Standardise inflow variable names and units for AEME

Attempts to match column names in an inflow data frame to AEME standard variable names using guess_aeme_vars(), then detects the likely input units of each variable from its values and converts to the units expected by the package (GLM-AED conventions).

Usage

standardise_inflow(
  inflow,
  model_controls = NULL,
  inf_vars = NULL,
  aeme_time = NULL,
  inflow_name = "inflow",
  model = NULL,
  pot_inf_vars = NULL,
  verbose = TRUE
)

Arguments

inflow: data.frame; inflow data with a time or Date column and one or more inflow variable columns.
model_controls: data.frame; model controls table containing at minimum columns var_aeme and inf_default. Used to fill missing state variables with default values. If NULL (default), the missing-variable fill step is skipped.
inf_vars: character; vector of required inflow state variable names (e.g. from model_controls$var_aeme). Variables in inf_vars that are absent from inflow will be filled with values from model_controls$inf_default. Ignored when model_controls is NULL.
aeme_time: named list or object; passed directly to check_time(). If NULL (default), the time-coverage check is skipped.
inflow_name: character(1); human-readable label for this inflow stream, used in check_time() messages (e.g. "inflow-tributary_1"). Ignored when aeme_time is NULL.
model: character(1); model identifier passed to check_time(). Ignored when aeme_time is NULL.
pot_inf_vars: character; column allowlist used for the final dplyr::select() step. Defaults to NULL, which retains all columns. Typical value: c("time", "HYD_flow", inf_vars, "model").
verbose: logical; if TRUE (default), emit cli_inform messages describing each detected unit conversion applied.

Value

The input data frame with column names remapped to AEME standard names, values converted to AEME standard units, missing state variables filled with defaults, time coverage validated, and columns trimmed to pot_inf_vars (when supplied). Columns that could not be matched are retained unchanged with a warning. A warning is also emitted if required variables (flow, temp, salt) are absent after renaming.

AEME standard inflow variables and units

Variable	Name	Unit	Required
Flow	`flow`	m3/day	Yes
Water temperature	`temp`	degC	Yes
Salinity	`salt`	PSU	Yes
Dissolved oxygen	`OXY_oxy`	mmol/m3	No
Phosphate-P	`PHS_frp`	mmol/m3	No
Dissolved organic P	`OGM_dop`	mmol/m3	No
Particulate organic P	`OGM_pop`	mmol/m3	No
Particulate inorganic P	`PHS_frp_ads`	mmol/m3	No
Ammoniacal nitrogen	`NIT_amm`	mmol/m3	No
Nitrate-N	`NIT_nit`	mmol/m3	No
Dissolved organic N	`OGM_don`	mmol/m3	No
Particulate organic N	`OGM_pon`	mmol/m3	No
Dissolved organic C	`OGM_doc`	mmol/m3	No
Particulate organic C	`OGM_poc`	mmol/m3	No
Dissolved inorganic C	`CAR_dic`	mmol/m3	No
Silica	`SIL_rsi`	mmol/m3	No
Suspended solids 1	`NCS_ss1`	g/m3	No
Suspended solids 2	`NCS_ss2`	g/m3	No
pH	`CHM_ph`	-	No

Unit detection logic

Nutrient concentrations (N, P, C fractions) are expected in mmol/m3. Detection thresholds are based on comparison of observed value ranges against the example inflow data distributed with AEME:

N fractions (NIT_amm, NIT_nit, OGM_don, OGM_pon): mmol/m3 typically 0-10. Median > 20 assumed to be mg/L and divided by the molar mass of N (14.007 g/mol).
P fractions (PHS_frp, OGM_dop, OGM_pop, PHS_frp_ads): mmol/m3 typically 0-5. Median > 10 assumed to be mg/L and divided by the molar mass of P (30.974 g/mol).
C fractions (OGM_doc, OGM_poc): mmol/m3 typically 0-100. Median > 100 assumed to be mg/L and divided by the molar mass of C (12.011 g/mol).
Dissolved inorganic C (CAR_dic): mmol/m3 typically 500-1000. Median > 2000 assumed to be mg/L.
Dissolved oxygen (OXY_oxy): mmol/m3 typically 200-400. Median < 50 assumed to be mg/L and multiplied by 1000/32 (molar mass of O2).
Silica (SIL_rsi): mmol/m3 typically 1-50. Median > 100 assumed to be mg/L and divided by molar mass of SiO2 (60.084).
Temperature (temp): degC expected. Median > 100 assumed to be Kelvin.