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eDNAjoint: R package for interpreting paired environmental DNA and traditional surveys #642

Open abigailkeller opened 1 month ago

abigailkeller commented 1 month ago

Submitting Author Name: Abigail Keller Submitting Author Github Handle: !--author1-->@abigailkeller<!--end-author1-- Repository: https://github.com/abigailkeller/eDNAjoint Version submitted: 0.1 Submission type: Stats Badge grade: silver Editor: !--editor-->@emitanaka<!--end-editor-- Reviewers: @chitrams, @smwindecker

Due date for @chitrams: 2024-07-02 Due date for @smwindecker: 2024-07-02

Archive: TBD Version accepted: TBD Language: en

Package: eDNAjoint
Title: Joint Modeling of Traditional and Environmental DNA Survey Data
Version: 0.1
Maintainer: Abigail G. Keller <agkeller@berkeley.edu>
Author: Abigail G. Keller
Authors@R: 
    c(person("Abigail G.", "Keller", role = c("aut", "cre"), email="agkeller@berkeley.edu"),
    person("Ryan P.", "Kelly", role = "ctb", email="rpkelly@uw.edu"))
Description: Models integrate environmental DNA (eDNA) detection data and traditional survey data to jointly estimate species catch rate (see package vignette: https://bookdown.org/abigailkeller/eDNAjoint_vignette/). Models can be used with count data via traditional survey methods (i.e., trapping, electrofishing, visual) and replicated eDNA detection/nondetection data via polymerase chain reaction (i.e., PCR or qPCR) from multiple survey locations. Estimated parameters include probability of a false positive eDNA detection, a site-level covariates that scale the sensitivity of eDNA surveys relative to traditional surveys, and catchability coefficients for traditional gear types. Models are implemented with a Bayesian framework (Markov chain Monte Carlo) using the 'Stan' probabilistic programming language.
License: GPL-3
URL: https://github.com/abigailkeller/eDNAjoint
BugReports: https://github.com/abigailkeller/eDNAjoint/issues
Encoding: UTF-8
Roxygen: list(markdown = TRUE, roclets = c ("namespace", "rd", "srr::srr_stats_roclet"))
RoxygenNote: 7.3.1
Biarch: true
Depends: 
    R (>= 3.4.0)
Imports: 
    bayestestR,
    dplyr,
    ggplot2,
    loo,
    magrittr,
    methods,
    Rcpp (>= 0.12.0),
    RcppParallel (>= 5.0.1), 
    rlist,
    rstan (>= 2.26.23),
    rstantools (>= 2.3.1.1),
    tidyr
LinkingTo: 
    BH (>= 1.66.0),
    Rcpp (>= 0.12.0),
    RcppEigen (>= 0.3.3.3.0),
    RcppParallel (>= 5.0.1),
    rstan (>= 2.26.23),
    StanHeaders (>= 2.26.22)
SystemRequirements: GNU make
LazyData: true
Suggests: 
    bayesplot,
    knitr,
    rmarkdown,
    testthat (>= 3.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3

Scope

Pre-submission Inquiry

General Information

The package eDNAjoint is useful for interpreting observations from paired environmental DNA (eDNA) and traditional surveys. The package runs a Bayesian model that integrates these two data streams to jointly estimate parameters like the false positive probability of eDNA detection and expected catch rate at a site. The package allows users to access pre-compiled models written in Stan. The target audience is environmental science researchers or managers who want to interpret environmental DNA data but do not have experience writing and implementing custom Bayesian models.

This is the first implementation of a model/algorithm developed in Keller et al. 2022.

Badging

Silver

Compliance with a good number of standards beyond those identified as minimally necessary.

Technical checks

Confirm each of the following by checking the box.

