Skip to contents

Resolve site, patch, and year indices for FINN inputs

Source: R/createInputs.R
resolveSiteIDs.Rd

Joins tree, environment, and observation tables; assigns integer indices for site, patch, period; standardizes species coding; and returns aligned data plus optional initial cohorts.

Usage

resolveSiteIDs(tree_dt, env_dt, obs_dt, createInitCohorts = T)

Arguments

tree_dt

data.table with tree-level data including siteName, patchName, year, species_name, dbh, status, living, and optional trees.

env_dt

data.table with environment data including siteName and year.

obs_dt

data.table with observations including siteName, patchName, year, species_name, and stand metrics (ba, dbh, trees, growth, mort, n_at_risk, n_died, reg), as returned by makeObsData.

createInitCohorts

logical. If TRUE, build FINN initial cohorts from trees with living == TRUE and year == 1. Default TRUE.

Value

A list with:

  • siteID_dt: site/patch/year index map.

  • tree_dt: tree table with indices and standardized species.

  • env_dt: environment table with indices.

  • obs_dt: site-aggregated observations by species.

  • obs_dt_patches: patch-level observations by species.

  • species_dt: species lookup (species, species_name).

  • initCohorts (optional): FINN CohortMat object.

  • initCohort_dt (optional): trees used to build cohorts.