cutpointr: Improved Estimation and Validation of Optimal Cutpoints in R

Thiele, Christian; Hirschfeld, Gerrit

doi:10.48550/arxiv.2002.09209

Cited by 7 publications

(7 citation statements)

References 16 publications

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“…We also considered alternative outcome measures, including the CM, NFTI, and Need for Emergent Intervention Within 6 Hours (NEI-6). 22 Analyses were performed using Stata, version 17.0 (StataCorp LLC) and the cutpointr, version 1.1.1 23 ; gamlss, version 5.4-1 24 ; and rms, version 6.2-0 25 packages in R, version 4.3.2 (R Foundation for Statistical Computing). A 2-sided P < .05 was considered significant for differences between sets of criteria.…”

Section: Discussionmentioning

confidence: 99%

Comparison of Vital Sign Cutoffs to Identify Children With Major Trauma

Gorski,

Chaudhari,

Spurrier

et al. 2024

JAMA Netw Open

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ImportanceVital signs are essential components in the triage of injured children. The Advanced Trauma Life Support (ATLS) and Pediatric Advanced Life Support (PALS) physiologic criteria are frequently used for trauma assessments.ObjectiveTo evaluate the performance of ATLS and PALS criteria vs empirically derived criteria for identifying major trauma in children.Design, Setting, and ParticipantsThis retrospective cohort study used 2021 American College of Surgeons Trauma Quality Improvement Program (TQIP) data contributed by US trauma centers. Included encounters involved pediatric patients (aged &lt;18 years) with severe injury, excluding those who experienced out-of-hospital cardiac arrest, were receiving mechanical ventilation, or were transferred from another facility. Data were analyzed between April 9 and December 21, 2023.ExposureInitial hospital vital signs, including heart rate, respiratory rate, and systolic blood pressure (SBP).Main Outcome and MeasuresMajor trauma, determined by the Standard Triage Assessment Tool, a composite measure of injury severity and interventions performed. Multivariable models developed from PALS and ATLS vital sign criteria were compared with models developed from the empirically derived criteria using the area under the receiver operating characteristic curve. Validation of the findings was performed using the 2019 TQIP dataset.ResultsA total of 70 748 patients (median [IQR] age, 11 [5-15] years; 63.4% male) were included, of whom 3223 (4.6%) had major trauma. The PALS criteria classified 31.0% of heart rates, 25.7% of respiratory rates, and 57.4% of SBPs as abnormal. The ATLS criteria classified 25.3% of heart rates, 4.3% of respiratory rates, and 1.1% of SBPs as abnormal. Among children with all 3 vital signs documented (64 326 [90.9%]), PALS had a sensitivity of 88.4% (95% CI, 87.1%-89.3%) and specificity of 25.1% (95% CI, 24.7%-25.4%) for identifying major trauma, and ATLS had a sensitivity of 54.5% (95% CI, 52.7%-56.2%) and specificity of 72.9% (95% CI, 72.6%-73.3%). The empirically derived cutoff vital sign z scores had a sensitivity of 80.0% (95% CI, 78.5%-81.3%) and specificity of 48.7% (95% CI, 48.3%-49.1%) and area under the receiver operating characteristic curve of 70.9% (95% CI, 69.9%-71.8%), which was similar to PALS criteria (69.6%; 95% CI, 68.6%-70.6%) and greater than ATLS criteria (65.4%; 95% CI, 64.4%-66.3%). Validation using the 2019 TQIP database showed similar performance to the derivation sample.Conclusions and RelevanceThese findings suggest that empirically derived vital sign criteria strike a balance between the sensitivity of PALS criteria and the specificity of ATLS criteria in identifying major trauma in children. These criteria may help to identify children at greatest risk of trauma-related morbidity and mortality.