This package:

Publication options

Code of conduct

ropensci-review-bot commented 1 month ago

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

ropensci-review-bot commented 1 month ago

:rocket:

Editor check started

:wave:

ropensci-review-bot commented 1 month ago

Checks for eDNAjoint (v0.1)

git hash: 8aecadf9

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

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

Package License: GPL-3

1. rOpenSci Statistical Standards (srr package)

This package is in the following category:

:heavy_check_mark: All applicable standards [v0.2.0] have been documented in this package (345 complied with; 50 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 | 302| |internal |stats | 33| |internal |eDNAjoint | 26| |internal |utils | 7| |internal |graphics | 3| |internal |parallel | 2| |imports |rstan | 30| |imports |Rcpp | 18| |imports |ggplot2 | 6| |imports |tidyr | 6| |imports |bayestestR | 5| |imports |dplyr | 4| |imports |magrittr | 2| |imports |loo | 1| |imports |methods | 1| |imports |RcppParallel | NA| |imports |rlist | NA| |imports |rstantools | NA| |suggests |bayesplot | NA| |suggests |knitr | NA| |suggests |rmarkdown | NA| |suggests |testthat | NA| |linking_to |rstan | 30| |linking_to |Rcpp | 18| |linking_to |BH | NA| |linking_to |RcppEigen | NA| |linking_to |RcppParallel | NA| |linking_to |StanHeaders | NA| Click below for tallies of functions used in each package. Locations of each call within this package may be generated locally by running 's <- pkgstats::pkgstats()', and examining the 'external_calls' table.

base

list (28), sum (20), length (19), for (16), col (14), as.data.frame (13), c (13), if (10), paste0 (10), q (10), apply (9), unlist (9), all (7), any (7), is.na (7), nrow (7), seq_along (7), unique (7), lapply (6), paste (6), round (6), by (5), seq (5), as.integer (4), as.matrix (4), beta (4), ifelse (4), vector (4), warning (4), as.character (2), cbind (2), colMeans (2), dim (2), exp (2), is.double (2), is.null (2), log (2), match (2), min (2), names (2), plot (2), rep (2), sapply (2), sqrt (2), stopifnot (2), dir.exists (1), matrix (1), ncol (1), qr (1), summary (1)

stats

median (9), cov (8), pnbinom (6), dnbinom (4), family (4), ppois (2)

rstan

extract (15), get_sampler_params (6), summary (6), sampling (2), stanc_builder (1)

eDNAjoint

div_check (4), init_joint_catchability (2), init_trad_catchability (2), all_checks (1), catchability_checks (1), covariate_checks (1), detectionCalculate (1), detectionCalculate_input_checks (1), detectionPlot (1), detectionPlot_input_checks (1), init_joint (1), init_joint_cov (1), init_joint_cov_catchability (1), init_trad (1), initial_values_checks (1), initial_values_checks_trad (1), jointModel (1), jointSelect (1), jointSelect_input_checks (1), jointSummarize (1), jointSummarize_input_checks (1)

Rcpp

loadModule (18)

utils

data (7)

ggplot2

aes (2), geom_line (2), ggplot (2)

tidyr

pivot_longer (6)

bayestestR

ci (5)

dplyr

case_when (2), mutate (2)

graphics

par (3)

magrittr

`% (2)

parallel

detectCores (2)

loo

loo_compare (1)

methods

new (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 C++ (18% in 19 files), C/C++ Header (0% in 1 files) and R (82% in 13 files) - 1 authors - 1 vignette - 2 internal data files - 12 imported packages - 7 exported functions (median 139 lines of code) - 74 non-exported functions in R (median 25 lines of code) - 19 C/C++ functions (median 26 lines of code) --- Statistical properties of package structure as distributional percentiles in relation to all current CRAN packages The following terminology is used: - `loc` = "Lines of Code" - `fn` = "function" - `exp`/`not_exp` = exported / not exported All parameters are explained as tooltips in the locally-rendered HTML version of this report generated by [the `checks_to_markdown()` function](https://docs.ropensci.org/pkgcheck/reference/checks_to_markdown.html) The final measure (`fn_call_network_size`) is the total number of calls between functions (in R), or more abstract relationships between code objects in other languages. Values are flagged as "noteworthy" when they lie in the upper or lower 5th percentile. |measure | value| percentile|noteworthy | |:------------------------|-----:|----------:|:----------| |files_R | 13| 68.2| | |files_src | 19| 96.3| | |files_inst | 1| 97.7| | |files_vignettes | 1| 68.4| | |files_tests | 8| 88.2| | |loc_R | 2126| 85.3| | |loc_src | 482| 46.1| | |loc_inst | 0| 0.0|TRUE | |loc_vignettes | 388| 71.5| | |loc_tests | 2107| 94.6| | |num_vignettes | 1| 64.8| | |data_size_total | 4212| 66.4| | |data_size_median | 2106| 69.0| | |n_fns_r | 81| 70.8| | |n_fns_r_exported | 7| 34.0| | |n_fns_r_not_exported | 74| 77.4| | |n_fns_src | 19| 44.7| | |n_fns_per_file_r | 6| 73.8| | |n_fns_per_file_src | 0| 0.0|TRUE | |num_params_per_fn | 5| 69.6| | |loc_per_fn_r | 29| 75.3| | |loc_per_fn_r_exp | 139| 95.2|TRUE | |loc_per_fn_r_not_exp | 25| 72.0| | |loc_per_fn_src | 26| 79.6| | |rel_whitespace_R | 25| 89.5| | |rel_whitespace_src | 28| 56.3| | |rel_whitespace_vignettes | 51| 84.4| | |rel_whitespace_tests | 18| 93.1| | |doclines_per_fn_exp | 77| 83.4| | |doclines_per_fn_not_exp | 0| 0.0|TRUE | |fn_call_network_size | 24| 50.3| | ---

