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[PRE REVIEW]: BinMat: an R package and Shiny application for processing binary data obtained from genetic fragment analysis methods #2742

Closed whedon closed 3 years ago

whedon commented 3 years ago

Submitting author: @CJMvS (Clarke van Steenderen) Repository: https://github.com/CJMvS/BinMat_JOSS Version: v0.1.2 Editor: Pending Reviewer: Pending Managing EiC: Daniel S. Katz

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Author instructions

Thanks for submitting your paper to JOSS @CJMvS. Currently, there isn't an JOSS editor assigned to your paper.

@CJMvS if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

The JOSS submission bot @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:

@whedon commands
whedon commented 3 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf
whedon commented 3 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=0.41 s (59.0 files/s, 10897.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JSON                             1              0              0           1279
HTML                             1             33              2            716
R                               16            298            327            635
TeX                              1             38              0            366
Markdown                         3            148              0            325
Rmd                              2             88            158             21
-------------------------------------------------------------------------------
SUM:                            24            605            487           3342
-------------------------------------------------------------------------------

Statistical information for the repository '7996e803680d5bae5cf46acb' was
gathered on 2020/10/12.
No commited files with the specified extensions were found.
whedon commented 3 years ago

PDF failed to compile for issue #2742 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:in parse': (a8c3174891a74b887edc939e/Paper/paper.md): could not find expected ':' while scanning a simple key at line 2 column 1 (Psych::SyntaxError) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:inparse_stream' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:325:in parse' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:252:inload' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:473:in block in load_file' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:472:inopen' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:472:in load_file' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon.rb:127:inload_yaml' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon.rb:87:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon/processor.rb:38:innew' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon/processor.rb:38:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/bin/whedon:58:inprepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:ininvoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:instart' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/bin/whedon:131:in <top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:inload' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in `

'

danielskatz commented 3 years ago

šŸ‘‹ @CJMvS - your paper.md is not formatted correctly - see https://joss.readthedocs.io/en/latest/submitting.html#example-paper-and-bibliography for what is needed. If you make changes, please add a new comment here with @whedon generate pdf to check to see if it compiles. You can also use @whedon check references to see if references have correct DOIs (as far as whedon can guess).

danielskatz commented 3 years ago

Also, due to the small size of your code, the editors will discuss the scope of the paper to see if we will review it. We should make a decision by the end of next week

danielskatz commented 3 years ago

@whedon query scope

whedon commented 3 years ago

Submission flagged for editorial review.

clarkevansteenderen commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

PDF failed to compile for issue #2742 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:in parse': (00934c39f12d19325df18b5e/Paper/paper.md): did not find expected key while parsing a block mapping at line 16 column 4 (Psych::SyntaxError) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:inparse_stream' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:325:in parse' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:252:inload' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:473:in block in load_file' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:472:inopen' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:472:in load_file' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon.rb:127:inload_yaml' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon.rb:87:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon/processor.rb:38:innew' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/lib/whedon/processor.rb:38:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/bin/whedon:58:inprepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:ininvoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:instart' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-d14a699185fb/bin/whedon:131:in <top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:inload' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in `

'

clarkevansteenderen commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

whedon commented 3 years ago

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

clarkevansteenderen commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

clarkevansteenderen commented 3 years ago

@whedon check references

clarkevansteenderen commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

clarkevansteenderen commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

clarkevansteenderen commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

clarkevansteenderen commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

clarkevansteenderen commented 3 years ago

@whedon commands

whedon commented 3 years ago

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository
clarkevansteenderen commented 3 years ago

@whedon check repository

whedon commented 3 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=0.05 s (453.9 files/s, 83094.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JSON                             1              0              0           1279
HTML                             1             33              2            716
R                               16            298            327            635
TeX                              1             38              0            367
Markdown                         3            112              0            189
Rmd                              1             71            123             21
-------------------------------------------------------------------------------
SUM:                            23            552            452           3207
-------------------------------------------------------------------------------

Statistical information for the repository 'e54b789413047443089f1c6b' was
gathered on 2020/10/12.
No commited files with the specified extensions were found.
clarkevansteenderen commented 3 years ago