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Section: Discussionmentioning

confidence: 99%

Comparison of Vital Sign Cutoffs to Identify Children With Major Trauma

Gorski,

Chaudhari,

Spurrier

et al. 2024

JAMA Netw Open

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“…The proposed CERA web tool, freely available at https://datascicence.shinyapps.io/ROCGPT/ , is developed using the shiny app [ 27 ], [ 8 ] R package and cutpointr function [ 28 ]. There are three versions of CERA tool.…”

Section: Methodsmentioning

confidence: 99%

“…For example, if the user defines a value of 0.7 for specificity, the performance measure results show the value with a minimum specificity of 0.7. This method works on cutpointr function [ 28 ].…”

Section: Methodsmentioning

confidence: 99%

ChatGPT-Enhanced ROC Analysis (CERA): A shiny web tool for finding optimal cutoff points in biomarker analysis

Agraz,

Mantzoros,

Karniadakis

2024

PLoS ONE

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Diagnostic tests play a crucial role in establishing the presence of a specific disease in an individual. Receiver Operating Characteristic (ROC) curve analyses are essential tools that provide performance metrics for diagnostic tests. Accurate determination of the cutoff point in ROC curve analyses is the most critical aspect of the process. A variety of methods have been developed to find the optimal cutoffs. Although the R programming language provides a variety of package programs for conducting ROC curve analysis and determining the appropriate cutoffs, it typically needs coding skills and a substantial investment of time. Specifically, the necessity for data preprocessing and analysis can present a significant challenge, especially for individuals without coding experience. We have developed the CERA (ChatGPT-Enhanced ROC Analysis) tool, a user-friendly ROC curve analysis web tool using the shiny interface for faster and more effective analyses to solve this problem. CERA is not only user-friendly, but it also interacts with ChatGPT, which interprets the outputs. This allows for an interpreted report generated by R-Markdown to be presented to the user, enhancing the accessibility and understanding of the analysis results.

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“…Models with AUC values greater than or equal to 0.70 are considered ‘useful’ and those with AUC values greater than 0.9 are considered ‘very good’ because sensitivity is high relative to the false positive rate [ 121 , 122 ]. The ‘ pROC ’ (v.1.16.2) and ‘ cutpointr ’ packages (v.1.0.32) [ 123 , 124 ] were used to conduct the ROC and AUC analysis of the models. The performance of each GAMM was assessed using the AUC value created from the training dataset and an evaluation dataset which consisted of the remaining 25% of the presence/absence data not used in the training dataset.…”

Section: Methodsmentioning

confidence: 99%

Seasonal habitat preference and foraging behaviour of post-moult Weddell seals in the western Ross Sea

et al. 2023

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Weddell seals ( Leptonychotes weddellii ) are important predators in the Southern Ocean and are among the best-studied pinnipeds on Earth, yet much still needs to be learned about their year-round movements and foraging behaviour. Using biologgers, we tagged 62 post-moult Weddell seals in McMurdo Sound and vicinity between 2010 and 2012. Generalized additive mixed models were used to (i) explain and predict the probability of seal presence and foraging behaviour from eight environmental variables, and (ii) examine foraging behaviour in relation to dive metrics. Foraging probability was highest in winter and lowest in summer, and foraging occurred mostly in the water column or just above the bottom; across all seasons, seals preferentially exploited the shallow banks and deeper troughs of the Ross Sea, the latter providing a pathway for Circumpolar Deep Water to flow onto the shelf. In addition, the probability of Weddell seal occurrence and foraging increased with increasing bathymetric slope and where water depth was typically less than 600 m. Although the probability of occurrence was higher closer to the shelf break, foraging was higher in areas closer to shore and over banks. This study highlights the importance of overwinter foraging for recouping body mass lost during the previous summer.

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cutpointr: Improved Estimation and Validation of Optimal Cutpoints in R

Cited by 7 publications

References 16 publications

Comparison of Vital Sign Cutoffs to Identify Children With Major Trauma

Comparison of Vital Sign Cutoffs to Identify Children With Major Trauma

ChatGPT-Enhanced ROC Analysis (CERA): A shiny web tool for finding optimal cutoff points in biomarker analysis

Seasonal habitat preference and foraging behaviour of post-moult Weddell seals in the western Ross Sea

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