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)

#### 3a. Continuous Integration Badges [![R-CMD-check.yaml](https://github.com/abigailkeller/eDNAjoint/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/abigailkeller/eDNAjoint/actions) [![pkgcheck](https://github.com/abigailkeller/eDNAjoint/workflows/pkgcheck/badge.svg)](https://github.com/abigailkeller/eDNAjoint/actions) **GitHub Workflow Results** | id|name |conclusion |sha | run_number|date | |----------:|:-------------------------------|:----------|:------|----------:|:----------| | 9005475404|.github/workflows/pkgcheck.yaml |failure |7eb425 | 14|2024-05-08 | | 9009886509|pkgcheck |success |8aecad | 17|2024-05-08 | | 9009886508|R-CMD-check |success |8aecad | 39|2024-05-08 | | 9009886511|test-coverage |success |8aecad | 39|2024-05-08 | --- #### 3b. `goodpractice` results #### `R CMD check` with [rcmdcheck](https://r-lib.github.io/rcmdcheck/) R CMD check generated the following error: 1. Error in proc$get_built_file() : Build process failed R CMD check generated the following check_fail: 1. no_import_package_as_a_whole #### Test coverage with [covr](https://covr.r-lib.org/) Package coverage: 85.06 #### Cyclocomplexity with [cyclocomp](https://github.com/MangoTheCat/cyclocomp) Error : Build failed, unknown error, standard output: * checking for file ‘eDNAjoint/DESCRIPTION’ ... OK * preparing ‘eDNAjoint’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘eDNAjoint.Rmd’ using rmarkdown Killed #### Static code analyses with [lintr](https://github.com/jimhester/lintr) [lintr](https://github.com/jimhester/lintr) found the following 15 potential issues: message | number of times --- | --- Avoid library() and require() calls in packages | 6 Avoid using sapply, consider vapply instead, that's type safe | 1 Lines should not be more than 80 characters. | 4 Use <-, not =, for assignment. | 4

5. Other Checks

Details of other checks (click to open)

:heavy_multiplication_x: The following function name is duplicated in other packages: - - `jointModel` from JM

Package Versions

|package |version | |:--------|:--------| |pkgstats |0.1.5.2 | |pkgcheck |0.1.2.22 | |srr |0.1.2.9 |

Editor-in-Chief Instructions:

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

abigailkeller commented 1 month ago

Hi! I'm not sure who to reach out to about this, but I'm curious about the R CMD check build failures associated with rcmdcheck and cyclocomp. My github workflows of R-CMD-check and pkgcheck pass without error. Do you know what the discrepancy could be?

mpadge commented 1 month ago

Sorry @abigailkeller I'm trying to resolve this. I've worked out that the build fails in building your vignette because of bayesplot, but that's clearly not your fault, and nor can I yet work out why. Main problem is that running checks on your package takes hours (on our system at least), so I've thus far only managed to that diagnosis and no further. Once I fix things, you should see a fresh dump of pkgcheck results appear here.

