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[PRE REVIEW]: faersquarterlydata : an R package to analyze adverse drug reactions in Food and Drug Administration (FDA) database #6077

Closed editorialbot closed 8 months ago

editorialbot commented 10 months ago

Submitting author: !--author-handle-->@luisgarcez11<!--end-author-handle-- (Luís Garcez Ferreira) Repository: https://github.com/luisgarcez11/faersquarterlydata Branch with paper.md (empty if default branch): master Version: 1.1.0 Editor: Pending Reviewers: Pending Managing EiC: Kevin M. Moerman

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Markdown: [![status](https://joss.theoj.org/papers/417c5e0e9be325963e2354b131b0fd28/status.svg)](https://joss.theoj.org/papers/417c5e0e9be325963e2354b131b0fd28)

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editorialbot commented 10 months ago

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

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

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editorialbot commented 10 months ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.06 s (388.0 files/s, 164271.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TeX                              1             83              0           5659
XML                              2              0              0           1796
R                               14            248            235            973
Markdown                         5            197              0            891
YAML                             1              8              3             39
Rmd                              1              9             12              7
-------------------------------------------------------------------------------
SUM:                            24            545            250           9365
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 10 months ago

Wordcount for paper.md is 3977

editorialbot commented 10 months ago

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

editorialbot commented 10 months ago

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editorialbot commented 10 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1111/J.1468-1331.2011.03501.X is OK
- 10.1016/0022-510X(95)00052-4 is OK
- 10.1093/eurheartj/ehy394 is OK
- 10.1161/CIRCULATIONAHA.122.062714 is OK
- 10.1093/eurheartj/ehad369 is OK
- 10.1111/jocs.14370 is OK
- 10.1016/S0140-6736(09)60552-3 is OK
- 10.1016/j.athoracsur.2005.05.005 is OK
- 10.1016/j.ahj.2022.01.017 is OK
- 10.12659/MSM.922957 is OK
- 10.1016/j.jtcvs.2020.03.164 is OK
- 10.1016/S0140-6736(19)31997-X is OK
- 10.1016/S0140-6736(21)02334-5 is OK
- 10.1161/CIRCULATIONAHA.108.842005 is OK
- 10.1016/S0140-6736(18)30423-9 is OK
- 10.1016/j.amjcard.2014.04.025 is OK
- 10.1016/j.ijcard.2016.09.055 is OK
- 10.1016/j.jacc.2006.11.048 is OK
- 10.1016/j.jcin.2015.10.044 is OK
- 10.1007/s11883-012-0226-3 is OK
- 10.1001/jamainternmed.2020.4748 is OK
- 10.1214/AOS/1013203451 is OK
- 10.1002/med.21528 is OK
- 10.1007/S00415-010-5609-1 is OK
- 10.1017/CBO9780511973000 is OK
- 10.18637/JSS.V014.I15 is OK
- 10.2307/2983604 is OK
- 10.1002/PDS.1001 is OK
- 10.1002/PDS.5105 is OK
- 10.1002/PDS.677 is OK
- 10.1111/1475-6773.12182 is OK
- 10.18637/JSS.V033.I01 is OK
- 10.18637/JSS.V097.I01 is OK
- 10.1023/A:1010933404324 is OK
- 10.18637/JSS.V033.I01 is OK
- 10.1201/9781315370279 is OK
- 10.1162/REST_A_00318 is OK
- 10.1037/0012-1649.44.2.395 is OK
- 10.1198/016214504000000647 is OK
- 10.1002/SIM.6004 is OK
- 10.1093/AJE/KWQ224 is OK
- 10.1080/00273171.2011.540475 is OK
- 10.18637/JSS.V042.I08 is OK
- 10.1093/PAN/MPL013 is OK
- 10.1016/J.JCLINEPI.2013.01.013 is OK
- 10.1037/A0014268 is OK
- 10.1093/AJE/KWQ472 is OK
- 10.1007/S11999-015-4239-4 is OK
- 10.1136/BMJ.328.7454.1490 is OK
- 10.1016/S0022-510X(99)00045-3 is OK
- 10.1183/23120541.00159-2017 is OK
