Using Ausfarm-Stock in APSIMUI

J.N.G. Hargreaves

05 Feb 2008

Summary

Introduction

The Ausfarm-Stock (Stock) component is used in APSIM to graze APSIM-Plant derived crops, such as Lucerne, Lablab and Wheat. The Ausfarm-Supplement (Supplement) component can also be used as a supplementary feed source for stock. Management operations can be carried out such as buying and selling of stock, supplementary feeding and moving stock to another paddock. Currently the paddock sizes are fixed at one hectare.

To use Stock in an APSIM simulation, three companion APSIMUI components are required – StockScienceConverter, StockHerbageConverter and FarmwiseSequencer.

e.g.

When Supplement is used, its companion SupplementScienceConverter is also required.

e.g.

All of these components are found in the APSIMUI Standard Toolbox in the Animals Folder. E.g.

A sample simulation (Wether_Lucerne_Supplement) of grazing wethers on lucerne with supplementary feeding of wheat is provided under the New menu.

APSIMUI components

· Stock

The Stock component initialises with default properties and no animals.

· StockScienceConverter

The StockScienceConverter initialises with the values specified in its properties grid e.g.

o Debug

o Stock_module

o Conversion_model

o Fraction_faeces_added

o Fraction_urine_added

· StockHerbageConverter

The StockHerbageConverter initialises with the values specified in its properties grid. E.g.

o Debug

o Conversion_model

o Herbage_model

o Herbage_module_name

· FarmwiseSequencer

The FarmwiseSequencer initialises with properties specified in its INI file. These properties translate APSIM events to Ausfarm events and should only be altered after consultation with the SEG.

· Supplement

Supplement initialises with the values specified in its properties grid.

o Spoilage_time

Supplement Store

The supplement store properties define the initial values of each supplement being used in the simulation.

· SupplementScienceConverter

The SupplementScienceConverter initialises with values specified in its properties grid. E.g.

o Debug

o Supplement_module

· Management

Pre-defined management rules of stock (cattle and sheep) and supplement feeding are found in the Stock folder under the Management folder in the Standard Toolbox.

E.g.

Pre-defined cattle management rules for buying, selling and moving stock.

Pre-defined sheep management rules for buying and selling stock.

Pre-defined supplement management rules for buying, mixing and feeding stock.

Stock Component Description

The STOCK component encapsulates the GRAZPLAN animal biology model, as described in:

Freer M, Moore AD & Donnelly JR (1997). GRAZPLAN: decision support systems for Australian grazing enterprises. II. The animal biology model for feed intake, production and reproduction and the GrazFeed DSS. Agricultural Systems 54 , 77-126.

The animals represented by a component instance are classified into groups . The members of each animal group have the same age class, but may have a range of ages (for example, an animal group containing mature animals may include four-year-old, five-year-old and six-year-old stock). The members of each animal group also have the same stage of pregnancy and/or lactation; the same number of suckling offspring; and occupy the same paddock. The set of animal groups changes as animals enter and leave the simulation, and as physiological events such as maturation, birth or weaning take place. Animal groups that become sufficiently similar are merged into a single group.

Each animal group has a unique, internally-assigned integer index , starting at 1. Because the set of groups present in a component instance is dynamic, the index number associated with a particular group may change over time.

Each animal group is also assigned a paddock . Paddocks are referred to by name in the STOCK component. It is the user's responsibility to ensure that paddock names correspond to instances of the PADDOCK component or other sources of necessary driving variables.

Each group also has a user-assigned tag and priority , which need not be unique. Tag values are generally used to manage distinct groups of animals in a common fashion. For example, all lactating ewes may be assigned the same tag value, which may then be used in management rules that keep them grazing together. Animal groups with different tag values are not merged even if they are otherwise similar. If tag values are assigned sequentially starting at 1, they can be used to generate summary variables. Priority values are used to allocate animals to paddocks in the draft event.

The initialisation variable set is nearly completely optional. The idea is to allow the user to specify a minimal information set as well as a maximally detailed initialisation.

Converts ram lambs to wether lambs, or bull calves to steers. If the animal group(s) denoted by group has no suckling young, has no effect.

If the number of male lambs or calves in a nominated group is greater than the number to be castrated, the animal group will be split; the sub-group with castrated offspring will remain at the original index and the sub-group with offspring that were not castrated will be added at the end of the set of animal groups.

Assigns paddocks to animals in such a way that animal groups with the lowest tag values are placed in the paddocks with the best pasture. This event has no parameters.

Ends lactation in cows that have already had their calves weaned. The event has no effect on other animals.

If the number of cows in a nominated group is greater than the number to be dried off, the animal group will be split; the sub-group that is no longer lactating will remain at the original index and the sub-group that continues lactating will be added at the end of the set of animal groups.

