This project presents a selection of the scripts and results associated with the paper titled "Quantification of norovirus internalization in lettuce from irrigation water and associated health risk ". The contents are summarized below :
| File | Description |
|---|---|
| dicaprio_leaf_all.csv | Contains leaf NoV load data from DiCaprio et. al (2012) , Fig 8C extracted from the image using WebPlotDigitizer. First column has labels and second column the values. Row 1 is mean log10 load without RNASE. Row 2 is mean log10 load without RNASE + std. dev. of log10 load without RNASE. Row 3 is mean log10 load with RNASE. Row 2 is mean log10 load with RNASE + std. dev. of log10 load without RNASE. Subsequent rows proceed in the same order for the remaining time points. |
| dicaprio_root_all.csv | Contains root NoV load data from DiCaprio et. al (2012) , Fig 8A extracted from the image using WebPlotDigitizer. First column has labels and second column the values. Row 1 is mean log10 load without RNASE. Row 2 is mean log10 load without RNASE + std. dev. of log10 load without RNASE. Row 3 is mean log10 load with RNASE. Row 2 is mean log10 load with RNASE + std. dev. of log10 load without RNASE. Subsequent rows proceed in the same order for the remaining time points. |
| hnv_fwater_dicaprio.csv | Contains feedwater NoV load data from DiCaprio et. al(2012), Fig 5. First column is the time points, second column is the log10 load. |
| irrigation.mat | Binary array (0 or 1) with 1s on the days lettuce is irrigated from Gallado et. al (1996), Fig 3. |
| secon.mat | NoV concentration (genome/mL) in secondary effluent used for irrigation, from Lim and Jiang (2016). |
| transpiration_gallardo.csv | Transpiration from Gallardo et. al (1996), Fig 3. |
This contains the scripts which utilize functions from the directory funcs to carry out different computations. Some of them read parameters from a coresponding text file and these are listed below :
| Filename | Description | Parameter filename |
|---|---|---|
| annrisk.m | Compute annual risk from daily risk. | - |
| consump_samples.m | Sample for consumption and bodyweight. | - |
| fitHydroponic.m | Fit data from DiCaprio et. al (2012) to hydroponically grown lettuce. | deparamlist.txt |
| getmodelopsH.m | Output hydroponic model simulation values. | moparamlist.txt |
| ppdH2.m | Find posterior prediction intervals for hydroponic lettuce. | ppdparams2.txt |
| riskH4.m | Daily risk of hydroponic lettuce. | rparamlistH4.txt |
| risklandscape1o3.m | Compute risk for range of values of attach-detach kinetic constants. | rlparams.txt |
| scaller2o3.m | Compute risk for soil grown lettuce. | sparams2o3.txt |
| calc_hypergeom.nb* | Compute the risk for the Hypergeometic model | - |
* Mathematica notebook
Detailed descriptions and comments can be found inside these files. Help can also be viewed for these files in the MATLAB console in the usual way. E.g, for annrisk.m, typing:
>> help annriskin the MATLAB console will print:
annrisk Annual risk from daily risk.
Computes distributions of annual risk of infection and annual disease burden of hydroponic/soil grown lettuce when supplied the daily risk distribution.
Additionally this directory also contains text files that the scripts read parameters from. The parameters are defined in a separate file to permit compilation of MATLAB code using the mcc command.
The results directory has the .mat files generated by the scripts. These are then used by other scripts or plotting functions. Each filename is prepended with a serial number for unique identification. No two files share the same serial number. These files described below :
| Filename | Generating script | Parameters |
|---|---|---|
| 1182236_DEMC_firsto_20000g32p0lb100ub30F0lam.mat | fitHydroponic.m | 20000,32,32,0.3,0,-9,6,2,1,1,1,1,0 |
| 1182237_DEMC_adscnt_20000g32p0lb100ub30F0lam.mat | fitHydroponic.m | 20000,32,32,0.3,0,-9,6,2,2,1,1,1,0 |
| 1182754_1182236_10000_modelopsH.mat | getmodelopsH.m | 20000 0.5 1182236_DEMC_firsto_20000g32p0lb100ub30F0lam.mat 6 32 |
| 1182755_1182237_10000_modelopsH.mat | getmodelopsH.m | 20000 0.5 1182237_DEMC_adscnt_20000g32p0lb100ub30F0lam.mat 6 32 |
| 2208542_s2o3_1182237_adscnt_10000.mat | scaller2o3.m | 1182237_DEMC_adscnt_20000g32p0lb100ub30F0lam.mat 6 8 10000 1 1 |
| 2208555_s2o3_1182237_adscnt_10000.mat | scaller2o3.m | 1182237_DEMC_adscnt_20000g32p0lb100ub30F0lam.mat 6 8 10000 6 6 |
| 2703562_1182236_firsto_10000sa10000bi6ouH4.mat* | riskH4.m | 10000 0.5 1182236_DEMC_firsto_20000g32p0lb100ub30F0lam.mat 1182754_1182236_10000_modelopsH.mat 6 10 2 800 8000 80000 |
| 2703562_1182237_firsto_10000sa10000bi6ouH4.mat* | riskH4.m | 10000 0.5 1182237_DEMC_adscnt_20000g32p0lb100ub30F0lam.mat 1182755_1182237_10000_modelopsH.mat 6 10 2 800 8000 80000 |
| 2703562_1182237_firsto_10000sa10000bi6ouH4_hyp.mat | calc_hypergeom | - |
| consumpsamp2.mat | consump_samples.m | - |
* See sparams2o3.txt inside `./scripts/`` for exact format.
This directory has auxiliary code required by the main scripts. It has the following files.
| Filename | Description |
|---|---|
| bpv.m | Vectorized beta-Poisson dose-response model. |
| DE_MC.m | Differential Evolution Markov Chain (ter Braak, 2006) |
| fp.m | Vectorized fractional Poisson dose-response model. |
| hyd_load_data.m | Load data for hydroponic lettuce |
| remout_simple.m | Naive outlier removal from a DE/DEMC solset object. |
| smodel2o1.m | Model for lettuce grown in the soil. |
| soil_load_data.m | Load data for soil lettuce |
| sse_water.m | Objective function value for a given set of parameters. |
| wmodel4o1.m | Model for lettuce grown hydroponically. |
Detailed comments are seen inside each file. Similar to scripts,help can be used. For e.g,
>> help bpvin the MATLAB console will print:
bpv Vectorized beta-Poisson dose-response model.
C = bpv(dose, alpha, beta) computes probability of infection assuming a beta-Poisson dose-response model. dose can be a vector. alpha and beta must be scalars.
If you use our code or part of it in your work, please cite the paper below:
Chandrasekaran, S., & Jiang, S. C. (2018). A dynamic transport model for quantification of norovirus internalization in lettuce from irrigation water and associated health risk. Science of The Total Environment, 643, 751–761. http://doi.org/10.1016/j.scitotenv.2018.06.158