spiro: Manage Data from Cardiopulmonary Exercise Testing

[smnnlt]

Date accepted: 2022-08-17
Submitting Author Name: Simon Nolte
Submitting Author Github Handle: @smnnlt
Repository: https://github.com/smnnlt/spiro
Version submitted: 0.0.5
Submission type: Standard
Editor: @melvidoni
Reviewers: @jameshunterbr, @manuramon

Due date for @jameshunterbr: 2022-07-11

Due date for @manuramon: 2022-07-22

Archive: TBD
Version accepted: TBD

Language: en

---

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

Package: spiro
Title: Manage Data from Cardiopulmonary Exercise Testing
Version: 0.0.5
Authors@R: 
    person(given = "Simon",
           family = "Nolte",
           role = c("aut", "cre"),
           email = "s.nolte@dshs-koeln.de",
           comment = c(ORCID = "0000-0003-1643-1860"))
Description: Import, process, summarize and visualize raw data from 
    metabolic carts.
License: MIT + file LICENSE
URL: https://github.com/smnnlt/spiro, https://smnnlt.github.io/spiro/
BugReports: https://github.com/smnnlt/spiro/issues
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.0
Imports: 
    ggplot2,
    xml2,
    readxl,
    knitr,
    cowplot,
    digest,
    signal
Suggests: 
    testthat (>= 3.0.0),
    rmarkdown,
    ggborderline
VignetteBuilder: knitr
Config/testthat/edition: 3

Scope

• Please indicate which category or categories from our package fit policies this package falls under: (Please check an appropriate box below. If you are unsure, we suggest you make a pre-submission inquiry.):

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

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

The spiro package allows to read and process data from raw data files of different metabolic carts.

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

This package is primarily written for researchers in exercise science, who want to make their analysis of cardiopulmonary exercise testing more standardized, reproducible and faster. It may also be used in a commercial context (e.g., training diagnostics business).

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

The whippr package has a different approach to the same problem. Compared to whippr, spiro has a more automated and simpler data workflow (basically one function for reading and processing data, and one function for summarizing or plotting). spiro has several relevant additional features, that whippr does not have: Automated detection and manual generation of exercise test protocols; data summary by load steps; adding and synchronizing external heart rate data; import of raw data file meta data; advanced data filtering methods (e.g., Butterworth filters; moving breath averages); Wasserman 9-Panel-Plots. Compared to whippr, the spiro package does not offer methods for VO2 kinetics analysis and automated outlier removal.

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

This package works with cardiopulmonary exercise data, which is per se sensitive health data. Meta data from the original raw data files is read and anonymized by default (with the exception of data on body mass, which is necessary to perform certain calculations of variables). The anonymization can optionally be deactivated by means of a function argument [spiro(anonymize = FALSE)], so that meta data is saved alongside the processed data. This may be helpful in some settings when there is no intent to share the data. Sharing of the resulting data in such situations could potentially reveal personal information, which is why this option is not activated by default.

• 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.

#537

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

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 using services such as Travis CI, Coveralls and/or CodeCov.

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.

[ropensci-review-bot]

🚀

Editor check started

👋

[ropensci-review-bot]

Checks for spiro (v0.0.5)

git hash: 92301b28

• ✔️ Package name is available
• ✔️ has a 'codemeta.json' file.
• ✔️ has a 'contributing' file.
• ✔️ uses 'roxygen2'.
• ✔️ 'DESCRIPTION' has a URL field.
• ✔️ 'DESCRIPTION' has a BugReports field.
• ✔️ Package has at least one HTML vignette
• ✖️ These functions do not have examples: [bw_filter, get_features, get_testtype, guess_device, knit_print.spiro, print.spiro, spiro_import_cortex, spiro_import_cosmed, spiro_import_vyntus, spiro_import_zan, spiro_interpolate, spiro_smooth].
• ✖️ Function names are duplicated in other packages
• ✔️ Package has continuous integration checks.
• ✔️ Package coverage is 91.3%.
• ✔️ R CMD check found no errors.
• ✔️ R CMD check found no warnings.