Commences mating of a particular group of animals. If the animals are not empty females, or if they are too young, has no effect.

Rearranges the list of animal groups in ascending order of tag value. This event has no parameters.

Creates two or more animal groups from the nominated group. One of these groups is placed at the end of the animal group list.

The division may only persist until the beginning of the next do_stock step, when sufficiently similar groups of animals are merged.

Weans some or all of the lambs or calves from an animal group. The newly weaned animals are added to the end of the list of animal groups, with males and females in separate groups.

Indicates the removal of herbage and seeds. This event is directed to each component instance that provides the Stock instance with a value for the plant2stock driving property.

Indicates the excretion of faeces and urine into a paddock. Different instances of this event are directed to each component subscribing to it, with parameters depending upon the name of the paddock component to which the subscribing component belongs.

If the following properties are not found, then alternative properties are subscribed to instead:

All initialisation properties are readable. In addition, the following owned properties are available:

Each entry in the following table describes between one and six variables: the named variable and five variants obtained by appending the texts: “_ yng ”, “_ all ”, “_ tag ”, “ _yng _ all ” and “ _yng _ tag ”.

Note that the animal model will automatically merge and split groups of animals, so that the index position of a particular group of animals in the array variables will not necessarily remain constant.

Drivers for the Stock Component

The Stock component implements alternative interfaces to obtain weather data; I have only provided the APSIM-compatible interface here.

The first six of these drivers will cause no difficulty. The wind driver is used in computing the energy requirement to maintain body temperature under cold conditions; it can be set to (say) a constant 2.0 m/s if wind speed data are not available. The waterlog driver is an index that describes the degree of waterlogging of the soil (which is modelled as affecting the time spent grazing); it is optional and can be ignored in your context.

In the Stock component, each group of animals is taken to reside in a paddock. The list of valid paddock names is obtained by looking for the components that have the area property and then obtaining the names of these components, i.e. a paddock is defined as any entity with an area. If no component in the simulation has the area property, then the Stock component sets itself up with a single “paddock” that has the null string for its name, an area of 1.0 ha and zero slope.

The slope values are used to compute the energy cost associated with movement.

The usual configuration is to have the paddock components/systems at the same level in the component tree as the Stock component.

At each time step, the Stock component requests the plant2stock driving property. Each value of plant2stock is allocated to one of the paddocks by parsing the name of the component sending it. The herbage present in each paddock is then summarised before being used in the computations of animal intake. In the case where no paddocks have been identified, all the “plant” components that provide plant2stock are allocated to the null paddock.

Once the intake rates of all animals have been computed, the rates for all animals in a paddock are summed and then allocated between the components in that paddock that provided a value for the plant2stock driver. Each such component is then sent a remove_herbage event that contains the rate of herbage removal for that plant component.

The fields of the sub-records in plant2stock : herbage and plant2stock : seed are:

One way to obtain a distribution of herbage mass into DMD classes is given on page 32 of the technical paper on GrazFeed that can be found via http://www.csiro.au/index.asp?type=faq&id=Grazplan .

At each time step, the Stock component requests the supp2stock driving property. This driving property is optional. The supp2stock property returns the amount and quality of supplementary feed that is present in each paddock. All animals resident in a paddock can access the corresponding quantity of supplementary feed (it is allocated between them in proportion to their maximum intake rate). To provide this property, include the Supplement component in the simulation.

The supp2stock driving property is an array of records. Each sub-record has the following fields:

Property	Type	Units	Required?	Description
breed	string		Yes	Name of the animal breed. The set of valid breed names is set out below. Implicit in the breed is the animal type (sheep or cattle).
cattle : number : sex : age : weight : max_prev_wt : pregnant : lactating : no_foetuses : no_suckling : birth_cs : calf_wt : paddock : tag : priority	record integer4 string double double double integer4 integer4 integer4 integer4 double double string integer4 integer4	d kg kg d d - kg	No	Initial state of each animal group for cattle. Not meaningful if breed is a sheep breed. • Number of animals. • Feasible values are ‘cow', ‘cows', ‘heifer', ‘heifers', ‘steer', ‘steers', ‘bull', ‘bulls'. • Age of the animals. • Unfasted live weight of the animals. • Highest weight recorded to date. • Zero denotes not pregnant; 1 or more denotes the time since conception. Only meaningful for females. • Zero denotes not lactating; 1 or more denotes the time since parturition. Only meaningful for females. • Number of foetuses. Only meaningful for females with pregnant > 0. • Number of suckling calves. Only meaningful for females with lactating > 0. • Condition score at parturition. Only meaningful for females with lactating > 0. • Unfasted live weight of suckling calves. Only meaningful for females with lactating > 0. • Paddock occupied by the animals. • Initial tag value for the animal group. • Priority accorded the animals in the draft event
conception	double[ ]	-	No	Expected rates of conception with 1, 2 and 3 young for mature ewes or cows in average body condition, over a mating period lasting 2.5 oestrus cycles. Only the first two elements are significant for cattle.
death_rate	double	/yr	No	Base rate of animal mortality. Default is 0.0.
fleece_yield	double	kg/kg	No	Clean fleece weight as a proportion of greasy fleece weight. Default is 0.70. Only meaningful for sheep.
male_breed	string		No	Name of the breed of rams or bulls to which ewes or cows in this component instance will be mated. The default is breed . The set of valid breed names is set out below.
male_srw	double	kg	No	Standard reference weight of the rams or bulls to which ewes or cows in this component instance will be mated.. The default value depends on male_breed .
max_fibre_diam	double	m m	No	Maximum average wool fibre diameter. The default depends on breed .
param_file	string		No	Name of a file containing genotypic parameters. Default behaviour is to use a default parameter set that is compiled into STOCK.DLL.
peak_milk	double	kg	No	Potential maximum milk yield per head, in 4% fat-corrected milk equivalents. Only significant for cattle. The default value is 20.0.
ref_fleece_wt	double	kg	No	Breed reference fleece weight. The default value depends on breed .
sheep : number : sex : age : weight : max_prev_wt : fleece_wt : fibre_diam : pregnant : lactating : no_young : birth_cs : lamb_wt : lamb_fleece_wt : paddock : tag : priority	record integer4 string double double double double double string integer4 integer4 integer4 integer4 double double double	d kg kg kg m m d d - kg kg	No	Initial state of each animal group for sheep. Not meaningful if breed is a cattle breed. • Number of animals. • Feasible values are ‘ewe', ‘ewes', ‘wether', ‘wethers', ‘ram', ‘rams', ‘crypto', ‘cryptos'. • Age of the animals. • Unfasted live weight of the animals. • Highest weight recorded to date. • Greasy fleece weight of the animals. • Average wool fibre diameter of the animals. • Paddock occupied by the animals. • Initial tag value for the animal group. • Zero denotes not pregnant; 1 or more denotes the time since conception. Only meaningful for ewes. • Zero denotes not lactating; 1 or more denotes the time since parturition. Only meaningful for ewes. • Number of foetuses or suckling lambs. Only meaningful for ewes. • Condition score at parturition. Only meaningful for ewes. • Unfasted live weight of suckling lambs. Only meaningful for ewes with lactating > 0. • Greasy fleece weight of suckling lambs. Only meaningful for ewes with lactating > 0.
srw	double	kg	No	Breed standard reference weight. The default value depends on breed .

Sheep breeds	Sheep breeds	Cattle breeds	Cattle breeds
‘black face x white face'	‘polwarth'	‘angus'	‘friesian'
‘border leicester'	‘polypay'	‘ayrshire'	‘friesian x british'
‘border leicester x merino'	‘romney'	‘beef shorthorn'	‘guernsey'
‘columbia'	‘ryeland'	‘brahman'	‘hereford'
‘corriedale'	‘southdown'	‘brahman x british'	‘holstein'
‘delaine-merino'	‘suffolk'	‘brown swiss'	‘holstein x british'
‘dorset x merino'	‘targhee'	‘charolais'	‘jersey'
‘dorset'	‘texel'	‘charolais x british'	‘limousin'
‘finnsheep'	‘US corriedale'	‘charolais x friesian'	‘sahiwal'
‘hampshire'	‘US romney'	‘charolais x holstein'	‘simmental'
‘large merino'	‘US southdown'	‘chianina'	‘south devon'
‘medium merino'	‘US suffolk'	‘dairy shorthorn'
‘merino'

Parameter	Type	Units	Description
number	integer4		Number of animals to be bought
sex	string		Sex of the animals. Feasible values are as for sheep : sex or cattle : sex , as appropriate.
age	double	months	Average age of the animals
weight	double	kg	Average unfasted live weight of the animals
fleece_wt	double	kg	Average greasy fleece weight of the animals. Only meaningful in sheep.
pregnant	integer4	d	Zero denotes not pregnant; 1 or more denotes the time since conception. Only meaningful for females.
lactating	integer4	d	Zero denotes not lactating; 1 or more denotes the time since parturition in lactating animals. Only meaningful for females.
no_young	integer4		Number of foetuses and/or suckling offspring.
young_wt	double	kg	Average unfasted live weight of any suckling lambs or calves.
young_fleece_wt	double	kg	Average greasy fleece weight of any suckling lambs.

