prepare_movement: Process raw movement 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 movement_table.

Usage

prepare_movement(
  csv,
  data = NULL,
  output_file = NULL,
  area_name = NULL,
  sep = "[,\t\r\n |;:]+",
  seed = NULL
)

Arguments

csv	File path of an input csv file. See the Detail section to know about form of input csv.
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.
area_name	If current_area and next_area are specified by character, specify integer area_id like c(barnA = 1, barnB = 2, ...).
sep	Separatator used in priority column. See explanation of priority in Detail section.
seed	Seed for a simulation.

Details

An input csv file can have following columns. The csv file must contain current_area, condition and next_area column.

• current_area

• condition

• next_area: A character like "1|2|3" will be converted to a numeric vector c(1, 2, 3). Separator (|) can be specifed by sep argument. (This transformation from character to numeric is necessary if you want to read data from a csv file.)

• priority: If NA, rep(1, length(next_area)) is set (which means all next_areas have the same priority and cows are randomly allocated among all next_areas). Values must be integer/numeric vectors of the same length with next_area or NA. Multiple values can be specified like next_area. For further detail of each variable, see movement_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.