structure (32), seq_len (31), as.numeric (30), unique (29), class (28), lapply (28), which (28), vapply (26), matrix (23), scale (23), abs (21), t (21), rep (20), as.POSIXct (18), is.na (18), sum (18), diff (17), min (17), body (16), do.call (16), max (16), format (15), seq (15), cos (14), logical (14), ncol (14), sin (14), dim (13), as.vector (11), round (11), split (11), col (10), if (10), file.path (9), merge (9), numeric (9), arrayInd (8), debug (8), drop (8), pi (8), pretty (8), setdiff (8), sort (8), write (8), cumsum (7), get (7), match (7), mean (7), units (7), unlist (7), vector (7), which.min (7), dirname (6), is.null (6), with (6), apply (5), as.integer (5), by (5), force (5), integer (5), ls (5), options (5), paste (5), seq_along (5), tempfile (5), all (4), as.data.frame (4), ifelse (4), Im (4), intersect (4), pmax (4), prod (4), range (4), Re (4), Reduce (4), return (4), strptime (4), url (4), any (3), atan2 (3), cbind (3), character (3), findInterval (3), grepl (3), labels (3), log (3), outer (3), paste0 (3), readLines (3), sequence (3), sqrt (3), tan (3), tryCatch (3), anyNA (2), array (2), asin (2), attr (2), ceiling (2), difftime (2), gamma (2), getwd (2), grep (2), inherits (2), is.finite (2), isTRUE (2), load (2), order (2), regexpr (2), regmatches (2), replicate (2), substr (2), system (2), table (2), tcrossprod (2), tolower (2), version (2), acos (1), Arg (1), args (1), as.character (1), as.double (1), as.list (1), as.matrix (1), asNamespace (1), basename (1), complex (1), Conj (1), emptyenv (1), file.exists (1), Filter (1), getOption (1), lengths (1), list.files (1), local (1), missing (1), nchar (1), new.env (1), norm (1), pmin (1), raw (1), rbind (1), rev (1), row.names (1), rowMeans (1), strftime (1), strsplit (1), sub (1), sweep (1), Sys.info (1), system.file (1), union (1), use (1)

GeoPressureR

param_create (30), map_expand (17), tag_create_detect (13), tag_create (11), graph_set_movement (10), mask_water (9), bird_create (8), geopressure_map (8), geolight_map (7), pressurepath_create (7), tag_set_map (7), edge_add_wind (6), geopressure_map_preprocess (6), ts2mat (6), twilight_create (6), graph_create (5), map_type (5), stap2flight (5), graph_simulation (4), graph_transition (4), ind2path (4), tag2map (4), datetime2floathour (3), format_minutes (3), geolight_calibrate (3), geolight_solar (3), geolight_solar_constants (3), graph_add_wind (3), path2edge (3), stap2duration (3), tag_status (3), twilight_include (3), download_geotiff (2), edge_add_wind_fill_var_fl (2), edge_add_wind_interp_path (2), edge_add_wind_nc_info (2), edge_add_wind_prepare_edges (2), edge_add_wind_segment_coords (2), edge_add_wind_weights (2), find_stap (2), fmt_row (2), geolight_fit_location (2), geolight_fit_location_objective (2), geolight_map_calibrate (2), geolight_solar_zenith (2), graph_compute_chunk_size (2), graph_create_bearing (2), graph_create_distance (2), graph_marginal (2), graph_most_likely (2), graph_status (2), light_matrix (2), map_create (2), palette_to_colors (2), path2twilight (2), speed2prob (2), tag_label (2), trainset_read_raw (2), ts2mat_to_long (2), twilight_label_read (2), bullets (1), cli_print_tbl (1), csv2tag (1), dim.map (1), edge_add_wind_check (1), func (1), geolight_map_aggregate (1), geolight_map_likelihood (1), geolight_solar_refracted (1), geolightviz (1), geopressure_map_likelihood (1), geopressure_map_mismatch (1), geopressure_timeseries (1), geopressuretemplate (1), geopressuretemplate_config (1), geopressuretemplate_graph (1), geopressuretemplate_pressurepath (1), geopressuretemplate_tag (1), geopressureviz (1), graph_assert (1), graph_create_coord_calc (1), graph_create_prune (1), haversine_bearing (1), haversine_distance (1), is_map_type (1), length.map (1), load_interim (1), mag_axes (1), map_add_mask_water (1), merge_params (1), path2elevation (1), plot_graph_movement (1), plot_path (1), plot_path_leaflet (1), plot_tag_acceleration (1), plot_tag_light (1), plot_tag_pressure (1), plot_tag_temperature (1), plot_tag_twilight (1), plot.map (1), plot.tag (1), prepare_twilight (1), pressure_diff_warning_data (1), rast.map (1), shiny_launch_browser (1), tag_create_dataframe (1), tag_create_datapackage (1), tag_create_dto (1), tag_prepare_likelihood (1)

