# Forest Informed Neural Networks

## Documentation for package ‘FINN’ version 0.1.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

ALE | Accumulated local effect plots
apply_env_scaling | Apply stored z-standardization to environmental predictors
array2obsDF | Transform Arrays to Observation Data Table
averageConditionalEffects | Average conditional effects of a FINN model
BA_stand | Calculate the Basal Area of a Stand
BA_stem | Calculate the basal area of a tree given the diameter at breast height (dbh)
binomial_from_bernoulli | Draw binomial counts from per-trial Bernoulli probabilities
climateDF2array | Convert a climate data frame to a FINN environment array
CohortMat | Cohort Matrix Class
competition | Compute the fraction of available light (light) for each cohort based on the given parameters
compute_env_scaling | Learn z-standardization for environmental predictors
conditionalEffects | Conditional effects of a FINN model
createHybrid | Define a hybrid (deep-neural-network) demographic process for FINN
createProcess | Define a demographic process for FINN
dbh2ba | Convert DBH to basal area
feature_importance | Permutation feature importance for FINN demographic rates
finn | Forest Informed Neural Network
FINN.seed | Set Seed for Reproducibility in R and Torch
fit | Fit FINN
growth | Calculate growth
height | Calculate the height of a tree based on its diameter at breast height and an allometry parameter
makeInitCohorts | Make initial cohorts for FINN
makeObsData | Create observation data from trees
mortality | Mortality
np_runif | Generate random numbers from a uniform distribution
obsDF2arrays | Convert observation data frame to arrays
plot.FINNale | Plot ALE curves of a FINN model
pred2DF | Convert Prediction Arrays to Data Frames
predict.finn_class | Predict from a FINN model
regeneration | Calculate the regeneration of forest patches based on the input parameters
resolveSiteIDs | Resolve site, patch, and year indices for FINN inputs
rweibull_cohorts | Generate Cohorts Using Weibull Distribution
simulateForest | Simulate
summary.finn_class | Summarise a fitted FINN model