What is the animal module and what does it do?
The animal module is one of the biophysical modules within RuFaS. It simulates each animal within the herd every day for the length of the simulation. In order to sufficiently simulate a herd, there are many inputs in the animal module covering herd performance and management. While overarching decisions about whether you’d like to provide the diet recipe or have RuFaS formulate one for you and whether or not you’d like to incorporate a feed additive will be included in the animal module, most ration-related inputs and functions will be described in the Feed Module description. Because this module houses all the animals, it is responsible for the initial generation of manure and the associated emissions.
Simulates Animal’s Lifecycle
The animal module is in charge of simulating individual animal’s daily activities within the herd. The module covers the lifecycle classes of a dairy bovine:
Birth and weaning (or selling surplus animals)
Growing and breeding heifers
Calving
Breeding
Drying off
Herd exits
For the youngstock in the herd, surplus animals (bull calves or excess heifers) are modeled as sold on the first day of life. All dairy female replacements make their way through the weaning process onto growing pens and to breeding. Within breeding, the specific type of reproductive protocol can be chosen for youngstock (estrus detection, timed artificial insemination, or a combination). Overall heifer insemination rate (sometimes referred to as the “heat detection rate”) and conception rate can be adjusted from the default values. If heifers reach an age (assigned by the user) at which they should no longer be given the chance to be bred, the heifer will be sold. All remaining animals will calve into the herd.
Once calving occurs, an animal immediately begins milk production. She will continue through her lactation, beginning breeding according to the reproductive protocols of the farm and continue until confirmed pregnant or reaching a days in milk where she is no longer eligible to be bred, and then leave the milking herd due to either a probabilistic chance of a health / disease (user can override default probability) related culling or death, failing to become pregnant, or successfully becoming pregnant and being dried off in preparation of entering a subsequent lactation.
Simulates ration formulation and enteric methane generation
As the module that houses the animal classes, the animal module also formulates (and reformulates at the frequency the user chooses) rations to meet the nutrient requirements of the animals. How rations are formulated from user entries is covered in more depth in the Feed Module. According to the ration and the animal class, the animal module calculates enteric methane. The default equation for simulating enteric methane production is the IPCC equation. This equation uses information from the ration fed to cows including crude protein, ether extract, NDF, and soluble residue to help calculate the amount of methane produced. There are other equation choices (Mills and Mutian) that can be selected, and IPCC is the default for all animal classes. Enteric methane inhibiting feed additives, including monensin and 3-NOP, can also be included in the diet within the animal module, though the default is to not include any feed additives.
Within the animal module, a user must choose whether they would like to use the specific ration formulation they provide or allow RuFaS to formulate a lowest cost ration using the ingredients offered by setting the ‘user_input parameter’ to true or false, respectively.
Simulates manure excretion and emissions
Lastly, the animal module houses the animals and their manure, even if only temporarily, so it is in this module that manure excretion is generated and manure housing emissions occur. Most manure emissions occur in manure storage/treatment and these emissions are covered in the Manure Module, however, ammonia is often lost immediately upon excretion and is therefore a common emission from housing in the animal module. Depending on the housing and manure management system, there will be varying amounts of other greenhouse gas emissions included as well. The animal module does simulate all nitrogen and phosphorus excretion, volatile solids, and total solids through feces and urine, which it will then pass onto the manure module for handling, treatment, and storage as applicable.
How and when do animals leave the herd?
There are currently a limited number of ways an animal can exit the herd.
Heifers who fail to become pregnant after reaching a user specified age are culled from the herd.
Heifers may also be sold or purchased when they are close to calving (heiferIII) in order to maintain a strict herd size. In order to alleviate the confusion with this process and allow the user to effectively utilize RuFaS outputs, it is suggested that a “net” number of heiferIIIs be calculated in all reports.
Cows who fail to become pregnant after reaching a user specified days in milk are designated “do not breed.” They will remain in the lactating herd until their milk production falls below a user specified milk production at which they are culled.
Cows are subject to a probabilistic health related culling event or death event. There are default values provided for these that can be overridden by the user. There is a parity specific cull probability and then if a cow is “chosen” to be culled, she will then be assigned a reason and a day in milk of culling according to the likelihood of each, as entered by the user.
