[PRE REVIEW]: tipr: An R package for sensitivity analyses for unmeasured confounders

[editorialbot]

Submitting author: !--author-handle-->@LucyMcGowan<!--end-author-handle-- (Lucy D'Agostino McGowan) Repository: https://github.com/LucyMcGowan/tipr Branch with paper.md (empty if default branch): joss Version: v0.4.1 Editor: !--editor-->@fabian-s<!--end-editor-- Reviewers: @gcskoenig, @MichaelSchomaker Managing EiC: Arfon Smith

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

The author's suggestion for the handling editor is @KristinaRiemer.

@LucyMcGowan 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).

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.03 s (1097.7 files/s, 161058.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
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R                               19            188            727           1460
TeX                              1            149              0           1079
Markdown                         4            104              0            405
YAML                             4              8              6             51
Rmd                              1             28             38             12
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SUM:                            29            477            771           3007
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gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 2517

[editorialbot]

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

OK DOIs

- None

MISSING DOIs

- 10.1007/s10552-018-1058-4 may be a valid DOI for title: Metformin use and incidence cancer risk: evidence for a selective protective effect against liver cancer
- 10.1037/h0037350 may be a valid DOI for title: Estimating causal effects of treatments in randomized and nonrandomized studies.
- 10.1111/rssb.12348 may be a valid DOI for title: Making sense of sensitivity: Extending omitted variable bias
- 10.1007/s10552-018-1058-4 may be a valid DOI for title: Metformin use and incidence cancer risk: evidence for a selective protective effect against liver cancer
- 10.1111/biom.13197 may be a valid DOI for title: Optimal approximate conversions of odds ratios and hazard ratios to risk ratios
- 10.1111/j.1365-3016.1992.tb00775.x may be a valid DOI for title: Prenatal events and the risk of subependymal/intraventricular haemorrhage in very low birthweight neonates
- 10.2307/1165073 may be a valid DOI for title: Dropping out of high school in the United States: An observational study
- 10.1093/aje/kwaa044 may be a valid DOI for title: Estimating risk ratios and risk differences using regression
- 10.1080/01621459.2016.1260466 may be a valid DOI for title: Balancing Covariates via Propensity Score Weighting
- 10.1037/h0037350 may be a valid DOI for title: Estimating causal effects of treatments in randomized and nonrandomized studies.
- 10.1002/sim.6607 may be a valid DOI for title: Moving towards best practice when using inverse probability of treatment weighting (IPTW) using the propensity score to estimate causal treatment effects in observational studies.
- 10.1515/ijb-2012-0030 may be a valid DOI for title: A Weighting Analogue to Pair Matching in Propensity Score Analysis
- 10.1177/0193841x08317586 may be a valid DOI for title: Weighting regressions by propensity scores.
- 10.1080/01621459.1994.10476818 may be a valid DOI for title: Estimation of Regression Coefficients When Some Regressors are not Always Observed
- 10.2307/2669390 may be a valid DOI for title: On Profile Likelihood: Comment
- 10.1016/j.jspi.2004.06.060 may be a valid DOI for title: Why prefer double robust estimators in causal inference?
- 10.1080/01621459.1999.10473870 may be a valid DOI for title: A Weighted Estimating Equation for Missing Covariate Data with Properties Similar to Maximum Likelihood
- 10.1214/07-sts227d may be a valid DOI for title: Comment: Performance of Double-Robust Estimators When “Inverse Probability” Weights Are Highly Variable
- 10.1002/sim.7231 may be a valid DOI for title: Stratification and weighting via the propensity score in estimation of causal treatment effects: a comparative study
- 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
- 10.1162/003465304323023697 may be a valid DOI for title: Finite-Sample Properties of Propensity-Score Matching and Weighting Estimators
- 10.3386/w14251 may be a valid DOI for title: Recent Developments in the Econometrics of Program Evaluation
