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swine_model_weekly-12fatpens-weight-FINAL-swIAVs.yaml
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swine_model_weekly-12fatpens-weight-FINAL-swIAVs.yaml
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---
# EMULSION (Epidemiological Multi-Level Simulation framework)
# ===========================================================
#
# Contributors and contact:
# -------------------------
#
# - Sébastien Picault (sebastien.picault@inrae.fr)
# - Yu-Lin Huang
# - Vianney Sicard
# - Sandie Arnoux
# - Gaël Beaunée
# - Pauline Ezanno (pauline.ezanno@inrae.fr)
#
# INRAE, Oniris, BIOEPAR, 44300, Nantes, France
#
#
# How to cite:
# ------------
#
# S. Picault, Y.-L. Huang, V. Sicard, S. Arnoux, G. Beaunée,
# P. Ezanno (2019). "EMULSION: Transparent and flexible multiscale
# stochastic models in human, animal and plant epidemiology", PLoS
# Computational Biology 15(9): e1007342. DOI:
# 10.1371/journal.pcbi.1007342
#
#
# License:
# --------
#
# Copyright 2016 INRAE and Univ. Lille
#
# Inter Deposit Digital Number: IDDN.FR.001.280043.000.R.P.2018.000.10000
#
# Agence pour la Protection des Programmes,
# 54 rue de Paradis, 75010 Paris, France
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
# __ __ _ _
# | \/ | | | | |
# | \ / | ___ __| | ___| |
# | |\/| |/ _ \ / _` |/ _ \ |
# | | | | (_) | (_| | __/ |
# |_| |_|\___/ \__,_|\___|_|
#
# _____ __ _ _
# |_ _| / _| | | (_)
# | | _ __ | |_ ___ _ __ _ __ ___ __ _| |_ _ ___ _ __
# | | | '_ \| _/ _ \| '__| '_ ` _ \ / _` | __| |/ _ \| '_ \
# _| |_| | | | || (_) | | | | | | | | (_| | |_| | (_) | | | |
# |_____|_| |_|_| \___/|_| |_| |_| |_|\__,_|\__|_|\___/|_| |_|
# NAME OF THE MODEL
model_name: hybrid_swine_model_metapop_weekly_weights_and_external_infection
# DESCRIPTION OF THE MODEL
model_info:
abstract: 'This model is a simple discrete-time, stochastic,
compartmental SEIR model of a swine population with different
life stages (i.e., gestation to finishing), sex, and age structure,
at the metapopulation scale where the finishing group is composed
of 12 pens.'
author: 'Jerrold M. Tubay (j.m.tubay@uu.nl)'
# _______ _
# |__ __(_)
# | | _ _ __ ___ ___
# | | | | '_ ` _ \ / _ \
# | | | | | | | | | __/
# |_| |_|_| |_| |_|\___|
# TIME INFORMATION
# This section defines the time unit (used e.g. for expressing
# durations, rates, etc.), the duration of the time step, the origin
# date and total duration of the simulation.
time_info:
time_unit: 'weeks'
delta_t: 1
origin: 'January 1, 2020' # IMPORTANT: Sync this date with the available data
total_duration: '170'
# _ _
# | | | |
# | | _____ _____| |___
# | | / _ \ \ / / _ \ / __|
# | |___| __/\ V / __/ \__ \
# |______\___| \_/ \___|_|___/
# ORGANIZATION LEVELS USED IN THE SIMULATION
# A hybrid model considers two levels: the population and
# its components (individuals)
levels:
metapop:
desc: 'level of the metapopulation'
aggregation_type: 'metapopulation'
# The metapopulation is explicitly linked to a specific class in a Python code add-on
file: 'movement_12fatpens_swIAVs.py'
class_name: Metapopulation
contains:
- herd
aggregate_vars:
- name: metapop_total_herd
collect: total_herd
operator: sum
- name: metapop_total_I
collect: total_I
