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Aflatoxin (AT) modelling project

The repository contains these folders:

Raw_data: here are the raw data files stored that where sent to me from Shannon McAmis R_data_wrangling: This folder contains an R project to clean the data provided by Shannon

PeanutAflatoxinProject

There are three different models to assess aflatoxin level in peanut.

Bowen (Auburn)

Objective

  • To develop a model to predict aflatoxin contamination in peanut in order to better manage a peanut crop to minimize this problem
  • To determine specific periods of temperature and moisture conditions prior to harvest that would define environments with high risk for aflatoxin contamination in peanuts

Details

  • Total aflatoxin concentrations (parts per billion, ppb) were averaged over these 16 samples and natural log-transformed (TPPB): ln(ppb + 1 ) to normalize the data prior to analyses.

  • The proportion of samples with greater than 20 ppb aflatoxins = PGT20

  • PGT20 = -328.5 + 3.34d3d.4wk + 9.136MaxT.6wk

  • PGT20 = 1.15 * d3d.4wk - 13.34, (MaxT.6wk <= 31.5)

  • PGT20 = 14.03 * d3d.4wk - 209.48 (MaxT.6wk > 31.5)

  • d3d.4wk : the cumulative number of 3 consecutive dry (,2.54 cm rain) days over the 4 wk period ending the day of inversion.

  • MaxT.6wk : the maximum daily temperature averaged over 6 wk prior to inversion.

  • PGT20 : the proportion of samples with ppb > 20 and is used to reflect risk for aflatoxin contamination.

  • At least 16 samples from each site-inversion date were assayed for aflatoxinscumulative number of 3-d-dry periods over 4 wk prior to harvest

    • no risk : TPPB = 0 and PGT20 = 0,
    • low : TPPB > 0 and PGT20 = 0,
    • moderate : TPPB > 0 and PGT20 > 0,
    • high : had PGT20 >= 30%.

APSIM (Australia)

Objective

  • the development of a new model, which uses a novel crop simulation approach to assess the risk of contamination, its validation and application in aflatoxin research and as a decision-support tool by peanut growers.

Columns

  • Date : Year-Month-Day

  • Days after planting : the date to start accumulating degree days, starting with the planting date, start date of the period = 0

  • Min Temp. (°C) : Minimum daily temperatures in degree Celsius.

  • Max Temp. (°C) : Maximum daily temperatures in degree Celsius.

  • Precip. & Irrigation (in) : the amount of daily rainfall and irrigation in inches

  • Weather Station ET (in) : to schedule irrigation system. The weather station calculate potential evapotranspiration, which is the amount of water lost from the soil due to evaporation and plant transpiration.

  • Daily GDD : (Max Temp.+ Min Temp.)/2 - Tbase, Tbase=13.3 in peanut Reference

  • Corrected GDD : If Daily GDD <= 0, Corrected GDD is 0. Otherwise, Corrected GDD = Daily GDD.

  • Cum. GDDs : a cumulative sum of Corrected GDD since yesterday + Corrected GDD today, Forecasting GDD accumulation helps growers in scheduling.

  • Root Depth (in) : = If Cum. GDDs <750, Root Depth = 12+(36-12)*((Cum.GDDs - starting day's Cum.GDDs)/(750-starting day's Cum.GDDs)). Otherwise, Root Depth is 36. Estimating soil water content in the root zone.

  • PAW (in) : Potential available Water = Available Water Capacity * Root Depth

  • Kc Curve : Crop coefficients (KC) are the ratio of the evapotranspiration of the crop to a reference crop, estimating crop irrigation requirements using meteorological data

    • 0.3 for 0<x<325,
    • 0.3 +((x-325)/475)*(1-0.3) for 325<x<800,
    • 1 for 800<x<1350,
    • 1+((x-1350)/300)*(0.6-1) for 1350<x<1650,
    • 0.6+((x-1650)/50)*(0.2-0.4) for 1650<x<1700,
    • 0.2 for x>1650
    • **x = Cum.GDDs)**

  • Available Water Capacity

    • Less than 0.10 : Sands, and loamy sands and sandy loams in which the sand is not dominated by very fine sand
    • 0.10 - 0.15 : Loamy sands and sandy loams in which very fine sand is the dominant sand fraction, and loams, clay loam, sandy clay loam, and sandy clay
    • 0.10 - 0.20 : Silty clay, and clay
    • 0.15 - 0.25 : Silt, silt loam, and silty clay loam

  • Final Soil Water Balance : Beginning soil water balance -(Weather Station ET * Kc Curve)+ Precip. Irrigation

  • Soil Water Balance : PAW for Final Soil Water Balance > PAW, and Final Soil Water Balance for Paw >= Final Soil Water Balance.

  • Irrigation Recommendation

    • "IRRIGATE" for Final Soil Water Balance<(0.51*PAW),
    • "CHECK FIELD" for Final Soil Water Balance<(0.6*PAW),
    • otherwise, "ADEQUATE SOIL MOISTURE ".

  • Afltoxin Drought Threshold : PAW * 0.2

  • Aflatoxin Temp Factor(ATF)

    • For daily mean soil temperature (STemp) <22 °C or >35 °C, ATF=0

    • For 22°C <= daily mean soil temperature < 30°C, ATF=(STemp-22)/(30-22)

    • For 30°C <= daily mean soil temperature < 35°C, ATF=(35-STemp)/(35-30)

      • ATF*3

  • ATF < 20% : ATF for Final Water Balance < Aflatoxin Drought Threshold, otherwise 0.

  • Aflatoxin Risk Index : =IF(SUMIFS(H2:H201,D2:D201,">1350")>100,100,SUMIFS(H2:H201,D2:D201,">1350"))

DSSAT-CROPGRO (Shannon McAmis)

Equation 1 
AFINFE(NPP)=AFINFE(NPP)+(SHELN(NPP)-AFINFE(NPP))*R_1*(1.0-SWBAR)*(1.0-SWFAC)*CURV('QDR^',22,33,35,45,ST(1))
  • Where:
    • AFINFE(NPP) : the number of aspergillus infected pods in a specific cohort
    • SHELN(NPP) : the number of shells in a specific cohort
    • R1 : a rate constant
    • SWBAR : soil water status of the first 15cm
    • SWFAC : an index of plant water stress and represents root water uptake divided by transpiration demand
    • CURV : temperature function dependent on base optimal and max temperatures of aspergillus infection
    • ST(1) : soil temperature of the first layer
Equation 2
AFMASS(NPP=AFMASS(NPP)+AFINFE(NPP)*R_3*(1.0-SWFAC)  *(CURV('QDR^',26,28,29,32,ST(1)))
  • Where:
    • AFMASS(NPP) : the aflatoxin mass of a specific cohort
    • AFINFE(NPP) : the number of aspergillus infected pods in a specific cohort
    • R3 : a rate constant
    • SWFAC : an index of plant water stress and represents root water uptake divided by transpiration demand
    • CURV : temperature function dependent on base optimal and max temperatures of aflatoxin production
    • ST(1) : soil temperature at 2.5 cm