@whedon check references

whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- None

MISSING DOIs

- 10.1016/j.biocontrol.2020.104426 may be a valid DOI for title: Addressing the red flags in cochineal identification: the use of molecular techniques to identify cochineal insects that are used as biological control agents for invasive alien cacti
- 10.1111/j.1442-9993.1993.tb00438.x may be a valid DOI for title: Non-parametric multivariate analyses of changes in community structure
- 10.1007/978-1-61779-870-2_10 may be a valid DOI for title: Automated scoring of AFLPs using RawGeno v 2.0, a free R CRAN library
- 10.1111/j.1365-294x.2004.02346.x may be a valid DOI for title: How to track and assess genotyping errors in population genetics studies
- 10.1080/10635150802044037 may be a valid DOI for title: Optimizing automated AFLP scoring parameters to improve phylogenetic resolution
- 10.1111/1755-0998.12559 may be a valid DOI for title: stratag: An R package for manipulating, summarizing and analysing population genetic data
- 10.1093/bioinformatics/btg412 may be a valid DOI for title: APE: analyses of phylogenetics and evolution in R language
- 10.1093/bioinformatics/btq706 may be a valid DOI for title: Phangorn: Phylogenetic analysis in R
- 10.1111/1365-2745.12869 may be a valid DOI for title: Intracontinental plant invader shows matching genetic and chemical profiles and might benefit from high defence variation within populations
- 10.1186/s12864-019-6073-7 may be a valid DOI for title: GENAVi: a shiny web application for gene expression normalization, analysis and visualization
- 10.1093/jis/1.1.8 may be a valid DOI for title: Individual and population variation in invertebrates revealed by Inter-simple Sequence Repeats (ISSRs)
- 10.1007/978-1-4615-5419-6_2 may be a valid DOI for title: Contributions of PCR-based methods to plant systematics and evolutionary biology
- 10.1016/0003-2697(91)90120-i may be a valid DOI for title: Fast and sensitive silver staining of DNA in polyacrylamide gels
- 10.1017/s0007485309990435 may be a valid DOI for title: Population genetic structure of economically important Tortricidae (Lepidoptera) in South Africa: a comparative analysis
- 10.1111/j.1462-2920.2004.00685.x may be a valid DOI for title: Assessing terminal restriction fragment length polymorphism suitability for the description of bacterial community structure and dynamics in hydrocarbon-polluted marine environments
- 10.1111/j.1574-6941.2008.00493.x may be a valid DOI for title: Evaluation of terminal-restriction fragment length polymorphism analysis in contrasting marine environments
- 10.1002/0470013192.bsa612 may be a valid DOI for title: Shepard diagram
- 10.1093/bioinformatics/14.1.68 may be a valid DOI for title: SplitsTree: analyzing and visualizing evolutionary data

INVALID DOIs

- None
clarkevansteenderen commented 3 years ago

@whedon check references

whedon commented 3 years ago

Checking the BibTeX entries failed with the following error:

Failed to parse BibTeX on value ".1111/mec.12844" (NAME) [#, "@", #, {:title=>["{Phylogeography of \textit{Heliconius cydno} and its closest relatives: disentangling their origin and diversification}"], :author=>["Arias, Carlos F and Salazar, Camilo and Rosales, Claudia and Kronforst, Marcus R and Linares, Mauricio and Bermingham, Eldredge and McMillan, W Owen"], :journal=>["Molecular Ecology"], :volume=>["23"], :number=>["16"], :pages=>["4137--4152"], :year=>["2014"], :doi=>"10"}]

clarkevansteenderen commented 3 years ago

@whedon check references

whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/j.biocontrol.2020.104426 is OK
- 10.1111/j.1442-9993.1993.tb00438.x is OK
- 10.1111/mec.12844 is OK
- 10.1016/j.biocontrol.2011.05.008 is OK
- 10.1016/j.biocontrol.2017.08.015 is OK
- 10.1007/978-1-61779-870-2_10 is OK
- 10.1111/j.1365-294X.2004.02346.x is OK
- 10.1038/nrg1707 is OK
- 10.1080/10635150802044037 is OK
- 10.1111/1755-0998.12559 is OK
- 10.1093/bioinformatics/btg412 is OK
- 10.1093/bioinformatics/btq706 is OK
- 10.5169/seals-268384 is OK
- 10.1111/1365-2745.12869 is OK
- 10.1186/s12864-019-6073-7 is OK
- 10.1016/S0167-7012(00)00153-6 is OK
- 10.1626/pps.12.88 is OK
- 10.1017/S0007485309990435 is OK
- 10.1111/j.1462-2920.2004.00685.x is OK
- 10.1111/j.1574-6941.2008.00493.x is OK
- 10.1371/journal.pone.0184259 is OK
- 10.1002/9781118445112.stat06268.pub2 is OK
- 10.1093/bioinformatics/14.1.68 is OK