cli

cli_abort (73), cli_bullets (51), cli_warn (33), cli_div (9), cli_progress_update (5), pb_name (4), col_blue (3), col_green (3), symbol$info (3), symbol$tick (3), cli_progress_along (1), cli_text (1), cli_verbatim (1), format_inline (1), pb_b (1), pb_bar (1), pb_current (1), pb_percent (1), pb_to (1)

stats

var (27), time (21), df (14), start (7), median (6), end (5), sd (5), approx (4), setNames (4), dt (3), kmeans (3), density (2), dgamma (2), filter (2), smooth (2), approxfun (1), ave (1), dist (1), line (1), optim (1), reshape (1)

utils

data (28), head (13), tail (11), read.delim (6), read.csv (5), askYesNo (3), timestamp (3), packageVersion (2), browseURL (1), fix (1), read.table (1), select.list (1)

ggplot2

aes (28), ggplot (12), theme (7), scale_y_continuous (5), scale_fill_manual (3), as_labeller (2), element_blank (2), facet_wrap (2), map_data (2), scale_fill_gradient (2), coord_cartesian (1)

grDevices

palette (52), colors (1), colours (1)

methods

is (13), as (9), new (1)

httr2

resp_body_json (6), req_perform (5), request (5), req_body_json (2), resp_body_string (2)

datasets

pressure (18)

graphics

par (5), text (3), grid (2), legend (2), title (1)

glue

glue (11)

lifecycle

deprecated (9)

Matrix

sparseMatrix (8), t (1)

terra

rast (3), as.matrix (2), plot (1), project (1), rasterize (1), vect (1)

jsonlite

toJSON (8)

ncdf4

ncvar_get (6), nc_open (2)

leaflet

leaflet (3), addProviderTiles (1), colorNumeric (1), layersControlOptions (1)

plotly

ggplotly (5)

RColorBrewer

brewer.pal (2), brewer.pal.info (1)

progressr

handlers (1), progressor (1)

readxl

read_excel (2)

tools

file_ext (2)

callr

r_bg (1)

EBImage

distmap (1)

ecmwfr

wf_set_key (1)

future

plan (1)

future.apply

future_lapply (1)

rnaturalearth

ne_countries (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 CSS (1% in 2 files), JavaScript (2% in 2 files), R (96% in 120 files) and YAML (0% in 1 files)
• 2 authors
• no vignette
• no internal data file
• 21 imported packages
• 84 exported functions (median 50 lines of code)
• 75 non-exported functions in R (median 22 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	93	98.9
files_inst	29	98.5
files_vignettes	0	0.0	TRUE
files_tests	31	97.9
loc_R	9216	97.9	TRUE
loc_inst	4976	94.7
loc_tests	1853	91.7
num_vignettes	0	0.0	TRUE
n_fns_r	159	94.0
n_fns_r_exported	84	92.8
n_fns_r_not_exported	75	93.4
n_fns_per_file_r	2	44.2
num_params_per_fn	4	54.7
loc_per_fn_r	31	76.6
loc_per_fn_r_exp	50	79.2
loc_per_fn_r_not_exp	22	87.9
rel_whitespace_R	15	97.1	TRUE
rel_whitespace_inst	9	97.1	TRUE
rel_whitespace_tests	19	94.6
doclines_per_fn_exp	50	64.3
doclines_per_fn_not_exp	6	86.3
fn_call_network_size	392	92.8

---

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
22893579051	format-check.yaml	success	92ba93	35	2026-03-10
22893579040	jarl-check	success	92ba93	35	2026-03-10
22893579043	pkgdown.yaml	success	92ba93	487	2026-03-10
22893579041	R-CMD-check.yaml	success	92ba93	519	2026-03-10
22893579057	test-coverage	success	92ba93	392	2026-03-10

