Make initial cohorts for FINN

This function prepares obs_df in the exact format expected by FINN::CohortMat$new() and calls it. The required long-table schema is:

• siteID integer index of sites \(1..S\).

• patchID integer index of patches within site \(1..P_s\).

• species integer species code \(1..sp\).

• dbh numeric DBH in cm (either exact or binned midpoints).

• trees integer count of trees in the cohort.

Usage

makeInitCohorts(
  init_trees,
  dbh_binsize = NULL,
  min_dbh = NULL,
  Nspecies,
  treeID_table = F,
  singleCohortTreeNames = NULL
)

Arguments

init_trees

data.table of initial trees with columns siteID, patchID, species, dbh, treeName; optional trees for pre-counted individuals.

dbh_binsize

numeric or NULL. Bin width in cm. If NULL, keep exact DBH.

min_dbh

numeric or NULL. Lower bound for binning. If NULL, uses min DBH.

Nspecies

integer. Number of species levels passed to sp.

treeID_table

logical. If TRUE, also return the cohort table used.

singleCohortTreeNames

character vector or NULL. Tree names excluded from binning and kept as single-tree cohorts.

Value

If treeID_table = FALSE, a FINN::CohortMat object. If TRUE, a list with:

• initCohort: the CohortMat object.

• init_trees: the obs_df passed to CohortMat$new().

Details

Aggregates initial trees into cohorts by DBH bins or exact DBH and constructs a FINN::CohortMat object.

Internally calls:

FINN::CohortMat$new(
  obs_df = <data.frame with columns siteID, patchID, species, dbh, trees>,
  dbh    = NULL,
  trees  = NULL,
  species= NULL,
  dims   = c(S, P, K),   # inferred from obs_df
  sp     = Nspecies,     # passed from argument
  device = "cpu"
)

Key fields of the resulting R6 object:

• dbh, trees, species: tensors per cohort.

• dims: integer vector c(S, P, K) for sites, patches, cohorts.

• sp: integer number of species.

• device: "cpu" or "cuda".

• dbh_r, trees_r, species_r: R arrays.

• obsDF2arrays: method converting obs_df into arrays.

See also

CohortMat