Fraxinus Survival and Mortality Model (version 0.7)
Provides probabilities and likelihood of mortality of street and park ash trees exposed to emerald ash borer
Installation requires devtools.
devtools::install_github("PlantEcology/FSMM")
Data should be organized trees in rows (tree10000 provided as example data set with 10,000 trees). The function will add mortality probability, mortality prediction (0,1 based on a threshold), and mortality year (1-3 after data year, not included by default) columns to the data output. Required data for models vary, however, bark splits and DBH are required for all models.
Tree = unique tree ID
BS = presence/absence of bark splits (1/0) [required for all model types]
DBH = diameter at breast height (cm) [required for all model types]
DB = percent crown dieback (5-100%) [required for "dieback" model type]
V = vigor rating (1-5, with 1 = healthiest and 5 = crown half dead) [required for "vigor" model type]
WP = presence/absence of woodpecker activity (1/0) [required for "woodpecker" model type]
Defines the variables to include in model predictions. Three model types are available each includes presence of bark splits (1,0) and diameter at breast height (DBH [cm]) ("dieback", "vigor", "woodpecker").
Type "dieback" provides model output using inputs of percent dieback, DBH, and bark splits. Clark et al. (2015) model had 83.8% correct prediction of mortality.
Type "vigor" provides model output using inputs of vigor, DBH, and bark splits. Clark et al. (2015) model had 86.5% correct prediction of mortality.
Type "woodpecker" provides model output using inputs of wood pecker activity, DBH, and bark splits. Clark et al. (2015) model had 75.7% correct prediction of mortality.
Default
type="dieback"
Probability of mortality that will define if a tree dies within 3 years. Mortality threshold defined by user as a continuous probability (0 to 1).
Default
threshold=0.65
Model can predict the year (after data collection) in which a tree will die. Year is a Boolean option. Clark et al. (2015) model had 71.6% correct prediction of mortality year. Requires inclusion of dieback if used with "vigor" or "woodpecker" type models.
Default
year=FALSE
This example would take the provided data tree10000 and produce a model based on vigor, DBH, bark splits, and a mortality threshold probability of 0.65 and output would include probability of mortality, a decision of mortality (1 or 0), and when mortality would occur (year).
FSMM(tree10000, type="vigor", threshold="0.65", year=TRUE)
Clark, RE, KN Boyes, LE Morgan, AJ Storer, and JM Marshall. 2015. Development and assessment of ash mortality models in relation to emerald ash borer infestation. Arboriculture & Urban Forestry 41, 270-278. https://doi.org/10.48044/jauf.2015.025