README.md

dfoliatR

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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.

Installation

dfoliatR is not yet on CRAN, to install it use the devtools function:

devtools::install_github("chguiterman/dfoliatR")

Once installed, dfoliatR can be called like any other R package.

library(dfoliatR)

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.

Overview

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 dplR with 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 dplR.

Begin using 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 dplr::chron() function.

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:

Questions, concerns, problems, ideas, or want to contribute?

Please contact the author, Chris Guiterman



chguiterman/bugr documentation built on Feb. 14, 2020, 3:53 p.m.