operator: sum
- name: metapop_total_Jn
collect: total_Jn
operator: sum
- name: metapop_total_Jnb
collect: total_Jnb
operator: sum
- name: metapop_total_Jf
collect: total_Jf
operator: sum
- name: metapop_total_A
collect: total_A
operator: sum
- name: metapop_total_G
collect: total_G
operator: sum
- name: metapop_total_F
collect: total_F
operator: sum
herd:
desc: 'level of the population'
aggregation_type: 'hybrid'
contains:
- animals
animals:
desc: 'level of the individuals'
#default_prototype: healthy
# _____
# | __ \
# | |__) | __ ___ ___ ___ ___ ___ ___ ___
# | ___/ '__/ _ \ / __/ _ \/ __/ __|/ _ \/ __|
# | | | | | (_) | (_| __/\__ \__ \ __/\__ \
# |_| |_| \___/ \___\___||___/___/\___||___/
# LIST OF PROCESSES (IN ORDER) TO BE EXECUTED DURING EACH TIME STEP
# In a hybrid model, processes take place at the population level
# (here, herd) and are managed by groupings
processes:
metapop:
- farmer_movement
- sample_I_from_fatteners
#- external_pathway
- third_trans_pathway
animals:
- sex: infection_by_sex
- age_group: sex_and_age
- health_state: infection_by_age
- parity: parities
# _____ _
# / ____| (_)
# | | __ _ __ ___ _ _ _ __ _ _ __ __ _
# | | |_ | '__/ _ \| | | | '_ \| | '_ \ / _` |
# | |__| | | | (_) | |_| | |_) | | | | | (_| |
# \_____|_| \___/ \__,_| .__/|_|_| |_|\__, |
# | | __/ |
# |_| |___/
# DESCRIPTION OF GROUPINGS, ASSOCIATED WITH PROCESSES WHICH ARE NOT
# DIRECTLY BASED ON STATE MACHINES
# A grouping is based on one or more variables. For instance, the
# grouping for managing the 'infection' process is based on the
# variable 'health_state' (coming from the state machine with the same
# name): hence, one group will be defined for all possible values of
# the health_state variable.
grouping:
herd:
infection_by_sex: [health_state, sex]
infection_by_age: [health_state, age_group]
sex_and_age: [sex, age_group]
parities: [parity]
# _____ _ _ __ __ _ _
# / ____| | | | | \/ | | | (_)
# | (___ | |_ __ _| |_ ___ | \ / | __ _ ___| |__ _ _ __ ___ ___
# \___ \| __/ _` | __/ _ \ | |\/| |/ _` |/ __| '_ \| | '_ \ / _ \/ __|
# ____) | || (_| | || __/ | | | | (_| | (__| | | | | | | | __/\__ \
# |_____/ \__\__,_|\__\___| |_| |_|\__,_|\___|_| |_|_|_| |_|\___||___/
# DESCRIPTION OF THE STATE MACHINES INVOLVED IN THE MODEL
state_machines:
sex:
desc: 'A state machine without transitions for representing male/female animals'
states:
- Female:
name: 'Female'
desc: 'Female animals'
fillcolor: 'orange'
default: yes
- Male:
name: 'Male'
desc: 'Male animals'
fillcolor: 'deepskyblue'
parity:
desc: 'A state machine without transitions, just for representing
the succession of relevant parities (number of successive
farrowings). The order of states defines a predecessor/successor
order used by keyword next_state in prototype next_parity'
states:
- P0:
name: 'Nulliparous'
desc: 'Nulliparous animal (no previous farrowing)'
fillcolor: 'orange'
- P1:
name: 'Parity 1'
desc: 'Animal with parity 1 (first farrowing)'
fillcolor: 'pink'
- P2:
name: 'Parity 2'
desc: 'Animal with parity 2'
fillcolor: 'red'
- P3:
name: 'Parity 3+'
desc: 'Animal with parity 3 and more'
fillcolor: 'purple'
age_group:
desc: 'The state machine which defines the evolution of age groups
from newborn piglets to gilt or sow.'
