Inverse meta-modelling to estimate soil available water capacity at high spatial resolution across a farm

Geo-referenced information on crop production that is both spatially- and temporally-dense would be useful for management in precision agriculture (PA). Crop yield monitors provide spatially but not temporally dense information. Crop growth simulation modelling can provide temporal density, but traditionally fail on the spatial issue. The research described was motivated by the challenge of satisfying both the spatial and temporal data needs of PA. The methods presented depart from current crop modelling within PA by introducing meta-modelling in combination with inverse modelling to estimate site-specific soil properties. The soil properties are used to predict spatially- and temporally-dense crop yields. An inverse meta-model was derived from the agricultural production simulator (APSIM) using neural networks to estimate soil available water capacity (AWC) from available yield data. Maps of AWC with a resolution of 10 m were produced across a dryland grain farm in Australia. For certain years and fields, the estimates were useful for yield prediction with APSIM and multiple regression, whereas for others the results were disappointing. The estimates contain ‘implicit information’ about climate interactions with soil, crop and landscape that needs to be identified. Improvement of the meta-model with more AWC scenarios, more years of yield data, inclusion of additional variables and accounting for uncertainty are discussed. We concluded that it is worthwhile to pursue this approach as an efficient way of extracting soil physical information that exists within crop yield maps to create spatially- and temporally-dense dataset

Data Pre-processing for Agricultural Simulations

The process of agricultural simulation using APSIM requires input meteorological data to be prepared in a specific format and the simulation setting file to be ready before the simulation processing starts. Because of possible time savings when conducting large number of simulations at once, it is preferable to create all the input and settings files for all the simulations beforehand and process the simulations in batches as large as possible. This article specifically deals with the data acquisition, transformation and preparation process. It also outlines initial testing and computing time estimations and discusses scheduling, parallel processing and other possible simulation optimization methods

Integrating pest population models with biophysical crop models to better represent the farming system

Farming systems frameworks such as the Agricultural Production Systems simulator (APSIM) represent fluxes through the soil, plant and atmosphere of the system well, but do not generally consider the biotic constraints that function within the system. We designed a method that allowed population models built in DYMEX to interact with APSIM. The simulator engine component of the DYMEX population-modelling platform was wrapped within an APSIM module allowing it to get and set variable values in other APSIM models running in the simulation. A rust model developed in DYMEX is used to demonstrate how the developing rust population reduces the crop's green leaf area. The success of the linking process is seen in the interaction of the two models and how changes in rust population on the crop's leaves feedback to the APSIM crop modifying the growth and development of the crop's leaf area. This linking of population models to simulate pest populations and biophysical models to simulate crop growth and development increases the complexity of the simulation, but provides a tool to investigate biotic constraints within farming systems and further moves APSIM towards being an agro-ecological framework

Integrating pest population models with biophysical crop models to better represent the farming system

Farming systems frameworks such as the Agricultural Production Systems simulator (APSIM) represent fluxes through the soil, plant and atmosphere of the system well, but do not generally consider the biotic constraints that function within the system. We designed a method that allowed population models built in DYMEX to interact with APSIM. The simulator engine component of the DYMEX population-modelling platform was wrapped within an APSIM module allowing it to get and set variable values in other APSIM models running in the simulation. A rust model developed in DYMEX is used to demonstrate how the developing rust population reduces the crop's green leaf area. The success of the linking process is seen in the interaction of the two models and how changes in rust population on the crop's leaves feedback to the APSIM crop modifying the growth and development of the crop's leaf area. This linking of population models to simulate pest populations and biophysical models to simulate crop growth and development increases the complexity of the simulation, but provides a tool to investigate biotic constraints within farming systems and further moves APSIM towards being an agro-ecological framework

Assessment of the potential impacts of plant traits across environments by combining global sensitivity analysis and dynamic modeling in wheat