---

3b. goodpractice results

Test coverage with covr

Package coverage: 65.49

The following files are not completely covered by tests:

file	coverage
R/edge_add_wind.R	0%
R/geolightviz.R	0%
R/geopressure_timeseries.R	62.16%
R/geopressuretemplate_config.R	45.71%
R/geopressuretemplate_graph.R	61.79%
R/geopressuretemplate_pressurepath.R	51.56%
R/geopressureviz.R	0%
R/graph_add_wind.R	0%
R/graph_create.R	69.74%
R/graph_transition.R	66.67%
R/load_interim.R	21.21%
R/path2twilight.R	67.9%
R/pressurepath_update.R	0%
R/read_stap.R	0%
R/shiny_run_app.R	0%
R/tag_assert.R	66.87%
R/tag_create_bas.R	0%
R/tag_create_dataframe.R	26.67%
R/tag_create_datapackage.R	0%
R/tag_create_soi.R	35.02%
R/tag_label_period.r	0%
R/tag_label_read.R	55.81%
R/tag_label.R	13.16%
R/tag_prepare_likelihood.R	68.42%
R/tag_set_map.R	68.47%
R/tag_stap_daily.R	56.94%
R/tag_update.R	0%
R/tag2map.R	66.67%
R/tag2path.R	69.44%
R/trainset.r	0%
R/zzz.R	57.89%

Cyclocomplexity with cyclocomp

The following functions have cyclocomplexity >= 15:

function	cyclocomplexity
tag_set_map	37
tag_status	36
edge_add_wind_check	33
edge_add_wind	32
tag_assert	31
geopressure_map_mismatch	28
print.tag	28
edge_add_wind_fill_var_fl	27
bird_create	25
geolight_fit_location	25
plot.map	25
tag_stap_daily	24
tag_prepare_likelihood	23
geopressure_map_preprocess	22
palette_to_colors	21
tag_label_stap	20
geopressure_timeseries	19
geopressureviz	19
tag_create_soi	19
tag2path	19
load_interim	18
tag_update	18
graph_create	17
graph_simulation	17
plot.tag	17
tag_create	17
geopressuretemplate_pressurepath	16
prepare_twilight	16
pressurepath_create	16
graph_create_prune	15
plot_graph_movement	15
tag_create_migratetech	15
trainset	15

Static code analyses with lintr

lintr found the following 1246 potential issues:

message	number of times
Avoid library() and require() calls in packages	12
Lines should not be more than 80 characters.	1234

---

Package Versions

package	version
pkgstats	0.2.2.15
pkgcheck	0.1.2.274

---

Editor-in-Chief Instructions:

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

This package has some noteworthy properties, see 'Package Statistics' details above.

[Rafnuss]

@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 GeoPressureR (v3.5.1)

git hash: 093951c6

• ✔️ Package name is available
• ✔️ has a 'contributing' file.
• ✔️ uses 'roxygen2'.
• ✔️ 'DESCRIPTION' has a URL field.
• ✔️ 'DESCRIPTION' has a BugReports field.
• ✖️ Package has no HTML vignettes
• ✔️ All functions have examples.
• ✔️ Package has continuous integration checks.
• ✔️ Package coverage is 81.6%.
• ✔️ R CMD check found no errors.
• ✔️ R CMD check found no warnings.
• 👀 Some goodpractice linters failed.
• 👀 Package has unusually large number of 21 Imports (> 98% of all packages)
• 👀 Examples should not use \dontrun{} unless really necessary.

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

(Checks marked with 👀 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	1892
internal	GeoPressureR	317
internal	grDevices	54
internal	datasets	18
internal	graphics	13
internal	tools	2
imports	cli	195
imports	stats	106
imports	utils	78
imports	ggplot2	66
imports	methods	23
imports	httr2	20
imports	glue	11
imports	lifecycle	9
imports	Matrix	9
imports	terra	9
imports	jsonlite	8
imports	leaflet	6
imports	plotly	5
imports	RColorBrewer	3
imports	progressr	2
imports	EBImage	1
imports	future	1
imports	future.apply	1
imports	config	NA
imports	pracma	NA
imports	suntools	NA
suggests	ncdf4	8
suggests	readxl	2
suggests	callr	1
suggests	ecmwfr	1
suggests	rnaturalearth	1
suggests	assertthat	NA
suggests	BiocManager	NA
suggests	covr	NA
suggests	knitr	NA
suggests	leaflet.providers	NA
suggests	maps	NA
suggests	rnaturalearthdata	NA
suggests	shiny	NA
suggests	shinyjs	NA
suggests	shinyWidgets	NA
suggests	testthat	NA
suggests	withr	NA
linking_to	NA	NA

