# Pan-European Phenological Data Analysis

## Documentation for package ‘pep725’ version 1.1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

add_country | Add Country Information to a Dataset Based on Latitude/Longitude
add_daylength | Add Daylength to Phenological Data
as.pep | Coerce to PEP725 Data Object
bbch_description | Get BBCH Phase Description
calc_daylength | Calculate Daylength (Photoperiod)
calc_max_daylength | Maximum Daylength at a Latitude
calc_thermal_sum | Calculate Thermal Sum at Phenological Events
calc_thermal_units | Calculate Thermal Units (Growing Degree Days)
get_phenology_doys | Compute CTRL and SCEN Phenology Day-of-Year Values
is.pep | Test if Object is a PEP725 Data Object
kendall_tau | Mann-Kendall Z-Statistic (deprecated alias for 'mann_kendall_z')
mann_kendall_z | Mann-Kendall Z-Statistic
new_pep | Create a PEP725 Phenological Data Object
pep-class | PEP725 Phenological Data Class
pep725_demo | Demonstrate the pep725 Package Functions
pep_cache_clear | Clear Cached PEP Data
pep_cache_info | Get Cache Information
pep_check_connectivity | Check Station-Year Connectivity
pep_check_phases | Check for Expected Phenological Phases
pep_check_phases_multi | Check Multiple Phases Across Species
pep_completeness | Assess Species and Phase Completeness of Phenological Data
pep_coverage | Assess Data Coverage of PEP725 Phenological Data
pep_download | Download Synthetic PEP725 Data
pep_flag_outliers | Flag Phenological Outliers
pep_import | Import and preprocess PEP725 phenological data
pep_outliers_leaflet | Interactive Leaflet Map of Outlier-Flagged Stations
pep_plot_outliers | Visualize Phenological Outliers for Inspection
pep_quality | Assess Data Quality of Phenological Observations
pep_second_events | Detect Second Flowering and Other Repeated Phenological Events
pep_seed | Minimal Seed Dataset for Synthetic Data Generation
pep_simulate | Simulate Synthetic PEP Data
pheno_anomaly | Calculate Phenological Anomalies
pheno_combine | Create Combined Phenological Time Series
pheno_gradient | Analyze Phenological Gradients with Elevation or Latitude
pheno_leaflet | Interactive Leaflet Map to Select PEP725 Stations
pheno_map | Plot Phenology Station Maps
pheno_normals | Calculate Phenological Normals (Climatology)
pheno_plot | Plot Phenological Time Series
pheno_plot_hh | Plot Phenological Time Series for Heading and Harvest
pheno_plot_timeseries | Plot Phenological Time Series
pheno_pls | Partial Least Squares Analysis for Phenology-Temperature Relationships
pheno_regional | Compile Regional Phenology Data and Climate Sensitivity Inputs
pheno_regional_hh | Compile Regional Phenological Time Series for Heading and Harvest
pheno_synchrony | Analyze Phenological Synchrony Across Stations
pheno_trend_turning | Detect Trend Turning Points in Phenological Time Series
plot.pep | Plot Method for PEP725 Data
plot.pep_completeness | Plot Method for Completeness Assessment
plot.pep_coverage | Plot Method for PEP Coverage
plot.pep_outliers | Plot Method for Outlier Detection Results
plot.pep_quality | Plot Method for Data Quality Assessment
plot.pheno_anomaly | Plot Method for Phenological Anomalies
plot.pheno_combined | Plot Method for Combined Time Series
plot.pheno_gradient | Plot Method for Phenological Gradient Analysis
plot.pheno_normals | Plot Method for Phenological Normals
plot.pheno_pls | Plot Method for PLS Phenology Results
plot.pheno_synchrony | Plot Method for Phenological Synchrony Analysis
plot.pheno_turning | Plot Method for Trend Turning Analysis
plot.second_events | Plot Method for Second Events Detection
plot_phenology_trends | Plot Robust Phenological Trends
print.pep | Print Method for PEP725 Data
print.pep_completeness | Print Method for Completeness Assessment
print.pep_coverage | Print Method for PEP Coverage
print.pep_outliers | Print Method for Outlier Detection Results
print.pep_quality | Print Method for Data Quality Assessment
print.phase_check | Print Method for Phase Check Results
print.phase_check_multi | Print Method for Multi-Species Phase Check
print.pheno_anomaly | Print Method for Phenological Anomalies
print.pheno_combined | Print Method for Combined Time Series
print.pheno_gradient | Print Method for Phenological Gradient Analysis
print.pheno_normals | Print Method for Phenological Normals
print.pheno_pls | Print Method for PLS Phenology Results
print.pheno_synchrony | Print Method for Phenological Synchrony Analysis
print.pheno_turning | Print Method for Trend Turning Analysis
print.second_events | Print Method for Second Events Detection
select_phase | Select and Label Phenophases from PEP Time Series
subspecies_report | Comprehensive Subspecies Availability Report
summarize_subspecies_availability | Summarize Subspecies Phenological Data Availability
summary.pep | Summary Method for PEP725 Data
summary.pep_completeness | Summary Method for Completeness Assessment
summary.pep_outliers | Summary Method for Outlier Detection Results
summary.pep_quality | Summary Method for Data Quality Assessment
summary.pheno_anomaly | Summary Method for Phenological Anomalies
summary.pheno_normals | Summary Method for Phenological Normals
summary.pheno_pls | Summary Method for PLS Phenology Results
summary.pheno_synchrony | Summary Method for Phenological Synchrony Analysis
summary.second_events | Summary Method for Second Events Detection
[.pep | Subset PEP725 Data While Preserving Class