Reference

Usage Identifying insect defoliation and outbreak events in tree-ing growth patterns is the goal of dfoliatR. Two functions perform the majority of the workload. They take indexed tree-ring data and find tree-level defoliation events [defoliate_trees()] and then composite all trees [outbreak()] to identify outbreak events.
defoliate_trees()	Identify defoliation events in host trees
outbreak()	Composite defoliation series to determine outbreak events
Graphics Objects created by the two functions above can be plotted via:
plot_defol()	Produce a Gantt plot of individual tree-ring series to show defoliation events in time
plot_outbreak()	Produce a stacked plot to present composited, site-level insect outbreak chronologies
Summary statistics
defol_stats()	Descriptive statistics for defoliation trees
outbreak_stats()	Outbreak statistics
Helpful functions
sample_depth()	Calculate the sample depth of a defol object
series_names()	Extract series names from a defol object
get_defol_events()	Defoliation event list
Data Tree-ring data from four sites in New Mexico are available for users to explore and test functions. These include two sets of Douglas-fir host series and two separate ponderosa pine non-host chronologies. The samples were collected to reconstruct western spruce budwork outbreak dynamics.
dmj_defol	Demi John dfol object
dmj_h	Demi John Douglas-fir
dmj_nh	Demi John area ponderosa pine
dmj_obr	Demi John outbreak object
ef_defol	East Fork defol object
ef_h	East Fork Jemez River Douglas-fir
ef_nh	East Fork Jemez area ponderosa pine
ef_obr	East Fork outbreak object
Background functions These functions are mainly used inside of other dfoliatR functions
events_table()	Create a runs table of events
gsi()	Calculate the growth suppression index
id_defoliation()	Identify defoliation events in a host series
is.defol()	Check if object is tree-level defoliation object: defol
plot(<defol>)	Plot a defol object
stack_defoliation()	Stack a defoliation list