Code and data used in the study: Estimating transition dates from status-based phenological observations: a test of methods

This is the code and data repository for the following study:

Taylor SD. 2019. Estimating transition dates from status-based phenology observations: a test of methods. PeerJ Preprints 7:e27629v1 https://doi.org/10.7287/peerj.preprints.27629v1

See the readme.md file for a full description of the analysis scripts. 

Study abstract:

The scale of phenological research has expanded due to the digitization of herbarium specimens and volunteer based contributions. These data are status-based, representing the presence or absence of a specific phenophase. Modelling the progress of plant dormancy to growth and reproduction and back to dormancy requires estimating the transition dates from these status-based observations. There are several methods available for this ranging from statistical moments using the day of year to newly introduced methods using concepts from other fields. Comparing the proficiency of different estimators is difficult since true transition dates are rarely known. Here I use a recently released dataset of in-situ flowering observations of the perennial forb Echinacea angustifolia. In this dataset, due to high sampling frequency and unique physiology, the transition dates of onset, peak, and end of flowering are known to within 3 days. I used a Monte Carlo analysis to test eight different estimators across two scales using a range of sample sizes and proportion of flowering presence observations. I evaluated the estimators accuracy in predicting the onset, peak, and end of flowering at the population level, and predicting onset and end of flowering for individual plants. Overall a method using a Weibull distribution performed the best for population level onset and end estimates, but other estimators may be more appropriate when there is a large amount of absence observations relative to presence observations. For individual estimates a method using the midway point between the first flower presence and most prior flower absence, within 7 days, is the best option as long as the restriction does not limit the final sample size. Otherwise the Weibull method is adequate for individual estimates as well. These methods allow practitioners to effectively utilize the large amount of status-based phenological observations currently available.