- 10.1136/JNNP-2014-310055 is OK
- 10.1002/MUS.26149 is OK
- 10.1016/S1474-4422(05)70326-4 is OK
- 10.1111/J.1600-0404.1983.TB04810.X is OK
- 10.1177/1756286419857040 is OK
- 10.1136/THORAX.57.3.192 is OK
- 10.1111/J.1467-9876.2005.00491.X is OK
- 10.1002/SIM.3450 is OK
- 10.3390/JCM7100352 is OK
- 10.3390/NU13082765 is OK
- 10.1371/JOURNAL.PONE.0177555 is OK
- 10.1080/21678421.2021.1946089 is OK
- 10.3386/T0283 is OK
- 10.1177/0193841X21992199 is OK
- 10.1080/03610918.2021.1963455 is OK
- 10.1007/978-3-319-19977-1 is OK
- 10.1016/S0022-510X(01)00614-1 is OK
- 10.1080/14660820310011728 is OK
- 10.1080/21678421.2019.1643374 is OK
- 10.1371/JOURNAL.PONE.0192243 is OK
- 10.3390/NU13082765 is OK
- 10.21105/JOSS.00296 is OK
- 10.1162/neco.1997.9.8.1735 is OK
- 10.1038/S41592-019-0686-2 is OK
- 10.1038/s41598-021-02476-9 is OK
- 10.1016/j.nicl.2016.10.008 is OK
- 10.1109/ICDMW.2018.00113 is OK
- 10.1212/WNL.53.5.1059 is OK
- 10.1046/j.1468-1331.2001.0222d.x is OK
- 10.1016/S0022-510X(99)00210-5 is OK
- 10.1002/SIM.4780080803 is OK
- 10.17576/jsm-2017-4603-15 is OK
- 10.1016/S0022-510X(99)00209-9 is OK
- 10.1212/WNL.53.2.278 is OK
- 10.22034/APJCP.2017.18.4.1077 is OK
- 10.3109/17482960802566824 is OK
- 10.1038/NN.4012 is OK
- 10.1038/NN.4012 is OK
- 10.1159/000351153 is OK
- 10.1007/S00109-015-1273-3 is OK
- 10.1212/WNL.36.4.511 is OK
- 10.1016/S1474-4422(07)70265-X is OK
- 10.3109/17482960802566824 is OK
- 10.1186/s12883-014-0197-9 is OK
- 10.1212/CPJ.0000000000000521 is OK
- 10.1136/jnnp.2009.175984 is OK
- 10.1007/s00415-015-7940-z is OK
- 10.1002/mus.26149 is OK
- 10.1136/thx.2011.160481 is OK
- 10.1371/journal.pone.0192243 is OK
- 10.1371/JOURNAL.PONE.0192243 is OK
- 10.1212/WNL.53.5.1123 is OK
- 10.1155/2018/6534150 is OK
- 10.1016/J.JCRC.2010.06.003 is OK
- 10.1080/21678421.2021.2004167 is OK
- 10.1080/01616412.2022.2029292 is OK
- 10.1001/ARCHNEUR.55.4.526 is OK
- 10.1136/JNNP-2015-312908 is OK
- 10.1002/ANA.24096 is OK
- 10.3389/fneur.2019.00109 is OK
- 10.1201/b12925-16 is OK
- 10.1136/jnnp.74.7.995 is OK
- 10.1016/S1474-4422(18)30089-9 is OK
- 10.1016/j.ebiom.2021.103732 is OK
- 10.1162/neco.1997.9.8.1735 is OK
- 10.1016/j.jalz.2013.10.003 is OK
- 10.1159/000488780 is OK
- 10.1016/j.neuroimage.2016.04.001 is OK
- 10.1186/s12911-020-01166-2 is OK
- 10.1016/j.jbi.2015.09.021 is OK
- 10.1016/j.nicl.2016.10.008 is OK
- 10.1016/S1474-4422(05)70326-4 is OK
- 10.1159/000499485 is OK
- 10.1080/14660820510043235 is OK
- 10.1007/s00415-021-10508-7 is OK
- 10.7287/peerj.preprints.3262v1 is OK
- 10.3892/etm.2019.7264 is OK
- 10.1016/j.eswa.2018.09.035 is OK
- 10.1016/j.clinph.2019.10.016 is OK
- 10.1007/s10618-017-0502-5 is OK
- 10.1145/3195833 is OK
- 10.1016/j.jbi.2015.09.021 is OK
- 10.2196/13433 is OK
- 10.1109/JSEN.2020.3035960 is OK
- 10.1038/s41467-019-08475-9 is OK
- 10.1038/s41598-018-36745-x is OK
- 10.1186/s12911-018-0710-y is OK
- 10.3978/j.issn.2305-5839.2016.01.16 is OK
- 10.3389/fninf.2018.00036 is OK
- 10.1038/s41598-018-36873-4 is OK
- 10.12688/f1000research.10476.1 is OK
- 10.3389/fphys.2016.00561 is OK
- 10.1186/s13015-014-0027-z is OK
- 10.1038/emm.2017.290 is OK
- 10.1007/s10618-017-0521-2 is OK
- 10.1080/21678421.2017.1349150 is OK
- 10.1007/s10618-014-0385-7 is OK
- 10.1016/S1474-4422(18)30089-9 is OK
- 10.1056/nejmra1814259 is OK
- 10.1214/aoms/1177729885 is OK
- 10.1177/009286150203600115 is OK
- 10.1177/1740774512447898 is OK
- 10.1002/(sici)1097-0258(19991230)18:24<3435::aid-sim365>3.0.co;2-o is OK
- 10.1111/j.1744-6171.2009.00193.x is OK
- 10.1192/apt.9.3.229 is OK
- 10.1016/J.GIE.2013.01.012 is OK
- 10.1007/s10916-014-0144-8 is OK
- 10.1093/geront/43.suppl_2.58 is OK
- 10.1177/1052562905276278 is OK
- 10.1111/1468-0009.00108 is OK
- 10.1016/J.CCT.2010.05.007 is OK
- 10.1007/s10916-014-0105-2 is OK
- 10.1016/J.ATHORACSUR.2011.06.101 is OK
- 10.2307/2533387 is OK