states:
- Jnb:
name: 'Juvenile new born'
desc: 'juvenile new born animals (farrowing stage)'
fillcolor: 'orange'
duration: 'weaning_time'
on_stay:
- set_var: age
value: age + delta_t
- set_var: weight
value: 'random_normal(mean_wean_weight, sd_wean_weight)'
- Jn:
name: 'piglets in the nursery'
desc: 'weaned piglets transferred to the nursery'
fillcolor: 'orchid'
duration: 'nursing_time'
on_stay:
- set_var: age
value: age + delta_t
- set_var: weight
value: 'random_normal(mean_fattening_weight, sd_fattening_weight)'
- Jf:
name: 'pigs for fattening until finishing'
desc: 'pigs that are transferred for fattening until finishing'
fillcolor: 'pink'
duration: 'finishing_time'
on_stay:
- set_var: age
value: age + delta_t
- Sold_fattener:
name: 'Sold fatteners'
desc: 'pigs that have been sold'
fillcolor: 'sienna'
on_enter:
- record_change: nb_fatteners_sold
autoremove: yes
- Sold_nursery:
name: 'sold pigs from the nursery'
desc: 'sold pigs from the nursery in excess of required number of fattening pigs'
on_enter:
- record_change: nb_nursery_pigs_sold
autoremove: yes
- A:
name: 'Non-gestating Adult'
desc: 'adult animals'
fillcolor: 'brown'
on_stay:
- set_var: age
value: age + delta_t
- G:
name: 'Gestating Adult'
desc: 'adult animals (producing new juveniles)'
fillcolor: 'deepskyblue'
on_enter:
- set_var: gestation_age
value: 0
on_stay:
- set_var: age
value: age + delta_t
- set_var: gestation_age
value: gestation_age + delta_t
on_exit:
- set_var: gestation_age
value: 0
- F:
name: 'Farrowing Sow'
desc: 'farrowing sow (providing milk for newborn piglets)'
duration: 'weaning_time'
on_stay:
- set_var: age
value: age + delta_t
- D:
name: 'Dead'
desc: 'compartment to put dead animals'
fillcolor: white
on_enter:
- record_change: dead_pigs
autoremove: yes
transitions:
- from: Jnb
to: Jn
proba: 1
cond: metapop_total_Jn < K_herd
- from: Jn
to: Jf
proba: 1
cond: Eq(metapop_total_Jf, 0)
- from: Jf
to: Sold_fattener
proba: 1
- from: A
to: D
rate: '(1 / avg_adult_death_age) + (is_I * mortality_I)'
escape: yes
desc: 'all Non-gestating Adults are subject to mortality due to old age'
- from: A
to: G
cond: 'OR(age >= adult_age, is_P1, is_P2, is_P3)'
rate: 'AND(StrictLessThan(metapop_total_G, K_sows), IfThenElse(is_P0, reproduction_g, reproduction_s))'
desc: 'non-gestating adult females start gestation at rate "reproduction_g" for gilts and "reproduction_s" for sows'
- from: G
to: F
cond: 'gestation_age >= dur_gestation'
rate: 1
on_cross:
- become: 'next_parity'
desc: 'at end of gestation, gestating adult females return to A state and
produce offspring. Their parity is updated using the prototype next_parity
which increments the value of discrete variable parity. Here, if the sow/gilt
is infectious, vertical transmission is possible to one of the newborn.'
- from: F
to: A
proba: 1
- from: G
to: D
rate: '1 / avg_adult_death_age + (is_I * mortality_I)'
desc: 'all Gestating Adults are subject to mortality due to old age -
this can occur even during gestation, hence escape is set to yes'
- from: Jnb
to: D
rate: mortality_weaning
escape: yes
desc: 'add additional mortality component if born infected'
- from: Jn
to: D
rate: mortality_nursery
escape: yes
- from: Jf
to: D
rate: mortality_fattening
escape: yes
#health states
health_state:
desc: 'Grouping of pigs from farrowing to fattening'
states:
- M:
name: 'Maternally immune individuals'
desc: 'piglets that are maternally immune to the disease'
fillcolor: 'teal'
- S:
name: 'Susceptible individuals'
desc: 'individuals that are susceptible to the disease'
fillcolor: 'forestgreen'
default: yes
- E:
name: 'Exposed individuals'
desc: 'individuals that has been exposed to the disease but not infectious yet'
fillcolor: 'bisque'
duration: 'latent_period'
- I:
name: 'Infectious individuals'