A crop can be viewed as a complex system with outputs (e.g. yield) that are affected by inputs of genetic, physiology, pedo-climatic and management information. Application of numerical methods for model exploration assist in evaluating the major most influential inputs, providing the simulation model is a credible description of the biological system. A sensitivity analysis was used to assess the simulated impact on yield of a suite of traits involved in major processes of crop growth and development, and to evaluate how the simulated value of such traits varies across environments and in relation to other traits (which can be interpreted as a virtual change in genetic background). The study focused on wheat in Australia, with an emphasis on adaptation to low rainfall conditions. A large set of traits (90) was evaluated in a wide target population of environments (4 sites x 125 years), management practices (3 sowing dates x 2 N fertilization) and $CO_2$ (2 levels). The Morris sensitivity analysis method was used to sample the parameter space and reduce computational requirements, while maintaining a realistic representation of the targeted trait x environment x management landscape ($\sim$ 82 million individual simulations in total). The patterns of parameter x environment x management interactions were investigated for the most influential parameters, considering a potential genetic range of +/- 20% compared to a reference. Main (i.e. linear) and interaction (i.e. non-linear and interaction) sensitivity indices calculated for most of APSIM-Wheat parameters allowed the identifcation of 42 parameters substantially impacting yield in most target environments. Among these, a subset of parameters related to phenology, resource acquisition, resource use efficiency and biomass allocation were identified as potential candidates for crop (and model) improvement.Comment: 22 pages, 8 figures. This work has been submitted to PLoS On

Predicting crop yields and soil‐plant nitrogen dynamics in the US Corn Belt

We used the Agricultural Production Systems sIMulator (APSIM) to predict and explain maize and soybean yields, phenology, and soil water and nitrogen (N) dynamics during the growing season in Iowa, USA. Historical, current and forecasted weather data were used to drive simulations, which were released in public four weeks after planting. In this paper, we (1) describe the methodology used to perform forecasts; (2) evaluate model prediction accuracy against data collected from 10 locations over four years; and (3) identify inputs that are key in forecasting yields and soil N dynamics. We found that the predicted median yield at planting was a very good indicator of end‐of‐season yields (relative root mean square error [RRMSE] of ∼20%). For reference, the prediction at maturity, when all the weather was known, had a RRMSE of 14%. The good prediction at planting time was explained by the existence of shallow water tables, which decreased model sensitivity to unknown summer precipitation by 50–64%. Model initial conditions and management information accounted for one‐fourth of the variation in maize yield. End of season model evaluations indicated that the model simulated well crop phenology (R2 = 0.88), root depth (R2 = 0.83), biomass production (R2 = 0.93), grain yield (R2 = 0.90), plant N uptake (R2 = 0.87), soil moisture (R2 = 0.42), soil temperature (R2 = 0.93), soil nitrate (R2 = 0.77), and water table depth (R2 = 0.41). We concluded that model set‐up by the user (e.g. inclusion of water table), initial conditions, and early season measurements are very important for accurate predictions of soil water, N and crop yields in this environment

Plant Modelling Framework: software for building and running crop models on the APSIM platform

The Plant Modelling Framework (PMF) is a software framework for creating models that represent the plant components of farm system models in the agricultural production system simulator (APSIM). It is the next step in the evolution of generic crop templates for APSIM, building on software and science lessons from past versions and capitalising on new software approaches. The PMF contains a top-level Plant class that provides an interface with the APSIM model environment and controls the other classes in the plant model. Other classes include mid-level Organ, Phenology, Structure and Arbitrator classes that represent specific elements or processes of the crop and sub-classes that the mid-level classes use to represent repeated data structures. It also contains low-level Function classes which represent generic mathematical, logical, procedural or reference code and provide values to the processes carried out by mid-level classes. A plant configuration file specifies which mid-level and Function classes are to be included and how they are to be arranged and parameterised to represent a particular crop model. The PMF has an integrated design environment to allow plant models to be created visually. The aims of the PMF are to maximise code reuse and allow flexibility in the structure of models. Four examples are included to demonstrate the flexibility of application of the PMF; 1. Slurp, a simple model of the water use of a static crop, 2. Oat, an annual grain crop model with detailed growth, development and resource use processes, 3. Lucerne, perennial forage model with detailed growth, development and resource use processes, 4. Wheat, another detailed annual crop model constructed using an alternative set of organ and process classes. These examples show the PMF can be used to develop models of different complexities and allows flexibility in the approach for implementing crop physiology concepts into model set up