mpadge commented 1 month ago

I think it was just an R4.4 update glitch which should be fixed now. @abigailkeller You can call check package yourself to start another one. (Checks take hours for your package, so you'll need to be patient ...)

abigailkeller commented 1 month ago

@ropensci-review-bot check package

ropensci-review-bot commented 1 month ago

Thanks, about to send the query.

ropensci-review-bot commented 1 month ago

:rocket:

Editor check started

:wave:

ropensci-review-bot commented 1 month ago

Checks for eDNAjoint (v0.1)

git hash: 8aecadf9

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

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

Package License: GPL-3

1. rOpenSci Statistical Standards (srr package)

This package is in the following category:

:heavy_check_mark: All applicable standards [v0.2.0] have been documented in this package (345 complied with; 50 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 | 302| |internal |stats | 33| |internal |eDNAjoint | 26| |internal |utils | 7| |internal |graphics | 3| |internal |parallel | 2| |imports |rstan | 30| |imports |Rcpp | 18| |imports |ggplot2 | 6| |imports |tidyr | 6| |imports |bayestestR | 5| |imports |dplyr | 4| |imports |magrittr | 2| |imports |loo | 1| |imports |methods | 1| |imports |RcppParallel | NA| |imports |rlist | NA| |imports |rstantools | NA| |suggests |bayesplot | NA| |suggests |knitr | NA| |suggests |rmarkdown | NA| |suggests |testthat | NA| |linking_to |rstan | 30| |linking_to |Rcpp | 18| |linking_to |BH | NA| |linking_to |RcppEigen | NA| |linking_to |RcppParallel | NA| |linking_to |StanHeaders | NA| Click below for tallies of functions used in each package. Locations of each call within this package may be generated locally by running 's <- pkgstats::pkgstats()', and examining the 'external_calls' table.

base

list (28), sum (20), length (19), for (16), col (14), as.data.frame (13), c (13), if (10), paste0 (10), q (10), apply (9), unlist (9), all (7), any (7), is.na (7), nrow (7), seq_along (7), unique (7), lapply (6), paste (6), round (6), by (5), seq (5), as.integer (4), as.matrix (4), beta (4), ifelse (4), vector (4), warning (4), as.character (2), cbind (2), colMeans (2), dim (2), exp (2), is.double (2), is.null (2), log (2), match (2), min (2), names (2), plot (2), rep (2), sapply (2), sqrt (2), stopifnot (2), dir.exists (1), matrix (1), ncol (1), qr (1), summary (1)

stats

median (9), cov (8), pnbinom (6), dnbinom (4), family (4), ppois (2)

rstan

extract (15), get_sampler_params (6), summary (6), sampling (2), stanc_builder (1)

eDNAjoint

div_check (4), init_joint_catchability (2), init_trad_catchability (2), all_checks (1), catchability_checks (1), covariate_checks (1), detectionCalculate (1), detectionCalculate_input_checks (1), detectionPlot (1), detectionPlot_input_checks (1), init_joint (1), init_joint_cov (1), init_joint_cov_catchability (1), init_trad (1), initial_values_checks (1), initial_values_checks_trad (1), jointModel (1), jointSelect (1), jointSelect_input_checks (1), jointSummarize (1), jointSummarize_input_checks (1)

Rcpp

loadModule (18)

utils

data (7)

ggplot2

aes (2), geom_line (2), ggplot (2)

tidyr

pivot_longer (6)

bayestestR

ci (5)

dplyr

case_when (2), mutate (2)

graphics

par (3)

magrittr

`% (2)

parallel

detectCores (2)

loo

loo_compare (1)