desc: 'individuals that are infected and infectious'
fillcolor: 'tomato'
- R:
name: 'Recovered individuals'
desc: 'individuals recovered from the disease'
transitions:
## S to E transistions are separated for each pig group to replicate the separation among the different areas in a pig farm
## This can also be combined in one transition and different force of infections can be considered per pig group
- from: M
to: S
rate: '1 / maternal_immunity_period'
desc: 'if maternally immune, it can be lost at the rate of 1 / maternal_immunity_period'
- from: S
to: E
rate: 'force_of_infection_int + trans_btwn_pens_frm_movement + trans_frm_3rd_path'
desc: 'horizontal and vertical transmission from piglets to farrowing sows is not possible for HEV'
- from: E
to: I
rate: 'NOT(OR(is_Jn, is_Jnb)) + OR(is_Jn, is_Jnb) * (1 / maternal_immunity_period)'
desc: 'newborn and nursing pigs have maternal immunity to HEV, however, nursing pigs can lose maternal immunity at the rate of 1/maternal_immunity_period'
- from: I
to: R
rate: 'recovery_rate'
## immunity wanes from the disease
- from: R
to: S
rate: 'waning_rate'
# _____ _
# | __ \ | |
# | |__) |_ _ _ __ __ _ _ __ ___ ___| |_ ___ _ __ ___
# | ___/ _` | '__/ _` | '_ ` _ \ / _ \ __/ _ \ '__/ __|
# | | | (_| | | | (_| | | | | | | __/ || __/ | \__ \
# |_| \__,_|_| \__,_|_| |_| |_|\___|\__\___|_| |___/
# PARAMETERS/FUNCTIONS/EXPRESSIONS USED IN THE MODEL
parameters:
init_herd_size_for_piglets:
desc: 'initial number of animals except sows in the herd (source: https://edepot.wur.nl/178589, average)'
value: 144
init_nb_nongestating:
desc: 'initial number of nongestating sows/gilts'
value: 'K_sows'
init_nb_gestating:
desc: 'initial number of gestating sows/gilts'
value: 'K_sows'
init_nb_farrowing:
desc: 'initial number of farrowing sows/gilts'
value: 'K_sows'
init_infected:
desc: 'initial number of infectious animals in the herd'
value: 1
init_prev:
desc: 'initial infection prevalence'
value: 0.1
init_prev_n:
desc: 'initial infection prevalence in nursing area'
value: 0.0
init_prev_f:
desc: 'initial infection prevalence in fattening area'
value: 0.1
K:
desc: 'farm`s carrying capacity (source: https://www.dutchnews.nl/2021/09/the-netherlands-has-fewer-pig-farms-but-each-one-has-more-pigs/)'
value: 1000
K_sows:
desc: 'average farm`s sow/gilt carrying capacity (source: https://edepot.wur.nl/178589)'
value: 24
K_herd:
desc: 'carrying capacity of a group (e.g. newborn, nursery, fatteners)'
value: 200
death:
desc: 'the death rate (/week)'
value: 0.07
dur_gestation:
desc: 'duration of gestation (weeks)'
value: 'ROUND(random_normal(16, 1))'
reproduction_g:
desc: 'reproduction rate of gilts (/week)'
value: 0.56
reproduction_s:
desc: 'reproduction rate of sows (/week)'
value: 0.63
reproduction:
desc: 'reproduction rate'
value: 'is_P0 * reproduction_g + NOT(is_P0) * reproduction_s'
avg_adult_death_age:
desc: 'mean longevity of adults (weeks)'
value: 72
adult_age:
desc: 'age when individuals become adults (weeks)'
value: 'random_integers(24,32)'
init_age_distrib:
desc: 'distribution of initial ages (weeks)'
value: 'adult_age + random_integers(0, 7)'
init_age_nursing:
desc: 'initial age of nursing piglets (farrowing area) in the initial population (weeks)'
value: 'random_uniform(0,3)'
init_age_nursery:
desc: 'initial age of piglets in the nursery for the initial population (weeks)'
value: 'weaning_time + random_uniform(6,8)'
init_age_fattener:
desc: 'initial age of fattening pigs in the initial population (weeks)'
value: 'weaning_time + random_uniform(6,8) + random_uniform(16,18)'
weaning_time:
desc: 'weaning time of animal (age in weeks)'
value: 3
nursing_time:
desc: 'nursing time of animal (age in weeks)'
value: 'random_integers(min_nt, max_nt)'
max_nt:
desc: 'maximum nursing time (age in weeks)'
value: 8
min_nt:
