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1.
    
When modeling competing risks (CR) survival data, several techniques have been proposed in both the statistical and machine learning literature. State-of-the-art methods have extended classical approaches with more flexible assumptions that can improve predictive performance, allow high-dimensional data and missing values, among others. Despite this, modern approaches have not been widely employed in applied settings. This article aims to aid the uptake of such methods by providing a condensed compendium of CR survival methods with a unified notation and interpretation across approaches. We highlight available software and, when possible, demonstrate their usage via reproducible R vignettes. Moreover, we discuss two major concerns that can affect benchmark studies in this context: the choice of performance metrics and reproducibility.  相似文献   

2.
We observed patch-use behavior by two gerbil species in a fieldsetting and investigated how aggression and intrinsic decision-makinginteract to influence patch residence times. Results were interpretedby using a competing risk analysis model, which uniquely enabledus to estimate the intrinsic patch-leaving decisions independentlyof external interruptions of foraging bouts by aggression. Theexperiment was conducted in two 1-ha field enclosures completelysurrounded by rodent-proof fences and included allopatric (onlyGerbillus andersoni allenbyi) and sympatric (G. a. allenbyiand G. pyramidum) treatments. We predicted that increased foodpatch quality (i.e., habitat quality) should decrease intrinsicpatch-leaving rates and increase rates of aggressive interactionsinvolving the forager feeding in the patch (i.e., the occupantindividual). We also anticipated that increasing populationdensity should result in an increase in the rate of aggressiveinteractions involving the occupant individual. Our resultssupported the first two predictions, indicating a trade-offbetween foraging and aggression. However, the third predictionwas realized only for G. a. allenbyi in allopatry. Furthermore,in allopatry, occupant G. a. allenbyi individuals with highcompetitive ranks were involved in aggressive interactions atlower rates than those with low competitive ranks. However,in sympatry, patch-use behavior of occupant G. a. allenbyi individualswas mainly influenced by aggressive behavior of G. pyramidum,which did not respond to their competitive rank. Thus, it shouldpay less for G. a. allenbyi to be aggressive in sympatric populations.The observed reduction in intraspecific aggression among individualG. a. allenbyi in the presence of G. pyramidum supports thisassertion. We suggest that this reduction likely weakens thenegative effect of intra- and interspecific density on the percapita growth rate of G. a. allenbyi. Because this would changethe slope of the isocline of G. a. allenbyi, it could be animportant mechanism promoting coexistence when habitat selectionis constrained.  相似文献   

3.
In the present paper, a variation of the methode of translation is discussed to generate bivariate or multivariate survival distributions starting a given bivariate or multivariate distribution which is not necessarily a life distribution. The new distribution has been called the dual of the given distribution. The duals of several bivariate and multivariate famílies of distributions are obtained, such as FRECHET'S , FARLIE -GUMBEL -MORGENSTERN'S , MARDIA'S and PLACKETT'S , among others. A necessary and sufficient condition is given for a bivariate distribution to be its own dual. Thus the present paper generates several survival distributions in addition to what are already available in the literature. These have important applications in competing risk theory or reliability of engineering systems.  相似文献   

4.
    
