search

openjournals / joss-reviews

Reviews for the Journal of Open Source Software
Creative Commons Zero v1.0 Universal
708 stars 38 forks source link

[PRE REVIEW]: haldensify: Highly adaptive lasso conditional density estimation in R #4411

Closed editorialbot closed 2 years ago

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@nhejazi<!--end-author-handle-- (Nima Hejazi) Repository: https://github.com/nhejazi/haldensify Branch with paper.md (empty if default branch): Version: v0.2.5 Editor: !--editor-->@majensen<!--end-editor-- Reviewers: @turgeonmaxime, @adibender Managing EiC: Kevin M. Moerman

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/e54c2bf1daca38bdcda505be275ecb65"><img src="https://joss.theoj.org/papers/e54c2bf1daca38bdcda505be275ecb65/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/e54c2bf1daca38bdcda505be275ecb65/status.svg)](https://joss.theoj.org/papers/e54c2bf1daca38bdcda505be275ecb65)

Author instructions

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

@nhejazi 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 @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

@editorialbot commands
editorialbot commented 2 years ago

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

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

@editorialbot commands

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

@editorialbot generate pdf
editorialbot commented 2 years ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.06 s (1335.2 files/s, 191648.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            28            676             97           4012
R                               22            270           1051           1601
Markdown                         7            170              0            759
TeX                              1             44              0            451
CSS                              3             98             52            442
JavaScript                       5             65             37            277
Rmd                              2             90            379             99
YAML                             5             15              4             95
XML                              1              0              0             84
make                             1              9              0             20
SVG                              1              0              1             11
-------------------------------------------------------------------------------
SUM:                            76           1437           1621           7851
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 2 years ago

Wordcount for paper.md is 2123

editorialbot commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1111/rssb.12362 is OK
- 10.5281/zenodo.3558313 is OK
- 10.21105/joss.02526 is OK
- 10.21105/joss.00512 is OK
- 10.1111/biom.13375 is OK
- 10.5281/zenodo.4070042 is OK
- 10.21105/joss.02447 is OK

MISSING DOIs

- 10.1007/978-3-319-65304-4_14 may be a valid DOI for title: Stochastic Treatment Regimes
- 10.1111/j.1541-0420.2011.01685.x may be a valid DOI for title: Population intervention causal effects based on stochastic interventions
- 10.2202/1557-4679.1356 may be a valid DOI for title: Super learner based conditional density estimation with application to marginal structural models
- 10.1007/978-3-319-65304-4_6 may be a valid DOI for title: Highly Adaptive Lasso (HAL)
- 10.1515/ijb-2015-0097 may be a valid DOI for title: A Generally Efficient Targeted Minimum Loss Based Estimator based on the Highly Adaptive Lasso
- 10.1109/dsaa.2016.93 may be a valid DOI for title: The highly adaptive lasso estimator
- 10.1515/jci-2014-0022 may be a valid DOI for title: A boosting algorithm for estimating generalized propensity scores with continuous treatments
- 10.1111/j.1541-0420.2005.00377.x may be a valid DOI for title: Doubly robust estimation in missing data and causal inference models
- 10.1162/neco.2008.10-07-628 may be a valid DOI for title: Nonparametric conditional density estimation using piecewise-linear solution path of kernel quantile regression
- 10.1016/s0167-9473(00)00046-3 may be a valid DOI for title: Bandwidth selection for kernel conditional density estimation
- 10.1007/978-1-4471-2097-1_162 may be a valid DOI for title: Estimation of conditional densities: A comparison of neural network approaches
- 10.1109/dsaa.2016.93 may be a valid DOI for title: The highly adaptive lasso estimator
- 10.2202/1544-6115.1036 may be a valid DOI for title: Asymptotic optimality of likelihood-based cross-validation
- 10.1016/j.stamet.2005.02.003 may be a valid DOI for title: Asymptotics of cross-validated risk estimation in estimator selection and performance assessment
- 10.1515/ijb-2015-0097 may be a valid DOI for title: A Generally Efficient Targeted Minimum Loss Based Estimator based on the Highly Adaptive Lasso
- 10.1002/sim.5907 may be a valid DOI for title: Estimation of the effect of interventions that modify the received treatment
- 10.1017/cbo9780511810725.016 may be a valid DOI for title: The central role of the propensity score in observational studies for causal effects
- 10.3150/bj/1093265631 may be a valid DOI for title: Semiparametric density estimation under a two-sample density ratio model
- 10.1093/biomet/85.3.619 may be a valid DOI for title: Inferences for case-control and semiparametric two-sample density ratio models
- 10.1007/bf00117832 may be a valid DOI for title: Stacked regressions
- 10.2202/1557-4679.1043 may be a valid DOI for title: Targeted maximum likelihood learning

