dfoliatR provides dendrochronologists with tools for identifying and analyzing the signatures of insect defoliators preserved in tree rings. The methods it employs closely follow (or exactly replicate) OUTBREAK, a FORTRAN program available from the Dendrochronological Program Library.
dfoliatR is not yet on CRAN, to install it use the
dfoliatR can be called like any other R package.
The package includes two sets of tree-ring data for examples and exploration.
For the full range of usage in
dfoliatR, please visit the introduction vignette.
The package requires users to input two sets of tree-ring data: standardized ring widths of individual host trees and a standardized tree-ring chronology from a local non-host tree species.
dfoliatR combines these to remove the climate signal represented by the non-host chronology from the host tree series. What's left should represent a disturbance signal. Then
dfoliatR identifies defoliation events in the host tree series.
We recommend that the input tree-ring data be standardized in either ARSTAN or the
dplR R package. These standardized ring-width series should be averaged to the tree level. In ARSTAN, make sure to output '.TRE' files and read them into R with the
read.compact() function in
dplR. If you choose to standardize raw ring widths in
detrend(), then use the
treeMean() function to generate tree-level series. All data input to
dfoliatR needs to be an
rwl object as defined in
dfoliatR by applying the
defoliate_trees() function that calls for these host tree series and a non-host site chronology. Note that the non-host chronology cannot include the "samp.depth" column commonly included in chronology files (e.g., .crn) and created by the
Analyses of the tree series (termed
defol objects) can be done via:
To identify ecologically-significant outbreak events, use the
outbreak() function. Various filters are available to aid users in defining outbreak thresholds. Analyses of outbreak series (termed
obr objects) can be done via:
Please contact the author, Chris Guiterman
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