NEWS

dfoliatR 0.3.0 (2023-08-09)

Updated defoliated_trees() to work without nonhost chronology #2
- Thanks for the contribution of @MaxenceMartin on this
- @chguiterman added a unit test, cleaned up a RCMD note, some linting, Also updated the function description for this new option
Changed use of {vdiffr} in testthat files to be conditional
- {vdiffr} does not load on Apply M1 machines, and thanks to @lionel- for code example on how to fix the issue https://github.com/lionel-/ggstance/commit/eac216f6
Removed Travis CI and implemented GitHub Actions
- Thanks to @brews for this helpful resource: https://deanattali.com/blog/migrating-travis-to-github/
New feature to allow users to change the y-axis label on the bottom tile of plot_outbreak()
- Thanks to Ann Lynch and Wojciech Kędziora for the suggestion. This should provide greater flexibility for users that are not only looking at defoliation but other causes of growth suppression
Removed ef_* data objects in preference for efk_* objects

Readme edits
Edits to function descriptions
Adding new logo
Fixed a bug in id_defoliation() regarding series_end_events
Added updated East Fork data, new objects are efk_*
Fix up plot_outbreak() with flexible Y-axis labels and shaded area
Address issues pertaining to ongoing defoliations when users select series_end_events = TRUE in defoliate_trees().
- Duration is no longer calculated for series-end-events in defol_stats()
- A new factor, "se_outbreak" was added to outbreak() results to identify ongoing events
- Duration and other statistics are not calculated for ongoing events in outbreak_stats()
Add examples to plotting functions
dfoliatR is now published in Dendrochronologia

Add data from Demi John; change built-in data naming scheme to help differentiate host series from nonhost chronologies
Added provision to prevent defoliation events two years following one, unless bridge_events is set to true.
Reduced event levels for more meaningful interpretation
Added Gantt plot to plotting options. This required adding several new helper functions, including the useful get_defol_events function
Revised defol_stats to catch series with no defol events
Gantt plot is now the default tree-level plotting option
Added unit tests to defoliate and outbreak functions
plotting is now stable to ggplot2 v3.2.0
testing of plots via vdiffr
Add "Maturing" as a lifecycle badge
Add new constructor functions to (re)establish object classes for defol and outbreak. This is particularly useful when batch processing with {purrr} functions like map
Changed the outbreak object code to obr. And updated several functions to account for the change.
Bug fix in get_defol_events() to pass non-defoliated series through to final table.
Spell check and code flow fixes
Added MIT License
Adding Zenodo DOI
Ready for v.0.0.4

preparation for CRAN release
adding examples to primary functions
checking spelling and code format
Updating man files with usethis::use_roxygen_md()
running diagnostic utilities in devtools
devtools::check() R CMD Check 0 errors, 0 warnings, 0 notes
devtools::check_rhub() 0 errors, 0 warnings, 1 note
The note relates to spelling of "Swetnam" and "dfoliatR" in the DESCRIPTION. Both are correct.
devtools::check_win_devel() seems to check out.
Update README
Update pkgdown site

Changed package name
Add parameter to allow for events that are ongoing at the time of sampling, called series end events. This is for users who know, with certainty, that they sampling during an outbreak event. The parameter allows for events to be recorded regardless of duration, but only the recent end of the series.
Add parameter to allow for bridging of two defoliation events on a single tree. This was done after observing instances where two successive events were separated by a single year, and in the case of western spruce budworm more likely represented a single, long event. The option should be used with caution and scrutinized closely.
Update author list to reflect significant contributions to dfoliatR development by Ann Lynch and Jodi Axelson.
Replaced the correct_host_series function with gsi to better capture the process of calculating the growth suppression index.

This version in response to validation trials with real data
Improve id_defoliation to prevent overlapping defol events
Add both corrected and normalized index series to outputs of defoliate_trees and outbreak functions

Initial uploads of basic functions
Includes detecting defoliation signals following protocols of Swetnam, Lynch, and Holmes studies and programs
Adds basic tree and site level stats
Adds basic plots for tree- and site-level objects
Add some data for educational purpose