Package: kwb.qmra 0.3.0

Michael Rustler

kwb.qmra: QMRA (quantitative microbial risk assessment)

QMRA for water supply systems.

Authors:Michael Rustler [aut, cre], Hauke Sonnenberg [aut], Wolfgang Seis [ctb, rev], Ralf Junghanns [ctb], Kompetenzzentrum Wasser Berlin gGmbH [cph], AquaNES [fnd], DEMOWARE [fnd], Smart-Control [fnd]

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kwb.qmra.pdf |kwb.qmra.html✨
kwb.qmra/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/kwb-r/kwb.qmra/issues

Datasets:
  • config_default_json - Config_dummy_json: dummy configuration for kwb.qmra::opencpu_simulate_risk() in JSON format
  • config_dummy_json - Config_default_json: default configuration developed by Christoph Sprenger for kwb.qmra::opencpu_simulate_risk() in JSON format
  • risk_dummy_json - Risk_dummy_json: example risk_json object returned by kwb.qmra::opencpu_simulate_risk

On CRAN:

project-aquanesproject-demowareproject-smartcontrolqmraqmra-webapp-backend-engine

40 exports 4 stars 0.61 score 91 dependencies 21 scripts

Last updated 3 years agofrom:9e096057da. Checks:OK: 1 ERROR: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 27 2024
R-4.5-winERRORAug 27 2024
R-4.5-linuxERRORAug 27 2024
R-4.4-winERRORAug 27 2024
R-4.4-macERRORAug 27 2024
R-4.3-winERRORAug 27 2024
R-4.3-macERRORAug 27 2024

Exports:%>%backcalc_infectionRisk_perDaycalc_health_riskcalc_infection_riskconfig_readconfig_writeconfig_write_dummycreate_random_distributiondefault_maxdefault_mindistribution_repeaterdr.betapoissondr.db_downloaddr.db_modeldr.expogenerate_random_valuesget_percentileopencpu_config_readopencpu_simulate_riskplot_doseresponseplot_effluentplot_event_dalysplot_event_doseplot_event_exposureplot_event_illnessProbplot_event_infectionProbplot_event_volumeplot_inflowplot_reductionplot_total_dalysplot_total_illnessProbplot_total_infectionProbpoisson_dosereport_workflowrun_appsimulate_exposuresimulate_inflowsimulate_risksimulate_treatmentwho_getTreatment

Dependencies:askpassbase64encbitbit64bslibcachemcellrangerclicliprcolorspacecommonmarkcpp11crayoncurldigestdplyrEnvStatsevaluatefansifarverfastmapfontawesomefsgenericsggplot2gluegtablehighrhmshtmltoolshttpuvhttrisobandjquerylibjsonliteknitrkwb.utilslabelinglaterlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmenortestopensslpillarpkgconfigplyrprettyunitsprogresspromisespurrrR6rappdirsRColorBrewerRcppreadrreadxlrematchrlangrmarkdownrvestsassscalesselectrsfsmiscshinysourcetoolsstringistringrsystibbletidyrtidyselecttinytextzdbutf8vctrsviridisLitevroomwithrxfunxml2xtableyaml

Dose-response modelling

Michael Rustler

Rendered fromdoseresponse.Rmdusingknitr::rmarkdownon Aug 27 2024.

Last update: 2021-02-22
Started: 2016-09-15

General workflow

Michael Rustler

Rendered fromgeneral.Rmdusingknitr::rmarkdownon Aug 27 2024.

Last update: 2018-01-17
Started: 2018-01-17

Inflow: Test Random Distributions

Michael Rustler

Rendered fromtest_random_distributions_inflow.Rmdusingknitr::rmarkdownon Aug 27 2024.

Last update: 2019-02-21
Started: 2019-02-21

Installation

Michael Rustler

Rendered frominstallation.Rmdusingknitr::rmarkdownon Aug 27 2024.

Last update: 2021-02-22
Started: 2018-01-16

Usage (Log10 Norm Inflow)

Michael Rustler

Rendered fromusage_log10_norm_inflow.Rmdusingknitr::rmarkdownon Aug 27 2024.

Last update: 2021-02-22
Started: 2019-02-12

Usage (Log10 Uniform Inflow)

Michael Rustler

Rendered fromusage_log10_uniform_inflow.Rmdusingknitr::rmarkdownon Aug 27 2024.

Last update: 2021-02-22
Started: 2019-02-12

Usage (Uniform Inflow)

Michael Rustler

Rendered fromusage.Rmdusingknitr::rmarkdownon Aug 27 2024.

Last update: 2021-02-22
Started: 2018-01-16

Web-app development with OpenCpu

Michael Rustler

Rendered fromweb_app.Rmdusingknitr::rmarkdownon Aug 27 2024.

Last update: 2021-02-22
Started: 2018-05-29

Readme and manuals

Help Manual

Help pageTopics
Backcalculate risk: infection (using optimise() function)backcalc_infectionRisk_perDay
Risk calculation: healthcalc_health_risk
Risk calculation: infectioncalc_infection_risk
config_dummy_json: dummy configuration for kwb.qmra::opencpu_simulate_risk() in JSON formatconfig_default_json
config_default_json: default configuration developed by Christoph Sprenger for kwb.qmra::opencpu_simulate_risk() in JSON formatconfig_dummy_json
Config: read configurationconfig_read
Config: create configurationconfig_write
Config: create dummy configurationconfig_write_dummy
Create random distributioncreate_random_distribution
Default Maxdefault_max
Default Mindefault_min
Helper function: distributon repeaterdistribution_repeater
Dose-response model: beta-poissondr.betapoisson
Download dose-response model database from QMRAwikidr.db_download
Generate table with different doses for dr.db_download()dr.db_model
Dose-response model: exponentialdr.expo
Create random distribution based on configuration filegenerate_random_values
Helper function: get percentileget_percentile
OpenCPU wrapper: import config from CSV and convert to JSONopencpu_config_read
OpenCPU wrapper: run risk calculation and convert results to JSON formatopencpu_simulate_risk
plot reductionplot_doseresponse
plot effluentplot_effluent
plot dalys_per_eventplot_event_dalys
plot dose per eventplot_event_dose
plot exposure per eventplot_event_exposure
plot illness probabilityplot_event_illnessProb
plot infection probabilityplot_event_infectionProb
plot volume per eventplot_event_volume
plot inflowplot_inflow
plot reductionplot_reduction
plot total DALYsplot_total_dalys
plot total illness probabilityplot_total_illnessProb
plot total infection probabilityplot_total_infectionProb
Helper function: poisson distribution based on exposure per eventpoisson_dose
Create report (not working for "shiny" reports)report_workflow
risk_dummy_json: example risk_json object returned by kwb.qmra::opencpu_simulate_risk()risk_dummy_json
Run shiny apprun_app
Simulate: exposuresimulate_exposure
Simulate: inflowsimulate_inflow
Simulate: risksimulate_risk
Simulate: treatmentsimulate_treatment
Treatment: get WHO reductionswho_getTreatment