prepare_cows: Process raw cow data to suitable form

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

Description

Transform an input csv into a suitable form, which is in a form of cow_table.

Usage

prepare_cows(
  csv,
  param,
  data = NULL,
  output_file = NULL,
  today = Sys.Date(),
  create_calf_data = F,
  modify_prevalence = NULL,
  area_name = NULL,
  seed = NULL
)

Arguments

csv	File path of an input csv file. See the Detail section to know about form of input csv.
param	See param.
data	data.frame as a input instead of csv. See the Detail section to know about form of input data.
output_file	The name of an output file (must be a csv file). If NULL, no output file is created.
today	A Date class object or a character in "YYYY/MM/DD" format. The date used to calculate age from date_birth when age is not set. today is automatically calculated when both of age and date_birth are filled and date_birth is in form of Date rather than number (which means that the cow was born $n$ month ago) and the value passed to this argument is ignored.
create_calf_data	logical or a numeric. Create data for young cows based on cow data in the input. Set this argument when the input does not contain data for young cows (e.g. when you use Nyuken data). If TRUE, create cows younger than the youngest cows in the input. If a numeric is set, create cows equal to or younger than that age.
modify_prevalence	One or two numbers within a range of 0 to 1. If the parameter is not NULL, modify infection_status column to make proportion of infected cows (when modify_prevalence is a number) orialandipl + eblcows (whenmodify_prevalence' is two numbers) accordingly.
area_name	If area_id is specified by character, specify integer area_id like c(barnA = 1, barnB = 2, ...).
seed	Seed for a simulation.

Details

An input csv file can have following columns. The csv file must contain age column.

• cow_id: It can be use-defined cow ID (not have to be a 9- or 10-digits code). If not set, cow_id is allocated sequencially (From 1 to the number of input cows).

• age: Age in month. Either one of age or date_birth must be set.

• date_birth: Birth day. If age is not set, age is calculated from this and today argument in the function.

• sex: One of "female", "male" or "freemartin". If not set, all cows are assumed to be "female".

• is_replacement: If a farm keeps non-replacement cows (e.g. a male newborn which will be send to a livestock market), set this parameter. If not set, age = 0 female cows are assumed to be a replacement according to prop_replacement parameter in param and all male cows are assumed to be a non-replacement.

• stage, parity, date_last_delivery, date_got_pregnant, date_dried: If not set, they will be calculated in according to parameters related with reproduction in param.

• is_to_test_pregnancy: If not set, FALSE is set.

• n_ai: If not set, it is assumed to be 0.

• infection_status: At least one of this variable or modify_prevalence argument must be set. Valid categories are follows: "al", "pl" and "ebl" (case insensitive). Other values or NA will be coerced to "s" (= non-infected). When modify_prevalence is set, prevalence is modified to make prevalence equal to the first value of modify_prevalence.

• date_ial, date_ipl, date_ebl: Specify the date when infection status was confirmed. If NULL, 0 is set.

• area_id: If not set, cows are divided to four areas based on stage ("calf" = 1, "heifer" = 2, "milking" = 3, "dry" = 4). If NAs are included, cows are allocated to areas in which cows with the same stage and parity are kept. If area_id is written in character, argument area_name must be set.

• months_in_area: If not set, it is assumed to be 0. This parameter has no effect when a farm does not use months_in_area as a criteria for area movement. See area_table for detail of area movement.

• chamber_id: If not set, it is randomly allocated later in setup_cows().

• is_isolated: If not set, FALSE is set.

For further detail of each variable, see cow_table.

Value

A csv file which can be used as an input for simulate_blv_spread().

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