desc: 'minimum nursing time (age in weeks)'
value: 6
finishing_time:
desc: 'finishing time of animal (age in weeks)'
value: 17
max_ft:
desc: 'maximum finishing time (age in weeks)'
value: 18
min_ft:
desc: 'minimum finishing time (age in weeks)'
value: 16
avg_dur_latency:
desc: 'average duration of latency'
value: 'random_uniform(0.5,5) / 7'
latent_period:
desc: 'latent period of exposed indviduals before they become infectious (weeks)'
value: 'random_uniform(0.5,5) / 7'
transmission_rate:
desc: 'disease transmission rate within a popoulation (/week) (Cador 2016)'
value: '2.43 * 7' #5.32250497
force_of_infection_int:
desc: 'the rate by which a disease is transmitted from I to S (/week)'
value: 'transmission_rate * total_I / total_herd'
mean_bp_trans:
desc: 'mean of between pen transmission rate'
value: '7 * (10 ** -8)'
min_bp_trans:
desc: 'minimum of between pen transmission rate'
value: '5 * (10 ** -9)'
max_bp_trans:
desc: 'maximum of between pen transmission rate'
value: '3 * (10 ** -7)'
sd_bp_trans:
desc: 'estimated standard deviation of between pen transmission rate'
value: '(max_bp_trans - min_bp_trans) / 4'
shape_bp_trans:
desc: 'shape of between pen transmission rate'
value: '(mean_bp_trans / sd_bp_trans) ** 2'
scale_bp_trans:
desc: 'scale of between pen transmission rate'
value: '(sd_bp_trans ** 2) / mean_bp_trans'
bp_trans:
desc: 'between pen transmission rate'
value: '7 * random_gamma(shape_bp_trans, scale_bp_trans)'
between_herd_trans:
desc: 'transmission rate between herds (Cador 2016)'
value: '1.41 * 7' #0.5524361
neighboring_herd_trans:
desc: 'transmission rate between neighboring fattening herds'
value: '1.41 * 7' #0.51157841
third_path_trans:
desc: 'transmission rate among areas in the farm via third pathway of infection (e.g., via air, fomites, vermin) (https://doi.org/10.1371/journal.pone.0106177)'
value: '2.43 * 7 / 178'
HEV_length:
desc: 'The length of the HEV genome is approximately 7.2 kilobases or 7,200 base pairs.'
value: 7200
waning_rate:
desc: 'waning rate of immunity from the disease per week'
value: '7 / 180' #https://doi.org/10.1371/journal.pone.0202493
recovery_rate:
desc: 'recovery rate of individuals from the disease'
value: '7 / 6.1' #'7 / 17'
mu_I:
desc: 'base mortality of infected individual'
value: 0.001
mortality_I:
desc: 'mortality due to infection'
value: 'mu_I * total_herd / K_herd'
maternal_immunity_period:
desc: 'period of time that a piglet is immune from the disease due to maternal immunity (weeks)'
value: 'weaning_time + nursing_time'
##other than vertical transmission, shedding from sow and sow acquired immunity
##can be considered in the disease transmission in a farrowing area
vert_trans:
desc: 'vertical transmission from sow to piglet'
value: 0.1
vert_trans_I:
desc: 'vertical transmission from infected sow to piglet'
value: 'vert_trans * is_I'
mortality_weaning:
desc: 'mortality of piglets before weaning'
value: 0
mortality_nursery:
desc: 'mortality of piglets at the nursery'
value: 0
mortality_fattening:
desc: 'mortality of piglets at the fattening stage'
value: 0
mean_pba:
desc: 'average pigs that are born alive'
value: 13.1
sd_pba:
desc: 'standard deviation of the number of pigs born alive'
value: 1.06
pba:
desc: 'number of pigs born alive'
value: 'ROUND(random_normal(mean_pba, sd_pba))'
## metapopulation
nb_herds:
desc: 'number of different populations'
value: 17
nb_infected_herds:
desc: 'number of infected herds'
value: 1
init_proba_mat_imm:
desc: 'initial probability of maternal immunity'
value: 0.5
init_portion_I:
desc: 'initial portion of infectious individuals from the initial prevalence; others are exposed'
value: 0.0
proba_removal_if_I:
desc: 'probability of being removed from population if infectious'
value: 0.0
proba_removal_if_E:
