[PRE REVIEW]: ssdtools v2: An R package to fit Species Sensitivity Distributions

editorialbot commented 1 month ago

Submitting author: !--author-handle-->@joethorley@fabian-s<!--end-editor-- Reviewers: @flor14, @nanhung Managing EiC: Kevin M. Moerman

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editorialbot commented 1 month ago

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editorialbot commented 1 month ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.09 s (3474.4 files/s, 232267.1 lines/s)
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Language                     files          blank        comment           code
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R                              132           1148           3382           7016
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Markdown                        18            503              0           1128
Rmd                              8            663           1410            961
TeX                              2             55              0            506
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YAML                             7             37             11            302
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SUM:                           303           2585           5316          12355
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Commit count by author:

  1424  Joe Thorley
   262  joethorley
    13  Nadine Hussein
     7  Sarah Lyons
     7  atillmanns
     5  stephhazlitt
     4  Nan-Hung Hsieh
     4  Rebecca Fisher
     3  cschwarz-stat-sfu-ca
     1  Angeline Tillmanns
     1  Hadley Wickham
     1  Seb Dalgarno
     1  Sergio Ibarra Espinosa
     1  Stephanie Hazlitt
     1  repo-mountie[bot]

editorialbot commented 1 month ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.21105/joss.02848 is OK
- 10.18637/jss.v064.i04 is OK
- 10.1007/978-0-387-98141-3 is OK
- 10.1007/b97636 is OK
- 10.1002/9780470094846 is OK
- 10.18637/jss.v070.i05 is OK
- 10.1002/etc.4925 is OK
- 10.25845/fm9b-7n28 is OK
- 10.25845/xtvt-yc51 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Improving Statistical Methods for Modeling Species...
- No DOI given, and none found for title: Species sensitivity distributions in ecotoxicology
- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- No DOI given, and none found for title: Burrlioz 2.0 Manual
- No DOI given, and none found for title: Methods of uncertainty analysis
- No DOI given, and none found for title: Revised Method for Deriving Australian and New Zea...
- No DOI given, and none found for title: Manual on the methodological framework to derive e...
- No DOI given, and none found for title: Derivation of Water Quality Guidelines for the Pro...
- No DOI given, and none found for title: Species Sensitivity Distribution (SSD) Toolbox.

❌ MISSING DOIs

- 10.32614/cran.package.ssddata may be a valid DOI for title: ssddata: Species Sensitivity Distribution Data
- 10.21105/joss.01082 may be a valid DOI for title: ssdtools: An R package to fit species sensitivity ...

❌ INVALID DOIs

- https://doi.org/10.1002/etc.5620190233 is INVALID because of 'https://doi.org/' prefix

editorialbot commented 1 month ago

Paper file info:

📄 Wordcount for paper.md is 1510

✅ The paper includes a Statement of need section

editorialbot commented 1 month ago

License info:

✅ License found: Apache License 2.0 (Valid open source OSI approved license)

editorialbot commented 1 month ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

editorialbot commented 1 month ago

Five most similar historical JOSS papers:

shinyssdtools: A web application for fitting Species Sensitivity Distributions (SSDs) Submitting author: @sebdalgarno Handling editor: @marcosvital (Active) Reviewers: @elimillera, @meenakshi-kushwaha, @nanhung Similarity score: 0.7713

shinyssd v1.0: Species Sensitivity Distributions for Ecotoxicological Risk Assessment Submitting author: @flor14 Handling editor: @karthik (Retired) Reviewers: @kylehamilton Similarity score: 0.7431

SSMSE: An R package for Management Strategy Evaluation with Stock Synthesis Operating Models Submitting author: @k-doering-NOAA Handling editor: @sbenthall (Active) Reviewers: @quang-huynh, @iagomosqueira Similarity score: 0.7015

fitODBOD: An R Package to Model Binomial Outcome Data using Binomial Mixture and Alternate Binomial Distributions. Submitting author: @Amalan-ConStat Handling editor: @csoneson (Active) Reviewers: @osorensen, @jjharden Similarity score: 0.6960

SurPyval: Survival Analysis with Python Submitting author: @derrynknife Handling editor: @dfm (Active) Reviewers: @CamDavidsonPilon, @MatthewReid854 Similarity score: 0.6846

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

joethorley commented 1 month ago

@editorialbot commands

editorialbot commented 1 month ago

Hello @joethorley, here are the things you can ask me to do:


# List all available commands
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# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

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@editorialbot check repository

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joethorley commented 1 month ago

@editorialbot set joss-paper as branch

editorialbot commented 1 month ago

Done! branch is now joss-paper

flor14 commented 1 month ago

Hi! I am interested in reviewing this article if that is possible. Thanks.

