Package: ambre 2.1.2

ambre: Multi-Barrier Approach for Water Reuse Risk Assessment

Provides a Quantitative Microbial Risk Assessment (QMRA) framework for the reuse of treated wastewater in agricultural irrigation. Following a multi-barrier approach, the package simulates pathogen inflow and removal along a treatment train, estimates human exposure, and computes health risk indicators such as infection probability, illness probability, and Disability-Adjusted Life Years (DALYs). It also supports an economic analysis of the treatment scenarios considered. For more details see <doi:10.36904/20240595>.

Authors:Flora Girard [aut, cre], Nicolas Forquet [ctb], Arthur Bréant [ctb], Colin Fay [ctb]

ambre_2.1.2.tar.gz
ambre_2.1.2.zip(r-4.7-any)ambre_2.1.2.zip(r-4.6-any)ambre_2.1.2.zip(r-4.5-any)
ambre_2.1.2.tgz(r-4.6-any)ambre_2.1.2.tgz(r-4.5-any)
ambre_2.1.2.tar.gz(r-4.7-any)ambre_2.1.2.tar.gz(r-4.6-any)
ambre_2.1.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ambre/json (API)

# Install 'ambre' in R:
install.packages('ambre', repos = c('https://floragirard.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

3.60 score 479 downloads 69 exports 67 dependencies

Last updated from:bd2cb35265. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK217
source / vignettesOK225
linux-releaseOK200
macos-releaseOK289
macos-oldrelOK214
windows-develOK241
windows-releaseOK252
windows-oldrelOK245
wasm-releaseOK114

Exports:annual_costcollective_treatment_cost_calculationcreate_random_distributioncreate_scenariocreate_scenario_from_dfdalys_calculationdistribution_repeaterdr.betapoissondr.expoenumerationfinal_dose_calculationgenerate_random_valuesget_exposure_value_or_stopget_infection_probget_risk_totalget_scheme_events_wideget_tbl_riskget_treatment_dataillness_probability_calculationinfection_probability_calculationinflow_concentrationinflow_concentration_custominitial_dose_calculationirrigation_need_calculationpercentage_irrigation_needperimeter_calculationplot_comparison_qmra_initial_vs_supplementary_processesplot_dalysplot_infection_probabilityplot_inflowplot_logreductionplot_volumesprocess_cost_calculationquery_barrierquery_cropquery_crop_heightquery_exp_pathquery_frequencyquery_irrigation_needquery_matrixquery_pathogenquery_popquery_volumeregulation_matrix_concentrationregulation_matrix_logretrieve_specific_barrierrun_economic_analysisrun_qmra_customrun_qmra_initial_situationrun_qmra_learning_caserun_qmra_supplementary_processsimulate_exposuresimulate_inflowsimulate_treatmenttotal_area_calculationtotal_investment_costtotal_irrigation_needupdate_concentrationupdate_frequencyupdate_frequency_with_desired_valueupdate_logreduction_decayupdate_logreduction_pathupdate_logreduction_specific_barrierupdate_monte_carloupdate_pathogenupdate_treatment_schemeupdate_volumeupdate_volume_with_desired_valuewater_price

Dependencies:base64encbslibcachemcellrangerclicolorspacecowplotcpp11crayondigestdplyrEnvStatsevaluatefarverfastmapfontawesomeformattablefsgenericsggplot2gluegtablehighrhmshtmltoolshtmlwidgetsisobandjquerylibjsonliteknitrlabelinglifecyclemagrittrMASSmemoisemimenortestpillarpkgconfigplyrprettyunitsprogresspurrrR6rappdirsRColorBrewerRcppreadxlrematchrlangrmarkdownS7sassscalessfsmiscstringistringrtibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunyaml

Costing a reuse scenario
The three levers | What the model computes | Run it | Getting the underlying numbers | Caveats worth flagging | Adapting the cost base
Rendered frome-economic-analysis.Rmdusingknitr::rmarkdown

Last update: 2026-09-04
Started: 2026-09-04

Get started with ambre
What ambre does, and for whom | Installation and the bundled example data | The scenario object | Your first run | Reading the four figures | Other figures | Where to go next
Rendered froma-get-started.Rmdusingknitr::rmarkdown

Last update: 2026-09-04
Started: 2026-09-04

Initial situation VS New scenario
Treatments and field barriers live in one table | How the Excel prepares two trains | The switch is a single line | Run and overlay the two strategies | Scope and current limits
Rendered fromb-initial-vs-new-scenario.Rmdusingknitr::rmarkdown

Last update: 2026-09-04
Started: 2026-09-04

Interpreting risk against the WHO target
The objective | From an event to a year | Why the result is a distribution | A worked example with the numbers | Reading the DALY plot | Concluding
Rendered fromd-interpreting-risk.Rmdusingknitr::rmarkdown

