SemiCompRisks: An R Package for the Analysis of Independent and Cluster-correlated Semi-competing Risks Data

Álvares, Danilo; Haneuse, Sebastien; Lee, Catherine; Lee, Kyu Ha

doi:10.32614/rj-2019-038

Cited by 26 publications

(26 citation statements)

References 43 publications

(54 reference statements)

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“…For the 3 most common mortality-causing events (chronic rejection, infection, and malignant disease), semicompeting risks Cox proportional hazards regression analyses compared event risks and postevent death risks between drugs. The semicompeting risks framework, intended to address possible informative censoring of nonfatal events by death due to other causes, is explained elsewhere by Alvares et al 21 and Haneuse and Lee, 22 authors of the SemiCompRisks R package. A reference manual is available at https://cran.r-project.org, and these methods have been previously applied by Jazić et al 23…”

Section: Methodsmentioning

confidence: 99%

Survival Associated With Sirolimus Plus Tacrolimus Maintenance Without Induction Therapy Compared With Standard Immunosuppression After Lung Transplant

et al. 2019

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Key Points Question Which immunosuppressive strategy is associated with the highest survival in lung transplantation? Findings In this cohort study of US recipients of lung transplants, sirolimus plus tacrolimus was associated with significantly better conditional survival from 1 year after transplant compared with mycophenolate mofetil plus tacrolimus (median survival, 8.9 vs 7.1 years after transplant). The highest conditional survival was observed in patients receiving sirolimus plus tacrolimus with no induction therapy (median survival, 10.7 years), which was significantly better than survival for those receiving mycophenolate mofetil plus tacrolimus with induction therapy (median survival, 7.4 years). Meaning Sirolimus plus tacrolimus was associated with improved patient survival compared with mycophenolate mofetil plus tacrolimus, and using no induction therapy with sirolimus plus tacrolimus was associated with the highest survival.

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Section: Methodsmentioning

confidence: 99%

Survival Associated With Sirolimus Plus Tacrolimus Maintenance Without Induction Therapy Compared With Standard Immunosuppression After Lung Transplant

et al. 2019

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“…Data were generated from the model ( 4 )-( 6 ) assuming Weibull baseline hazard functions using simID from the SemiCompRisks package [ 42 , 43 ] in R [ 40 ]. We set model parameters to those obtained from fitting the model to dementia data, where the nonterminal and terminal events were dementia diagnosis and death, the origin was age 65, the left-truncation time was study entry, and a dichotomous variable was included as a covariate in all three regression models.…”

Section: Methodsmentioning

confidence: 99%

Fitting a shared frailty illness-death model to left-truncated semi-competing risks data to examine the impact of education level on incident dementia

Lee

Gilsanz

Haneuse

2021

BMC Med Res Methodol

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Background Semi-competing risks arise when interest lies in the time-to-event for some non-terminal event, the observation of which is subject to some terminal event. One approach to assessing the impact of covariates on semi-competing risks data is through the illness-death model with shared frailty, where hazard regression models are used to model the effect of covariates on the endpoints. The shared frailty term, which can be viewed as an individual-specific random effect, acknowledges dependence between the events that is not accounted for by covariates. Although methods exist for fitting such a model to right-censored semi-competing risks data, there is currently a gap in the literature for fitting such models when a flexible baseline hazard specification is desired and the data are left-truncated, for example when time is on the age scale. We provide a modeling framework and openly available code for implementation. Methods We specified the model and the likelihood function that accounts for left-truncated data, and provided an approach to estimation and inference via maximum likelihood. Our model was fully parametric, specifying baseline hazards via Weibull or B-splines. Using simulated data we examined the operating characteristics of the implementation in terms of bias and coverage. We applied our methods to a dataset of 33,117 Kaiser Permanente Northern California members aged 65 or older examining the relationship between educational level (categorized as: high school or less; trade school, some college or college graduate; post-graduate) and incident dementia and death. Results A simulation study showed that our implementation provided regression parameter estimates with negligible bias and good coverage. In our data application, we found higher levels of education are associated with a lower risk of incident dementia, after adjusting for sex and race/ethnicity. Conclusions As illustrated by our analysis of Kaiser data, our proposed modeling framework allows the analyst to assess the impact of covariates on semi-competing risks data, such as incident dementia and death, while accounting for dependence between the outcomes when data are left-truncated, as is common in studies of aging and dementia.

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“…Specifically, the semi-competing risks framework addresses a potential dependence between respiratory events and death by adding a patient-specific frailty to the standard proportional hazard regression model. A more detailed description of the semi-competing risks framework is available from Haneuse and colleagues,55 56 and an example of its application is described elsewhere 57. To compare with the results of semi-competing risk models, we also implemented standard Cox proportional hazards (censoring death) and Fine-Gray competing-risk models 49…”

Section: Methodsmentioning

confidence: 99%

Respiratory events associated with concomitant opioid and sedative use among Medicare beneficiaries with chronic obstructive pulmonary disease

Park

Choi

et al. 2020

BMJ Open Resp Res

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BackgroundOpioids and sedatives are commonly prescribed in chronic obstructive pulmonary disease (COPD) patients for symptoms of dyspnoea, pain, insomnia, depression and anxiety. Older adults are advised to avoid these medications due to increased adverse events, including respiratory events. This study examines respiratory event risks associated with concomitant opioid and sedative use compared with opioid use alone in older adults with COPD.MethodsA 5% nationally representative sample of Medicare beneficiaries with COPD and opioid use between 2009 and 2013 was used for this retrospective cohort study. Current and past concomitant use were identified using drug dispensed within 7 days from the censored date: at respiratory event, at death, or at 12 months post index. Concomitant opioid and sedative use were categorised into no overlap (opioid only), 1 to 10, 11 to 30, 31 to 60 and >60 days of total overlap. The primary outcome was hospitalisation or emergency department (ED) visits for respiratory events (COPD exacerbations or respiratory depression). Propensity score matching was implemented and semi-competing risk models were used to address competing risk by death.ResultsAmong 48 120 eligible beneficiaries, 1810 (16.7%) concomitant users were matched with 9050 (83.3%) opioid only users. Current concomitant use of 1 to 10, 11 to 30 and 31 to 60 days was associated with increased respiratory events (HRs (95% CI): 2.8 (1.2 to 7.3), 9.3 (4.9 to 18.2) and 5.7 (2.5 to 12.5), respectively), compared with opioid only use. Current concomitant use of >60 days or past concomitant use of ≤60 days was not significantly associated with respiratory events. Consistent findings were found in sensitivity analyses, including in subgroup analysis of non-benzodiazepine sedatives. Additionally, current concomitant use significantly increased risk of death.ConclusionShort-term and medium-term current concomitant opioid and sedative use significantly increased risk of respiratory events and death in older COPD Medicare beneficiaries. Long-term past concomitant users, however, demonstrated lower risks of these outcomes, possibly reflecting a healthy user effect or developed tolerance to the effects of these agents.

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SemiCompRisks: An R Package for the Analysis of Independent and Cluster-correlated Semi-competing Risks Data

Cited by 26 publications

References 43 publications

Survival Associated With Sirolimus Plus Tacrolimus Maintenance Without Induction Therapy Compared With Standard Immunosuppression After Lung Transplant

Survival Associated With Sirolimus Plus Tacrolimus Maintenance Without Induction Therapy Compared With Standard Immunosuppression After Lung Transplant

Fitting a shared frailty illness-death model to left-truncated semi-competing risks data to examine the impact of education level on incident dementia

Respiratory events associated with concomitant opioid and sedative use among Medicare beneficiaries with chronic obstructive pulmonary disease

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