joethorley commented 1 month ago

Thanks @flor14 . A second possible reviewer is jhollist at the USEPA or failing that nanhung a toxicologist who reviewed the manuscript for v0.0.3.

joethorley commented 1 month ago

@editorialbot check references

editorialbot commented 1 month ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.21105/joss.02848 is OK
- 10.1002/etc.4373 is OK
- 10.18637/jss.v064.i04 is OK
- 10.1007/978-0-387-98141-3 is OK
- 10.1007/b97636 is OK
- 10.1002/9780470094846 is OK
- 10.18637/jss.v070.i05 is OK
- 10.1002/etc.4925 is OK
- 10.25845/fm9b-7n28 is OK
- 10.25845/xtvt-yc51 is OK
- 10.23645/epacomptox.11971392.v2 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Improving Statistical Methods for Modeling Species...
- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- No DOI given, and none found for title: Burrlioz 2.0 Manual
- No DOI given, and none found for title: Revised Method for Deriving Australian and New Zea...
- No DOI given, and none found for title: Manual on the methodological framework to derive e...
- No DOI given, and none found for title: Derivation of Water Quality Guidelines for the Pro...

❌ MISSING DOIs

- 10.32614/cran.package.ssddata may be a valid DOI for title: ssddata: Species Sensitivity Distribution Data
- 10.21105/joss.01082 may be a valid DOI for title: ssdtools: An R package to fit species sensitivity ...

❌ INVALID DOIs

- https://doi.org/10.1002/etc.5620190233 is INVALID because of 'https://doi.org/' prefix

joethorley commented 1 month ago

@editorialbot check references

editorialbot commented 1 month ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.1002/etc.5620190233 is OK
- 10.21105/joss.02848 is OK
- 10.1002/etc.4373 is OK
- 10.18637/jss.v064.i04 is OK
- 10.1007/978-0-387-98141-3 is OK
- 10.1007/b97636 is OK
- 10.1002/9780470094846 is OK
- 10.18637/jss.v070.i05 is OK
- 10.1002/etc.4925 is OK
- 10.25845/fm9b-7n28 is OK
- 10.25845/xtvt-yc51 is OK
- 10.23645/epacomptox.11971392.v2 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Improving Statistical Methods for Modeling Species...
- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- No DOI given, and none found for title: Burrlioz 2.0 Manual
- No DOI given, and none found for title: Revised Method for Deriving Australian and New Zea...
- No DOI given, and none found for title: Manual on the methodological framework to derive e...
- No DOI given, and none found for title: Derivation of Water Quality Guidelines for the Pro...

❌ MISSING DOIs

- 10.32614/cran.package.ssddata may be a valid DOI for title: ssddata: Species Sensitivity Distribution Data
- 10.21105/joss.01082 may be a valid DOI for title: ssdtools: An R package to fit species sensitivity ...

❌ INVALID DOIs

- None

joethorley commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

editorialbot commented 1 month ago

Five most similar historical JOSS papers:

shinyssdtools: A web application for fitting Species Sensitivity Distributions (SSDs) Submitting author: @sebdalgarno Handling editor: @marcosvital (Active) Reviewers: @elimillera, @meenakshi-kushwaha, @nanhung Similarity score: 0.7717

shinyssd v1.0: Species Sensitivity Distributions for Ecotoxicological Risk Assessment Submitting author: @flor14 Handling editor: @karthik (Retired) Reviewers: @kylehamilton Similarity score: 0.7438

SSMSE: An R package for Management Strategy Evaluation with Stock Synthesis Operating Models Submitting author: @k-doering-NOAA Handling editor: @sbenthall (Active) Reviewers: @quang-huynh, @iagomosqueira Similarity score: 0.7017

fitODBOD: An R Package to Model Binomial Outcome Data using Binomial Mixture and Alternate Binomial Distributions. Submitting author: @Amalan-ConStat Handling editor: @csoneson (Active) Reviewers: @osorensen, @jjharden Similarity score: 0.6960

SurPyval: Survival Analysis with Python Submitting author: @derrynknife Handling editor: @dfm (Active) Reviewers: @CamDavidsonPilon, @MatthewReid854 Similarity score: 0.6849

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

Kevin-Mattheus-Moerman commented 1 month ago

@joethorley Dear author, thanks for this submission. I am the AEiC on this track and here to help process the initial steps. Before we proceed, please can you have a look at the following points:

[ ] Please study the above reference check :point_up: and see if you can address any of the reported potential DOI issues. You can add/amend DOI entries in your .bib file, and call @editorialbot check references here to check them again.