- 10.1016/J.CCT.2018.01.003 is OK
- 10.1016/S0003-4975(01)03222-2 is OK
- 10.1002/mdc3.12388 is OK
- 10.1371/journal.pone.0029522 is OK
- 10.1371/currents.RRN1184 is OK
- 10.1186/s13063-015-0653-x is OK
- 10.1186/s13063-015-0653-x is OK
- 10.1016/j.cct.2010.05.007 is OK
- 10.1007/0-387-27782-X is OK
- 10.1111/j.1740-9713.2011.00521.x is OK
- 10.1007/s10120-015-0533-9 is OK
- 10.1177/1740774507087554 is OK
- 10.1186/1745-6215-12-S1-A55 is OK
- 10.1007/s10120-015-0533-9 is OK
- 10.1177/1740774507087554 is OK
- 10.1186/1471-2288-5-11 is OK
- 10.4155/CLI.14.116 is OK
- 10.1198/tech.2004.s740 is OK
- 10.1198/tech.2004.s740 is OK
- 10.1080/03610918208812265 is OK
- 10.2196/jmir.2001 is OK
- 10.1177/1740774512447898 is OK
- 10.1197/jamia.M3144 is OK
- 10.4212/cjhp.v62i4.812 is OK
- 10.1186/gm239 is OK
- 10.1109/MSP.2010.103 is OK
- 10.1016/S0169-7161(08)00015-1 is OK
- 10.1371/journal.pone.0028071 is OK
- 10.1080/09332480.2004.10554908 is OK
- 10.1161/STROKEAHA.107.482414 is OK
- 10.1016/j.ahj.2012.10.015 is OK
- 10.2307/1905335 is OK
- 10.1016/j.jtcvs.2007.07.021 is OK
- 10.2307/2684560 is OK
- 10.2307/2684560 is OK
- 10.1016/S0140-6736(08)60694-7 is OK
- 10.1002/ccd.25884 is OK
- 10.1186/1755-7682-2-27 is OK
- 10.1016/S0895-4356(96)00236-3 is OK
- 10.1016/j.ahj.2012.10.015 is OK
- 10.1161/STROKEAHA.110.608638 is OK
- 10.4244/EIJV9I3A56 is OK
- 10.1161/CIRCOUTCOMES.112.965269 is OK
- 10.1586/erc.12.16 is OK
- 10.1007/s11886-012-0287-5 is OK
- 10.1016/j.ijcard.2012.05.017 is OK
- 10.1002/sim.3278 is OK
- 10.1002/sim.1903 is OK
- 10.1002/sim.1903 is OK
- 10.1002/sim.1047 is OK
- 10.1111/j.1468-0262.2006.00655.x is OK
- 10.1016/j.jclinepi.2005.07.004 is OK
- 10.1002/pst.433 is OK
- 10.1002/sim.2277 is OK
- 10.1037/a0014268 is OK
- 10.1016/S1573-4463(99)03012-6 is OK
- 10.1016/j.optm.2007.12.009 is OK
- 10.1111/j.1742-7843.2006.pto_293.x is OK
- 10.1002/sim.2580 is OK
- 10.1002/sim.2328 is OK
- 10.1177/0962280210394483 is OK
- 10.1002/sim.3150 is OK
- 10.2307/2074954 is OK
- 10.1080/00273171.2011.568786 is OK
- 10.1186/s12874-015-0017-y is OK
- 10.1162/003465304323023651 is OK
- 10.1089/act.2014.20604 is OK
- 10.1001/jamaoncol.2015.0735 is OK
- 10.1111/j.1467-9752.1996.tb00390.x is OK
- 10.1111/gcb.12272 is OK
- 10.2307/2532812 is OK
- 10.2307/2533392 is OK
- 10.1002/(SICI)1099-095X(199905/06)10:3<261::AID-ENV351>3.0.CO;2-O is OK
- 10.1002/sim.6607 is OK
- 10.1080/00031305.1985.10479383 is OK
- 10.1186/s12874-015-0049-3 is OK
- 10.1093/icb/44.2.163 is OK
- 10.1016/j.cjca.2015.05.015 is OK
- 10.1093/aje/kwj047 is OK
- 10.1002/(SICI)1097-0258(19981015)17:19<2265::AID-SIM918>3.0.CO;2-B is OK
- 10.1093/aje/kwj149 is OK
- 10.1093/aje/kwg115 is OK
- 10.1093/aje/kwm069 is OK
- 10.1093/aje/kwi192 is OK
- 10.1002/ajmg.a.34338 is OK
- 10.7326/0003-4819-137-8-200210150-00015 is OK
- 10.1212/WNL.0000000000012777 is OK
- 10.1177/0272989X09341755 is OK
- 10.1016/j.cmpbup.2021.100018 is OK
- 10.1002/PDS.668 is OK
- 10.3390/HEALTHCARE10030420 is OK
- 10.1164/rccm.201604-0848OC is OK
- 10.1016/j.cmpbup.2021.100018 is OK
- 10.1007/s00415-014-7564-8 is OK
- 10.1177/0193841X21992199 is OK
- 10.1097/JTO.0B013E3181EC173D is OK
- 10.1038/s41598-019-49656-2 is OK
- 10.3389/fnins.2019.00135 is OK
- 10.1097/WCO.0000000000000795 is OK
- 10.1016/j.jbi.2019.103350 is OK
- 10.1080/14660820310011728 is OK
- 10.1097/MAJ.0000000000000517 is OK
- 10.1159/000380855 is OK
- 10.1186/s12874-021-01273-2 is OK
- 10.22034/APJCP.2017.18.4.1077 is OK
- 10.15585/MMWR.MM6650A3 is OK
- 10.1136/JNNP-2015-312908 is OK
- 10.1001/ARCHNEUROL.2009.1 is OK
- 10.1016/J.JALZ.2013.12.014 is OK
- 10.1038/s41598-018-37769-z is OK
- 10.7726/AJAD.2013.1002 is OK
- 10.3389/fnagi.2017.00077 is OK
- 10.1016/j.neuroimage.2012.01.062 is OK
- 10.1093/brain/awu176 is OK
- 10.1093/brain/awy089 is OK
- 10.1016/S1474-4422(13)70044-9 is OK
- 10.1177/1740774513494504 is OK

