<b>mstate</b>: An<i>R</i>Package for the Analysis of Competing Risks and Multi-State Models

Introduction: In Malawi, HIV-infected pregnant and breastfeeding women are offered lifelong antiretroviral therapy (ART) regardless of CD4 count or clinical stage (Option B+). Their HIV-exposed children are enrolled in the national prevention of mother-to-child transmission (PMTCT) programme, but many are lost to follow-up. We estimated the cumulative incidence of vertical HIV transmission, taking loss to follow-up into account. Methods: We abstracted data from HIV-exposed children enrolled into care between September 2011 and June 2014 from patient records at 21 health facilities in central and southern Malawi. We used competing risk models to estimate the probability of loss to follow-up, death, ART initiation and discharge, and used pooled logistic regression and inverse probability of censoring weighting to estimate the vertical HIV transmission risk. Results: A total of 11,285 children were included; 9285 (82%) were born to women who initiated ART during pregnancy. At age 30 months, an estimated 57.9% (95% CI 56.6–59.2) of children were lost to follow-up, 0.8% (0.6–1.0) had died, 2.6% (2.3–3.0) initiated ART, 36.5% (35.2–37.9) were discharged HIV-negative and 2.2% (1.5–2.8) continued follow-up. We estimated that 5.3% (95% CI 4.7–5.9) of the children who enrolled were HIV-infected by the age of 30 months, but only about half of these children (2.6%; 95% CI 2.3–2.9) were diagnosed. Conclusions: Confirmed mother-to-child transmission rates were low, but due to poor retention only about half of HIV-infected children were diagnosed. Tracing of children lost to follow-up and HIV testing in outpatient clinics should be scaled up to ensure that all HIV-positive children have access to early ART.

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“…We fitted the model in the R package mstate [22,23]. The structure of the model is shown in Figure 2.…”

Section: Methodsmentioning

confidence: 99%

HIV transmission and retention in care among HIV‐exposed children enrolled in Malawi's prevention of mother‐to‐child transmission programme

Haas

Oosterhout

Tenthani

et al. 2017

Journal of the International AIDS Society

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“…All patients had pre-treatment staging with a lung CT-scan to rule out the presence of metastasis. Thirty-four patients were excluded from analysis (presentation with metastases (11), recurrent disease (16), no operative treatment (7)) resulting in a cohort of 127 patients (mean age at time of diagnosis: 48 years (range five to 91), including nine children; male/female ratio 1:0.87).…”

Section: Methodsmentioning

confidence: 99%

High-grade soft tissue sarcomas of the extremities: surgical margins influence only local recurrence not overall survival

Willeumier

Fiocco

Nout

et al. 2015

International Orthopaedics (SICOT)

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Purpose After surgical treatment of high-grade soft tissue sarcomas, local recurrences, metastases and survival remain a great concern. Further knowledge on factors with a possible impact on these endpoints, specifically resection margins, is relevant for decision-making regarding the aggressiveness of local treatment. The aim of this study is to investigate the impact of prognostic factors on local recurrence and overall survival for patients with high-grade soft tissue sarcomas of the extremities. Methods In a retrospective cohort study of 127 patients (mean age 48 years, range five to 91; median follow-up 71 months) the prognostic effect of margin status and other clinicopathologic characteristics on local recurrence and overall survival were analysed by employing a multivariate Cox regression. Results Five-year cumulative incidence of local recurrence and distant metastases was 26 % and 40 %, respectively. The estimated five-year overall survival was 59 %. Tumour size proved a consistent adverse prognostic factor for local recurrence (hazard ratio (HR) 3.9), distant metastasis (HR 4.9) and overall survival (HR 2.4). The significant association of resection margins with local recurrence (HR 10.2) was confirmed. Margins were however not significantly associated with the occurrence of distant metastasis or overall survival. The occurrence of local recurrence had a significant impact on overall survival (HR 2.0). Conclusions The results of this study confirm the critical role of tumour size on survival and margins on local recurrence, and stress the need for further investigation concerning the association between margins, local recurrence and survival.

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“…Statistical analyses were performed by R 3.0 with survey, mstate, rms, clinfun, and pec packages. [30][31][32][33][34][35][36] …”

Section: Statistical Analysesmentioning

confidence: 99%

Self-Reported Health Status Predicts Other-Cause Mortality in Men with Localized Prostate Cancer: Results from the Prostate Cancer Outcomes Study

et al. 2015

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BACKGROUND: Guidelines recommend against treating localized prostate cancer (PCa) in men with a greater than10-year life expectancy. However, physicians have difficulty accurately estimating life expectancy. OBJECTIVE: We used data from a population-based observational study to develop a nomogram to estimate long-term other-cause mortality based on self-reported health status (SRHS), race/ethnicity, and age at diagnosis. DESIGN: This was an observational study. SUBJECTS: Men diagnosed with localized PCa from October 1994 through October 1995 participated in the study. MAIN MEASURES: Initial measures obtained 6 months after diagnosis included sociodemographic and tumor characteristics, treatment, and a single item on the SRHS, with response options ranging from excellent to poor. We used Surveillance, Epidemiology, and End-Results program data to determine date and cause of death through December 2010. We estimated other-cause mortality with proportional hazards survival analyses, accounting for competing risks. KEY RESULTS: We evaluated 2,695 men, of whom 74 % underwent aggressive therapy (surgery or radiotherapy). At the initial survey, 18 % reported excellent (E), 36 % very good (VG), 31 % good (G), and 15 % fair/poor (F/P) health. Healthier men were younger, and more likely to be white, better educated, and to undergo surgery. At follow-up, 44 % of the cohort had died; 78 % of deaths were from causes other than PCa. SRHS predicted other-cause mortality; for men reporting E, VG, G, F/P health, the cumulative incidences of other-cause mortality were 20 %, 29 %, 40 %, and 53 %, respectively, p<0.001. Compared to a reference of excellent SRHS, multivariable hazard ratios (95 % CI) for other-cause mortality for men reporting VG, G, and F/P health were 1.22 (0

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mstate: AnRPackage for the Analysis of Competing Risks and Multi-State Models

Cited by 330 publications

References 14 publications

HIV transmission and retention in care among HIV‐exposed children enrolled in Malawi's prevention of mother‐to‐child transmission programme

HIV transmission and retention in care among HIV‐exposed children enrolled in Malawi's prevention of mother‐to‐child transmission programme

High-grade soft tissue sarcomas of the extremities: surgical margins influence only local recurrence not overall survival

Self-Reported Health Status Predicts Other-Cause Mortality in Men with Localized Prostate Cancer: Results from the Prostate Cancer Outcomes Study

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