Click below for tallies of functions used in each package. Locations of each call within this package may be generated locally by running 's <- pkgstats::pkgstats(<path/to/repo>)', and examining the 'external_calls' table.

base

c (297), list (242), length (60), for (56), formals (56), nrow (48), file (45), names (39), data.frame (36), seq_len (31), as.numeric (29), which (29), lapply (28), structure (28), unique (27), vapply (26), class (24), matrix (23), scale (23), abs (21), t (21), rep (20), as.POSIXct (18), is.na (18), sum (18), diff (17), min (17), body (16), do.call (16), max (16), format (15), if (15), seq (15), cos (14), logical (14), ncol (14), sin (14), dim (13), as.vector (11), round (11), split (11), col (10), return (10), numeric (9), arrayInd (8), debug (8), drop (8), pi (8), pretty (8), setdiff (8), sort (8), write (8), cumsum (7), get (7), is.null (7), match (7), mean (7), units (7), unlist (7), vector (7), which.min (7), dirname (6), with (6), apply (5), as.integer (5), file.path (5), force (5), integer (5), ls (5), merge (5), options (5), paste (5), seq_along (5), tempfile (5), all (4), as.data.frame (4), ifelse (4), Im (4), interactive (4), intersect (4), pmax (4), prod (4), range (4), Re (4), Reduce (4), strptime (4), url (4), any (3), atan2 (3), cbind (3), character (3), grepl (3), labels (3), log (3), outer (3), paste0 (3), readLines (3), sequence (3), sqrt (3), tan (3), tryCatch (3), anyNA (2), array (2), asin (2), by (2), ceiling (2), difftime (2), file.exists (2), findInterval (2), gamma (2), getOption (2), getwd (2), grep (2), inherits (2), is.finite (2), isTRUE (2), load (2), order (2), regexpr (2), regmatches (2), replicate (2), substr (2), system (2), table (2), tcrossprod (2), tolower (2), version (2), acos (1), Arg (1), args (1), as.double (1), as.list (1), as.matrix (1), asNamespace (1), attr (1), basename (1), complex (1), Conj (1), emptyenv (1), Filter (1), lengths (1), list.files (1), local (1), missing (1), nchar (1), new.env (1), norm (1), pmin (1), rev (1), row.names (1), rowMeans (1), strftime (1), strsplit (1), sub (1), sweep (1), Sys.info (1), system.file (1), use (1)

GeoPressureR

param_create (26), map_expand (17), tag_create_detect (13), graph_set_movement (10), tag_create (10), mask_water (9), bird_create (8), geopressure_map (8), geolight_map (7), tag_set_map (7), edge_add_wind (6), pressurepath_create (6), tag_create_tabular_read (6), ts2mat (6), geopressure_map_preprocess (5), graph_create (5), map_type (5), stap2flight (5), twilight_create (5), graph_simulation (4), graph_transition (4), ind2path (4), tag2map (4), datetime2floathour (3), format_minutes (3), geolight_calibrate (3), geolight_solar (3), geolight_solar_constants (3), graph_add_wind (3), path2edge (3), stap2duration (3), tag_status (3), twilight_include (3), download_geotiff (2), edge_add_wind_fill_var_fl (2), edge_add_wind_interp_path (2), edge_add_wind_nc_info (2), edge_add_wind_prepare_edges (2), edge_add_wind_segment_coords (2), edge_add_wind_weights (2), find_stap (2), fmt_row (2), geolight_fit_location (2), geolight_fit_location_objective (2), geolight_map_calibrate (2), geolight_solar_zenith (2), graph_compute_chunk_size (2), graph_create_bearing (2), graph_create_distance (2), graph_marginal (2), graph_most_likely (2), graph_status (2), light_matrix (2), map_create (2), palette_to_colors (2), path2twilight (2), speed2prob (2), tag_label (2), trainset_read_raw (2), ts2mat_to_long (2), twilight_label_read (2), bullets (1), cli_print_tbl (1), csv2tag (1), dim.map (1), edge_add_wind_check (1), func (1), geolight_map_aggregate (1), geolight_map_likelihood (1), geolight_solar_refracted (1), geolightviz (1), geopressure_map_likelihood (1), geopressure_map_mismatch (1), geopressure_timeseries (1), geopressuretemplate (1), geopressuretemplate_config (1), geopressuretemplate_graph (1), geopressuretemplate_pressurepath (1), geopressuretemplate_tag (1), geopressureviz (1), graph_assert (1), graph_create_coord_calc (1), graph_create_prune (1), haversine_bearing (1), haversine_distance (1), is_map_type (1), length.map (1), load_interim (1), mag_axes (1), map_add_mask_water (1), merge_params (1), path2elevation (1), plot_graph_movement (1), plot_path (1), plot_path_leaflet (1), plot_path_static (1), plot_tag_acceleration (1), plot_tag_light (1), plot_tag_pressure (1), plot_tag_temperature (1), plot_tag_twilight (1), plot.map (1), plot.tag (1), prepare_twilight (1), pressure_diff_warning_data (1), rast.map (1), shiny_launch_browser (1), tag_create_csv (1), tag_create_dto (1), tag_create_soi (1), tag_create_tabular (1), tag_prepare_likelihood (1)

