Function reference • qraLm

qraLm

R package for quantitative risk assessment of Listeria monocytogenes in food

qraLm qraLm-package: qraLm: Functions to develop quantitative risk assessment for Listeria monocytogenes in foods

Dose-Response Models

An updated DR model was developed to take into account class of strain virulence and age-sex group, as a surrogate for susceptibility, as determined by underlying health conditions

DRForModel(): Dose-response model function for the qraLm models

RiskEurope(): Risk Europe

Summary and Plots

Functions to summarise and plot the Monte-Carlo simulation results

plotLotsECDF.qraLm(): plotLotsECDF Generic plot function to plot the ECDF

plotRisk.qraLm(): Generic plot function for risk per serving

printMC.qraLm(): Generic print function to print the MC results

summaryLot.qraLm(): summaryLot Generic print function to print the between lots MC summary statistics

summaryServings.qraLm(): summaryServings Generic function to print the within lots (between servings) MC summary statistics

summaryUnits.qraLm(): summaryUnits Generic function to print the within lots (between units) MC summary statistics

summaryRiskLot.qraLm(): summaryRiskLot generic function to print the risk summary statistics at lot level

summaryRiskServings.qraLm(): summaryRiskServings generic function to print the risk summary statistics

plotLotRisk.qraLm(): Generic plot function for risk

plotUnitsECDF.qraLm(): plotUnitsECDF Generic plot function to plot the ECDF

printPrevContUnits.qraLm(): printPrevContUnits function to print the prevalence of contaminated units

Generate Data

Functions to generate the simulated data

LotGen(): Generation of contaminated lots

Lot2LotGen(): Generation of contaminated lots with variability in prevalence and concentration

Frozen Vegetables

The stages represented in the model considered pre-conditioned vegetables as the raw material and included processing (blanching and packaging), environmental contamination, and consumer handling practices (defrosting and cooking)

fvBlanching(): Effect of blanching on L. monocytogenes in processed vegetables

fvPartitioningCC(): Cross-contamination during freezing/packaging and partitioning into packed units

fvCooking(): Microbial reduction due to cooking at home

fvDefrost(): Defrosting of frozen vegetables at home

fvReductionPostpack(): Effect of a potential intervention step post-packaging

fvPortioning(): Portioning of the contents of a pack at home

fvTesting() sfTesting(): Application of a testing regime for L. monocytogenes in a sample of food units from a lot

Diced RTE Cantaloupe

The model considered a full production-to-consumption chain representing pre-harvest, harvest and storage, cleaning and washing, processing, cold chain storage, and consumer handling practices

caGrowthBaranyi(): Growth of L. monocytogenes in cantaloupe flesh

caHomeRTE(): Storage of RTE diced cantaloupe packs at home

caRet2HomeRTE(): Transport of RTE diced cantaloupe packs from retail to home

caRetRTE(): Display of RTE diced cantaloupe packs at retail

caTrans2RetRTE(): Transport of RTE diced cantaloupe packs from the end of processing to retail

caBrush(): Cleaning cantaloupes by brushing

caHarvestCC(): Cross-contamination of cantaloupe rind by L. monocytogenes during harvest

caPartitioningCC(): Cross-contamination of cantaloupe during dicing and partitioning into packed units

caDicing(): Dicing of cantaloupe for preparation of RTE pre-cut cantaloupe

caFlumeTank(): Cantaloupe washing in flume tank

caFlumeTankCC(): Cantaloupe cross-contamination during washing in flume tank

caHoldingTime(): Holding time of cantaloupes post-harvest

caIrrig2rind(): Route of contamination of cantaloupe from irrigation water to rind

caPrimaryProduction(): Contamination of cantaloupe rind from soil and irrigation water

caSoil2rind(): Route of contamination of cantaloupe from soil to rind

caTesting(): Application of a testing regime for L. monocytogenes in a sample of RTE cantaloupe from a lot/sublot

Cold-smoked RTE Fish

The model considered a full production-to-consumption chain including primary processing, secondary processing, cold-chain, and consumer handling

sfGrowthLPD(): Growth of L. monocytogenes in raw fish

sfBrineORsaltCC(): Cross-contamination of fish fillets during brine injection or dry-salting

sfBriningCC(): Internal contamination of fish fillets during brine injection

sfSmearingCC(): External cross-contamination of fish fillets during smearing with salt, sugar or spices

sfMaceration(): Reduction of L. monocytogenes due to maceration of fish fillets with gravlax curing agents

sfSmoking(): Reduction of L. monocytogenes due to smoking brined or dry-salted fish

sfRawFishStorage(): Storage of raw fish (whole or fillets) during processing

sfSlicer(): Cross-contamination during slicing of raw fish or processed fillets

sfPackaging(): Packaging of slices of ready-to-eat seafood

fvTesting() sfTesting(): Application of a testing regime for L. monocytogenes in a sample of food units from a lot

sfCharacteristics(): Sampling of the RTE smoked fish characteristics

sfMejlholmDalgaard(): Secondary growth rate model of L. monocytogenes in RTE seafood

sfMejlholmDalgaardLAB(): Secondary growth rate model of Lactic Acid Bacteria (LAB) in RTE seafood

sfGrowthJameson(): Growth model of L. monocytogenes in RTE seafood including background flora competition

sfColdChain(): Cold chain logistics for ready-to-eat seafood

sfPortioning(): Portioning of the contents of a seafood pack at home

expandedjamesonC(): Integrate the growth model with Jameson effect

expandedjamesonC_set_params(): Set the parameters to integrate the growth model with Jameson effect

qraLmShiny

Shiny application for simulation

runExample(): Shiny application for qraLm package