Piecewise Weibull proportional hazard models were used to investigate the effect of genetic and nongenetic factors on functional and true longevity traits of the Slovenian Brown cattle breed. Records of 37 908 Brown cows from 2401 Slovenian herds were used. As these herds were characterised by a relatively small average herd size starting from 6.7 in 1999 and increasing to 8.7 Brown cows per herd in 2008, milk yield classification was made within different herd size groups. The hazard rate was the lowest in the first part of each lactation and was increasing for later stages. Culling risk was lower for cows from herds increasing in size, for cows with higher milk production and for cows from a region with smaller herd sizes and tougher conditions for cattle breeding. The latter result is surprising and may be related to better attention to maintain the animals, despite their lower milk production. The introduction of the milk quota system and drought was found to have an important effect on culling policy between the last seasons of the years 2001 and 2003. Seasonal effects were not related to the milk quota year (from April to March), but to the effect of shortage in fodder during the winter time. The effect of age at first calving and the interaction between year and milk yield class were not found to be significant. Heritability for functional and for true longevity were similar at around 10% each. Inclusion of a correction for class of milk yield to approximate functional longevity increased the herd-year random effect variance by 53%, whereas the sire variance increased by only 14%. The correlation coefficient between ranks of breeding values for functional and true longevity was high (0.91), whereas genetic trends were not found to be significant. To assess their predictive ability, models were compared looking at the survival rate of 4212 second-crop daughters not included in the initial models. The average correlation between estimated breeding values and survival at different stages was 0.39 for true longevity and 0.43 for functional longevity. Results showed that ranking milk yield at population level is appropriate to correct for voluntary culling on low production in small herds.  相似文献   

5.
    
Abstract The longevity of a leaf is related to the benefit that the plant is able to derive from it. This benefit varies among seasons and as more leaves emerge, such that leaf lifespan can be limited by canopy position rather than physiological age. Using interval‐censored failure time analysis, we investigate leaf lifespan for 34 Mediterranean species in a previously published dataset involving species with different life forms and functional strategies. Failure time regression models were used to determine leaf lifespan, and to investigate how these effects varied among species. Median lifespan estimated for each species with two methods differed by less than 10% on average, but varied from 0.02–19.5% depending on the shape of the underlying failure time distribution. Within shoots, later‐emerging leaves had shorter lifespans for species with longer periods of leaf emergence, and the reverse was true for species with short emergence. Having accounted for the within‐shoot effect, leaves emerging in spring had shorter lifespans, particularly herbaceous species, whereas the reverse was true woody species. These effects were consistent among life forms and successional stages, and consistent with theories of within‐shoot translocation of resources following self‐shading.  相似文献   

6.
    
The relationship between type traits and longevity was studied in the French Holstein breed using a survival analysis model. In this model, the phenotypic value adjusted for systematic fixed effects, the estimated breeding value, or the residual value (defined as the difference between the adjusted phenotypic value and the estimated breeding value) of the cow for each type trait was included as a risk factor. This was done separately for two subpopulations (registered and nonregistered herds) and with or without adjustment for production traits, i.e., considering true or functional longevity. For both types of herds, udder traits (and above all, udder depth) clearly influenced the length of productive life. There seemed to be a more pronounced voluntary culling on type traits in registered herds. The correction for the within herd-year class of production traits, as a way to approximate functional longevity, increased the importance of udder traits and decreased the weight of capacity traits. The same results were obtained when the phenotypic value of the cow for type was replaced by her estimated breeding value, whereas residuals had little impact. The relationship between longevity and type traits was most often nonlinear, in particular for udder traits, but in this study, no trait with a clear intermediate optimum was found.  相似文献   

7.
    
Many research questions involve time-to-event outcomes that can be prevented from occurring due to competing events. In these settings, we must be careful about the causal interpretation of classical statistical estimands. In particular, estimands on the hazard scale, such as ratios of cause-specific or subdistribution hazards, are fundamentally hard to interpret causally. Estimands on the risk scale, such as contrasts of cumulative incidence functions, do have a clear causal interpretation, but they only capture the total effect of the treatment on the event of interest; that is, effects both through and outside of the competing event. To disentangle causal treatment effects on the event of interest and competing events, the separable direct and indirect effects were recently introduced. Here we provide new results on the estimation of direct and indirect separable effects in continuous time. In particular, we derive the nonparametric influence function in continuous time and use it to construct an estimator that has certain robustness properties. We also propose a simple estimator based on semiparametric models for the two cause-specific hazard functions. We describe the asymptotic properties of these estimators and present results from simulation studies, suggesting that the estimators behave satisfactorily in finite samples. Finally, we reanalyze the prostate cancer trial from Stensrud et al. (2020).  相似文献   