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

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	311
internal	spiro	139
internal	utils	121
internal	stats	55
internal	mgcv	1
imports	ggplot2	51
imports	xml2	9
imports	readxl	6
imports	signal	2
imports	cowplot	1
imports	knitr	NA
imports	digest	NA
suggests	testthat	NA
suggests	rmarkdown	NA
suggests	ggborderline	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 (57), data.frame (24), file (23), list (18), which (16), as.numeric (13), nrow (12), max (10), seq_along (10), attr (8), raw (8), rep.int (8), round (7), length (6), diff (5), lapply (5), range (5), vapply (5), as.data.frame (4), cbind (4), names (4), switch (4), drop (3), for (3), is.na (3), suppressWarnings (3), colnames (2), do.call (2), mean (2), min (2), numeric (2), rep (2), rev (2), rownames (2), split (2), strsplit (2), suppressMessages (2), unique (2), anyDuplicated (1), apply (1), as.character (1), character (1), duplicated (1), factor (1), grepl (1), levels (1), list.files (1), ls (1), mapply (1), paste0 (1), rbind (1), row.names (1), seq_len (1), seq.int (1), sum (1), system.file (1), unlist (1)

spiro

get_data (29), get_meta (10), spiro_smooth (10), get_sex (4), to_seconds (4), to_number (3), add_bodymass (2), add_protocol (2), bw_smooth_extract (2), calo.internal (2), check_bb (2), dupl (2), get_id (2), get_smooth_data (2), get_wrongcol_string (2), getstepmeans (2), gettime (2), hr_import (2), import_xml (2), replace_intna (2), smooth_match (2), spiro_import (2), spiro_interpolate (2), spiro_interpolate.internal (2), spiro_plot.guess_units (2), spiro_plot.internal (2), add_hr (1), bw_filter (1), calo (1), const (1), get_features (1), get_protocol (1), get_testtype (1), guess_device (1), hr_interpolate (1), knit_print.spiro (1), mavg (1), pre (1), print.spiro (1), set_protocol (1), set_protocol_manual (1), set_protocol_manual.data.frame (1), set_protocol_manual.default (1), spiro (1), spiro_anonymize (1), spiro_example (1), spiro_import_cortex (1), spiro_import_cosmed (1), spiro_import_vyntus (1), spiro_import_zan (1), spiro_max (1), spiro_plot (1), spiro_plot_EQ (1), spiro_plot_EQCO2 (1), spiro_plot_HR (1), spiro_plot_Pet (1), spiro_plot_RER (1), spiro_plot_VE (1), spiro_plot_vent (1), spiro_plot_VO2 (1), spiro_plot_vslope (1), spiro_smooth.internal (1), spiro_summary (1), steps (1), theme_spiro (1)

utils

data (106), read.delim (7), head (5), read.csv (3)

stats

smooth (20), time (13), approx (7), df (7), reshape (5), filter (2), end (1)

ggplot2

aes (20), ggplot (8), labs (7), scale_colour_manual (5), scale_y_continuous (3), sec_axis (3), aes_ (2), scale_color_manual (1), scale_fill_manual (1), theme_minimal (1)

xml2

xml_find_all (3), xml_text (3), read_xml (2), xml_children (1)

readxl

read_excel (6)

signal

butter (1), filtfilt (1)

cowplot

plot_grid (1)

mgcv

s (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 15 files) and
• 1 authors
• 2 vignettes
• no internal data file
• 7 imported packages
• 31 exported functions (median 20 lines of code)
• 103 non-exported functions in R (median 15 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	15	73.0
files_vignettes	2	85.7
files_tests	11	91.7
loc_R	1563	79.1
loc_vignettes	208	50.8
loc_tests	275	62.3
num_vignettes	2	89.2
n_fns_r	134	83.0
n_fns_r_exported	31	79.2
n_fns_r_not_exported	103	84.4
n_fns_per_file_r	5	67.1
num_params_per_fn	2	11.9
loc_per_fn_r	16	49.2
loc_per_fn_r_exp	20	46.7
loc_per_fn_r_not_exp	15	49.5
rel_whitespace_R	17	77.3
rel_whitespace_vignettes	37	54.2
rel_whitespace_tests	18	55.9
doclines_per_fn_exp	32	36.7
doclines_per_fn_not_exp	0	0.0	TRUE
fn_call_network_size	124	82.6

