Function reference • dfoliatR

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

as_defol(): Cast data frame to list-like defol object

as_obr(): Cast data frame to list-like obr object

as.defol(): Alias to as_defol()

as.obr(): Alias to as_obr()

is.defol(): Check if object is tree-level defoliation object: defol

is.obr(): Check if object is outbreak, meaning site-level outbreak object

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

efk_defol: East Fork defol object

efk_h: East Fork Jemez River Douglas-fir

efk_nh: Baca ponderosa pine chronology

efk_obr: East Fork outbreak object

Miscileaneous

These functions are mainly called internally, but could assist in troubleshooting or in other unusual situations.

gsi(): Calculate the growth suppression index

id_defoliation(): Identify defoliation events in a host series

stack_defoliation(): Stack a defoliation list

defol(): Constructor for S3 defol class

obr(): Constructor for an obr object.

plot(<defol>): Plot a defol object