Package: dfoliatR 0.3.0

dfoliatR: Detection and Analysis of Insect Defoliation Signals in Tree Rings

Tools to identify, quantify, analyze, and visualize growth suppression events in tree rings that are often produced by insect defoliation. Described in Guiterman et al. (2020) <doi:10.1016/j.dendro.2020.125750>.

Authors:Chris Guiterman [aut, cre], Ann Lynch [aut], Jodi Axelson [aut]

dfoliatR_0.3.0.tar.gz
dfoliatR_0.3.0.zip(r-4.7)dfoliatR_0.3.0.zip(r-4.6)dfoliatR_0.3.0.zip(r-4.5)
dfoliatR_0.3.0.tgz(r-4.6-any)dfoliatR_0.3.0.tgz(r-4.5-any)
dfoliatR_0.3.0.tar.gz(r-4.7-any)dfoliatR_0.3.0.tar.gz(r-4.6-any)
dfoliatR_0.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
dfoliatR/json (API)

# Install 'dfoliatR' in R:

install.packages('dfoliatR', repos = c('https://chguiterman.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/chguiterman/dfoliatr/issues

Pkgdown/docs site:https://chguiterman.github.io

Datasets:

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

On CRAN:

budworm defoliators dendrochronology dendroecology disturbance forests insects outbreak tree-rings

4.98 score 7 stars 27 scripts 291 downloads 20 exports 87 dependencies

Last updated from:e5a3470f9f. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	168
source / vignettes	OK	218
linux-release-x86_64	OK	158
macos-release-arm64	OK	173
macos-oldrel-arm64	OK	258
windows-devel	OK	128
windows-release	OK	108
windows-oldrel	OK	119
wasm-release	OK	131

Exports:as_defol as_obr as.defol as.obr defol defol_stats defoliate_trees get_defol_events gsi id_defoliation is.defol is.obr obr outbreak outbreak_stats plot_defol plot_outbreak sample_depth series_names stack_defoliation

Dependencies:abind backports boot broom car carData cli colorspace corrplot cowplot cpp11 Deriv digest doBy dplR dplyr farver forcats forecast Formula fracdiff generics ggplot2 ggpubr ggrepel ggsci ggsignif glue gridExtra gtable isoband labeling lattice lifecycle lme4 lmtest magrittr MASS Matrix MatrixModels matrixStats mgcv microbenchmark minqa modelr nlme nloptr nnet numDeriv pbkrtest pillar pkgconfig png polynom purrr quantreg R.methodsS3 R.oo R.utils R6 rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack reformulas rlang rstatix S7 scales signal SparseM stringi stringr survival tibble tidyr tidyselect timeDate urca utf8 vctrs viridisLite withr XML zoo

Introduction to dfoliatR

Installation | Data | Performance

Rendered fromintro-to-dfoliatR.Rmdusingknitr::rmarkdown

Last update: 2023-08-09
Started: 2019-12-06

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Cast data frame to list-like 'defol' object	as_defol
Cast data frame to list-like 'obr' object	as_obr
Alias to 'as_defol()'	as.defol
Alias to 'as_obr()'	as.obr
Constructor for S3 defol class	defol
Descriptive statistics for defoliation trees	defol_stats
Identify defoliation events in host trees	defoliate_trees
Demi John dfol object	dmj_defol
Demi John Douglas-fir	dmj_h
Demi John area ponderosa pine	dmj_nh
Demi John outbreak object	dmj_obr
East Fork defol object	efk_defol
East Fork Jemez River Douglas-fir	efk_h
Baca ponderosa pine chronology	efk_nh
East Fork outbreak object	efk_obr
Defoliation event list	get_defol_events
Calculate the growth suppression index	gsi
Identify defoliation events in a host series	id_defoliation
Check if object is tree-level defoliation object: 'defol'	is.defol
Check if object is outbreak, meaning site-level outbreak object	is.obr
Constructor for an 'obr' object.	obr
Composite defoliation series to determine outbreak events	outbreak
Outbreak statistics	outbreak_stats
Produce a Gantt plot of individual tree-ring series to show defoliation events in time	plot_defol
Produce a stacked plot to present composited, site-level insect outbreak chronologies	plot_outbreak
Plot a 'defol' object	plot.defol
Calculate the sample depth of a defol object	sample_depth
Extract series names from a defol object	series_names
Stack a defoliation list	stack_defoliation