methods

new (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 C++ (18% in 19 files), C/C++ Header (0% in 1 files) and R (82% in 13 files) - 1 authors - 1 vignette - 2 internal data files - 12 imported packages - 7 exported functions (median 139 lines of code) - 74 non-exported functions in R (median 25 lines of code) - 19 C/C++ functions (median 26 lines of code) --- Statistical properties of package structure as distributional percentiles in relation to all current CRAN packages The following terminology is used: - `loc` = "Lines of Code" - `fn` = "function" - `exp`/`not_exp` = exported / not exported All parameters are explained as tooltips in the locally-rendered HTML version of this report generated by [the `checks_to_markdown()` function](https://docs.ropensci.org/pkgcheck/reference/checks_to_markdown.html) The final measure (`fn_call_network_size`) is the total number of calls between functions (in R), or more abstract relationships between code objects in other languages. Values are flagged as "noteworthy" when they lie in the upper or lower 5th percentile. |measure | value| percentile|noteworthy | |:------------------------|-----:|----------:|:----------| |files_R | 13| 68.2| | |files_src | 19| 96.3| | |files_inst | 1| 97.7| | |files_vignettes | 1| 68.4| | |files_tests | 8| 88.2| | |loc_R | 2126| 85.3| | |loc_src | 482| 46.1| | |loc_inst | 0| 0.0|TRUE | |loc_vignettes | 388| 71.5| | |loc_tests | 2107| 94.6| | |num_vignettes | 1| 64.8| | |data_size_total | 4212| 66.4| | |data_size_median | 2106| 69.0| | |n_fns_r | 81| 70.8| | |n_fns_r_exported | 7| 34.0| | |n_fns_r_not_exported | 74| 77.4| | |n_fns_src | 19| 44.7| | |n_fns_per_file_r | 6| 73.8| | |n_fns_per_file_src | 0| 0.0|TRUE | |num_params_per_fn | 5| 69.6| | |loc_per_fn_r | 29| 75.3| | |loc_per_fn_r_exp | 139| 95.2|TRUE | |loc_per_fn_r_not_exp | 25| 72.0| | |loc_per_fn_src | 26| 79.6| | |rel_whitespace_R | 25| 89.5| | |rel_whitespace_src | 28| 56.3| | |rel_whitespace_vignettes | 51| 84.4| | |rel_whitespace_tests | 18| 93.1| | |doclines_per_fn_exp | 77| 83.4| | |doclines_per_fn_not_exp | 0| 0.0|TRUE | |fn_call_network_size | 24| 50.3| | ---

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)

#### 3a. Continuous Integration Badges [![R-CMD-check.yaml](https://github.com/abigailkeller/eDNAjoint/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/abigailkeller/eDNAjoint/actions) [![pkgcheck](https://github.com/abigailkeller/eDNAjoint/workflows/pkgcheck/badge.svg)](https://github.com/abigailkeller/eDNAjoint/actions) **GitHub Workflow Results** | id|name |conclusion |sha | run_number|date | |----------:|:-------------------------------|:----------|:------|----------:|:----------| | 9005475404|.github/workflows/pkgcheck.yaml |failure |7eb425 | 14|2024-05-08 | | 9009886509|pkgcheck |success |8aecad | 17|2024-05-08 | | 9009886508|R-CMD-check |success |8aecad | 39|2024-05-08 | | 9009886511|test-coverage |success |8aecad | 39|2024-05-08 | --- #### 3b. `goodpractice` results #### `R CMD check` with [rcmdcheck](https://r-lib.github.io/rcmdcheck/) R CMD check generated the following error: 1. Error in proc$get_built_file() : Build process failed R CMD check generated the following check_fail: 1. no_import_package_as_a_whole #### Test coverage with [covr](https://covr.r-lib.org/) Package coverage: 85.06 #### Cyclocomplexity with [cyclocomp](https://github.com/MangoTheCat/cyclocomp) Error : Build failed, unknown error, standard output: * checking for file ‘eDNAjoint/DESCRIPTION’ ... OK * preparing ‘eDNAjoint’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘eDNAjoint.Rmd’ using rmarkdown Killed #### Static code analyses with [lintr](https://github.com/jimhester/lintr) [lintr](https://github.com/jimhester/lintr) found the following 15 potential issues: message | number of times --- | --- Avoid library() and require() calls in packages | 6 Avoid using sapply, consider vapply instead, that's type safe | 1 Lines should not be more than 80 characters. This line is 546 characters. | 1 Lines should not be more than 80 characters. This line is 81 characters. | 1 Lines should not be more than 80 characters. This line is 82 characters. | 1 Lines should not be more than 80 characters. This line is 87 characters. | 1 Use <-, not =, for assignment. | 4

5. Other Checks

Details of other checks (click to open)

:heavy_multiplication_x: The following function name is duplicated in other packages: - - `jointModel` from JM