8.
水曲柳和落叶松细根寿命的估计   总被引：9，自引：3，他引：6       下载免费PDF全文
树木细根(直径≤2 mm)是控制树木与其周围环境进行能量交换和物质分配的主要器官,其寿命的长短决定了每年被分配到土壤中碳和养分的数量。我们使用微根管技术监测了水曲柳(Fraxinus mandshurica)和落叶松(Larix gmelinii)细根生长、衰老、死亡的动态过程,运用Kaplan-Meier方法估计细根存活率及中位值寿命(Median root lifespan,MRL),做存活曲线(Survival curve)。用对数秩检验(Log-rank test)比较不同树种、不同土壤层次、不同季节出生的细根寿命差异程度。研究结果表明,随观测期延长,细根存活率逐渐下降,在观测期内的各个时点上,水曲柳细根存活率显著高于落叶松(p<0.001),说明水曲柳细根寿命明显长于落叶松,两树种的MRL分别为111±7 d和77±4 d。无论是水曲柳还是落叶松,土壤下层(20~40 cm)的细根存活率始终高于上层(0~20 cm),差异程度均达到显著水平(p落=0.001, p水<0.001),落叶松上下两层的MRL分别为62±11 d 和95±11 d,水曲柳为111±6 d和124±20 d,这与土壤环境因子的垂直分布有关,下层土壤延长细根寿命。不同同龄根群(Root cohort)的细根寿命不同。落叶松夏季产生的细根存活率显著高于春季(p=0.042),中位值寿命分别是MRL春=47±13 d,MRL夏=82±6 d。水曲柳不同细根同龄根群与落叶松具有相似的季节性,夏季产生的细根存活率在同一时间点上要显著高于春季(p=0.014)。  相似文献   

9.
    
Macrocentrus grandii which develop within Nosema pyrausta-infected larvae of the European corn borer, Ostrinia nubilalis, develop direct systemic infections from the ingestion of spores at the time of larval emergence from the host. Infections adversely affect pupal development and adult longevity. Infected females are unable to transmit the microsporidian to additional corn borer hosts. Pathogen development in the parasite host appears identical to its development in the corn borer host and mature spores show no morphological differences in size or shape when observed at the ultrastructural level. The prevalence of infection in natural parasite populations is 53.8% and closely parallels the 56.7% prevalence of infection in corn borer populations. Results suggest N. pyrausta may play a significant role in limiting M. grandii populations when levels of N. pyrausta in corn borers are high.  相似文献   

10.
    
Line Rosef 《应用植被学》2008,11(2):223-230
Questions: Could the seed bank increase biodiversity during restoration of abandoned, species‐poor, formerly cultivated vegetation? Is it possible to identify how climate, soil and former and present management and vegetation affected the seed bank? Location: The study sites were eight abandoned grasslands, four in Orkdal, central Norway and four in Gaular, western Norway. Methods: 144 seed bank samples were collected from three depths. Each sample was sown and placed in a greenhouse. After three months, the trays were dried and stored at 4°C in a dry place for two months. This was repeated twice. Results: There was a separation of the two regions along the first DCA axis in both the seed bank and in the vegetation analysis and also a clear separation of the seed bank from the vegetation along the second axis. These results are caused by differences in former management as well as temperature, precipitation and soil type between Gaular and Orkdal. We found more annuals, short‐lived species and species demanding light open conditions in the seed bank than in the vegetation probably because these species have the capacity for producing persistent seeds. Most of the species found only in the seed bank were found in very few samples and with few individuals. Conclusion: These results suggest that it may be difficult to increase vegetation biodiversity through restoration of grasslands such as those investigated if the natural soil seed bank is the main seed source.  相似文献   

11.
    
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12.
    
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13.
    