- 10.1198/jcgs.2011.09219 may be a valid DOI for title: Optimal Matching of an Optimally Chosen Subset in Observational Studies
- 10.1093/biomet/asn055 may be a valid DOI for title: Dealing with limited overlap in estimation of average treatment effects
- 10.1017/cbo9780511810725.017 may be a valid DOI for title: Assessing sensitivity to an unobserved binary covariate in an observational study with binary outcome
- 10.1214/12-aos1058 may be a valid DOI for title: On the definition of a confounder
- 10.1093/med/9780199682898.003.0007 may be a valid DOI for title: Confounding
- 10.18637/jss.v011.i10 may be a valid DOI for title: Econometric Computing with HC and HAC Covariance Matrix Estimators
- 10.18637/jss.v016.i09 may be a valid DOI for title: Object-Oriented Computation of Sandwich Estimators
- 10.1093/jnci/22.1.173 may be a valid DOI for title: Smoking and lung cancer: recent evidence and a discussion of some questions.
- 10.1093/oxfordjournals.aje.a112581 may be a valid DOI for title: Assessing effects of confounding variables.
- 10.1017/cbo9780511810725.017 may be a valid DOI for title: Assessing sensitivity to an unobserved binary covariate in an observational study with binary outcome
- 10.1093/ije/25.6.1107 may be a valid DOI for title: Basic methods for sensitivity analysis of biases
- 10.2307/2533848 may be a valid DOI for title: Assessing the sensitivity of regression results to unmeasured confounders in observational studies.
- 10.1002/pds.1200 may be a valid DOI for title: Sensitivity analysis and external adjustment for unmeasured confounders in epidemiologic database studies of therapeutics
- 10.7326/0003-4819-137-4-200208200-00012 may be a valid DOI for title: Postmenopausal hormone replacement therapy and the primary prevention of cardiovascular disease
- 10.1016/s0140-6736(98)05066-1 may be a valid DOI for title: Cardiovascular and cancer morbidity and mortality and sudden cardiac death in postmenopausal women on oestrogen replacement therapy (ERT)
- 10.1016/0021-9681(66)90062-2 may be a valid DOI for title: Spurious effects from an extraneous variable
- 10.1093/oxfordjournals.aje.a112863 may be a valid DOI for title: RE:“Assessing Effects of Confounding Variables”
- 10.1093/biomet/71.1.191 may be a valid DOI for title: Case-control studies: assessing the effect of a confounding factor
- 10.1002/ajim.4700130107 may be a valid DOI for title: Indirect methods of assessing the effects of tobacco use in occupational studies
- 10.1002/ajim.4700130108 may be a valid DOI for title: Indirect corrections for confounding under multiplicative and additive risk models
- 10.1002/sim.1657 may be a valid DOI for title: Sensitivity analyses for unmeasured confounding assuming a marginal structural model for repeated measures
- 10.1007/978-1-4612-1284-3_1 may be a valid DOI for title: Sensitivity Analysis for Selection bias and unmeasured Confounding in missing Data and Causal inference models
- 10.1016/0021-9681(67)90080-x may be a valid DOI for title: Pertinency of an extraneous variable
- 10.1111/0272-4332.214136 may be a valid DOI for title: Sensitivity Analysis, Monte Carlo Risk Analysis, and Bayesian Uncertainty Assessment
- 10.1198/01621450338861905 may be a valid DOI for title: The Impact of Prior Distributions for Uncontrolled Confounding and Response Bias
- 10.1093/aje/kwi192 may be a valid DOI for title: Adjusting Effect Estimates for Unmeasured Confounding with Validation Data using Propensity Score Calibration
- 10.1002/pds.1200 may be a valid DOI for title: Sensitivity analysis and external adjustment for unmeasured confounders in epidemiologic database studies of therapeutics
- 10.1002/sim.2711 may be a valid DOI for title: Bayesian sensitivity analysis for unmeasured confounding in observational studies
- 10.1016/j.jclinepi.2007.05.006 may be a valid DOI for title: A sensitivity analysis using information about measured confounders yielded improved uncertainty assessments for unmeasured confounding
- 10.1097/ede.0b013e3181f74493 may be a valid DOI for title: Bias Formulas for Sensitivity Analysis of Unmeasured Confounding for General Outcomes, Treatments, and Confounders
- 10.1002/sim.4354 may be a valid DOI for title: Sensitivity analysis for interactions under unmeasured confounding
- 10.1111/j.1541-0420.2008.01024.x may be a valid DOI for title: Sensitivity analysis: distributional assumptions and confounding assumptions
- 10.1097/ede.0b013e3181810e29 may be a valid DOI for title: Causal directed acyclic graphs and the direction of unmeasured confounding bias
