coevolve: Fit Bayesian Generalized Dynamic Phylogenetic Models using 'Stan'

[ScottClaessens]

Submitting Author Name: Scott Claessens
Submitting Author Github Handle: @ScottClaessens
Other Package Authors Github handles: @ErikRingen
Repository: https://github.com/ScottClaessens/coevolve
Version submitted: 0.1.0.9005
Submission type: Stats
Badge grade: gold
Editor: @natydasilva
Reviewers: TBD
Due dates: TBD
Archive: TBD
Version accepted: TBD
Language: en

---

Package: coevolve
Title: Fit Bayesian Generalized Dynamic Phylogenetic Models using 'Stan'
Version: 0.1.0.9005
Authors@R: 
    c(person("Scott", "Claessens", , "scott.claessens@gmail.com", 
             role = c("aut", "cre"), comment = c(ORCID = "0000-0002-3562-6981")),
      person("Erik", "Ringen", , "erikjacob.ringen@uzh.ch", 
             role = c("aut")))
Description: Fit Bayesian generalized dynamic phylogenetic models using 'Stan'. 
    The package allows an abritrary number of variables with different response 
    distributions to coevolve on a phylogenetic tree via an Ornstein-Uhlenbeck 
    evolutionary process, allowing users to assess directionality between 
    coevolving variables.
License: GPL (>= 3)
URL: https://github.com/ScottClaessens/coevolve, https://scottclaessens.github.io/coevolve/
BugReports: https://github.com/ScottClaessens/coevolve/issues
Encoding: UTF-8
Roxygen: list(markdown = TRUE, roclets = c("namespace", "rd", "srr::srr_stats_roclet"))
RoxygenNote: 7.3.2
Suggests: 
    knitr,
    rmarkdown,
    testthat (>= 3.0.0),
    tibble,
    withr
Config/testthat/edition: 3
Imports: 
    ape,
    bayesplot,
    cmdstanr,
    colorspace,
    dplyr,
    ggplot2,
    gridExtra,
    Matrix,
    methods,
    patchwork,
    phangorn,
    phaseR,
    phytools,
    posterior,
    purrr,
    readr,
    rlang,
    stats,
    stringr,
    tidyr
VignetteBuilder: knitr
Depends: 
    R (>= 3.5.0)
LazyData: true
Additional_repositories: https://stan-dev.r-universe.dev/
Remotes:
    stan-dev/cmdstanr,
    mjg211/phaseR

Scope

• Please indicate which of our statistical package categories this package falls under. (Please check one or more appropriate boxes below):

  Statistical Packages

  • Bayesian and Monte Carlo Routines
  • Dimensionality Reduction, Clustering, and Unsupervised Learning
  • Machine Learning
  • Regression and Supervised Learning
  • Exploratory Data Analysis (EDA) and Summary Statistics
  • Spatial Analyses
  • Time Series Analyses
  • Probability Distributions

Pre-submission Inquiry

• A pre-submission inquiry has been approved in issue coevolve - presubmission inquiry #715

General Information

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

The target audience is researchers in the life sciences and cultural evolution who would like to model how multiple variables have coevolved over evolutionary time. The coevolve package allows users to fit Bayesian generalised dynamic phylogenetic models in Stan. These models estimate the autoregressive and cross-lagged effects of variables along the branches of a phylogenetic tree. The current version of the package allows users to model different data types (e.g., binary, ordinal, continuous, count) while accounting for measurement error, missing data, and repeated measures.

• Paste your responses to our General Standard G1.1 here, describing whether your software is:

This is the first implementation of a novel algorithm.

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I don't think these guidelines apply to this package.

Badging

• What grade of badge are you aiming for?

gold

• If aiming for silver or gold, describe which of the four aspects listed in the Guide for Authors chapter the package fulfils (at least one aspect for silver; three for gold)

1. Compliance with a good number of standards beyond those identified as minimally necessary.
2. Demonstrating excellence in compliance with multiple standards from at least two broad sub-categories.
3. Internal aspects of package structure and design.

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 have another maintainer identified.
• I/we have read the Statistical Software Peer Review Guide for Authors.
• I/we have run autotest checks on the package, and ensured no tests fail.
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• The pkgcheck() function confirms this package may be submitted - alternatively, please explain reasons for any checks which your package is unable to pass.

Currently, the pkgcheck() function is failing due to a failing R CMD check workflow run on macOS. We are hoping that this is temporary failure due to GitHub runner caching.

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.

