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How to analyse seed germination data using statistical time-to-event analysis: non-parametric and semi-parametric methods

https://doi.org/10.1017/S0960258511000547

Seed germination experiments are conducted in a wide variety of biological disciplines. Numerous methods of analysing the resulting data have been proposed, most of which fall into three classes: intuition-based germination indexes, classical non-linear regression analysis and time-to-event analysis (also known as survival analysis, failure-time analysis and reliability analysis). This paper briefly reviews all three of these classes, and argues that time-to-event analysis has important advantages over the other methods but has been underutilized to date. It also reviews in detail the types of time-to-event analysis that are most useful in analysing seed germination data with standard statistical software. These include non-parametric methods (life-table and Kaplan–Meier estimators, and various methods for comparing two or more groups of seeds) and semi-parametric methods (Cox proportional hazards model, which permits inclusion of categorical and quantitative covariates, and fixed and random effects). Each method is illustrated by applying it to a set of real germination data. Sample code for conducting these analyses with two standard statistical programs is also provided in the supplementary material available online (at http://journals.cambridge.org/). The methods of time-to-event analysis reviewed here can be applied to many other types of biological data, such as seedling emergence times, flowering times, development times for eggs or embryos, and organism lifetimes.