outbreak {dfoliatR} | R Documentation |
Composite defoliation series to determine outbreak events
Description
outbreak()
takes a defol
object from
defoliate_trees()
and composites it into a site-level object.
Function parameters allow the user to filter the tree-level series in various
ways to optimize thresholds of what constitutes an "outbreak" level event
recorded by the host trees.
Usage
outbreak(x, filter_perc = 25, filter_min_series = 3, filter_min_defol = 1)
Arguments
x |
a defol object |
filter_perc |
the minimum percentage of defoliated trees to be considered an outbreak. Default is 25 percent. |
filter_min_series |
The minimum number of trees required for an outbreak event. Default is 3 trees. |
filter_min_defol |
The minimum number of trees recording a defoliation event. Default is 1 tree. |
Value
A data.frame obr
object for the site that includes all trees in the
host defol
object. Columns in the obr
include:
-
year
for every year in the set of host trees, -
num_defol
the number of trees recording a defoliation event, -
percent_defol
the percent of trees recording a defoliation, -
num_max_defol
the number of trees recording a maximum growth suppression (or peak of that event on that tree), -
perc_max_defol
the percent of trees at maximum defoliation, -
mean_gsi
the average of all trees growth suppression index (gsi
), -
mean_ngsi
the average of all trees normalized growth suppression index (ngsi
), -
outbreak_status
whether that year constitutes an outbreak based on the filters applied to the function.
Examples
data("dmj_defol")
head(outbreak(dmj_defol))