{"id":13724641,"url":"https://github.com/chguiterman/dfoliatR","last_synced_at":"2025-05-07T18:33:16.878Z","repository":{"id":56413967,"uuid":"104808563","full_name":"chguiterman/dfoliatR","owner":"chguiterman","description":"Detection and analysis of insect defoliators in tree rings","archived":false,"fork":false,"pushed_at":"2023-08-09T20:04:54.000Z","size":3497,"stargazers_count":7,"open_issues_count":8,"forks_count":4,"subscribers_count":2,"default_branch":"master","last_synced_at":"2024-06-11T18:15:21.053Z","etag":null,"topics":["budworm","defoliators","dendrochronology","dendroecology","disturbance","forests","insects","outbreak","tree-rings"],"latest_commit_sha":null,"homepage":"https://chguiterman.github.io/dfoliatR/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/chguiterman.png","metadata":{"files":{"readme":"README.Rmd","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2017-09-25T22:29:31.000Z","updated_at":"2023-07-02T01:50:49.000Z","dependencies_parsed_at":"2023-01-21T21:46:45.843Z","dependency_job_id":null,"html_url":"https://github.com/chguiterman/dfoliatR","commit_stats":{"total_commits":328,"total_committers":2,"mean_commits":164.0,"dds":"0.0030487804878048808","last_synced_commit":"e5a3470f9ff3446724d15347e0dc920f9786bd2a"},"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/chguiterman%2FdfoliatR","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/chguiterman%2FdfoliatR/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/chguiterman%2FdfoliatR/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/chguiterman%2FdfoliatR/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/chguiterman","download_url":"https://codeload.github.com/chguiterman/dfoliatR/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":219864702,"owners_count":16554086,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["budworm","defoliators","dendrochronology","dendroecology","disturbance","forests","insects","outbreak","tree-rings"],"created_at":"2024-08-03T01:02:00.963Z","updated_at":"2024-11-14T14:31:33.582Z","avatar_url":"https://github.com/chguiterman.png","language":"R","funding_links":[],"categories":["Biosphere"],"sub_categories":["Forest Modeling and Analysis"],"readme":"---\noutput: github_document\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, include = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"man/figures/README-\",\n  out.width = \"100%\"\n)\n```\n\n# dfoliatR \u003cimg src=\"man/figures/logo.png\" align=\"right\" width=\"120\" /\u003e\n\n\u003c!-- badges: start --\u003e\n[![R build status](https://github.com/chguiterman/dfoliatR/workflows/R-CMD-check/badge.svg)](https://github.com/chguiterman/dfoliatR/actions)\n[![Coverage Status](https://coveralls.io/repos/github/chguiterman/dfoliatR/badge.svg?branch=master)](https://coveralls.io/github/chguiterman/dfoliatR?branch=master)\n[![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/dfoliatR)](https://cran.r-project.org/package=dfoliatR)\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3626135.svg)](https://doi.org/10.5281/zenodo.3626135)\n\n\n\u003c!-- badges: end --\u003e\n\nThe 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/). \n\nWhen using `dfoliatR` in a publication, please cite the paper:\n\n\u003eGuiterman, 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.\n\n## Installation\n\nYou can install the released version of dfoliatR from [CRAN](https://CRAN.R-project.org) with:\n\n``` r\ninstall.packages(\"dfoliatR\")\n```\n\nAnd the development version from [GitHub](https://github.com/) with:\n\n``` r\n# install.packages(\"devtools\")\ndevtools::install_github(\"chguiterman/dfoliatR\")\n```\n\n## Usage\n\nThe 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. \n\nWe 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`.\n\n\n## Example\n\nHere we briefly explore defoliation and outbreaks patterns for a Douglas-fir site in New Mexico. These data are included in the package\n\n```{r }\nlibrary(dfoliatR)\n## load the data\ndata(\"dmj_h\")\ndata(\"dmj_nh\")\n```\n\nTo start out, we identify *defoliation* events on individual trees,\n```{r }\n## Identify defoliation signals\ndmj_defol \u003c- defoliate_trees(host_tree = dmj_h, nonhost_chron = dmj_nh)\n\n## Plot the results\nplot_defol(dmj_defol)\n```\n\nAnd then scale up to *outbreaks* by compositing across the site via\n```{r }\n## Identify site-level outbreak patterns\ndmj_obr \u003c- outbreak(dmj_defol)\n\n## Plot those results\nplot_outbreak(dmj_obr)\n```\n\n## Further resources\n\nAnalyses of the tree series (termed `defol` objects) can be done via:\n\n* `plot_defol()`\n* `defol_stats()`\n* `get_defol_events()`\n* `sample_depth()`\n\nTo 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:\n\n* `plot_outbreak()`\n* `outbreak_stats()`\n\nFor the full range of usage in `dfoliatR`, please visit the [introduction vignette](https://chguiterman.github.io/dfoliatR/articles/intro-to-dfoliatR.html). \n\n#### Questions, concerns, problems, ideas, or want to contribute?\nPlease contact the author, Chris Guiterman\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fchguiterman%2FdfoliatR","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fchguiterman%2FdfoliatR","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fchguiterman%2FdfoliatR/lists"}