---

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

GitHub Workflow Results

id	name	conclusion	sha	run_number	date
2462665426	pages build and deployment	success	33cc31	26	2022-06-08
2459834392	pkgdown	success	92301b	68	2022-06-08
2459834396	R-CMD-check	failure	92301b	40	2022-06-08
2459834394	test-coverage	success	92301b	39	2022-06-08

---

3b. goodpractice results

R CMD check with rcmdcheck

rcmdcheck found no errors, warnings, or notes

Test coverage with covr

Package coverage: 91.29

Cyclocomplexity with cyclocomp

No functions have cyclocomplexity >= 15

Static code analyses with lintr

lintr found no issues with this package!

---

4. Other Checks

Details of other checks (click to open)

✖️ The following 4 function names are duplicated in other packages:

• • const from arpr, CMLS, labdsv, sketch, timereg
• • get_id from CVXR, epicontacts, eventr, IOHanalyzer, panelr, rbenvo, rmonad, seqmagick
• • pre from DAMisc, html5, htmltools, pre, supernova, yonder
• • steps from amt, ddpcr, fitbitr, shiny.semantic

---

Package Versions

package	version
pkgstats	0.0.4.75
pkgcheck	0.0.3.60

---

Editor-in-Chief Instructions:

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

[smnnlt]

Hi, I have added examples and renamed the functions that may lead to namespace conflicts.

[mpadge]

Thanks @smnnlt , we've recently added an ability for submitting authors to directly call ˋ@ropensci-review-bot check packageˋ. Feel free to give that a try, to re-run the checks. (You'd get to be the first author to do so 🚀)

[smnnlt]

@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 spiro (v0.0.5.9000)

git hash: b5db6e6e

• ✔️ Package name is available
• ✔️ has a 'codemeta.json' file.
• ✔️ has a 'contributing' file.
• ✔️ uses 'roxygen2'.
• ✔️ 'DESCRIPTION' has a URL field.
• ✔️ 'DESCRIPTION' has a BugReports field.
• ✔️ Package has at least one HTML vignette
• ✔️ All functions have examples.
• ✔️ Package has continuous integration checks.
• ✔️ Package coverage is 91.3%.
• ✔️ R CMD check found no errors.
• ✔️ R CMD check found no warnings.

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	311
internal	spiro	139
internal	utils	121
internal	stats	56
internal	mgcv	1
imports	ggplot2	51
imports	xml2	9
imports	readxl	6
imports	signal	2
imports	cowplot	1
imports	knitr	NA
imports	digest	NA
suggests	testthat	NA
suggests	rmarkdown	NA
suggests	ggborderline	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 (57), data.frame (24), file (23), list (18), which (16), as.numeric (13), nrow (12), max (10), seq_along (10), attr (8), raw (8), rep.int (8), round (7), length (6), diff (5), lapply (5), range (5), vapply (5), as.data.frame (4), cbind (4), names (4), switch (4), drop (3), for (3), is.na (3), suppressWarnings (3), colnames (2), do.call (2), mean (2), min (2), numeric (2), rep (2), rev (2), rownames (2), split (2), strsplit (2), suppressMessages (2), unique (2), anyDuplicated (1), apply (1), as.character (1), character (1), duplicated (1), factor (1), grepl (1), levels (1), list.files (1), ls (1), mapply (1), paste0 (1), rbind (1), row.names (1), seq_len (1), seq.int (1), sum (1), system.file (1), unlist (1)