cli

cli_abort (74), cli_bullets (51), cli_warn (31), cli_div (9), cli_progress_update (5), pb_name (4), col_blue (3), col_green (3), symbol$info (3), symbol$tick (3), cli_progress_along (1), cli_text (1), cli_verbatim (1), format_inline (1), pb_b (1), pb_bar (1), pb_current (1), pb_percent (1), pb_to (1)

stats

var (25), time (21), df (10), median (6), end (5), sd (5), start (5), approx (4), setNames (4), dt (3), kmeans (3), density (2), dgamma (2), filter (2), line (2), smooth (2), approxfun (1), ave (1), dist (1), optim (1), reshape (1)

utils

data (35), head (13), tail (11), read.delim (6), read.csv (5), timestamp (3), packageVersion (2), browseURL (1), fix (1), read.table (1)

ggplot2

aes (28), ggplot (12), theme (7), scale_y_continuous (5), scale_fill_manual (3), as_labeller (2), element_blank (2), facet_wrap (2), map_data (2), scale_fill_gradient (2), coord_cartesian (1)

grDevices

palette (52), colors (1), colours (1)

methods

is (13), as (9), new (1)

httr2

resp_body_json (6), req_perform (5), request (5), req_body_json (2), resp_body_string (2)

datasets

pressure (18)

graphics

par (5), text (3), grid (2), legend (2), title (1)

glue

glue (11)

lifecycle

deprecated (9)

Matrix

sparseMatrix (8), t (1)

terra

rast (3), as.matrix (2), plot (1), project (1), rasterize (1), vect (1)

jsonlite

toJSON (8)

ncdf4

ncvar_get (6), nc_open (2)

leaflet

leaflet (3), addProviderTiles (1), colorNumeric (1), layersControlOptions (1)

plotly

ggplotly (5)

RColorBrewer

brewer.pal (2), brewer.pal.info (1)

progressr

handlers (1), progressor (1)

readxl

read_excel (2)

tools

file_ext (2)

callr

r_bg (1)

EBImage

distmap (1)

ecmwfr

wf_set_key (1)

future

plan (1)

future.apply

future_lapply (1)

rnaturalearth

ne_countries (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 CSS (1% in 2 files), JavaScript (2% in 2 files), R (96% in 116 files) and YAML (0% in 1 files)
• 2 authors
• no vignette
• no internal data file
• 21 imported packages
• 82 exported functions (median 50 lines of code)
• 75 non-exported functions in R (median 20 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	89	98.8
files_inst	29	98.5
files_vignettes	0	0.0	TRUE
files_tests	34	98.3
loc_R	8918	97.8	TRUE
loc_inst	4976	94.7
loc_tests	2260	93.5
num_vignettes	0	0.0	TRUE
n_fns_r	157	93.9
n_fns_r_exported	82	92.5
n_fns_r_not_exported	75	93.4
n_fns_per_file_r	2	44.4
num_params_per_fn	4	54.7
loc_per_fn_r	31	76.6
loc_per_fn_r_exp	50	79.2
loc_per_fn_r_not_exp	20	86.4
rel_whitespace_R	15	96.8	TRUE
rel_whitespace_inst	9	97.1	TRUE
rel_whitespace_tests	18	95.6	TRUE
doclines_per_fn_exp	50	65.2
doclines_per_fn_not_exp	6	86.3
fn_call_network_size	385	92.7

---

2a. Network visualisation

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

---

3. goodpractice and other checks

Details of goodpractice checks (click to open)

