geoffreyogutu / wofost_crop_parameters

Parameter sets for the WOFOST crop simulation model implemented in YAML

Parameter sets for the WOFOST crop simulation model

This repository contains the parameter sets for 22 crops for the WOFOST crop simulation model.

Format and structure of the parameter files

The parameters are stored in a data serialization format called YAML. YAML is similar to XML or JSON but has a strong focus on human readability and therefore is much more suited to store parameter sets that often have to be edited manually. Moreover, YAML is language independent and YAML parsers are available for a variety of languages.

The parameter files are organized by crop type and within each file different crop ecotypes and crop varieties can be defined. To accomodate the definition of different crop varieties in one file, the parameter files have been organized in a clear structure. This can be most easily explained with an example (barley in this case):

Version: 1.0.0
CropParameters:
    GenericC3: &GenericC3

        ## All parameters for C3 crops go here

    GenericC4: &GenericC4

        ## All parameters for C4 crops go here

    EcoTypes:
        springbarley: &springbarley
            <<: *GenericC3           # Ecotype springbarley inherits from GenericC3

            ## All parameters specific for springbarley go here

    Varieties:
        Spring_barley_301:
            <<: *springbarley        # Variety Spring_barley_301 inherits from ecotype springbarley
            TSUM1:
            -  800
            - temperature sum from emergence to anthesis
            - ['C.d']
            TSUM2:
            -  750
            - temperature sum from anthesis to maturity
            - ['C.d']

The parameter file starts with a version number that is used to identify the file structure. Next, the crop parameters are defined starting at the tag CropParameters. First all parameters that are generic for C3 and C4 crops are defined by the tags GenericC3 and GenericC4. These parameters mainly have to do with CO₂ response on assimilation and transpiration. Moreover they define two anchors &GenericC3 and &GenericC4 that can be used to refer to in later sections.

Second, the parameter file defines the EcoTypes. These can be regarded as distinct sets of crop parameters that define the properties of groups of varieties. The parameter definitions of EcoTypes have to be complete (all crop parameters have to be present) and they have to inherit from either GenericC3 or GenericC4 by providing a reference to the anchor. For example, the ecotype 'springbarley' refers to the anchor GenericC3 through the syntax <<: *GenericC3. Each ecotype defines an anchor to itself that can be used to refer to later on.

Finally, the parameter file defines the varieties for the given crop (often called cultivars). Varieties in the parameter file inherit all parameters from one of the defined EcoTypes and redefine one or more parameters that are specific for the given variety. In the example above, the variety 'Spring_barley_301' inherits its parameters from the EcoType 'springbarley' while it redefines the parameters TSUM1 and TSUM2 to values specific for this variety.

Parameters themselves are defined by a tag that is the name of the parameter and a list of three items: 1) the value of the parameter, 2) a description of the parameter and 3) the units of the parameter. The units are defined in such way that they can be easily parsed and used by software that supports units during model definition and simulation.

The indenting and general structure of the parameter files are part of the YAML syntax and not only enhance readability of the file, but also are essential for YAML to parse it.

How to use the parameter files

The crop parameter files have been designed to work with the Python Crop Simulation Environment (PCSE) which provides a DataProvider that can directly use the YAML crop parameter files:

>>> from pcse.fileinput import YAMLCropDataProvider
>>> cropd = YAMLCropDataProvider()
>>> cropd.print_crops_varieties()
crop 'mungbean', available varieties:
 - 'Mungbean_VanHeemst_1988'
crop 'millet', available varieties:
 - 'Millet_VanHeemst_1988'
crop 'chickpea', available varieties:
 - 'Chickpea_VanHeemst_1988'
crop 'soybean', available varieties:
 - 'Soybean_906'
 - 'Soybean_904'

.....

crop 'potato', available varieties:
 - 'Potato_701'
 - 'Potato_703'
 - 'Potato_702'
 - 'Potato_704'
crop 'sorghum', available varieties:
 - 'Sorghum_VanHeemst_1988'
>>> cropd.set_active_crop('soybean', 'Soybean_906')
>>> print(cropd)
YAMLCropDataProvider - current active crop 'soybean' with variety 'Soybean_906'
Available crop parameters:
 {'DTSMTB': [0.0, 0.0, 7.0, 0.0, 30.0, 23.0, 45.0, 38.0], 'NLAI_NPK': 1.0, 'NRESIDLV': 0.0093, 'KCRIT_FR': 1.0,

 ....

 720.0, 0.9, 1000.0, 0.9, 2000.0, 0.9], 'TSUM2': 1300, 'TSUM1': 500, 'TSUMEM': 90}

Moreover, the PCSE AgroManager is designed to work with the YAMLCropDataProvider and the parameters files by referring to the crop type (crop_name) and crop variety (variety_name) in its definition of the agromanagement:

Version: 1.0.0
AgroManagement:
- 1998-01-01:
    CropCalendar:
        crop_name: soybean
        variety_name: Soybean_906
        crop_start_date: 1998-05-15
        crop_start_type: sowing
        crop_end_date:
        crop_end_type: maturity
        max_duration: 150
    TimedEvents:
    StateEvents:
- 1999-01-01:

Within the agromanagement definition (also defined in YAML) the crop_name and variety_name tags within the CropCalendar definition directly refer to the name of the parameter file ('soybean') and the variety ('Soybean_906') that is defined in the crop parameter file.

Note that crop_name and variety_name in the agromanagement definition are case sensitive!

Limitations

A limitation of the current version of the parameter files is that the metadata concerning the different ecotypes and varieties has not yet been defined in the file. In a subsequent version of the parameter files this will be taken into account including information like:

• region where the variety can be applied
• contact person
• reference dataset
• reference publication
• etc.