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

Abstract

Biomass and nitrogen partitioning Integrated design environment Phenological and morphological development Reusable organ and function classes a b s t r a c tThe 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.

An integrated phenology modelling framework in r

“…For example, the code required to partially reproduce a study by Basler (2016) relied on a mere 15 r commands (see run_model_comparison.r in the phenor manuscript github repository), while the models used are easily readable and well documented. Furthermore, adding model structures is easy compared to other frameworks which rely on either low level languages, are closed source or do not work cross-platform (Brown et al, 2014;Chuine, Garcia Cortazar Atauri, Kramer, & Hänninen, 2013;Hänninen & Kramer, 2007 (Basler, 2016;Clark et al, 2014;Fisher et al, 2007;Linkosalo et al, 2006).…”

Climate trends account for stalled wheat yields in Australia since 1990

“…We deployed the cropping system simulation model APSIM (Version 7.7) to determine water-limited yield potential (Yw). We chose APSIM to simulate Yw because it is well validated for wheat (Asseng et al, 1998;Wang et al, 2003;Hochman et al, 2007;Brown et al, 2014) and fallow periods (Dolling et al, 1996;Probert et al, 1998;Zeleke et al, 2014) in Australia. APSIM has been used in many climate change and climate adaptation studies, and it is able to capture the CO 2 enrichment effects on photosynthesis via modifiers of radiation use efficiency (RUE).…”

Responses to atmospheric CO2 concentrations in crop simulation models: a review of current simple and semicomplex representations and options for model development

“…This could involve comparison of the simulation accuracy of plant models/modelling approaches differing in complexity for one (or more) particular plant species (separately) against experimental field data. For this purpose, the Plant Modelling Framework (PMF; Brown et al ., ) could be used within the APSIM framework. The PMF, resulting from a recent initiative to create generic plant model code within APSIM, makes use of a library of several plant organ and process models (which can differ in model complexity) that can be combined in a model for a specific plant.…”