dfoliatR

Provide dendrochronologists with tools for identifying and analyzing the signatures of insect defoliators preserved in tree rings.
https://github.com/chguiterman/dfoliatr

Category: Biosphere
Sub Category: Forest Modeling and Analysis

Keywords

budworm defoliators dendrochronology dendroecology disturbance forests insects outbreak tree-rings

Last synced: about 20 hours ago
JSON representation

Repository metadata

Detection and analysis of insect defoliators in tree rings

• Host: GitHub
• URL: https://github.com/chguiterman/dfoliatr
• Owner: chguiterman
• Created: 2017-09-25T22:29:31.000Z (over 7 years ago)
• Default Branch: master
• Last Pushed: 2023-08-09T20:04:54.000Z (over 1 year ago)
• Last Synced: 2025-04-18T04:10:41.675Z (9 days ago)
• Topics: budworm, defoliators, dendrochronology, dendroecology, disturbance, forests, insects, outbreak, tree-rings
• Language: R
• Homepage: https://chguiterman.github.io/dfoliatR/
• Size: 3.33 MB
• Stars: 7
• Watchers: 1
• Forks: 5
• Open Issues: 8
• Releases: 3
• Metadata Files:
  • Readme: README.Rmd

README.Rmd

          ---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# dfoliatR 


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[![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/dfoliatR)](https://cran.r-project.org/package=dfoliatR)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3626135.svg)](https://doi.org/10.5281/zenodo.3626135)




The goal of `dfoliatR` is to provide dendrochronologists with tools for identifying and analyzing the signatures of insect defoliators preserved in tree rings. The methods it employs closely follow (or in some cases exactly replicate) OUTBREAK, a FORTRAN program available from the [Dendrochronological Program Library](https://www.ltrr.arizona.edu/pub/dpl/). 

When using `dfoliatR` in a publication, please cite the paper:

>Guiterman, CH, AM Lynch, and JN Axelson (2020) [`dfoliatR`: An R package for detection and analysis of insect defoliation signals in tree rings.](https://authors.elsevier.com/sd/article/S1125786520300898) _Dendrochronologia_. DOI: 10.1016/j.dendro.2020.125750.

## Installation

You can install the released version of dfoliatR from [CRAN](https://CRAN.R-project.org) with:

``` r
install.packages("dfoliatR")
```

And the development version from [GitHub](https://github.com/) with:

``` r
# install.packages("devtools")
devtools::install_github("chguiterman/dfoliatR")
```

## Usage

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 or climate series. `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. If there is more than one ring-width series from the same tree, these should be standardized and 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`.


## Example

Here we briefly explore defoliation and outbreaks patterns for a Douglas-fir site in New Mexico. These data are included in the package

```{r }
library(dfoliatR)
## load the data
data("dmj_h")
data("dmj_nh")
```

To start out, we identify *defoliation* events on individual trees,
```{r }
## Identify defoliation signals
dmj_defol <- defoliate_trees(host_tree = dmj_h, nonhost_chron = dmj_nh)

## Plot the results
plot_defol(dmj_defol)
```

And then scale up to *outbreaks* by compositing across the site via
```{r }
## Identify site-level outbreak patterns
dmj_obr <- outbreak(dmj_defol)

## Plot those results
plot_outbreak(dmj_obr)
```

## Further resources

Analyses of the tree series (termed `defol` objects) can be done via:

* `plot_defol()`
* `defol_stats()`
* `get_defol_events()`
* `sample_depth()`

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:

* `plot_outbreak()`
* `outbreak_stats()`

For the full range of usage in `dfoliatR`, please visit the [introduction vignette](https://chguiterman.github.io/dfoliatR/articles/intro-to-dfoliatR.html). 

#### Questions, concerns, problems, ideas, or want to contribute?
Please contact the author, Chris Guiterman

        

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Owner metadata

• Name: Chris Guiterman
• Login: chguiterman
• Email:
• Kind: user
• Description:
• Website: https://cires.colorado.edu/researcher/chris-guiterman
• Location:
• Twitter: ChrisGuiterman
• Company: CIRES/CU-Boulder, NOAA/NCEI Paleo, @ltrr-arizona-edu
• Icon url: https://avatars.githubusercontent.com/u/15913450?u=fc6f63f2a4d61491c751367001da80a046b70b14&v=4
• Repositories: 21
• Last ynced at: 2024-06-11T15:47:34.642Z
• Profile URL: https://github.com/chguiterman

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Last Year

• Fork event: 1

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Committers metadata

Last synced: 6 days ago

Name	Email	Commits
Chris Guiterman	c****n@e****u	327
Maxence Martin	m****7@e****a	1

Committer domains:

• etu.uqac.ca: 1
• email.arizona.edu: 1

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Last synced: 2 days ago

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Package metadata

• Total packages: 1
• Total downloads:
  • cran: 279 last-month
• Total dependent packages: 0
• Total dependent repositories: 0
• Total versions: 3
• Total maintainers: 1

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Dependencies

Score: 9.035986984831405