MISSING DOIs

- 10.1093/jis/1.1.8 may be a valid DOI for title: Individual and population variation in invertebrates revealed by Inter-simple Sequence Repeats (ISSRs)
- 10.1007/978-1-4615-5419-6_2 may be a valid DOI for title: Contributions of PCR-based methods to plant systematics and evolutionary biology
- 10.1016/0003-2697(91)90120-i may be a valid DOI for title: Fast and sensitive silver staining of DNA in polyacrylamide gels

INVALID DOIs

- 10.1128/AEM.67.10.4863ā€“4873.2001 is INVALID
clarkevansteenderen commented 3 years ago

@whedon check references

whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/j.biocontrol.2020.104426 is OK
- 10.1111/j.1442-9993.1993.tb00438.x is OK
- 10.1111/mec.12844 is OK
- 10.1016/j.biocontrol.2011.05.008 is OK
- 10.1016/j.biocontrol.2017.08.015 is OK
- 10.1007/978-1-61779-870-2_10 is OK
- 10.1111/j.1365-294X.2004.02346.x is OK
- 10.1038/nrg1707 is OK
- 10.1080/10635150802044037 is OK
- 10.1111/1755-0998.12559 is OK
- 10.1093/bioinformatics/btg412 is OK
- 10.1093/bioinformatics/btq706 is OK
- 10.5169/seals-268384 is OK
- 10.1111/1365-2745.12869 is OK
- 10.1186/s12864-019-6073-7 is OK
- 10.1093/jis/1.1.8 is OK
- 10.1007/978-1-4615-5419-6_2 is OK
- 10.1016/S0167-7012(00)00153-6 is OK
- 10.1016/0003-2697(91)90120-i is OK
- 10.1626/pps.12.88 is OK
- 10.1017/S0007485309990435 is OK
- 10.1111/j.1462-2920.2004.00685.x is OK
- 10.1111/j.1574-6941.2008.00493.x is OK
- 10.1371/journal.pone.0184259 is OK
- 10.1002/9781118445112.stat06268.pub2 is OK
- 10.1093/bioinformatics/14.1.68 is OK

MISSING DOIs

- None

INVALID DOIs

- 10.1128/AEM.67.10.4863ā€“4873.2001 is INVALID
clarkevansteenderen commented 3 years ago

Thank you for the update @danielskatz. I managed to successfully compile the .md file.

clarkevansteenderen commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

clarkevansteenderen commented 3 years ago

@whedon check references

whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/j.biocontrol.2020.104426 is OK
- 10.1111/j.1442-9993.1993.tb00438.x is OK
- 10.1111/mec.12844 is OK
- 10.1016/j.biocontrol.2011.05.008 is OK
- 10.1016/j.biocontrol.2017.08.015 is OK
- 10.1007/978-1-61779-870-2_10 is OK
- 10.1111/j.1365-294X.2004.02346.x is OK
- 10.1038/nrg1707 is OK
- 10.1080/10635150802044037 is OK
- 10.1111/1755-0998.12559 is OK
- 10.1093/bioinformatics/btg412 is OK
- 10.1093/bioinformatics/btq706 is OK
- 10.5169/seals-268384 is OK
- 10.1111/1365-2745.12869 is OK
- 10.1186/s12864-019-6073-7 is OK
- 10.1093/jis/1.1.8 is OK
- 10.1007/978-1-4615-5419-6_2 is OK
- 10.1016/S0167-7012(00)00153-6 is OK
- 10.1016/0003-2697(91)90120-i is OK
- 10.1626/pps.12.88 is OK
- 10.1017/S0007485309990435 is OK
- 10.1111/j.1462-2920.2004.00685.x is OK
- 10.1111/j.1574-6941.2008.00493.x is OK
- 10.1371/journal.pone.0184259 is OK
- 10.1002/9781118445112.stat06268.pub2 is OK
- 10.1093/bioinformatics/14.1.68 is OK

MISSING DOIs

- None

INVALID DOIs

- None
kyleniemeyer commented 3 years ago

@CJMvS Unfortunately, the JOSS editors have decided that this submission does not meet the substantial scholarly effort criterion for review by JOSS. Please see https://joss.readthedocs.io/en/latest/submitting.html#other-venues-for-reviewing-and-publishing-software-packages for other suggestions for how you might receive credit for your work.

kyleniemeyer commented 3 years ago

@whedon reject

whedon commented 3 years ago

Paper rejected.