Package index • hydroSense

Example data

leachate_demo(): Synthetic leachate-impacted water-quality data (demo)

Leachate detection (LMF)

End-member mixing analysis to quantify the leachate-mixing fraction of a sample.

add_lmf(): Compute the Leachate Mixing Fraction (LMF) for water quality samples
to_meq(): Convert analyte concentrations to milliequivalents per litre

Chemistry imputation

Domain-agnostic Bayesian multivariate imputation of below-detection and missing analyte concentrations, plus deterministic co-analyte imputation.

fit_imputation_model(): Fit the Bayesian multivariate imputation model(s)
impute_group(): Declare an imputation group
leachate_impute_groups(): Leachate imputation-group preset
impute_chemistry(): Impute missing and BDL chemistry using a fitted imputation model
impute_coanalytes(): Impute missing normalisation co-analytes from the fitted chemistry PCA
bdl_cap_summary(): Inspect detection-limit cap activations from impute_chemistry()

Toxicity & single-substance PAF

Species sensitivity distributions and the potentially affected fraction for an individual analyte.

ssd_paf(): Estimate the fraction of species potentially affected at a concentration.
ssd_pct(): Quick point-estimate only (no CI, no bootstrapping).
ssd_hc50(): Return HC50 for use in Concentration Addition (msPAF).

Multi-substance PAF (msPAF)

Concentration- and response-addition mixture PAF with Added-Risk local background adjustment. Includes the static and temporal (contemporaneous) ARA reference paths.

mspaf_pipeline(): Run the full chronic msPAF pipeline end to end
add_mspaf(): Compute the Adjusted multi-substance PAF (msPAF) for water quality samples
mspaf_daily(): Continuous daily msPAF time series from interpolated grab chemistry
prepare_reference(): Prepare reference chemistry for msPAF background subtraction
fit_reference_model(): Fit a temporal reference model for contemporaneous ARA background subtraction
fit_target_model(): Fit a season-blind predictive model of the site impact
loo_anchor_coverage(): Leave-one-anchor-out coverage of the daily Kalman bands
ara_summary(): Retrieve per-cell ARA diagnostics from an add_mspaf() result
analyte_pafs(): Per-analyte PAF breakdown from add_mspaf()
summarise_draws(): Summarise a draw-carrier frame to posterior median and credible interval
draw_measurement_error(): Expand observed measurements into lognormal posterior-predictive draws

Water chemistry & normalisation

Bioavailability and physicochemical adjustments that bring measured concentrations to the SSD index condition.

correct_ammonia_ph_temp(): Correct total ammonia-N to the ANZG reference pH and temperature
derive_hardness(): Three-way reconciliation between Ca, Mg, and hardness
estimate_water_temp(): Estimate water temperature from air temperature measurements
get_silo_air_temp(): Fetch daily mean air temperature from SILO for an Australian location
get_silo_rainfall(): Fetch daily rainfall from SILO for an Australian location

Screening & temporal aggregation

Detection-frequency prescreening and chronic time-weighted averaging.

prescreen_analytes(): Pre-screen analytes by detection frequency
time_weighted_aggregate(): Time-weighted chronic aggregation for any long-format value column
expand_focal_dates(): Generate a sequence of focal dates for chronic msPAF computation