How does RuFaS model herd milk production?
RuFaS asks for, but does not require, annual herd milk production. If the user elects to have RuFaS simulate the amount of milk that would be produced, rather than attempt to match the amount of milk produced on a herd, the annual herd milk production input must be “null.” If the user would like RuFaS to, as closely as possible, match the observed milk production on a herd, the user should input the total annual milk production on a farm (including all milk fed to calves) in kg. RuFaS does require a parity distribution in order to simulate the annual milk production of the herd. RuFaS uses the Wood’s lactation curve as its basis for stimulating milk production and can adjust the height of the curve to match the total annual milk production desired.
In RuFaS, milk production is influenced by the ration fed, just as it is in real life. Within the animal module, a user must choose whether or not the ration should be a user input (meaning RuFaS creates and feeds a ration with specific % dry matter as inputted by the user to animals) or not (meaning RuFaS uses the ingredients listed but creates a lowest cost, balanced ration using ingredients in different proportions than inputted by the user). A user can set limits for how much milk production is impacted by the ration in the feed module through the milk reduction maximum parameter. If milk reduction maximum is set to anything greater than 0, RuFaS will undergo an iterative process to match milk production given the nutrient requirements of the animals in the herd, to the nutrients offered in the ration.
How does RuFaS group animals?
RuFaS groups animals by animal class in pens according to the user defined pens. A user must have at least one pen for each group of animals (calves, growing heifers, dry cows, and lactating cows). These pen designations help RuFaS to simulate housing conditions, energy requirements (especially given how far lactating cows need to walk to the parlor), and are linked to the manure and feed modules for manure management and ration formulation. In the animal module, a user must designate the pen size (number of stalls and stocking density), distance from the parlor, and the manure management scenario (which will be designed later).
What are the inputs for the animal module?
Herd demographic inputs:
Number of animals by age class (heiferI = preweaning, heiferII = post weaning through close up, heiferIII = close up heifers, cows) and parity distribution
RuFaS does not ask for the number of dry cows as this number will be simulated knowing the other information from the inputs.
Breed and body weight
Annual milk production, % fat, and % protein
Reproductive inputs:
Reproductive programs for cows and heifers (estrus detection, a limited list of timed artificial insemination, and combination programs are available to choose from.) See Dairy Cattle Reproduction Council for more information on protocols.
Conception rates and insemination rates for cows and heifers
Age and days in milk cut offs for stopping reproductive protocols
Stillborn rate
Non reproduction / production associated culls:
Parity cull and death distributions
Probabilities of culling by reason
Ration related inputs:
User defined ration, formulation interval
Feed additive and amount fed
What are the outputs for the animal module?
While the total list of animal module outputs can be accessed through use of the model, a few key outputs of interest include:
Production outputs:
Milk production
Herd demographics (# animals in each age class, lactation group %, # animals leaving the herd and the reason)
Dry matter intake and feed efficiency
Environmental outputs (available by animal class):
Enteric methane(CH4)
Manure nutrients (N, P, volatile and total solids)
Manure housing emissions (NH3, CH4, and N2O)
Feed emissions, assuming the feeds are purchased, not homegrown
What is the future for the animal module?
Semen updates: RuFaS currently only accepts one type of semen to be chosen across the herd. If a herd uses 30% sexed, 70% beef semen currently, the user needs to update the male calf rate input parameter to simulate this. In the future, multiple semen types will be able to be used and improvements will also allow specific animals to be bred with the semen types to better simulate dairy management practices.
Genomics updates: RuFaS currently does not have the capacity for generational genetic or phenotypic improvement. In future updates, genomic index will be incorporated so that improvement in the index can be modeled through various breeding decisions and associated production outcomes will also update.
Health updates: Today, in order to simulate health outcomes, the impact of health events on milk production, reproduction and culling must be separately inputted into RuFaS. In the future, a health submodule will be added to RuFaS so that users can directly model changing risk factors and/or disease incidence to determine the production and environmental impacts of diseases specific to dairy cattle.