Kevin-Mattheus-Moerman commented 1 month ago

Note to editors, a prior paper for this project exists: https://joss.theoj.org/papers/10.21105/joss.01082

Kevin-Mattheus-Moerman commented 1 month ago

@joethorley you noted that this new submission (wrt the previous paper) now also features changes like:

The first update (v1) included the addition of four new distributions and a switch to the R package TMB. The second major release (v2) includes critical updates to ensure that the HC and HP estimates satisfy the inversion principle as well as bootstrap methods to obtain confidence intervals (CIs) with more appropriate coverage.

If you could share a bit more detail on the major changes since the previous paper, e.g. a list here, that would be helpful for the handling editor. Thanks.

Kevin-Mattheus-Moerman commented 1 month ago

@editorialbot invite @lucydot as editor

editorialbot commented 1 month ago

Invitation to edit this submission sent!

lucydot commented 1 month ago

Apologies @Kevin-Mattheus-Moerman I'm now editing my maximum number of papers (4) so can't take this one on.

joethorley commented 1 month ago

@Kevin-Mattheus-Moerman - I reviewed all the dois previously (see futher up in chain) and fixed all that I can. The missing ones do not exist.

joethorley commented 1 month ago

@Kevin-Mattheus-Moerman The following is a relatively short summary of the major changes since the previous paper (v0.0.3)

ssdtools 2.0.0

The following arguments were added to ssd_hc() and ssd_hp()

multi_est = TRUE to calculate model averaged estimates treating the distributions as constituting a single mixture distribution (previously it was effectively FALSE).
method_ci = "weighted_samples" to specify whether to use "weighted_samples", "weighted_arithmetic", "multi_free" or "multi_fixed" methods to generate confidence intervals (previously it was effectively "weighted_arithmetic").

In addition, the following functions and arguments were added.

scale_fill_ssd() for color-blind fill scale.

ssdtools 1.0.0

An important change to the functionality of ssd_fit_dists() was to switch from model fitting using fitdistrplus to TMB which has resulted in improved handling of censored data. Although it was hoped that model fitting would be faster this is currently not the case.

As a result of an international collaboration British Columbia and Canada and Australia and New Zealand selected a set of recommended distributions for model averaging and settings when generating final guidelines.

The distributions are

> ssd_dists_bcanz()
[1] "gamma"       "lgumbel"     "llogis"      "lnorm"       "lnorm_lnorm" "weibull"

The following distributions were added (or in the case of burrIII3 readded) to the new version

burrIII3 - burrIII three parameter distribution
invpareto - inverse pareto (with bias correction in scale order statistic)
lnorm_lnorm log-normal/log-normal mixture distribution
llogis_llogis log-logistic/log-logistic mixture distribution

The function ssd_fit_burrlioz() was added to approximate the behaviour of Burrlioz.

Added following plotting functions

geom_ssdsegment() to allow plotting of the range of a censored data points using segments.
scale_colour_ssd() (and scale_color_ssd()) to provide an 8 color-blind scale.

Soft-deprecated

geom_ssd() for geom_ssdpoint().

ssdtools 0.3.0

Soft-deprecated pareto distribution as poor fit on SSD data.

ssdtools 0.2.0

Deprecated burrIII2 distribution for llogis as identical.
Replaced burrIII2 with (identical) llogis distribution in default set.

ssdtools 0.1.0

Default distributions changed to burrIII2, gamma and lnorm from gamma, gompertz, lgumbel, llog, lnorm and weibull.

Added

Burr Type-III Two-Parameter Distribution (burrIII2).
Added Burr Type-III Three-Parameter Distribution (burrIII3).

fabian-s commented 3 weeks ago

@Kevin-Mattheus-Moerman i can edit this

joethorley commented 3 weeks ago

Thanks @fabian-s - we appreciate you being the editor!

flor14 commented 1 week ago

Hello,

Regarding the review process: Is there any difference in the reviewers' checklist for a second version of a software package that has already been published? I couldn’t find any mention of this in the reviewers' guide.

fabian-s commented 1 week ago

@editorialbot add @fabian-s as editor

editorialbot commented 1 week ago

Assigned! @fabian-s is now the editor

fabian-s commented 1 week ago

@editorialbot add @flor14 as reviewer

editorialbot commented 1 week ago

@flor14 added to the reviewers list!

fabian-s commented 1 week ago

@jhollist @nanhung

would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

fabian-s commented 1 week ago

@flor14 thanks for volunteering to review!

Is there any difference in the reviewers' checklist for a second version of a software package that has already been published?

I don't think there is. We'll start the review once I've found a 2nd reviewer, sorry for the delay.

nanhung commented 1 week ago

@fabian-s Sure! I am happy to review this package.

fabian-s commented 1 week ago

@editorialbot add @nanhung as reviewer

editorialbot commented 1 week ago

@nanhung added to the reviewers list!

fabian-s commented 1 week ago

@editorialbot start review

editorialbot commented 1 week ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/7492.

openjournals / joss-reviews