desc: 'probability of being removed from population if exposed'
value: 0.0
biosec_remove_risky_move:
desc: 'indicator parameter for avoiding risky movement: 1 = avoid, 0 = no restriction'
value: 0
# weight-related parameters
# sources: https://www.prrs.com/expertise/publications/prrsflex-increases-average-daily-weight-gain-dutch-finishing-pigs
# doi:10.1017/S175173111900346X
# https://porcinehealthmanagement.biomedcentral.com/articles/10.1186/s40813-021-00225-y
mean_wean_weight:
desc: 'mean weight of weaning piglets'
value: 6.34
sd_wean_weight:
desc: 'sd weight of weaning piglets'
value: 0.7
min_wean_weight:
desc: 'minimum weaning weight for piglets (https://www.mdpi.com/2076-2615/10/6/1017)'
value: 5.5
mean_fattening_weight:
desc: 'mean weight of fattening piglets'
value: 30
sd_fattening_weight:
desc: 'sd weight of fattening piglets'
value: 5
min_fattening_weight:
desc: 'minimum fattening weight for piglets'
value: 24
# transmission probabilities for transmission from outside the farm
proba_encounter:
desc: 'max probability of encountering infectious agent'
value: 0.9
proba_trans:
desc: 'max probability of transmission from an infectious agent'
value: 0.9
proba_ext_I:
desc: 'max probability that external agent is infectious'
value: 0.9
proba_success_biosec_opt:
desc: 'optimistic probability of success of biosecurity measure'
value: 1.0
proba_success_biosec_ml:
desc: 'most likely probability of success of biosecurity measure'
value: 0.75
proba_success_biosec_pes:
desc: 'most likely probability of success of biosecurity measure'
value: 0.5
# _____ _ _
# / ____| | | |
# | (___ | |_ __ _| |_ _____ ____ _ _ __ ___
# \___ \| __/ _` | __/ _ \ \ / / _` | '__/ __|
# ____) | || (_| | || __/\ V / (_| | | \__ \
# |_____/ \__\__,_|\__\___| \_/ \__,_|_| |___/
statevars:
age:
desc: 'age of the animal'
weight:
desc: 'weight of the animal'
gestation_age:
desc: 'gestation age of the animal'
nb_fatteners_sold:
desc: 'number of fatteners sold'
nb_nursery_pigs_sold:
desc: 'number of nursery pigs sold'
dead_pigs:
desc: 'number of dead pigs'
nb_piglets_I_from_vert_trans:
desc: 'number of piglets that are born infected'
initial_prevalence:
desc: 'Initial prevalence in the population'
initial_herd_size:
desc: 'initial number of animals in the herd (source: https://edepot.wur.nl/178589, average)'
trans_btwn_pens_frm_movement:
desc: 'transmission between pens from farmer movement'
initial_nongestating_herd_size:
desc: 'initial number of nongestating sows and gilts'
initial_gestating_herd_size:
desc: 'initial number of gestating sows and gilts'
initial_newborn_herd_size:
desc: 'initial number of unweaned piglets'
initial_farrowing_herd_size:
desc: 'initial number of farrowing sows'
initial_nursery_herd_size:
desc: 'initial number of pigs in the nursery'
initial_fattening_herd_size:
desc: 'initial number of pigs in the growing/fattening area'
nb_of_sampled_I_Jf:
desc: 'number of sampled fatteners that are infected'
nb_new_farrowing_sows:
desc: 'number of new farrowing sows at each time step'
external_infection:
desc: 'probability of infection from external sources e.g. vermin, visitors, delivery vehicles, wild animals'
trans_frm_3rd_path:
desc: 'force of infection that comes from other areas in a farm via a third transmission pathway (e.g., via air, fomites, vermin, etc)'
# _____ _ _
# | __ \ | | | |
# | |__) | __ ___ | |_ ___ | |_ _ _ _ __ ___ ___
# | ___/ '__/ _ \| __/ _ \| __| | | | '_ \ / _ \/ __|
# | | | | | (_) | || (_) | |_| |_| | |_) | __/\__ \
# |_| |_| \___/ \__\___/ \__|\__, | .__/ \___||___/
# __/ | |
# |___/|_|
# PROTOTYPES describe typical individuals, characterized by specific
# values of their variables
prototypes:
herd:
- nongestating_population:
desc: 'population initially of nongestating sows and gilts'
initial_prevalence: init_prev
