Reference

All functions

bounding_box()

calculate the median bounding box for a yearly section

circular_linear_plot()

Create species-specific linear and/or circular plot of phenology data Linear plots show full time-series Circular plots show annual means

climate_ccf()

cross-correlations species pheno data with climate data

consecutive_timeline_sp()

for fourier analysis, no missing years can be incorporated. If missing years within a timeline, then only the longest consecutive timeline is kept.

dist_point_to_line()

distance between a point and a line (orthogonal) (2D)

dist_point_to_point()

point to point distance (pythagoras theorem) (2D)

event_length()

Calculates event length and timing

extract_annotations()

Extract all phenology dates

format_zoo_data()

Reads in Jungle Rhythms classification output file (CSV) and cleans up the data by dropping early values (trials) etc

intersect_line_circle()

line circle intersection (2D) calculates line intersections with a circle with origin at start, only intersections with y > start_y are reported

line_intersection()

Calculate line intersection when provided four coordinaes defining two lines

line_sections()

Extract line sections from annotations

luki_circular_linear_plot()

Create linear plot of phenology data

missing_years()

In the full dataset, for each individual, obervation years without phenophase events observed (leaf event, flowering, fruiting, seed dispersal) had been removed as missing. Thereby, some timelines of individuals do not have consecutive dates Here, these missing dates are filled with phenological value of NA, within the individual-specific start-end years

overview_stats()

Calculates summary statistics / characteristics at species-level including number of individuals, start/end year, number of observed events, total nr of observation years across individuals

panel_plot()

Panel plot of annotations

peak_detection()

Peak detection and cyclicity using fourier transform

plot_raw_annotations()

Plot raw annotations

plot_weekly_annotations()

Plot weekly annotations

proj_point_on_line()

orthogonal projection of a point onto a line (2D)

row_locations()

calculate the approximate location of the rows

standlevel_phen()

stand-level annual phenological signal species-specific annual signals are weighted by their basal area

standlevel_phen_plotlevel() standlevel_phen_plotlevel()

plot-level annual phenological signal species-specific annual signals are weighted by their basal area at the plot level

summarize_annotations()

Summarize annotations into weekly values