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

Code of conduct

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[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 coevolve (v0.1.0.9005)

git hash: 097c50f4

• ✔️ 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 fails continuous integration checks.
• ✔️ Package coverage is 98.2%.
• ✔️ This is a statistical package which complies with all applicable standards
• ✔️ R CMD check found no errors.
• ✔️ R CMD check found no warnings.
• 👀 Some goodpractice linters failed.
• 👀 Function names are duplicated in other packages
• 👀 Package has unusually large number of 20 Imports (> 98% of all packages)

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

(Checks marked with 👀 may be optionally addressed.)

Package License: GPL (>= 3)

---

1. rOpenSci Statistical Standards (srr package)

This package is in the following category:

• Bayesian and Monte Carlo

✔️ All applicable standards [v0.2.0] have been documented in this package (470 complied with; 24 N/A standards)

Click to see the report of author-reported standards compliance of the package with links to associated lines of code, which can be re-generated locally by running the srr_report() function from within a local clone of the repository.

---

2. 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	329
internal	coevolve	44
internal	utils	28
internal	graphics	6
internal	grDevices	2
imports	ggplot2	46
imports	stats	30
imports	posterior	15
imports	dplyr	7
imports	stringr	7
imports	ape	4
imports	cmdstanr	3
imports	Matrix	2
imports	phangorn	2
imports	tidyr	2
imports	bayesplot	1
imports	purrr	1
imports	readr	1
imports	colorspace	NA
imports	gridExtra	NA
imports	methods	NA
imports	patchwork	NA
imports	phaseR	NA
imports	phytools	NA
imports	rlang	NA
suggests	tibble	2
suggests	knitr	NA
suggests	rmarkdown	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

for (33), c (26), length (18), names (18), seq_along (16), paste0 (13), list (12), which (12), is.na (11), t (9), ncol (8), nrow (7), seq_len (7), apply (6), as.character (6), as.numeric (6), colnames (6), drop (6), ifelse (6), rep (6), unlist (6), matrix (5), max (5), mean (5), any (4), factor (4), lapply (4), unique (4), data.frame (3), if (3), is.numeric (3), match (3), deparse (2), duplicated (2), is.null (2), levels (2), min (2), sample (2), scale (2), sub (2), substitute (2), sum (2), all (1), array (1), as.data.frame (1), as.list (1), as.matrix (1), ceiling (1), chol (1), col (1), diag (1), dim (1), dimnames (1), do.call (1), expand.grid (1), formals (1), gsub (1), intersect (1), labels (1), mode (1), numeric (1), paste (1), seq (1), solve (1), sort (1), summary (1), switch (1), tempfile (1), tryCatch (1), vector (1)

ggplot2

element_blank (19), aes (7), element_text (5), theme (3), element_rect (2), guide_colourbar (2), unit (2), after_stat (1), element_line (1), facet_wrap (1), geom_line (1), ggplot (1), theme_classic (1)

coevolve

coev_calculate_theta (3), coev_pred_series (3), coev_make_stancode (2), coev_make_standata (2), extract_samples (2), lmod (2), plot_diag (2), choose_plot_type (1), coev_calculate_delta_theta (1), coev_fit (1), coev_plot_delta_theta (1), coev_plot_flowfield (1), coev_plot_pred_series (1), coev_plot_predictive_check (1), coev_plot_selection_gradient (1), coev_plot_trait_values (1), coev_simulate_coevolution (1), extract_samples.coevfit (1), ou (1), ou_sde (1), plot_lower_tri (1), plot_upper_tri (1), plot.coevfit (1), print_format (1), print.coevfit (1), print.coevsummary (1), run_checks (1), run_checks_data (1), run_checks_dist_cov (1), run_checks_dist_mat (1), run_checks_effects_mat (1), run_checks_id (1), run_checks_measurement_error (1), run_checks_plot_trait_values (1), run_checks_pred_series (1)

stats

median (10), quantile (9), sd (3), mad (2), time (2), line (1), nobs (1), sigma (1), var (1)

utils

data (27), modifyList (1)

posterior

as_draws_rvars (8), draws_of (2), ndraws (2), as_draws_matrix (1), rvar_mad (1), rvar_median (1)

dplyr

sym (5), across (1), group_by (1)

stringr

str_starts (4), str_extract (2), fixed (1)

graphics

text (2), title (2), contour (1), points (1)

ape

keep.tip (1), node.depth (1), node.depth.edgelength (1), read.tree (1)

cmdstanr

write_stan_file (2), cmdstan_model (1)

grDevices

palette (2)