3a. Continuous Integration Badges

GitHub Workflow Results

id	name	conclusion	sha	run_number	date
22950379354	format-check.yaml	success	093951	45	2026-03-11
22950379367	jarl-check	success	093951	45	2026-03-11
22950379327	pkgdown.yaml	success	093951	498	2026-03-11
22950379338	R-CMD-check.yaml	success	093951	529	2026-03-11
22950379325	test-coverage	success	093951	402	2026-03-11

---

3b. goodpractice results

Test coverage with covr

Package coverage: 81.59

Cyclocomplexity with cyclocomp

The following functions have cyclocomplexity >= 15:

function	cyclocomplexity
tag_set_map	38
tag_status	36
edge_add_wind_check	33
edge_add_wind	32
tag_assert	31
geopressure_map_mismatch	28
print.tag	28
edge_add_wind_fill_var_fl	27
bird_create	25
geolight_fit_location	25
plot.map	25
tag_stap_daily	24
tag_prepare_likelihood	23
geopressure_map_preprocess	22
palette_to_colors	21
tag_label	21
tag_label_stap	20
geopressure_timeseries	19
geopressureviz	19
tag_create	19
tag_create_crop	19
tag_create_soi	19
tag2path	19
graph_create	17
graph_simulation	17
plot.tag	17
geopressuretemplate_pressurepath	16
prepare_twilight	16
pressurepath_create	16
graph_create_prune	15
load_interim	15
plot_graph_movement	15
tag_create_migratetech	15
trainset	15

Static code analyses with lintr

lintr found the following 1235 potential issues:

message	number of times
Avoid library() and require() calls in packages	12
Lines should not be more than 80 characters.	1223

---

Package Versions

package	version
pkgstats	0.2.2.15
pkgcheck	0.1.2.274

---

Editor-in-Chief Instructions:

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

This package has some noteworthy properties, see 'Package Statistics' details above.

[Rafnuss]

✖️ Package has no HTML vignettes

The package currently does not include an HTML vignette because the full documentation and workflow examples are provided in a dedicated Quarto manual: https://raphaelnussbaumer.com/GeoPressureManual/

This manual serves the same purpose as a vignette, but allows substantially richer documentation than what can realistically be maintained inside a package vignette.

The rOpenSci guideline requesting an HTML vignette aims to ensure that users have clear, workflow-oriented documentation of package functionality. The Quarto manual fulfills this role and goes substantially beyond what a typical vignette would provide.

Because this documentation is already maintained externally in a dedicated manual, duplicating it as a vignette would introduce redundancy and risk divergence between the two sources.

[emilyriederer]

Hi @Rafnuss -- thanks for your submission. To help us better ground the package, could you please share a bullet point on how it fits into each of the criteria that you mention? For example, if you see our categories, data retrieval is for "accessing and downloading data from online sources with scientific applications" while data extraction is "retrieving data from unstructured sources". Does this package do both? From your initial description, I was not also clear how "data deposition" is relevant.

[Rafnuss]

Hi @emilyriederer, thanks for this clarification.

You are right that my initial scope text was too broad. I've removed "scientific software wrappers" (not really coorect) and "data deposition" (performed in associated GeoLocatoR package)

Here is a category-by-category mapping for GeoPressureR:

• data retrieval: GeoPressureR retrieves external environmental data (ERA5), e.g. tag_download_wind() (ERA5 via CDS/ecmwfr) and GeoPressureAPI/GEE queries in geopressure_map_*() and pressurepath_create().
• data extraction: GeoPressureR parses raw files from geolocator manufacturers (e.g. SOI .pressure/.glf, MigrateTech .deg/.lux, BAS .lig, Lund .xlsx, PresTag .txt) into standardized R structures via tag_create().
• data munging: GeoPressureR transforms those extracted/retrieved data into analysis-ready objects (labeling, stationary periods, likelihood maps, movement graphs, reconstructed paths).
• workflow automation: geopressuretemplate() automates the full end-to-end workflow (tag creation, map building, graph inference, pressurepath outputs).
• geospatial data: core outputs are likelihood maps (rasters) and trajectories (polylines), with geospatial map operations throughout the workflow and integrations of terra package.

For your specific question: yes, the package does both retrieval (online ERA5/API sources) and extraction (raw logger file parsing), but no data deposition.

Hope this clarify your questions. Feel free to make suggestions on these categories if I missunderstood them.
Thanks!

[emilyriederer]

@ropensci-review-bot check package

[ropensci-review-bot]

Thanks, about to send the query.

[ropensci-review-bot]

🚀

Editor check started

👋