Package Versions

|package |version | |:--------|:--------| |pkgstats |0.1.5.2 | |pkgcheck |0.1.2.34 | |srr |0.1.2.9 |

Editor-in-Chief Instructions:

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

abigailkeller commented 1 month ago

@mpadge Thanks! I just ran the check again. It looks like the same issue is happening?

jooolia commented 1 month ago

Thank you for your submission @abigailkeller ! And thanks @mpadge for looking into the issues running the checks on our system. Based on the pre-submission issue and the checks (minus the failures that Mark is investigating), I think the only package will be ready to pass on to a handing editor. @abigailkeller do you plan on addressing the duplicated function name "jointModel from JM"? Thanks, Julia

abigailkeller commented 1 month ago

Hi @jooolia, sounds great!

As of now, I am not planning on changing the duplicated function name, but I'm also definitely open to addressing the duplication if you all suggest. The JM package seems like it is different enough that a user would not have both packages loaded at once, but I also would defer to suggestions from reviewers and editors here.

Thanks! Abby

abigailkeller commented 1 month ago

Update: since my vignette compilation time was causing build failures (see issue here), I removed the vignette from the package and instead will direct users/reviewers to a copy of my vignette outside the package in this book. This book is linked in the package DESCRIPTION, as well as in the documentation in all functions.

jooolia commented 1 month ago

@ropensci-review-bot assign @emitanaka as editor

ropensci-review-bot commented 1 month ago

Assigned! @emitanaka is now the editor

abigailkeller commented 3 weeks ago

@ropensci-review-bot check package

ropensci-review-bot commented 3 weeks ago

Thanks, about to send the query.

ropensci-review-bot commented 3 weeks ago

:rocket:

Editor check started

:wave:

emitanaka commented 3 weeks ago

@ropensci-review-bot seeking reviewers

ropensci-review-bot commented 3 weeks ago

I'm sorry @emitanaka, I'm afraid I can't do that. That's something only editors are allowed to do.

mpadge commented 3 weeks ago

@abigailkeller Your checks failed because GitHub returned an "unexpected error". Please try again. @emitanaka Sorry, that was an oversight on our part; should now be fixed so please try again. :smile:

abigailkeller commented 3 weeks ago

@ropensci-review-bot check package

ropensci-review-bot commented 3 weeks ago

Thanks, about to send the query.

ropensci-review-bot commented 3 weeks ago

:rocket:

Editor check started

:wave:

ropensci-review-bot commented 3 weeks ago

Checks for eDNAjoint (v0.1)

git hash: 606414b5

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

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

Package License: GPL-3

1. rOpenSci Statistical Standards (srr package)

This package is in the following category:

:heavy_check_mark: Your code includes the following standard which are not actual standards: [BS4.2]

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 | 302| |internal |stats | 33| |internal |eDNAjoint | 26| |internal |utils | 7| |internal |graphics | 3| |internal |parallel | 2| |imports |rstan | 30| |imports |Rcpp | 18| |imports |ggplot2 | 6| |imports |tidyr | 6| |imports |bayestestR | 5| |imports |dplyr | 4| |imports |magrittr | 2| |imports |loo | 1| |imports |methods | 1| |imports |RcppParallel | NA| |imports |rlist | NA| |imports |rstantools | NA| |suggests |bayesplot | NA| |suggests |knitr | NA| |suggests |rmarkdown | NA| |suggests |testthat | NA| |linking_to |rstan | 30| |linking_to |Rcpp | 18| |linking_to |BH | NA| |linking_to |RcppEigen | NA| |linking_to |RcppParallel | NA| |linking_to |StanHeaders | NA| Click below for tallies of functions used in each package. Locations of each call within this package may be generated locally by running 's <- pkgstats::pkgstats()', and examining the 'external_calls' table.