Matrix

expm (1), nearPD (1)

phangorn

Ancestors (2)

tibble

tibble (2)

tidyr

expand_grid (1), pivot_longer (1)

bayesplot

pp_check (1)

purrr

map2 (1)

readr

parse_number (1)

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

---

3. 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 23 files) and
• 2 authors
• 1 vignette
• 3 internal data files
• 20 imported packages
• 21 exported functions (median 75 lines of code)
• 82 non-exported functions in R (median 37 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	23	83.6
files_vignettes	2	81.9
files_tests	17	93.3
loc_R	3701	91.3
loc_vignettes	703	84.1
loc_tests	5382	97.9	TRUE
num_vignettes	1	58.4
data_size_total	67929	80.3
data_size_median	8815	77.9
n_fns_r	103	75.5
n_fns_r_exported	21	68.4
n_fns_r_not_exported	82	77.8
n_fns_per_file_r	3	47.6
num_params_per_fn	4	51.1
loc_per_fn_r	41	85.4
loc_per_fn_r_exp	75	87.9
loc_per_fn_r_not_exp	37	83.9
rel_whitespace_R	1	23.3
rel_whitespace_vignettes	24	78.3
rel_whitespace_tests	1	49.6
doclines_per_fn_exp	69	78.7
doclines_per_fn_not_exp	0	0.0	TRUE
fn_call_network_size	249	89.9

---

3a. Network visualisation

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

---

4. 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 check_fail:

1. cyclocomp

Test coverage with covr

Package coverage: 98.23

Cyclocomplexity with cyclocomp

The following functions have cyclocomplexity >= 15:

function	cyclocomplexity
write_model_block	63
run_checks_variables	51
coev_make_standata	41
run_checks_plot_trait_values	37
run_checks_pred_series	36
write_gen_quantities_block	34
coev_plot_flowfield	32
coev_plot_predictive_check	32
coev_pred_series	31
coev_plot_selection_gradient	28
coev_simulate_coevolution	28
run_checks_sim	27
coev_plot_trait_values	26
summary.coevfit	26
write_transformed_pars_block	24
coev_plot_delta_theta	22
run_checks	19
write_transformed_data_block	19
coev_calculate_theta	18
coev_make_stancode	18
coev_plot_pred_series	18
print.coevsummary	18
coev_calculate_delta_theta	17

Static code analyses with lintr

lintr found no issues with this package!

---

5. Other Checks

Details of other checks (click to open)

✖️ The following 3 function names are duplicated in other packages:

• • extract_samples from adnuts, tidybayes
• • stancode from brms
• • standata from brms

---

Package Versions

package	version
pkgstats	0.2.0.64
pkgcheck	0.1.2.207
srr	0.1.4.8

---

Editor-in-Chief Instructions:

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

[mpadge]

Hi @ScottClaessens, sorry for slow start here. We're trying to find an editor to handle this submission. You'll see progress as soon as that's happened.

[ldecicco-USGS]

Sorry for the delay @ScottClaessens , we've had a lot of editors on vacation this month, but people are trickling back in!

[ldecicco-USGS]

@ropensci-review-bot assign @natydasilva editor

[ropensci-review-bot]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@ropensci-review-bot help

[ldecicco-USGS]

@ropensci-review-bot assign @natydasilva as editor

[ropensci-review-bot]

Assigned! @natydasilva is now the editor

[mpadge]

@ScottClaessens Sorry about delays in getting back to you here, but can you give us an update of the state of the package? The previous lot of checks showed that CI tests were failing. Has that been fixed? If so, please ask the bot here to check package and confirm that we're good to proceed.

[ScottClaessens]

@mpadge Thank you for following up! The package hasn't changed since I submitted this issue.

I just re-ran the CI tests. As before, they pass on Windows and Linux but fail on Mac (see here). From the logs, it's something to do with the phaseR package that was removed from CRAN. I added mjg211/phaseR to Remotes to fix this. You previously suggested that the resulting Mac-specific error was likely a temporary GitHub runner caching issue, but this seems unlikely as it's been a few months now and the issue still hasn't resolved. I'm not entirely sure how to fix this!

Happy to work with you to get this resolved quickly.

[ScottClaessens]

Ah, the issue was solved by a very small change to my GitHub workflow. So sorry about that @mpadge!

I can confirm that all checks are now passing in the most recent 0.1.0.9007 version.