initial_nongestating_herd_size: init_nb_nongestating
initial_gestating_herd_size: 0
initial_farrowing_herd_size: 0
initial_newborn_herd_size: 0
initial_nursery_herd_size: 0
initial_fattening_herd_size: 0
trans_btwn_pens_frm_movement: 0
external_infection: 0
trans_frm_3rd_path: 0
- gestating_population:
desc: 'population initially of gestating sows and gilts'
initial_prevalence: init_prev
initial_nongestating_herd_size: 0
initial_gestating_herd_size: init_nb_gestating
initial_farrowing_herd_size: 0
initial_newborn_herd_size: 0
initial_nursery_herd_size: 0
initial_fattening_herd_size: 0
trans_btwn_pens_frm_movement: 0
nb_new_farrowing_sows: 0
external_infection: 0
trans_frm_3rd_path: 0
- farrowing_population:
desc: 'population initially of farrowing sows and nursing piglets'
initial_prevalence: init_prev
initial_nongestating_herd_size: 0
initial_gestating_herd_size: 0
initial_farrowing_herd_size: init_nb_farrowing
initial_newborn_herd_size: init_herd_size_for_piglets
initial_nursery_herd_size: 0
initial_fattening_herd_size: 0
trans_btwn_pens_frm_movement: 0
external_infection: 0
trans_frm_3rd_path: 0
- nursery_population:
desc: 'population initially of pigs in the nursery area'
initial_prevalence: init_prev_n
initial_nongestating_herd_size: 0
initial_gestating_herd_size: 0
initial_farrowing_herd_size: 0
initial_newborn_herd_size: 0
initial_nursery_herd_size: init_herd_size_for_piglets
initial_fattening_herd_size: 0
trans_btwn_pens_frm_movement: 0
external_infection: 0
trans_frm_3rd_path: 0
- fattening_population1:
desc: 'population initially of growing and fattening pigs'
initial_prevalence: init_prev_f
initial_nongestating_herd_size: 0
initial_gestating_herd_size: 0
initial_farrowing_herd_size: 0
initial_newborn_herd_size: 0
initial_nursery_herd_size: 0
initial_fattening_herd_size: 12
trans_btwn_pens_frm_movement: 0
external_infection: 0
trans_frm_3rd_path: 0
- fattening_population2:
desc: 'population initially of growing and fattening pigs'
initial_prevalence: init_prev_f
initial_nongestating_herd_size: 0
initial_gestating_herd_size: 0
initial_farrowing_herd_size: 0
initial_newborn_herd_size: 0
initial_nursery_herd_size: 0
initial_fattening_herd_size: 12
trans_btwn_pens_frm_movement: 0
external_infection: 0
trans_frm_3rd_path: 0
- fattening_population3:
desc: 'population initially of growing and fattening pigs'
initial_prevalence: init_prev_f
initial_nongestating_herd_size: 0
initial_gestating_herd_size: 0
initial_farrowing_herd_size: 0
initial_newborn_herd_size: 0
initial_nursery_herd_size: 0
initial_fattening_herd_size: 12
trans_btwn_pens_frm_movement: 0
external_infection: 0
trans_frm_3rd_path: 0
- fattening_population4:
desc: 'population initially of growing and fattening pigs'
initial_prevalence: init_prev_f
initial_nongestating_herd_size: 0
initial_gestating_herd_size: 0
initial_farrowing_herd_size: 0
initial_newborn_herd_size: 0
initial_nursery_herd_size: 0
initial_fattening_herd_size: 12
trans_btwn_pens_frm_movement: 0
external_infection: 0
trans_frm_3rd_path: 0
- fattening_population5:
desc: 'population initially of growing and fattening pigs'
initial_prevalence: init_prev_f
initial_nongestating_herd_size: 0
initial_gestating_herd_size: 0
initial_farrowing_herd_size: 0
initial_newborn_herd_size: 0
initial_nursery_herd_size: 0
initial_fattening_herd_size: 12
trans_btwn_pens_frm_movement: 0
external_infection: 0
trans_frm_3rd_path: 0
- fattening_population6:
desc: 'population initially of growing and fattening pigs'
initial_prevalence: init_prev_f
initial_nongestating_herd_size: 0
initial_gestating_herd_size: 0
initial_farrowing_herd_size: 0
initial_newborn_herd_size: 0
initial_nursery_herd_size: 0
initial_fattening_herd_size: 12
trans_btwn_pens_frm_movement: 0
external_infection: 0
trans_frm_3rd_path: 0
