R Pipeline for Calculation of APSIM Parameters and Generating the XML File

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<p>A pipeline for APSIM parameters calculation was developed to process the 2018 dataset.</p>

<p>The R script "Pipeline" is used to generate the XML parameter file. Other R scripts are functions created separately that can be called into the Pipeline when needed. R script "conf" defines the input files and output files. The working directory is set in Pipeline to read in the weather file and parameter file using the function "MetFile" and "ParameterParse". Thermal time is calculated using the function "ThermalTime" and accumulated thermal time from emergence is calculated using the function "LeafNumber".</p>

<p>After calculating the accumulated thermal time for different leaf numbers, leaf appearance rate (LAR) is determined using the Function "phyllochronDE". This function uses DE optimization, so slightly different results are obtained each time you run this function. The LAR output is used to calculate the dynamic Leaf Area Index (LAI) using the function "LeafSizes" based on the calculated leaf number using LAR and the input data such as leaf size distribution parameters, final tiller number, and observed final leaf number.</p>

<p>The next step is calculating k using the function "K" based on the calculated LAI and observed canopy cover data. With the calculated k and LAI, we can derive the dynamic canopy cover curve and estimate the radiation interception accumulation.</p>

<p>Radiation Use Efficiency (RUE) is calculated using the radiation interception accumulation and observed biomass.</p>

<p>After getting all of the parameters, the genotype file and XML file can be written through function "utils" and "GenotypeBuilder".   </p>

<p>The parameter file is "SorghumXMLOutput".</p>