Many infectious diseases are well prevented by proper vaccination. However, when a vaccine is not completely efficacious, there is great interest in determining how the vaccine effect differs in subgroups conditional on measured immune responses postvaccination and also according to the type of infecting agent (eg, strain of a virus). The former is often called correlate of protection (CoP) analysis, while the latter has been called sieve analysis. We propose a unified framework for simultaneously assessing CoP and sieve effects of a vaccine in a large Phase III randomized trial. We use flexible parametric models treating times to infection from different agents as competing risks and estimated maximum likelihood to fit the models. The parametric models under competing risks allow for estimation of both cumulative incidence-based contrasts and instantaneous rates. We outline the assumptions with which we can link the observable data to the causal contrasts of interest, propose hypothesis testing procedures, and evaluate our proposed methods in an extensive simulation study.  相似文献   

14.
    
Data on doe longevity in a rabbit population were analysed using a semiparametric log-Normal animal frailty model. Longevity was defined as the time from the first positive pregnancy test to death or culling due to pathological problems. Does culled for other reasons had right censored records of longevity. The model included time dependent covariates associated with year by season, the interaction between physiological state and the number of young born alive, and between order of positive pregnancy test and physiological state. The model also included an additive genetic effect and a residual in log frailty. Properties of marginal posterior distributions of specific parameters were inferred from a full Bayesian analysis using Gibbs sampling. All of the fully conditional posterior distributions defining a Gibbs sampler were easy to sample from, either directly or using adaptive rejection sampling. The marginal posterior mean estimates of the additive genetic variance and of the residual variance in log frailty were 0.247 and 0.690.  相似文献   

15.
    
Halyomorpha halys (Hemiptera: Pentatomidae) occurs in sweet persimmon orchards from late July to early September and its damage level is negligible before mid‐July. It rarely appears in persimmon orchards after mid‐September, but is easily found in soybean fields. From the phenological observation of H. halys, it is assumed that seasonal migration of H. halys to sweet persimmon orchards may be related to the content of soluble tannin in sweet persimmon fruits. The feeding preference of H. halys was evaluated on sweet and astringent persimmon fruits, and the effects of persimmon fruits and purified persimmon tannin were tested on the survival of H. halys. Numbers of visiting bugs and feeding spots on the fruits were significantly higher on sweet persimmon than those on astringent persimmon. There was no significant difference in survivorships of H. halys fed sweet persimmon and soybean. However, the number of eggs laid by sweet persimmon fed adult females was significantly lower than those fed soybean. The higher concentration of persimmon tannin caused higher mortality of H. halys. Male and female H. halys fed with 3% persimmon tannin showed the lowest survival. Longevities of male H. halys fed with 0, 0.01, 0.1 and 1% persimmon tannin were 14.9, 12.7, 14.5 and 16.3 days, respectively. However, males fed with 3% tannin lived only 6.4 days. The longevities of female H. halys were similar to those of male (10.1, 14.4, 13.8, 12.0 and 6.1 days for 0, 0.01, 0.1, 1 and 3% tannin concentration, respectively). These results suggest that H. halys invades sweet persimmon orchards during late July and early September when more suitable foods, e.g. soybean, are in short supply and sweet persimmon fruits become suitable for feeding (e.g. lower tannin content).  相似文献   

16.
In this paper, we respond to comments on our paper, “Instrumental variable estimation of the causal hazard ratio.”  相似文献   

17.
    