spiro

get_data (29), get_meta (10), spiro_smooth (10), get_sex (4), to_seconds (4), add_bodymass (2), add_protocol (2), bw_smooth_extract (2), calo.internal (2), check_bb (2), dupl (2), get_anonid (2), get_smooth_data (2), get_wrongcol_string (2), getstepmeans (2), gettime (2), hr_import (2), import_xml (2), replace_intna (2), smooth_match (2), spiro_import (2), spiro_interpolate (2), spiro_interpolate.internal (2), spiro_plot.guess_units (2), spiro_plot.internal (2), to_number (2), add_hr (1), bw_filter (1), calo (1), get_features (1), get_protocol (1), get_testtype (1), guess_device (1), hr_interpolate (1), knit_print.spiro (1), mavg (1), print.spiro (1), pt_const (1), pt_pre (1), pt_steps (1), pt_wu (1), set_protocol (1), set_protocol_manual (1), set_protocol_manual.data.frame (1), set_protocol_manual.default (1), spiro (1), spiro_anonymize (1), spiro_example (1), spiro_import_cortex (1), spiro_import_cosmed (1), spiro_import_vyntus (1), spiro_import_zan (1), spiro_max (1), spiro_plot (1), spiro_plot_EQ (1), spiro_plot_EQCO2 (1), spiro_plot_HR (1), spiro_plot_Pet (1), spiro_plot_RER (1), spiro_plot_VE (1), spiro_plot_vent (1), spiro_plot_VO2 (1), spiro_plot_vslope (1), spiro_smooth.internal (1), spiro_summary (1), theme_spiro (1)

utils

data (106), read.delim (7), head (5), read.csv (3)

stats

smooth (20), time (13), approx (7), df (7), reshape (5), filter (2), dt (1), end (1)

ggplot2

aes (20), ggplot (8), labs (7), scale_colour_manual (5), scale_y_continuous (3), sec_axis (3), aes_ (2), scale_color_manual (1), scale_fill_manual (1), theme_minimal (1)

xml2

xml_find_all (3), xml_text (3), read_xml (2), xml_children (1)

readxl

read_excel (6)

signal

butter (1), filtfilt (1)

cowplot

plot_grid (1)

mgcv

s (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 15 files) and
• 1 authors
• 2 vignettes
• no internal data file
• 7 imported packages
• 23 exported functions (median 14 lines of code)
• 111 non-exported functions in R (median 16 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	15	73.0
files_vignettes	2	85.7
files_tests	11	91.7
loc_R	1563	79.1
loc_vignettes	208	50.8
loc_tests	275	62.3
num_vignettes	2	89.2
n_fns_r	134	83.0
n_fns_r_exported	23	71.4
n_fns_r_not_exported	111	85.7
n_fns_per_file_r	5	67.1
num_params_per_fn	3	33.6
loc_per_fn_r	16	49.2
loc_per_fn_r_exp	14	33.2
loc_per_fn_r_not_exp	16	52.7
rel_whitespace_R	17	77.2
rel_whitespace_vignettes	37	54.2
rel_whitespace_tests	18	55.9
doclines_per_fn_exp	40	50.1
doclines_per_fn_not_exp	0	0.0	TRUE
fn_call_network_size	124	82.6

---

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

GitHub Workflow Results

id	name	conclusion	sha	run_number	date
2468348888	pages build and deployment	success	cd779d	27	2022-06-09
2468334160	pkgdown	success	b5db6e	70	2022-06-09
2468334164	R-CMD-check	failure	b5db6e	42	2022-06-09
2468334158	test-coverage	success	b5db6e	41	2022-06-09

---

3b. goodpractice results

R CMD check with rcmdcheck

rcmdcheck found no errors, warnings, or notes

Test coverage with covr

Package coverage: 91.29

Cyclocomplexity with cyclocomp

No functions have cyclocomplexity >= 15

Static code analyses with lintr

lintr found the following 1 potential issues:

message	number of times
Lines should not be more than 80 characters.	1

---

Package Versions

package	version
pkgstats	0.0.4.75
pkgcheck	0.0.3.60

---

Editor-in-Chief Instructions:

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

[emilyriederer]

Hi @smnnlt ! Thank you for the full submission and your proactive work addressing the bots feedback. I'm currently seeking a handling editor and hope to kick-off the full review soon.

[emilyriederer]

@ropensci-review-bot assign @melvidoni as editor

[ropensci-review-bot]

Assigned! @melvidoni is now the editor