INVALID DOIs

- None
editorialbot commented 2 years ago

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

Kevin-Mattheus-Moerman commented 2 years ago

@nhejazi can you check those potentially missing DOIs? :point_up: If those papers are not cited in the paper please remove them from the bib file. You can call @editorialbot check references to repeat the check.

Kevin-Mattheus-Moerman commented 2 years ago

@nhejazi I have just assigned the waitlisted label here, since the editors for this domain are currently preoccupied with other submissions. We will assign an editor once one becomes available.

Kevin-Mattheus-Moerman commented 2 years ago

@marcosvital would you be able to edit this once you are available?

nhejazi commented 2 years ago

@editorialbot commands

editorialbot commented 2 years ago

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


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

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

# Generates the pdf paper
@editorialbot generate pdf

# Get a link to the complete list of reviewers
@editorialbot list reviewers
nhejazi commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

Checking the BibTeX entries failed with the following error: 

Failed to parse BibTeX on value "url" (NAME) [#<BibTeX::Bibliography data=[4]>, "@", #<BibTeX::Entry >, {:title=>["Super learner based conditional density estimation with application to marginal structural models"], :author=>["D{\\'\\i}az, Iv{\\'a}n and {van der Laan}, Mark J"], :journal=>["International Journal of Biostatistics"], :volume=>["7"], :number=>["1"], :pages=>["1--20"], :year=>["2011"], :publisher=>["De Gruyter"], :doi=>["10.2202/1557-4679.1356"]}]
nhejazi commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

Checking the BibTeX entries failed with the following error: 

Failed to parse BibTeX on value "url" (NAME) [#<BibTeX::Bibliography data=[25]>, "@", #<BibTeX::Entry >, {:title=>["Asymptotics of cross-validated risk estimation in estimator selection and performance assessment"], :author=>["Dudoit, Sandrine and {van der Laan}, Mark J"], :journal=>["Statistical Methodology"], :volume=>["2"], :number=>["2"], :pages=>["131--154"], :year=>["2005"], :publisher=>["Elsevier"], :doi=>["10.1016/j.stamet.2005.02.003"]}]
nhejazi commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1007/978-3-319-65304-4_14 is OK
- 10.2202/1557-4679.1356 is OK
- 10.1111/rssb.12362 is OK
- 10.1007/978-3-319-65304-4_6 is OK
- 10.1515/ijb-2015-0097 is OK
- 10.5281/zenodo.3558313 is OK
- 10.21105/joss.02526 is OK
- 10.1109/dsaa.2016.93 is OK
- 10.1515/jci-2014-0022 is OK
- 10.1111/j.1541-0420.2005.00377.x is OK
- 10.1162/neco.2008.10-07-628 is OK
- 10.1016/s0167-9473(00)00046-3 is OK
- 10.1007/978-1-4471-2097-1_162 is OK
- 10.21105/joss.00512 is OK
- 10.2202/1544-6115.1036 is OK
- 10.1016/j.stamet.2005.02.003 is OK
- 10.1515/ijb-2015-0097 is OK
- 10.1111/biom.13375 is OK
- 10.1002/sim.5907 is OK
- 10.1017/cbo9780511810725.016 is OK
- 10.3150/bj/1093265631 is OK
- 10.1093/biomet/85.3.619 is OK
- 10.1007/bf00117832 is OK
- 10.5281/zenodo.4070042 is OK
- 10.21105/joss.02447 is OK
- 10.2202/1557-4679.1043 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1111/j.1541-0420.2011.01685.x is INVALID because of 'https://doi.org/' prefix
nhejazi commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1007/978-3-319-65304-4_14 is OK
- 10.1111/j.1541-0420.2011.01685.x is OK
- 10.2202/1557-4679.1356 is OK
- 10.1111/rssb.12362 is OK
- 10.1007/978-3-319-65304-4_6 is OK
- 10.1515/ijb-2015-0097 is OK
- 10.5281/zenodo.3558313 is OK
- 10.21105/joss.02526 is OK
- 10.1109/dsaa.2016.93 is OK
- 10.1515/jci-2014-0022 is OK
- 10.1111/j.1541-0420.2005.00377.x is OK
- 10.1162/neco.2008.10-07-628 is OK
- 10.1016/s0167-9473(00)00046-3 is OK
- 10.1007/978-1-4471-2097-1_162 is OK
- 10.21105/joss.00512 is OK
- 10.2202/1544-6115.1036 is OK
- 10.1016/j.stamet.2005.02.003 is OK
- 10.1515/ijb-2015-0097 is OK
- 10.1111/biom.13375 is OK
- 10.1002/sim.5907 is OK
- 10.1017/cbo9780511810725.016 is OK
- 10.3150/bj/1093265631 is OK
- 10.1093/biomet/85.3.619 is OK
- 10.1007/bf00117832 is OK
- 10.5281/zenodo.4070042 is OK
- 10.21105/joss.02447 is OK
- 10.2202/1557-4679.1043 is OK

