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
dfoliatR v0.2.0
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
dfoliatR v0.1.0
Edits to DESCRIPTION
Accepted to CRAN
dfoliatR v0.0.4
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
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
dfoliatR v0.0.39999
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
dfoliatR v0.0.3
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.
bugr v0.0.2
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
bugr v0.0.1
Initial uploads of basic functions
Includes detecting defoliation signals following protocols of
Swetnam, Lynch, and Holmes studies and programs