Last update: 2026-09-04
Started: 2026-09-04

Preparing your input file
Anatomy of the file | Validity bounds and empty cells | The allowed values | Known pitfalls | Validate your file
Rendered fromc-input-file.Rmdusingknitr::rmarkdown

Last update: 2026-09-04
Started: 2026-09-04

The config_ambre database
Overview: 8 slots, 16 CSVs | The entity-relation keys | The barrier families | Anatomy of a distribution | Customizing the database for your case | Known pitfalls | See also
Rendered fromh-config-ambre.Rmdusingknitr::rmarkdown

Last update: 2026-09-04
Started: 2026-09-04

The Monte-Carlo engine
Two dimensions: repeats and events | The distribution catalog | From min/max to a spread | A special case worth knowing | Why barrier credits add up | Reproducibility
Rendered fromg-monte-carlo-engine.Rmdusingknitr::rmarkdown

Last update: 2026-09-04
Started: 2026-09-04

What-if: calibrating exposure
How exposure is set by default | Inspect the base numbers | Override for a what-if | Modelling management measures | A mini sensitivity study | Technical notes and caveats
Rendered fromf-what-if-exposure.Rmdusingknitr::rmarkdown

Last update: 2026-09-04
Started: 2026-09-04

Readme and manuals

Help Manual

Help pageTopics
Annual costannual_cost
Collective treatment cost calculationcollective_treatment_cost_calculation
config_ambreconfig_ambre
Create random distributioncreate_random_distribution
Create Exposure Scenariocreate_scenario
Create Exposure Scenario from a data.framecreate_scenario_from_df
Dalys calculationdalys_calculation
Helper function: distribution repeaterdistribution_repeater
Dose-response model: beta-poissondr.betapoisson
Dose-response model: exponentialdr.expo
Enumerate Elementsenumeration
Final dose calculationfinal_dose_calculation
Create random distribution based on configuration filegenerate_random_values
Get exposure value or stopget_exposure_value_or_stop
Get infection probability valuesget_infection_prob
Get risk totalget_risk_total
Calculate Wide-Format Treatment Scheme Eventsget_scheme_events_wide
Get table riskget_tbl_risk
Simulate treatment data for pathogen processesget_treatment_data
Illness probability calculationillness_probability_calculation
Infection probability calculationinfection_probability_calculation
Inflow concentrationinflow_concentration
Inflow concentration custominflow_concentration_custom
Initial dose concentrationinitial_dose_calculation
Irrigation need calculationirrigation_need_calculation
Percentage irrigation needpercentage_irrigation_need
Perimeter calculationperimeter_calculation
Plot comparison QMRA calculation with initial vs supplementary processesplot_comparison_qmra_initial_vs_supplementary_processes
Plot dalysplot_dalys
Plot infection probabilityplot_infection_probability
Plot inflow concentrationplot_inflow
Plot log reductionplot_logreduction
Plot volumeplot_volumes
Barrier Cost Calculationprocess_cost_calculation
Barrier Queryquery_barrier
Crop Queryquery_crop
Query crop heightquery_crop_height
Path Queryquery_exp_path
Query frequencyquery_frequency
Query irrigation needquery_irrigation_need
Query Matrixquery_matrix
Pathogen Queryquery_pathogen
Population Queryquery_pop
Query volumequery_volume
Concentration reduction matrix calculationregulation_matrix_concentration
Log reduction matrix calculationregulation_matrix_log
Apply barriers' specific log-reduction to a configretrieve_specific_barrier
Run economic analysisrun_economic_analysis
Run QMRA customrun_qmra_custom
Run QMRA on initial situationrun_qmra_initial_situation
QMRA on learning caserun_qmra_learning_case
Run QMRA on addition processrun_qmra_supplementary_process
Simulate: exposuresimulate_exposure
Simulate: inflowsimulate_inflow
Simulate Treatmentsimulate_treatment
Total areatotal_area_calculation
Total investment costtotal_investment_cost
Total irrigation needtotal_irrigation_need
Update concentration with desired valueupdate_concentration
Frequency updateupdate_frequency
Updated frequency with desired valueupdate_frequency_with_desired_value
Update log reduction for decay barrierupdate_logreduction_decay
Update log reduction for specific pathupdate_logreduction_path
Update log reduction with specific valueupdate_logreduction_specific_barrier
Update monte carlo valueupdate_monte_carlo
Pathogen updateupdate_pathogen
Update treatment schemeupdate_treatment_scheme
Volume updateupdate_volume
Update volume with desired valueupdate_volume_with_desired_value
Water chargewater_price