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
There are three different models to assess aflatoxin level in peanut.
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%. 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.
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
**x = Cum.GDDs)**
Available Water Capacity
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),"ADEQUATE SOIL MOISTURE "
.Afltoxin Drought Threshold
: PAW
* 0.2
Aflatoxin Temp Factor(ATF)
For 30°C <= daily mean soil temperature < 35°C, ATF=(35-STemp)/(35-30)
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"))
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))
AFINFE(NPP)
: the number of aspergillus infected pods in a specific cohortSHELN(NPP)
: the number of shells in a specific cohortR1
: a rate constantSWBAR
: soil water status of the first 15cmSWFAC
: an index of plant water stress and represents root water uptake divided by transpiration demandCURV
: temperature function dependent on base optimal and max temperatures of aspergillus infectionST(1)
: soil temperature of the first layerEquation 2
AFMASS(NPP=AFMASS(NPP)+AFINFE(NPP)*R_3*(1.0-SWFAC) *(CURV('QDR^',26,28,29,32,ST(1)))
AFMASS(NPP)
: the aflatoxin mass of a specific cohortAFINFE(NPP)
: the number of aspergillus infected pods in a specific cohortR3
: a rate constantSWFAC
: an index of plant water stress and represents root water uptake divided by transpiration demandCURV
: temperature function dependent on base optimal and max temperatures of aflatoxin productionST(1)
: soil temperature at 2.5 cm