- 10.1007/s10654-013-9770-6 may be a valid DOI for title: Unmeasured confounding and hazard scales: sensitivity analysis for total, direct, and indirect effects
- 10.1093/ije/dyp332 may be a valid DOI for title: Sensitivity analyses to estimate the potential impact of unmeasured confounding in causal research
- 10.1161/jaha.116.005379 may be a valid DOI for title: Comparative Safety of Sulfonylurea and Metformin Monotherapy on the Risk of Heart Failure: A Cohort Study
- 10.1016/j.annepidem.2008.05.007 may be a valid DOI for title: Poor Quality of Reporting Confounding Bias in Observational Intervention Studies: A Systematic Review
- 10.7326/m16-2607 may be a valid DOI for title: Sensitivity Analysis in Observational Research: Introducing the E-Value.
- 10.1007/s11886-001-0021-1 may be a valid DOI for title: The risk of congestive heart failure: sobering lessons from the Framingham Heart Study.
- 10.1016/j.ahj.2004.08.005 may be a valid DOI for title: Characteristics and outcomes of patients hospitalized for heart failure in the United States: rationale, design, and preliminary observations from the first 100,000 cases in the Acute Decompensated Heart Failure National Registry (ADHERE).
- 10.1001/archinte.150.4.769 may be a valid DOI for title: Trends in hospitalization rates for heart failure in the United States, 1973-1986. Evidence for increasing population prevalence.
- 10.2105/ajph.84.1.20 may be a valid DOI for title: Estimating clinical morbidity due to ischemic heart disease and congestive heart failure: the future rise of heart failure.
- 10.1016/s0145-4145(08)01014-9 may be a valid DOI for title: Ultrafiltration versus intravenous diuretics for patients hospitalized for acute decompensated heart failure.
- 10.1111/j.1365-2362.2005.01572.x may be a valid DOI for title: Frailty predicts long-term mortality in elderly subjects with chronic heart failure.
- 10.1002/dmrr.2743 may be a valid DOI for title: Where frailty meets diabetes
- 10.1007/s10654-014-9891-6 may be a valid DOI for title: Frailty prevalence and 10-year survival in community-dwelling older adults: results from the ESTHER cohort study
- 10.1371/journal.pone.0087958 may be a valid DOI for title: Prevalence and Outcomes of Frailty in Korean Elderly Population: Comparisons of a Multidimensional Frailty Index with Two Phenotype Models
- 10.1007/s12603-011-0134-1 may be a valid DOI for title: Physical frailty in older adults is associated with metabolic and atherosclerotic risk factors and cognitive impairment independent of muscle mass
- 10.1002/sim.3697 may be a valid DOI for title: Balance diagnostics for comparing the distribution of baseline covariates between treatment groups in propensity-score matched samples
- 10.1002/pds.2251 may be a valid DOI for title: Balance measures for propensity score methods: a clinical example on beta-agonist use and the risk of myocardial infarction
- 10.1080/01621459.2016.1260466 may be a valid DOI for title: Balancing Covariates via Propensity Score Weighting
- 10.1016/j.jclinepi.2013.01.013 may be a valid DOI for title: Prognostic score–based balance measures can be a useful diagnostic for propensity score methods in comparative effectiveness research
- 10.1017/cbo9780511810725.030 may be a valid DOI for title: Using Propensity Scores to Help Design Observational Studies: Application to the Tobacco Litigation
- 10.1016/s1062-1458(97)82166-6 may be a valid DOI for title: The effectiveness of right heart catheterization in the initial care of critically III patients
- 10.1515/ijb-2012-0030 may be a valid DOI for title: A Weighting Analogue to Pair Matching in Propensity Score Analysis
- 10.1214/09-aoas315 may be a valid DOI for title: The Sensitivity of Linear Regression Coefficients’ Confidence Limits to the Omission of a Confounder
- 10.1002/sim.5991 may be a valid DOI for title: Variance reduction in randomised trials by inverse probability weighting using the propensity score
- 10.1111/biom.12101 may be a valid DOI for title: Calibrating Sensitivity Analyses to Observed Covariates in Observational Studies
- 10.1198/000313004x5824 may be a valid DOI for title: Model Selection, Confounder Control, and Marginal Structural Models
- 10.1093/aje/163.suppl_11.s222-c may be a valid DOI for title: Bayesian propensity score analysis for observational data.
- 10.1111/j.1541-0420.2012.01830.x may be a valid DOI for title: Model Feedback in Bayesian Propensity Score Estimation
- 10.1080/00031305.2015.1111260 may be a valid DOI for title: The Central Role of Bayes’ Theorem for Joint Estimation of Causal Effects and Propensity Scores