Parameter	Type	Units	Description
group	integer4		Index number of the animal group, the lambs or calves of which are to be castrated. A value of zero denotes that each animal group should be processed in turn until the nominated number of offspring has been castrated.
number	integer4		Number of male lambs or calves to be castrated.

Parameter	Type	Units	Description
group	integer4		Index number of the animal group for which lactation is to end. A value of zero denotes that each animal group should be processed in turn until the nominated number of cows has been dried off.
number	integer4

Property	Alternative	Type	Units	Event:State	Number	Description
weather	maxt	double	ºC	do_stock :0	1	Maximum air temperature.
weather	mint	double	ºC	do_stock :0	1	Minimum air temperature.
weather	rain	double	mm	do_stock :0	1	Precipitation in all forms other than snow.
weather	wind	double	m/s	do_stock :0	1	Average wind speed

Version	Date	Changes
0.1	12 Dec 1997	First draft
0.2	17 Dec 1997	Second draft
0.3	4 Aug 1998	Third draft
0.4	10 Dec 2003	Revised to match pre-release version of component. *_tag properties added
0.5	15 Dec 2003	supp_eaten added

Field	Type	Units	Description
herbage	array of records		Mass and quality of the herbage on offer. The herbage is split into a number of pools that are distinguished by their DM digestibility; each of these pools is described by one element of the array. The fields of the sub-records are set out below.
propn_green	double	-	Proportion of the total herbage mass that is green
legume	double	-	Proportion of the total herbage mass that is legume. Usually 0.0 or 1.0
select_factor	double	-	Species-specific effect on the relationship between digestibility and voluntary intake. Typical values are 0.0 for C3 grasses and legumes and 0.16 for C4 grasses.
seed	array of records		Mass and quality of unripe and ripe seeds (elements 1 and 2, respectively). The fields of the sub-records are the same as for the herbage field.
seed_class	array of integer4	-	“Equivalent digestibility class” for unripe and ripe seeds (elements 1 and 2, respectively). Valid values are 1-6 or 0, where 1 denotes that seeds will be selected at the same time as 80% digestible herbage, 2 corresponds to 70% herbage, etc. A zero value denotes that seeds are not grazed.

Property	Type	Units	Description
name	string		Fully-qualified name of the component.
type	string		Value is “Stock”.
version	string		Value is “1.0”.
author	string		Value is “CSIRO Plant Industry”.
active	Boolean		Denotes whether or not the component is active.
state	string		SDML description of the current state.

Field	Type	Units	Description
dm	double	kg/ha	Mass (dry matter basis) of the herbage or seed pool
dmd	double	-	Dry matter digestibility (0-1, not percentage)
cp_conc	double	kg/kg	Crude protein concentration. Can be estimated as 6.25 x [N]
p_conc	double	kg/kg	Phosphorus concentration. Can reasonably be estimated by assuming a fixed N:P ratio.
s_conc	double	kg/kg	Sulphur concentration. Can reasonably be estimated by assuming a fixed N:S ratio.
prot_dg	double	kg/kg	Protein degradability. In the absence of better information, can be estimated as dmd +0.10
ash_alk	double	mol/kg	Ash alkalinity.
height_ratio	double	-	An index of the bulk density of the herbage. The height ratio for herbage should be computed as 100/(0.03 x BD ), where BD is the herbage bulk density in g/m 3 . This value should be set to 1.0 for seed pools.

Field	Type	Units	Description
paddock	string		Name of a paddock
amount	double	kg	Amount of supplementary feed present in the paddock
roughage	boolean		TRUE i.f.f. the feed is a roughage.
dm_content	double	kg/kg	Dry matter content of the feed.
dmd	double	-	Dry matter digestibility of the feed (not including any portion that passes the gut undamaged).
me_content	double	MJ/kg	Metabolizable energy content of the feed.
cp_conc	double	kg/kg	Crude protein content of the feed.
prot_dg	double	kg/kg	Protein degradability of the feed.
p_conc	double	kg/kg	Phosphorus content of the feed.
s_conc	double	kg/kg	Sulphur content of the feed.
ee_conc	double	kg/kg	Ether-extractable content of the feed.
adip2cp	double	kg/kg	Proportion of crude protein that is insoluble in acid detergent.
ash_alk	double	mol/kg	Ash alkalinity of the feed.
max_passage	double	kg/kg	Maximum proportion of the feed that will pass undamaged through the gut of ruminants.

Using Ausfarm-Stock in APSIMUI

Summary

Introduction

APSIMUI components

· Stock

· StockScienceConverter

· StockHerbageConverter

· FarmwiseSequencer

· Supplement

· SupplementScienceConverter

· Management

Stock Component Description

3.1. do_stock

Drivers for the Stock Component