param: Parameters about a simulation which should be set by users

In fmsan51/blvibmjp: Individual Based Model of Bovine Leukemia Virus Spread in a Dairy Herd in Japan

Description

Parameters about a simulation

Usage

param

Format

An object of class list of length 27.

Details

Parameters related with simulation:

• simulation_length (integer): Length of simulation (months). (default: 60)

• n_simulation (integer): The number of simulation. (default: 1)

• simulation_start (1-12): The month simulation starts (1 = Jan, 2 = Feb, ...). (default: 1)

• output_dir (character): Directory to output files. (default: data/output)

• output_filename (character): The name of the output files. (default: "simulation")

Parameters depends on a farm:

• prop_female (0-1): Proportion of female of newborns. (default: average in Hokkaido)

• prop_replacement (0-1): Proportion of calves to be replacements in female newborns. (default: average in Hokkaido)

• prop_died (1-0): Proportion of dead cows in removed cows (Died / (Died + Slaughtered)). (default: average in Hokkaido)

• prop_heat_detected (0-1): Proportion of detected heats in total heats. (default: average in Hokkaido)

• calving_interval (numeric): Calving interval in day. (default: average in Hokkaido)

• age_first_delivery (numeric): Age (in month) or the first delivery. (default: average in Hokkaido)

• age_first_ai (numeric): Age (in month) of the first AI for heifers. (default: average in Hokkaido)

• day_start_ai (numeric): Day of first AI after a delivery. (default: average in Hokkaido)

• days_milking (numeric): Length of milking period (in days). (default: average in Hokkaido)

• days_open (numeric): Length of open period (in days). (default: average in Hokkaido)

• n_introduced c(calf, heifer, delivered): The number of introduced cows for five years. (default: c(0, 0, 0))

• capacity_in_head c(lower, upper): Lower/upper limit of the herd size. Set either this or capacity_as_ratio below.

• capacity_as_ratio c(lower, upper): Lower/upper limit of the herd as ratio to the initial herd size (lower limit = lower * initial_herd_size, upper limit = upper * initial_herd_size). Set either this or capacity_in_head above. When both of capacity_in_head and capacity_as_ratio is NA, capacity_as_ratio is set to c(0.9, 1.1).

• prob_seroconversion_in_pasture (0-1): probability of seroconversion when a cow is send to a communal pasture. (default: random value from 0 to 1)

• days_qualantine (integer): Length of qualantine period (in days) for introduced cows in which introduced cows contacted no cows but introduced ones at the same time. (default: 0)

• control_insects (logical or 0-1): wheter conduct control measures against insects. When specified by a number from 0 to 1, it means that the number of bloodsucking insects decrease to this proportion (i.e., control_insects = 0.8 means that the number of insects becomes 80%). When TRUE, it is assumed that insects in a farm decrease to 50%. (default: FALSE)

• change_gloves (logical): whether use one glove for one cow for rectal palpation. (default: TRUE)

• feed_raw_colostrum (logical): wheter feed non-pasteurized colostrum milk to newborn calves. (default: FALSE)

• cull_infected_cows ("no"/"all"/"highrisk"): Whether cull infected cows. "all" means cull infected cows even when they do not show simptoms and "highrisk" means cull PL or EBL cows only. Culling is conducted when a new female calf is born and you can set frequency of culling by cull_frequency described next.

• culling_frequency (numeric): This parameter can be set to specify the frequency of culling to cull an infected cow to every $n$ (= culling_frequency) female calves.

• test_frequency (1-12): Frequency of BLV tests in a year. Only integers can be set.

• test_method ("immunodiffusion"/"ELISA"/"PHA"/"nested PCR"/"real-time PCR" or two numerics (0-1)): Method of BLV test. Character indicating test method or a vector consisted of two numerics which mean sensitivity and specificity of the test.

fmsan51/blvibmjp documentation built on Sept. 2, 2020, 9:04 p.m.