base

list (28), sum (20), length (19), for (16), col (14), as.data.frame (13), c (13), if (10), paste0 (10), q (10), apply (9), unlist (9), all (7), any (7), is.na (7), nrow (7), seq_along (7), unique (7), lapply (6), paste (6), round (6), by (5), seq (5), as.integer (4), as.matrix (4), beta (4), ifelse (4), vector (4), warning (4), as.character (2), cbind (2), colMeans (2), dim (2), exp (2), is.double (2), is.null (2), log (2), match (2), min (2), names (2), plot (2), rep (2), sapply (2), sqrt (2), stopifnot (2), dir.exists (1), matrix (1), ncol (1), qr (1), summary (1)

stats

median (9), cov (8), pnbinom (6), dnbinom (4), family (4), ppois (2)

rstan

extract (15), get_sampler_params (6), summary (6), sampling (2), stanc_builder (1)

eDNAjoint

div_check (4), init_joint_catchability (2), init_trad_catchability (2), all_checks (1), catchability_checks (1), covariate_checks (1), detectionCalculate (1), detectionCalculate_input_checks (1), detectionPlot (1), detectionPlot_input_checks (1), init_joint (1), init_joint_cov (1), init_joint_cov_catchability (1), init_trad (1), initial_values_checks (1), initial_values_checks_trad (1), jointModel (1), jointSelect (1), jointSelect_input_checks (1), jointSummarize (1), jointSummarize_input_checks (1)

Rcpp

loadModule (18)

utils

data (7)

ggplot2

aes (2), geom_line (2), ggplot (2)

tidyr

pivot_longer (6)

bayestestR

ci (5)

dplyr

case_when (2), mutate (2)

graphics

par (3)

magrittr

`% (2)

parallel

detectCores (2)

loo

loo_compare (1)

methods

new (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 C++ (18% in 19 files), C/C++ Header (0% in 1 files), HTML (0% in 1 files) and R (82% in 13 files) - 1 authors - no vignette - 2 internal data files - 12 imported packages - 7 exported functions (median 139 lines of code) - 74 non-exported functions in R (median 25 lines of code) - 19 C/C++ functions (median 26 lines of code) --- Statistical properties of package structure as distributional percentiles in relation to all current CRAN packages The following terminology is used: - `loc` = "Lines of Code" - `fn` = "function" - `exp`/`not_exp` = exported / not exported All parameters are explained as tooltips in the locally-rendered HTML version of this report generated by [the `checks_to_markdown()` function](https://docs.ropensci.org/pkgcheck/reference/checks_to_markdown.html) The final measure (`fn_call_network_size`) is the total number of calls between functions (in R), or more abstract relationships between code objects in other languages. Values are flagged as "noteworthy" when they lie in the upper or lower 5th percentile. |measure | value| percentile|noteworthy | |:-----------------------|-----:|----------:|:----------| |files_R | 13| 68.2| | |files_src | 20| 96.5| | |files_inst | 1| 97.7| | |files_vignettes | 0| 0.0|TRUE | |files_tests | 8| 88.2| | |loc_R | 2132| 85.4| | |loc_src | 482| 46.1| | |loc_inst | 0| 0.0|TRUE | |loc_tests | 2163| 94.7| | |num_vignettes | 0| 0.0|TRUE | |data_size_total | 4212| 66.4| | |data_size_median | 2106| 69.0| | |n_fns_r | 81| 70.8| | |n_fns_r_exported | 7| 34.0| | |n_fns_r_not_exported | 74| 77.4| | |n_fns_src | 19| 44.7| | |n_fns_per_file_r | 6| 73.8| | |n_fns_per_file_src | 0| 0.0|TRUE | |num_params_per_fn | 5| 69.6| | |loc_per_fn_r | 29| 75.3| | |loc_per_fn_r_exp | 139| 95.2|TRUE | |loc_per_fn_r_not_exp | 25| 72.0| | |loc_per_fn_src | 26| 79.6| | |rel_whitespace_R | 25| 89.5| | |rel_whitespace_src | 45| 66.0| | |rel_whitespace_tests | 18| 93.5| | |doclines_per_fn_exp | 78| 83.8| | |doclines_per_fn_not_exp | 0| 0.0|TRUE | |fn_call_network_size | 24| 50.3| | ---

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)