- fattening_population7:
desc: 'population initially of growing and fattening pigs'
initial_prevalence: init_prev_f
initial_nongestating_herd_size: 0
initial_gestating_herd_size: 0
initial_farrowing_herd_size: 0
initial_newborn_herd_size: 0
initial_nursery_herd_size: 0
initial_fattening_herd_size: 12
trans_btwn_pens_frm_movement: 0
external_infection: 0
trans_frm_3rd_path: 0
- fattening_population8:
desc: 'population initially of growing and fattening pigs'
initial_prevalence: init_prev_f
initial_nongestating_herd_size: 0
initial_gestating_herd_size: 0
initial_farrowing_herd_size: 0
initial_newborn_herd_size: 0
initial_nursery_herd_size: 0
initial_fattening_herd_size: 12
trans_btwn_pens_frm_movement: 0
external_infection: 0
trans_frm_3rd_path: 0
- fattening_population9:
desc: 'population initially of growing and fattening pigs'
initial_prevalence: init_prev_f
initial_nongestating_herd_size: 0
initial_gestating_herd_size: 0
initial_farrowing_herd_size: 0
initial_newborn_herd_size: 0
initial_nursery_herd_size: 0
initial_fattening_herd_size: 12
trans_btwn_pens_frm_movement: 0
external_infection: 0
trans_frm_3rd_path: 0
- fattening_population10:
desc: 'population initially of growing and fattening pigs'
initial_prevalence: init_prev_f
initial_nongestating_herd_size: 0
initial_gestating_herd_size: 0
initial_farrowing_herd_size: 0
initial_newborn_herd_size: 0
initial_nursery_herd_size: 0
initial_fattening_herd_size: 12
trans_btwn_pens_frm_movement: 0
external_infection: 0
trans_frm_3rd_path: 0
- fattening_population11:
desc: 'population initially of growing and fattening pigs'
initial_prevalence: init_prev_f
initial_nongestating_herd_size: 0
initial_gestating_herd_size: 0
initial_farrowing_herd_size: 0
initial_newborn_herd_size: 0
initial_nursery_herd_size: 0
initial_fattening_herd_size: 12
trans_btwn_pens_frm_movement: 0
external_infection: 0
trans_frm_3rd_path: 0
- fattening_population12:
desc: 'population initially of growing and fattening pigs'
initial_prevalence: init_prev_f
initial_nongestating_herd_size: 0
initial_gestating_herd_size: 0
initial_farrowing_herd_size: 0
initial_newborn_herd_size: 0
initial_nursery_herd_size: 0
initial_fattening_herd_size: 12
trans_btwn_pens_frm_movement: 0
external_infection: 0
trans_frm_3rd_path: 0
- dressing_room1:
desc: 'dressing room 1 in a farm'
initial_prevalence: 0
initial_nongestating_herd_size: 0
initial_gestating_herd_size: 0
initial_farrowing_herd_size: 0
initial_newborn_herd_size: 0
initial_nursery_herd_size: 0
initial_fattening_herd_size: 0
trans_btwn_pens_frm_movement: 0
external_infection: 0
trans_frm_3rd_path: 0
- dressing_room2:
desc: 'dressing room 2 in a farm'
initial_prevalence: 0
initial_nongestating_herd_size: 0
initial_gestating_herd_size: 0
initial_farrowing_herd_size: 0
initial_newborn_herd_size: 0
initial_nursery_herd_size: 0
initial_fattening_herd_size: 0
trans_btwn_pens_frm_movement: 0
external_infection: 0
trans_frm_3rd_path: 0
animals:
- nongestating:
desc: 'initial healthy sows'
age_group: A
parity: P0
beta_i: 0
beta_i_max: 0
weight: 0
- nongestating_S:
desc: 'susceptible initial healthy sows'
age_group: A
age: init_age_distrib
sex: Female
parity: random
health_state: S
beta_i: 0
beta_i_max: 0
weight: 0
- nongestating_E:
desc: 'initial infected animals'
age_group: A
age: init_age_distrib
sex: Female
parity: random
health_state: E
beta_i: 0
beta_i_max: 0
weight: 0
- nongestating_I:
desc: 'initial infectious animals'
age_group: A
age: init_age_distrib
sex: Female
parity: random
health_state: I
beta_i: 0
beta_i_max: 0
weight: 0
- newborn_M:
desc: 'newly created animals with maternal immunity'
age_group: Jnb
sex: random
age: 0
parity: P0
health_state: M
beta_i: 0
beta_i_max: 0
weight: 0
- newborn_S:
desc: 'newly created animals that are susceptible'