cow_table: A data.table to store status of cows

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

Description

cow_table is a data.table to store status of cows. Status of all the cows in a farm is stored in one cow_table. The rows are consists of a_new_calf, which indicates one cow.

Usage

a_new_calf

cow_table_cols

Format

data.table

An object of class character of length 33.

Details

date_xxx variables are expressed as month. The month when the simulation starts is 0. eg. The date_birth of a cow which is 20 months old at the simulation start is -20. day_xxx variables are days in the month.

• cow_id

• age: Age in month.

• stage: One of "calf", "heifer", "milking" or "dry".

• sex: One of "female" (Holstern), "male" (Holstein), "freemartin" (female Hostein), "f1-female" (Hostein x Japanese black), "f1-male" (Holstein x Japanese black), "black-female" (Japanese black), "black-male" (Japanese black).

• date_birth: Date of birth.

• date_removal: Date of death. The value is NA while the cow is alive. It is set after the cow died.

• date_removal_expected: Expected date of death. It is calculated when a calf is born or when a cow is introduced to the herd.

• is_owned: Whether the cow is owned by the simulated herd. It is set FALSE when the cow is sold or died.

• cause_removal:

  • "died": died.

  • "slaughtered": slaughtered not due to the disease.

  • "culled": culled due to the disease.

  • "sold": send to a market or another farm.

  • "will_die": (still alive and) will die.

  • "will_be_slaughtered": (still alive and) will be slaughtered.

• is_replacement: TRUE: The cow will be kept in the farm as replacement. FALSE: The cow Will be sold to beef operations.

• parity

• date_last_delivery: 'Delivery' here includes abortions and stillbirths. NA means that the cow is heifer (pairty = 0).

• date_got_pregnant: NA means that the cow is open.

• date_dried: NA means that the cow is milking.

• n_ai: The number of AI from last delivery. The value is set as 0 when the cow got pregnant.

• day_heat: Day in month of the NEXT heat.

• day_last_detected_heat: Day in month of the LAST heat.

• is_to_test_pregnancy: Whether to be served for a pregnancy test (= AI was conducted to the cow and heats were not observed from then).

• infection_status: One of "s" (susceptible = non-infected), "ial" (aleukemia), "ipl" (PL) and "ebl".

• is_detected: Whether BLV infection is detected. Sometimes even a non-infected cow can be TRUE when false-positive in BLV test occurs.

• date_ial: The month when infection_status changes from "s" to "ial".

• date_ipl: The month when infection_status changes from "ial" to "ipl".

• date_ipl_expected: The expected month when infection_status changes from "ial" to "ipl". It is calculated when infection_status becomes "ial".

• date_ebl: The month when infection_status changes from "ipl" to "ebl".

• date_ebl_expected: The exppected month when infection_status changes from "ial" to "ebl". It is calculated when infection_status becomes "ial".

• cause_infection: The reason why the cow is infected. It is set when the cow gets infected.

  • "initial": already be infected at the start of the start of a simulation.

  • "tie_exposed_baseline": by insects (the cow is kept in a tie-stall barn and has an infected neighbor and infection was NOT due to the neighbor.)

  • "tie_exposed_risk": by insects (the cow is kept in a tie-stall barn and has an infected neighbor and infection was due to the neighbor.)

  • "tie_non_exposed": by insects (the cow is kept in a tie-stall barn and does not have an infected neighbor.)

  • "free": by insects (the cow is kept in an free-stall barn or at outside.)

  • "rp": by rectal palpation.

  • "vertical": vertical transimisson (intrauterine and by the dam milk).

  • "introduced": for a introduced cow which is infected before introduction (a home-bred cow infected from introduced cow is not categorized as this).

  • "pasture": infected at a communal pasture.

• susceptibility_ial_to_ipl: Genetic susceptibility to disease progress (Ial -> Ipl).

• susceptibility_ipl_to_ebl: Genetic susceptibility to disease progress (Ipl -> EBL).

• area_id: Area ID.

• months_in_area: The number of month a cow stayed in the current area.

• chamber_id: ID of the chamber in which the cow kept for a cow in a tie-stall barn. NA_real_ for a cow in a free-stall barn. 0 for a cow in a tie-stall barn but to it a chamber is not assigned (a free-roaming cow).

• is_isolated: Whether the cow is isolated for a cow in a tie-stall barn. NA_real_ for a cow in a free-stall barn.

• i_month: The number of months past from the start of a simulation.

See Also

tie_stall_table area_table movement_table rp_table

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