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Plot a species' growth curve against its references

plot_growth_calibration.Rd

Reproduces the layout of the source parameterization figures: the fitted LANDIS-II trajectory in black, the ICH-SORTIE reference in dark grey, the TIPSY yield curve in purple, and ground-plot observations coloured by BEC subzone and shaped by sample-establishment type.

Usage

plot_growth_calibration(
  species,
  curve,
  reference,
  x_max = NULL,
  mature_window = c(100L, Inf),
  density = FALSE,
  density_bins = 34L,
  density_points_max = 150L
)

Arguments

species

Character. Modelled species code.

curve

A tibble with age and aboveground_c_mg_ha.

reference

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

x_max

Numeric or NULL. Upper age limit for the panel. NULL (the default) extends to the last age present in the data, so a longer run is never silently clipped.

mature_window

Numeric length-2. Fitting window to shade; NULL to omit.

density

Logical. Draw the ground-plot cloud as a WEIGHTED hexagonal density instead of one point per plot, with individual points kept only for the best-matched plots. Off by default, because it is worth it only where the cloud is dense enough to be unreadable as points: a species with a hundred plots gets a sparse, blocky panel that says less than the points did. Requires the 'hexbin' package.

density_bins

Integer. Number of bins across the x range of the hexagonal grid when density is TRUE.

density_points_max

Integer. When density is TRUE, how many of the best-matched plots stay drawn individually over the density. A COUNT rather than a fraction of the maximum weight, because a fraction does not control the number drawn: the weight distribution differs by species, and at 60% of maximum one species keeps 989 plots where another keeps 65. Requires a plot_weight column; without one every plot counts equally.

Value

A ggplot.

Details

Deciduous plots are shown by their RAW leading species, because cottonwood and birch are modelled as trembling aspen but observed separately.

The fitting window is shaded, so a reviewer can see at a glance which part of the curve the fit statistic is actually responding to.

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_curves(), 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_candidate(), plot_growth_factorial_sensitivity(), plot_growth_structures(), read_growth_scoring(), read_landscape_cohort_structures(), scale_linetype_growth_reference(), write_growth_review_bundle()