In the context of time-to-event analysis, a primary objective is to model the risk of experiencing a particular event in relation to a set of observed predictors. The Concordance Index (C-Index) is a statistic frequently used in practice to assess how well such models discriminate between various risk levels in a population. However, the properties of conventional C-Index estimators when applied to left-truncated time-to-event data have not been well studied, despite the fact that left-truncation is commonly encountered in observational studies. We show that the limiting values of the conventional C-Index estimators depend on the underlying distribution of truncation times, which is similar to the situation with right-censoring as discussed in Uno et al. (2011) [On the C-statistics for evaluating overall adequacy of risk prediction procedures with censored survival data. Statistics in Medicine 30(10), 1105–1117]. We develop a new C-Index estimator based on inverse probability weighting (IPW) that corrects for this limitation, and we generalize this estimator to settings with left-truncated and right-censored data. The proposed IPW estimators are highly robust to the underlying truncation distribution and often outperform the conventional methods in terms of bias, mean squared error, and coverage probability. We apply these estimators to evaluate a predictive survival model for mortality among patients with end-stage renal disease.  相似文献   

18.
    
Growing evidence has revealed that long noncoding RNAs (lncRNAs) have an important impact on tumorigenesis and tumor progression via a mechanism involving competing endogenous RNAs (ceRNAs). However, their use in predicting the survival of a patient with hepatocellular carcinoma (HCC) remains unclear. The aim of this study was to develop a novel lncRNA expression–based risk score system to accurately predict the survival of patients with HCC. In our study, using expression profiles downloaded from The Cancer Genome Atlas database, the differentially expressed messenger RNAs (mRNAs), lncRNAs, and microRNAs (miRNAs) were explored in patients with HCC and normal liver tissues, and then a ceRNA network constructed. A risk score system was established between lncRNA expression of the ceRNA network and overall survival (OS) or recurrence-free survival (RFS); it was further analyzed for associations with the clinical features of patients with HCC. In HCC, 473 differentially expressed lncRNAs, 63 differentially expressed miRNAs, and 1417 differentially expressed mRNAs were detected. The ceRNA network comprised 41 lncRNA nodes, 12 miRNA nodes, 24 mRNA nodes, and 172 edges. The lncRNA expression–based risk score system for OS was constructed based on six lncRNAs (MYLK-AS1, AL359878.1, PART1, TSPEAR-AS1, C10orf91, and LINC00501), while the risk score system for RFS was based on four lncRNAs (WARS2-IT1, AL359878.1, AL357060.1, and PART1). Univariate and multivariate Cox analyses showed the risk score systems for OS or RFS were significant independent factors adjusted for clinical factors. Receiver operating characteristic curve analysis showed the area under the curve for the risk score system was 0.704 for OS, and 0.71 for RFS. Our result revealed a lncRNA expression–based risk score system for OS or RFS can effectively predict the survival of patients with HCC and aid in good clinical decision-making.  相似文献   

19.
    
We propose new resampling‐based approaches to construct asymptotically valid time‐simultaneous confidence bands for cumulative hazard functions in multistate Cox models. In particular, we exemplify the methodology in detail for the simple Cox model with time‐dependent covariates, where the data may be subject to independent right‐censoring or left‐truncation. We use simulations to investigate their finite sample behavior. Finally, the methods are utilized to analyze two empirical examples with survival and competing risks data.  相似文献   

20.
Objective: This study compared self‐reported subjective life expectancy (i.e., probability of living to age 75) for normal‐weight, overweight, and obese weight groups to examine whether individuals are internalizing information about the health risks due to excessive weight. Research Methods and Procedures: Using data from the Health and Retirement Study, a total of 9035 individuals 51 to 61 years old were analyzed by BMI category. The primary outcome measure was individuals’ reports about their own expectations of survival to age 75. Absolute and relative risks of survival were compared with published estimates of survival to age 75. Results: Consistently, higher levels of BMI were associated with lower self‐estimated survival probabilities. Differences relative to normal weight ranged from 4.9% (p < 0.01) for male nonsmokers to 8.8% (p < 0.001) for female nonsmokers. However, these differences were substantially less than those obtained from published survival curve estimates, suggesting that obese individuals tended to underestimate mortality risks. Discussion: Individuals appeared to underestimate the mortality risks of excessive weight; thus, knowledge campaigns about the risks of obesity should remain a top priority.  相似文献   

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