calc_prev: Calculate prevalence from 'cow_table' or a csv file

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

Description

Calculate monthly prevalences from csv files or list of cow_table. Set either one of output_dir+output_filename or csv.

Usage

calc_prev(
  param,
  output_filename = param$output_filename,
  output_dir = param$output_dir,
  i_simulation = seq_len(param$n_simulation),
  list_cows = NULL,
  type = c("prop", "count", "status", "route"),
  gather = T,
  drop = T,
  by_simulation = F
)

Arguments

param, output_filename, output_dir	See param.
i_simulation	csvs with this numbers are used.
list_cows	List consisted of cow_tables. Specify one of output_dir+output_filename or list_cows.
type	prop means proportion of infected cows. count means the number of infected and non-infected cows. status means the number of s (non-infected), ial (asymptomatic), ipl (persistent lymphositosis) and ebl cows. route means the number of infected cows by each infection route.
gather	When type is "route", whether infection routes as "tie_exposed_baseline", "tie_exposed_risk", "tie_non_exposed" and "free" should be gathered to one category "insects" or treated as-is.
by_simulation	Whether calculate median of all simulations (FALSE) or calculate by each simualtion (TRUE).

Value

A data.table contains monthly prevalences.

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