Summarise supported diagnostics without fabricating missing properties

Usage

rri_property_scores(
  res,
  rec = NULL,
  soil_df = NULL,
  eac_col = "EAC",
  edc_col = "EDC",
  humic_col = NULL,
  connectivity_method = "cross_domain_magnitude",
  H_weight = 0.5,
  I_weight = 0.5,
  forcing_window = NULL
)

Arguments

res: RRI result.
rec: Optional recovery table.
soil_df: Optional soil capacity measurements.
eac_col, edc_col, humic_col: Capacity-related columns.
connectivity_method: Association or network summary.
H_weight, I_weight: Memory-diagnostic weights.
forcing_window: Optional timescale for the recovery speed score.

Value

Scores and a provenance table. Unavailable properties stay NA. Capacity here is an oxidative-oriented feature composite, Connectivity an association/topology descriptor, Kinetics a recovery-speed descriptor, and Memory a persistent-displacement descriptor. None proves the named mechanism.

Which inputs each property needs

Only Connectivity is derived from res alone. The other three require an additional argument, and are returned as NA with method "unavailable" when it is absent:

Capacity needs soil_df containing the columns named by eac_col and edc_col. Passing only res and rec is the usual reason Capacity comes back NA.
Kinetics and Memory need rec, the table returned by rri_recovery_metrics().

A message names any missing input. NA here means "not supplied", never "measured and found to be zero".

Examples

sim <- simulate_redox_holobiont(
  n_plot = 2, n_depth = 2, n_plant = 2, n_time = 40, p_micro = 10,
  seed = 2026
)
res <- suppressWarnings(rri_pipeline_st(
  ROS_flux = sim$ROS_flux, Eh_stability = sim$Eh_stability,
  micro_data = sim$micro_data, id = sim$id
))
rec <- rri_recovery_metrics(
  res = res, id = sim$id, time_col = "time",
  group_cols = c("plot", "depth", "plant_id"),
  perturb_start = 12, perturb_end = 22
)

## All four properties available: soil_df supplies Capacity, rec supplies
## Kinetics and Memory.
full <- rri_property_scores(res, rec = rec, soil_df = sim$soil_data)
full$property_table
#>       property     score                                         method
#> 1     Capacity 0.5188017 Oxidative-oriented feature composite; not Cacc
#> 2 Connectivity 0.5555565                         cross_domain_magnitude
#> 3     Kinetics 0.5000000                 Cohort-relative recovery speed
#> 4       Memory 0.1657948   Loop-area/persistent-displacement diagnostic
#>   available
#> 1      TRUE
#> 2      TRUE
#> 3      TRUE
#> 4      TRUE

## Omitting soil_df leaves Capacity unavailable, and says so.
partial <- rri_property_scores(res, rec = rec)
#> Unavailable property returned as NA.
#>   Capacity: supply `soil_df` with EAC/EDC columns (see `eac_col`, `edc_col`)
partial$property_table
#>       property     score                                       method available
#> 1     Capacity        NA                                  unavailable     FALSE
#> 2 Connectivity 0.5555565                       cross_domain_magnitude      TRUE
#> 3     Kinetics 0.5000000               Cohort-relative recovery speed      TRUE
#> 4       Memory 0.1657948 Loop-area/persistent-displacement diagnostic      TRUE