MISSING DOIs

- 10.1136/pgmj.53.621.419 may be a valid DOI for title: Aids to the examination of the peripheral nervous system
- 10.1101/2021.05.13.21254848 may be a valid DOI for title: Identifying Patterns of ALS Progression from Sparse Longitudinal Data
- 10.1186/s13063-018-2941-8 may be a valid DOI for title: Monitoring performance of sites within multicentre randomised trials : a systematic review of performance metrics
- 10.1186/s13063-018-2940-9 may be a valid DOI for title: Development of a standardised set of metrics for monitoring site performance in multicentre randomised trials : a Delphi study
- 10.1186/s13063-018-2941-8 may be a valid DOI for title: Monitoring performance of sites within multicentre randomised trials : a systematic review of performance metrics
- 10.1186/s13063-018-2940-9 may be a valid DOI for title: Development of a standardised set of metrics for monitoring site performance in multicentre randomised trials : a Delphi study
- 10.4324/9781315267227-2 may be a valid DOI for title: Keywords :
- 10.1007/978-3-319-52636-2_191 may be a valid DOI for title: De-identifying clinical trials data
- 10.1201/9780203753781-6 may be a valid DOI for title: Generalized additive models
- 10.7326/0003-4819-137-8-200210150-00015 may be a valid DOI for title: Rare outcomes, common treatments: analytic strategies using propensity scores.
- 10.1093/biostatistics/3.2.179 may be a valid DOI for title: Propensity score modeling strategies for the causal analysis of observational data
- 10.2307/2528036 may be a valid DOI for title: The effectiveness of adjustment by subclassification in removing bias in observational studies.
- 10.1201/9780203753781-6 may be a valid DOI for title: Generalized Additive Models
- 10.3386/t0283 may be a valid DOI for title: Simple and Bias-Corrected Matching Estimators for Average Treatment Effects
- 10.1017/cbo9780511810725.007 may be a valid DOI for title: Matching to Remove Bias in Observational Studies
- 10.4324/9781315129945-23 may be a valid DOI for title: Factors relevant to the validity of experiments in social settings.
- 10.1353/obs.2015.0010 may be a valid DOI for title: Observational Studies
- 10.1017/pan.2019.11 may be a valid DOI for title: Why propensity score should not be used for matching
- 10.1136/bjophthalmol-2015-306727 may be a valid DOI for title: First Diabetic Retinopathy Prevalence Study in Portugal: RETINODIAB Study-Evaluation of the Screening Programme for Lisbon and Tagus Valley Region
- 10.1017/cbo9780511810725.018 may be a valid DOI for title: Reducing bias in observational studies using subclassification on the propensity score
- 10.7249/tl136.1 may be a valid DOI for title: Toolkit for Weighting and Analysis of Nonequivalent Groups: A tutorial for the twang package

