This is the code and primary data for the above study.
The analysis develops and tests a method, the Weibull Grid, to estimate flowering onset across large-scales using only observations of flowering presence. It uses a Weibull estimator (from the phest package) integrated into a spatially explicit ensemble. The method is tested with a simulation study and then applied to actually phenology data derived from iNaturalist.
Code for the Weibull Grid model and making flowering simulations is in the flowergrids R package.
Data sources:
iNaturalist
Phenocam
USA National Phenology Network*
iDigBio*
*These data sources were only used to show historic trends in data collection, not in the main analysis.
data/ : All original data used in the analysis.
results/ : Results from the simulation analysis
inat_data_prep/ : Scripts and config files for downloading and scoring the iNaturalist photographs for the two species.
prior_study_phenology : Notes and data on prior measurements of onset for the two species analysed.
install_packages.R : Install the packages used in this analysis
config.R : Setup for the simulation analysis parameters.
run_estimators.R : Runs the simulation analysis.
analysis_simulation_errors.R : Produce the figures and tables related to the simulations.
conceptual_figures.R : Create Figure 1 from the introduction.
phenocam_site_explore.R : Mapping out the different phenocam sites for selection.
process_phenocam_data.R : Downloading and process the phenocam data used in the analysis
inaturalist_onset_models.R : Fit the iNaturalist models for the 2 species and create the figure comparing them to phenocam onset
supplemental_figure_simulation_example.R : Create the supplemental figures showing the example simulations.
other_dataset_comparison.R : Create Figure 5 showing the sample size of different data sources over time.