MISSING DOIs

- None

INVALID DOIs

- None
nhejazi commented 2 years ago

thanks @Kevin-Mattheus-Moerman, I've now added all of the missing DOIs and validated them against the checks from the editorial bot. no problem to wait until editors/reviewers are available.

danielskatz commented 2 years ago

👋 @majensen - would you be willing to edit this submission?

danielskatz commented 2 years ago

@editorialbot invite @majensen as editor

editorialbot commented 2 years ago

Invitation to edit this submission sent!

majensen commented 2 years ago

@editorialbot assign me as editor

editorialbot commented 2 years ago

Assigned! @majensen is now the editor

majensen commented 2 years ago

@nhejazi thanks for the submission. Are you able to suggest one or two possible reviewers? Thanks

nhejazi commented 2 years ago

@majensen sure, thanks for reminding me about this. here are a few possible referees from the JOSS list: stefanocoretta, mhu48, turgeonmaxime, graystatistics, stmcg

nhejazi commented 2 years ago

@majensen, no rush at all, but let me know if I can work on anything else related to starting this review

majensen commented 2 years ago

Apologies @nhejazi - Thanks for the ping. I will get some reviewer requests out today.

majensen commented 2 years ago

Hi @stefanocoretta - I appreciate your interest in reviewing for JOSS! Are you available to review this work? Your expertise here would be very helpful; please have a look at the review guidelines, and if you are interested, please repond in this thread. Thanks for your consideration! --@majensen

majensen commented 2 years ago

Hello @turgeonmaxime - thanks for your interest in reviewing for JOSS. I believe your interests and expertise align with this submitted work. Would you have time to review? Please have a look at the review guidelines, and let us know by responding in this thread. If you have suggestions for other possible reviewers, that would be welcome as well. Many thanks for your consideration --@majensen

turgeonmaxime commented 2 years ago

@majensen Yes, I'm available to review this manuscript.

majensen commented 2 years ago

Thanks so much @turgeonmaxime

majensen commented 2 years ago

@editorialbot add @turgeonmaxime as reviewer

editorialbot commented 2 years ago

@turgeonmaxime added to the reviewers list!

majensen commented 2 years ago

Hi @adibender - I am seeking one review for this work for JOSS. Would you have time and be willing to review? Your expertise would be right on target. Thanks for your consideration! --@majensen

adibender commented 2 years ago

Hello @majensen , happy to do so.

majensen commented 2 years ago

@editorialbot add @adibender as reviewer

editorialbot commented 2 years ago

@adibender added to the reviewers list!

majensen commented 2 years ago

@turgeonmaxime @adibender thanks so much for your willingness to review - I will open the review issue, which will close this current one. Further discussion will take place there. cc @nhejazi

majensen commented 2 years ago

@editorialbot start review

editorialbot commented 2 years ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/4522.

stefanocoretta commented 2 years ago

Hi @stefanocoretta - I appreciate your interest in reviewing for JOSS! Are you available to review this work? Your expertise here would be very helpful; please have a look at the review guidelines, and if you are interested, please repond in this thread. Thanks for your consideration! --@majensen

Hello! Sorry for the late reply but I was away. I assume the review task has been taken over by someone already?

majensen commented 2 years ago

Thanks so much @stefanocoretta - yes we are all set now. Catch you next time I hope-