Data from: Dead before detection: addressing the effects of left truncation on survival estimation and ecological inference for neonates

1. Neonate survival is a key life history trait, yet remains challenging to measure in wild populations because neonates can be difficult to capture at birth. Estimates of survival from neonates that are opportunistically captured might be inaccurate because some individuals die before sampling, resulting in data that are left truncated. The resulting overestimation of survival rates can further affect ecological inference through biased estimates of covariate effects in survival models, yet is not addressed in most studies of animal survival. Here, we quantify the effects of left truncation on survival estimates and subsequent ecological inference. 2. Vaginal implant transmitters (VITs) enable capture of ungulates at birth, yielding data without left truncation. The effects of left truncation on survival estimation were quantified using age-dependent survival models for VIT and opportunistically captured neonatal deer. Differences in daily survival rates (DSRs) and cumulative survival probability were calculated for the first 70 days of life. In addition, left truncation was simulated by removing fawns that died during the first 1 or 2 days of life from the VIT-caught sample, isolating the effect of left truncation. 3. Cumulative probability of survival during the first 70 days of life was overestimated by 7–23% for fawns caught opportunistically compared with those caught by VIT, depending on model design. Differences in DSRs were large at age 1 day, but had converged by age 30 days. Simulated left truncation resulted in overestimates of survival of up to 31%. Model selection and covariate coefficients were strongly affected by left truncation, producing spurious ecological inference, including changes to sign and/or magnitude of inferred effects of all covariates. 4. We recommend (i) every effort be made to capture neonates; (ii) consistent capture methods, using at least in part non-truncating techniques, be implemented across years and study areas; and (iii) exclusion of left-truncated data from survival estimates until DSRs converge with those calculated from non-truncated data. This work emphasizes the importance of accounting for left truncation in survival estimation for any species with strong age-dependent survival in order to prevent biased conclusions produced by sampling method rather than true ecological effects.1. 新生幼体（neonate）存活率是核心的生活史性状，但在野生种群中难以精准测定，原因在于新生幼体在出生时难以被捕获。通过偶遇捕获的新生幼体得到的存活率估算值可能存在偏差：部分个体在采样前便已死亡，导致数据出现左截断问题。由此产生的存活率高估问题，还会通过生存模型中协变量效应的有偏估计进一步干扰生态推断，但多数动物存活率研究并未对此问题加以关注。本研究量化了左截断对存活率估算及后续生态推断的影响。 2. 阴道植入式发射器（vaginal implant transmitters, VITs）可实现有蹄类动物（ungulates）出生时的捕获，从而获得无左截断的数据。本研究针对通过VIT捕获的新生鹿群与偶遇捕获的新生鹿群，构建年龄依赖型生存模型，量化左截断对存活率估算的影响；同时计算了幼鹿（fawns）出生后前70天的日存活率（daily survival rates, DSRs）差异与累积存活概率差异。此外，本研究通过从VIT捕获的样本中移除出生后1或2天内死亡的幼鹿，模拟左截断场景，以分离左截断的单独效应。 3. 与VIT捕获的幼鹿相比，偶遇捕获的幼鹿在出生后前70天的累积存活概率被高估7%~23%，高估幅度取决于模型设定。日存活率的差异在幼鹿1日龄时最为显著，但在30日龄时趋于一致。模拟左截断场景可导致存活率高估幅度最高达31%。左截断会显著影响模型选择与协变量系数，进而产生虚假的生态推断结果，包括所有协变量推断效应的符号和/或强度发生改变。 4. 本研究提出以下建议：（1）尽一切努力捕获新生幼体；（2）在不同年份与研究区域统一采用至少部分采用无截断技术的捕获方法；（3）在日存活率与非截断数据计算结果趋于一致前，排除左截断数据用于存活率估算。本研究强调，对于存在显著年龄依赖型生存特征的物种，在存活率估算中必须考虑左截断问题，以避免因采样方法而非真实生态效应产生有偏结论。