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Build one species' reference curves on a common age grid

growth_reference_curves.Rd

Everything the scorer needs, computed once per species rather than once per parameter combination: each reference series evaluated at the same ages, and each series' plateau level.

Usage

growth_reference_curves(
  reference,
  window,
  bin = 20L,
  plot_quantile = 0.5,
  min_plots = 50L,
  n_grid = 60L,
  use_tipsy = FALSE,
  use_vdyp = FALSE,
  site = NULL,
  weight = NULL
)

Arguments

reference

A data frame of reference observations, with columns source ("SORTIE", "TIPSY", "VDYP" or "Ground plots"), age and aboveground_c_mg_ha.

window

Numeric length-2. The fitting window.

bin, plot_quantile, min_plots

Ground-plot controls; min_plots is advisory and only sets plots_sparse. See growth_bin_observations() and read_growth_scoring().

n_grid

Integer. Number of ages in the common grid.

use_tipsy

Logical. Score against TIPSY as well.

use_vdyp

Logical. Score against VDYP as well. VDYP is the British Columbia Variable Density Yield Projection model, whose curves are natural (unmanaged) stand yields; it is a separate series from TIPSY, which projects MANAGED stands, because a natural-disturbance model wants the former and the distinction must not be lost in the outputs.

site

Optional column name identifying the sampling location of a ground-plot observation. Passed to growth_bin_observations(); when given, n_plots counts distinct locations rather than visits.

weight

Optional column name holding a per-observation climatic weight. Passed to growth_bin_observations(); see growth_climatic_weight().

Value

A list with ages, series, levels, n_plots, n_bins, plots_sparse.

Details

Interpolation uses rule = 1, so a series is NA outside its own age range and nothing is ever scored against an extrapolation of a reference that simply stops.

See also

Other growth calibration helpers: extract_landscape_cohort_structures(), growth_add_objective(), growth_auto_window(), growth_best_candidates(), growth_bin_observations(), growth_calibration_design(), growth_calibration_partition(), growth_calibration_work_root(), growth_climatic_distance(), growth_climatic_weight(), growth_expand_over_pseudo_species(), growth_factorial_ratio_grid(), growth_fitting_windows(), growth_identifiability(), growth_inflation_factor(), growth_mortality_onset_frac(), growth_plot_palette(), growth_pseudo_species_name(), growth_reference_inflection(), growth_score_fit(), growth_scoring_for(), growth_smooth_observations(), growth_structure_cell_curves(), growth_structure_cohort_table(), growth_structure_design(), growth_structure_summary(), growth_window_for(), plot_growth_calibration(), plot_growth_candidate(), plot_growth_factorial_sensitivity(), plot_growth_structures(), read_growth_scoring(), read_landscape_cohort_structures(), scale_linetype_growth_reference(), write_growth_review_bundle()