#### 3a. Continuous Integration Badges [![R-CMD-check.yaml](https://github.com/abigailkeller/eDNAjoint/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/abigailkeller/eDNAjoint/actions) **GitHub Workflow Results** | id|name |conclusion |sha | run_number|date | |----------:|:-------------------------------|:----------|:------|----------:|:----------| | 9005475404|.github/workflows/pkgcheck.yaml |failure |7eb425 | 14|2024-05-08 | | 9303551629|pkgcheck |failure |606414 | 22|2024-05-30 | | 9303551630|R-CMD-check |success |606414 | 44|2024-05-30 | | 9303551632|test-coverage |success |606414 | 44|2024-05-30 | --- #### 3b. `goodpractice` results #### `R CMD check` with [rcmdcheck](https://r-lib.github.io/rcmdcheck/) R CMD check generated the following notes: 1. checking installed package size ... NOTE installed size is 553.2Mb sub-directories of 1Mb or more: libs 552.4Mb 2. checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements. R CMD check generated the following check_fails: 1. cyclocomp 2. no_import_package_as_a_whole 3. rcmdcheck_gnu_make_required 4. rcmdcheck_reasonable_installed_size #### Test coverage with [covr](https://covr.r-lib.org/) Package coverage: 84.91 #### Cyclocomplexity with [cyclocomp](https://github.com/MangoTheCat/cyclocomp) The following functions have cyclocomplexity >= 15: function | cyclocomplexity --- | --- detectionCalculate | 117 detectionPlot | 117 jointSummarize | 105 jointModel | 66 traditionalModel_input_checks | 38 all_checks | 27 traditionalModel | 26 initial_values_checks | 21 detectionPlot_input_checks | 18 detectionCalculate_input_checks | 17 muCritical_input_checks | 16 #### Static code analyses with [lintr](https://github.com/jimhester/lintr) [lintr](https://github.com/jimhester/lintr) found the following 9 potential issues: message | number of times --- | --- Avoid using sapply, consider vapply instead, that's type safe | 1 Lines should not be more than 80 characters. This line is 546 characters. | 1 Lines should not be more than 80 characters. This line is 81 characters. | 1 Lines should not be more than 80 characters. This line is 82 characters. | 1 Lines should not be more than 80 characters. This line is 87 characters. | 1 Use <-, not =, for assignment. | 4

5. Other Checks

Details of other checks (click to open)

:heavy_multiplication_x: The following function name is duplicated in other packages: - - `jointModel` from JM

Package Versions

|package |version | |:--------|:--------| |pkgstats |0.1.5.2 | |pkgcheck |0.1.2.42 | |srr |0.1.3.2 |

Editor-in-Chief Instructions:

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

emitanaka commented 3 weeks ago

@ropensci-review-bot seeking reviewers

ropensci-review-bot commented 3 weeks ago

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

[![Status at rOpenSci Software Peer Review](https://badges.ropensci.org/642_status.svg)](https://github.com/ropensci/software-review/issues/642)

Furthermore, if your package does not have a NEWS.md file yet, please create one to capture the changes made during the review process. See https://devguide.ropensci.org/releasing.html#news

emitanaka commented 2 weeks ago

@ropensci-review-bot add @chitrams to reviewers

ropensci-review-bot commented 2 weeks ago

@chitrams added to the reviewers list. Review due date is 2024-07-02. Thanks @chitrams for accepting to review! Please refer to our reviewer guide.

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

ropensci-review-bot commented 2 weeks ago

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

emitanaka commented 2 weeks ago

@ropensci-review-bot add @smwindecker to reviewers

ropensci-review-bot commented 2 weeks ago

@smwindecker added to the reviewers list. Review due date is 2024-07-02. Thanks @smwindecker for accepting to review! Please refer to our reviewer guide.

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

ropensci-review-bot commented 2 weeks ago

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

emitanaka commented 2 weeks ago

Please note that @smwindecker is mentoring @chitrams for their review and their review will be considered one (not two). I am still seeking one more reviewer for this.

abigailkeller commented 3 days ago

@emitanaka Hi! I'm wondering if it is too late in the review process to express interest in publishing in Methods in Ecology and Evolution? I am thinking that publishing in this journal may make the package more visible to my intended audience. However, I know that this was something I should have indicated when creating this issue, so I understand if it is not possible!

Thanks, Abby

ropensci-review-bot commented 1 day ago

:calendar: @chitrams you have 2 days left before the due date for your review (2024-07-02).

ropensci-review-bot commented 1 day ago

:calendar: @smwindecker you have 2 days left before the due date for your review (2024-07-02).