Identify defoliation events in a host series

After calculating the growth suppression index in gsi(), id_defoliation() performs a runs analysis on the normalized growth suppression index, or ngsi, in which sequences of negative departures are assessed as possible defoliation events. id_defoliation() is the workhorse for defoliate_trees(), performing much of the necessary criteria evaluation used in OUTBREAK. The defaults for most parameters originate from OUTBREAK. Two new features distinguish the dfoliatR version: bridging events that occur in close sequence and allowing for the recent end of a series to be evaluated for defoliation regardless of the event duration. See parameter specifics for details.

id_defoliation(input_series, duration_years = 8, max_reduction = -1.28,
  bridge_events = FALSE, series_end_event = FALSE)

Arguments

input_series	A data frame with 5 columns, as generated by gsi().
duration_years	The minimum length of time in which the tree is considered to be in defoliation.
max_reduction	The minimum value of ngsi required to be considered a defoliation event. If a sequence of negative ngsi values does not reach this threshold, the potential event is rejected. Defaults to -1.28.
bridge_events	Binary, defaults to FALSE. This option allows for successive events that are separated by a single year to be bridged and become one event. It should be used cautiously and closely evaluated to ensure the likelihood that the two (or more) events are actually one long event.
series_end_event	Binary, defaults to FALSE. This option allows the user to identify an event occurring at the time of sampling as a defoliation event, regardless of duration. Including it will help to quantify periodicity and extent of an outbreak. This should only be used if the user has direct knowledge of an ongoing defoliation event when the trees were sampled.

Value

After performing runs analyses, the function adds a column to the input data frame that distinguishes years of defoliation and the maximum defoliation year (ie. the year the greatest negative growth departure within the event).

Note

id_defoliation() is called by defoliate_trees(). It might only be used by the user for troubleshooting.