INVALID DOIs

- None

[editorialbot]

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

[LucyMcGowan]

Thank you! For reviewer suggestions, someone with R and epidemiology experience would be ideal. A few suggestions: masalmon, tgerke, noamross, corinne-riddell, jenniferthompson, darrendahley

[arfon]

@LucyMcGowan - thanks for your submission to JOSS. We're currently managing a large backlog of submissions and the editor most appropriate for your area is already rather busy.

For now, we will need to waitlist this paper and process it as the queue reduces. Thanks for your patience!

[Kevin-Mattheus-Moerman]

@editorialbot invite @fabian-s as editor

[editorialbot]

Invitation to edit this submission sent!

[fabian-s]

@editorialbot invite @fabian-s as editor

Alright, I can take this on, too.

[fabian-s]

:wave: @wxwx1993 @tedinburgh @stmcg

would 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

[stmcg]

I'm sorry, I won't be able to review this submission. This caught me at a busy time. Thanks for the invitation

[Kevin-Mattheus-Moerman]

@editorialbot assign @fabian-s as editor

[editorialbot]

Assigned! @fabian-s is now the editor

[fabian-s]

:wave: @corinne-riddell @tgerke

would 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]

:wave: @csinva @AvianaGlobal @wxwx1993 @tedinburgh @corinne-riddell @tgerke

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

[tedinburgh]

Sorry @fabian-s, I'm away on holiday for a few weeks, so unfortunately won't be able help with this

[fabian-s]

:wave: @csinva @AvianaGlobal @gcskoenig @Alex-Markham

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]

@LucyMcGowan sorry for the delay, as you can see I'm having a hard time finding reviewers...

To speed things up once we actually get going, in the meantime:

1. please add the missing DOIs that the bot is complaining about
2. consider shortening your paper -- it's currently more than double the typical/recommended length for JOSS papers (~ 500 - 1000 words, yours is 2500). For example, you could consider moving the "tipping point" example into a package vignette and link the vignette from your paper. I'm also not convinced the full listing of all package functions is necessary in the article.

[Alex-Markham]

@fabian-s I'd be willing if it were in Python, but I think I'm unfortunately not familiar enough with R

[fabian-s]

:wave: @gcskoenig @dandls @csinva @AvianaGlobal

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]

@LucyMcGowan sorry for the delay, as you can see I'm having a hard time finding reviewers...

To speed things up once we actually get going, in the meantime:

1. please add the missing DOIs that the bot is complaining about

2. consider shortening your paper -- it's currently more than double the typical/recommended length for JOSS papers (~ 500 - 1000 words, yours is 2500). For example, you could consider moving the "tipping point" example into a package vignette and link the vignette from your paper. I'm also not convinced the full listing of all package functions is necessary in the article.

reposted so it does not get lost here.

[gcskoenig]

I am currently in vacation until the week after next week, but afterwards I can do a review.

However, if you find someone with more R expertise in the meantime, I am happy to pass on the reviewer role.

[fabian-s]

@editorialbot add @gcskoenig as reviewer

TY Gunnar! If two other people I asked eventually deign to reply and reply affirmatively, I'll remove you from the list again....

[editorialbot]

@gcskoenig added to the reviewers list!

[LucyMcGowan]

@fabian-s thank you so much! I've corrected the DOIs and removed several examples to shorten the paper. Do I need to do something to trigger the updates to propagate to the joss repo?

I also realized in my reviewer suggestions above I had the wrong handle for Maëlle Salmon, it should have been @ maelle

Thank you, again!

[fabian-s]

@editorialbot generate pdf

@LucyMcGowan this triggers re-rendering ;)

[editorialbot]

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

[fabian-s]

@editorialbot check references

.. and this checks the DOIs

[editorialbot]

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

OK DOIs

- 10.1093/jnci/22.1.173 is OK
- 10.1093/oxfordjournals.aje.a112581 is OK
- 10.1016/0021-9681(66)90062-2 is OK
- 10.1097/EDE.0000000000000457 is OK
- 10.1111/j.2517-6161.1983.tb01242.x is OK
- 10.2307/2533848 is OK
- 10.7326/M16-2607 is OK
- 10.1111/rssb.12348 is OK
- 10.1007/978-0-387-87959-8 is OK
- 10.1002/(SICI)1097-0258(19981015)17:19<2265::AID-SIM918>3.0.CO;2-B is OK
- 10.1037/h0037350 is OK
- 10.1214/12-aos1058 is OK
- 10.1159/000315883 is OK
- 10.3102/10769986011003207 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[fabian-s]

:wave: @maelle would 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

[maelle]

@fabian-s sorry, no I wouldn't have time. Thanks for asking!

[LucyMcGowan]

@editorialbot generate pdf

[editorialbot]

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

[fabian-s]

@editorialbot add @MichaelSchomaker as reviewer

[editorialbot]

@MichaelSchomaker added to the reviewers list!

[fabian-s]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/4495.