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Thursday, July 6 • 5:30pm - 5:35pm
The cutpointr package: Improved and tidy estimation of optimal cutpoints

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Keywords: cutpoints, tidy
Webpages: https://github.com/Thie1e/cutpointr
Clinicians often use cutpoints or decision-thresholds to decide e.g. whether or not a patient with a depression score of “20” needs treatment for her or his depression. The R package cutpointr allows for estimating such optimal cutpoints for binary decisions by maximizing a specified metric or by using kernel estimation or distribution-based methods (Fluss, Faraggi, and Reiser 2005; Leeflang et al. 2008). The package includes a parallelizable bootstrapping routine to provide estimates of the cutpoints’ variability and their out-of-bag performance. cutpointr follows current tidy programming practices to allow for efficient estimation and use in simulation studies as well as interplay with functions from the tidyverse. Furthermore, cutpointr accepts user defined functions and includes existing functions (López-Ratón et al. 2014) to calculate optimal cutpoints. We also discuss future plans for cutpointr, specifically a Shiny-interface to make the package more accessible.
References Fluss, Ronen, David Faraggi, and Benjamin Reiser. 2005. “Estimation of the Youden Index and Its Associated Cutoff Point.” Biometrical Journal 47 (4): 458–72. http://onlinelibrary.wiley.com/doi/10.1002/bimj.200410135/full.

Leeflang, Mariska MG, Karel GM Moons, Johannes B. Reitsma, and Aielko H. Zwinderman. 2008. “Bias in Sensitivity and Specificity Caused by Data-Driven Selection of Optimal Cutoff Values: Mechanisms, Magnitude, and Solutions.” Clinical Chemistry, no. 4: 729–38. http://go.galegroup.com/ps/i.do?id=GALE%7CA209106300&sid=googleScholar&v=2.1&it=r&linkaccess=fulltext&issn=00099147&p=AONE&sw=w.

López-Ratón, Mónica, María Xosé Rodríguez-Álvarez, Carmen Cadarso-Suárez, and Francisco Gude-Sampedro. 2014. “OptimalCutpoints: An R Package for Selecting Optimal Cutpoints in Diagnostic Tests.” Journal of Statistical Software 061 (i08). http://econpapers.repec.org/article/jssjstsof/v_3a061_3ai08.htm.




Speakers


Thursday July 6, 2017 5:30pm - 5:35pm
3.01 Wild Gallery

Attendees (68)