Mapping Temperature Data to Phenological Time Uncovers Distinct Phases Governing Leaf Senescence Timing

This is the software and data publication associated with the manuscript "Mapping Temperature Data to Phenological Time Uncovers Distinct Phases Governing Leaf Senescence Timing". All code was written in R, in total 19 R scripts accompany the manuscript. Scripts preceded by 01_ are related to the 1st major investigation outlined in the paper, i.e. the investigation of apple on German scale. Consequently, scripts preceded by 02_ are related to the 2nd investigation, i.e. apple on European scale, and those preceded by 03_ are related to the 3rd investigation of other species. One script preceded by 04_ provides an overview map relating to all major investigations. SOFTWAREBelow, the steps performed in the different scripts, and the figures created for manuscript and supplement as well as the data files supplied with this repository are outlined in detail:01: Investigation of apple on German scale01a_Uniting_Cleaning_Database.R: Uniting phenology and cultivar data and removal of quality flagged data, producing Phenology_observations.csv 01b_Extracing_T_data_stations.R: In this script, DWD temperature data is downloaded and extracted for all phenology observations, producing data in dwd_dwd.7z01c_Extracting_T_data_periods.R: For each observation, mean temperatures for the 10-day increments between 0 and 360 DBLF50 and associated periods are calculated 01d_SPEI.R: Entails the calculation of SPEI and the extraction of annual mean SPEI values for all German phenology observations; data further analyzed in 01e01e_Analysis.R: All data analysis on the DWD phenology data, producing Figs. 1, S1, S2, S3, S12, S1301f_EOBS_extraction_analysis.R: A rudimentary version of analysis 1e, but based on E-OBS instead of DWD temperature data, producing data in dwd_eobs.7z01g_T_Accumulation.R: Accumulation of growing degree hours, producing Fig. S401h_Phenology_TemporalTrends.R: Analysis of trends in bud break, leaf fall and season length; producing Fig. S14 02: Investigation of apple on European scale02a_Extracting_t_data_PEP.R: E-OBS temperature data is extracted for all PEP725 phenology observations, producing data in europe_eobs.7z02b_Extracting_T_data_IPG.R: E-OBS temperature data is extracted for all IPG phenology observations02c_Uniting_PEP_IPG.R: PEP and IPG phenology observations are united to one dataset for subsequent analyses02d_SRTM_Extraction.R: Download of SRTM data, investigation of elevational heterogeneity within an E-OBS cell; producing Fig. S702e_Analysis_Europe.R: All data analysis on the PEP725 and IPG phenology data, producing Figs. 2, S5, S6, S8, S9, S10, S11 03: Investigation of other species03a_Pyrus_communis.R: Extraction of temperature data and entire analysis for pear, producing figure united to Fig. 3 in 03e03b_Prunus_avium.R: Extraction of temperature data and entire analysis for cherry, producing figure united to Fig. 3 in 03e03c_Fagus_sylvatica.R: Extraction of temperature data and entire analysis for beech, producing figure united to Fig. 3 in 03e03d_Quercus_robur.R: Extraction of temperature data and entire analysis for oak, producing Fig. S1503e_Uniting_Species_Plots.R: United single plots created in 03a - 03c into Fig. 3. 04_Mapping_Phenology_Observations.R: Created the location overview maps shown in Figs. S16, S17. 05_Calendar_Phenological_Time_GraphicalAbstract.R: Produced part of the graphical abstract figure, the rest is produced in 01e_Analysis.R DATAAs we do not have permission to share phenology observations from PEP725 and IPG (which are available free of charge via the respective data portals), we can only share DWD phenology observations. In addition, we provide the temperature time series we extracted for the investigations for apple, i.e. for the DWD phenology data once with DWD temperature data and once with E-OBS temperature data as well as the european-scale analysis. The filename of each .csv-file containing temperature data refers in all circumstances to the site ID provided either by the DWD, PEP725 or IPG databases. Phenology_observations.csv: Entails all DWD observations, created in script 01adwd_dwd.7z: Entails timelines based on DWD temperature data for all DWD phenology observations, created in script 01bdwd_eobs.7z: Entails timelines baed on E-OBS temperature data for all DWD phenology observations, created in script 01feurope_eobs.7z: Entails timelines based on E-OBS temperature data for all IPG and PEP725 phenology observations, created in script 02a and 02b