chguiterman/dfoliatr

Detection and analysis of insect defoliators in tree rings

dfoliatr's Issues

Try to match results of OUTBREAK as best as possible.

This includes a lot of tedious checking

Units tests

Include Travis checks

Preparation for CRAN launch

fix outbreak_stats after changed to defoliate_trees and otubreak

In `defol_stats()`, remove "series_end_event"s from duration stats

add short-series warning to `id_defoliation`

As presented by Cody Dangerfield, if a series has only 1 year, the runs analysis, rle will fail with an NA that cascades into the for loop and fails on line 93 of "utils.R".
Need some way to catch NA in the departure runs and skip the loop.

bridge successive events

Allow user to combine 2 events if there are separated by a single year. This is response to observations that occasional successive events probably best reflect a single long event, but there are too many positive excursions to be objectively allowed. This option is being tested and should be scrutinized by users.

plotting functions broken due to changes in main.R

Include non-defoliated series in plot_defol

Series that lack identified defoliation events are ignored in plot_defol(). This also triggers an error in get_defol_events() which is actually caused bu events_table() yielded a null return.

Add %defol line to `plot_outbreak()`

This can't be done after the fact...so the "filter_prop" variable must be passed to the obr object, probably as an "attr". then it has ot be called by plot_outbreak().

Back-to-back defolations

Somehow, it's possible to have two defolations, back-to-back without a break. Needs exploration and validation in id_defoliation

Add example to `plot_defol()`

Especially showing the use of the breaks argument

Spell check everything

Document data included in package

Add examples to functions

Add sort function for use in plotting

see burnr::sort.fhx()

Ongoing defoliations

If the last year of a series has a positive index, it is not allowed as an excursion in the defoliation event, and the event is cut-off. But if the user knows the event is ongoing, it should not cut-off.

Allow `defoliate_trees` to run in host-only mode

Currently defoliate_trees can be only be done with a host and non-host chronology. Allow it to run with only a host set of tree-ring series, assuming the user has already performed series correction.

tree-level list of defoliation events

Depreciate and remove EF data

Updating the East Fork data, and removing the ef_* data objects. New data are labeled efk_*

Change package name

Add flexibility for non-host chronologies

Need to ignore samp.depth. For chronology files with multiple types (std, res, ars), need to add warning message for user to select which they want and subset the input data.

series_end_events label

Currently, the "series_end_event" tag in defol objects is placed regardless of whether series_end_event = TRUE in defoliate_trees(). The tag should only be placed where the variable is set to TRUE.

Change name of "corrected"series

Flexible labels in `plot_oubreak()`

Currently only "GSI" displays in the y-axis label for plot_outbreak(). It would be better if it reflected whether the plot shows the ngsi (default) or gsi (only other option).