INVALID DOIs

- 10.3389/FNEUR.2019.00143/BIBTEX is INVALID
- 10.1007/S00068-017-0786-6/METRICS is INVALID
- 10.1186/1472-684X-12-23/FIGURES/2 is INVALID
- 10.1513/ANNALSATS.202002-169OC/SUPPL_FILE/DISCLOSURES.PDF is INVALID
- 10.3233/JAD-161201.Prediction is INVALID
- 10.1093/biostatistics/output is INVALID
- 10.1159/000488780.Estimating is INVALID
- 10.1016/j.jmb.2018.05.037.Patient is INVALID
- 10.2337/dc06 is INVALID
- 10.1002/sim is INVALID
- 10.3837/tiis.0000.00.000 is INVALID
- 10.1002/sim.3782.Improving is INVALID
- 10.1002/sim is INVALID
- 10.1.1.335.7044 is INVALID
- 10.1002/sim is INVALID
- 10.1186/S12883-021-02187-8/TABLES/4 is INVALID
Kevin-Mattheus-Moerman commented 10 months ago

@luisgarcez11 thanks for this submission. I am the AEiC for this track and here to help process initial steps.

For the moment I have the following comments:

Note that I have just added the query-scope label here. This is because I am requesting some help from the editorial board to review if this work is in scope for JOSS. In particular we'll determine if it confirms to our substantial scholarly effort criteria. This review may take several weeks to complete.

luisgarcez11 commented 10 months ago

Hi @Kevin-Mattheus-Moerman ,

I took into account your comments and changed the package accordingly.

To review the package, I would recommend Yafei Wang, darinddv, ajbaird, metelkin.

Thank you!

Luis

Kevin-Mattheus-Moerman commented 9 months ago

@editorialbot check references

editorialbot commented 9 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1002/PDS.668 is OK
- 10.1002/PDS.677 is OK
- 10.3390/HEALTHCARE10030420 is OK
- 10.2307/2983604 is OK

MISSING DOIs

- None

INVALID DOIs

- None
Kevin-Mattheus-Moerman commented 9 months ago

@luisgarcez11 The bib file looks cleaned up now. However, the README still has not been updated. Please fully extend your README (and include and refer to contributing guidelines too), here is a nice guide for instance: https://www.freecodecamp.org/news/how-to-write-a-good-readme-file/.

luisgarcez11 commented 9 months ago

@Kevin-Mattheus-Moerman sorry. Now the readme file is done.

luisgarcez11 commented 9 months ago

And it is ready for review.

Kevin-Mattheus-Moerman commented 8 months ago

@luisgarcez11 the editorial board has concluded the scope review. Apologies for the delay as this took longer than usual over the holiday period. Unfortunately it was determined that this work is not in scope for JOSS as it stands. Given its relatively small size and relative immaturity it does not conform to our substantial scholarly effort criteria. We will now proceed to reject this submission. Note that the above conclusion does not mean the work is not of a high quality, or not useful, it merely means that based on size and extent of functionality offered it is not in scope for JOSS.

We hope you will consider JOSS for any future (re)submissions of a more substantial nature.

Kevin-Mattheus-Moerman commented 8 months ago

@editorialbot reject

editorialbot commented 8 months ago

Paper rejected.