plot_route: Plot monthly infection routes nicely

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

Description

Plot average (median) monthly prevalences by each infection route from csv files or list of cow_table. Set either one of output_dir+output_filename or csv.

Usage

plot_route(
  param,
  output_filename = param$output_filename,
  output_dir = param$output_dir,
  i_simulation = seq_len(param$n_simulation),
  list_cows = NULL,
  language = "English",
  drop = T,
  route_levels = NULL,
  route_labels = NULL,
  gather = T,
  max_ylim = NULL,
  title = T,
  legend_title = T,
  xlab = T,
  ylab = T,
  gray = F,
  area_color = NULL,
  border = F,
  border_color = NULL,
  font = NULL
)

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.
language	Language to which translate messages. At present, only English and Japanese is implemented.
drop	Drop infection routes not in csv or cows from a legend.
route_levels, route_labels, gather	See redefine_route_levels
max_ylim	Upper limit of the y-axis of the plot.
title, legend_title, xlab, ylab	logical or character. Plot a title, a legend title, a label for x-axis and a label for y-axis. When TRUE, the default value is used. When FALSE or NULL, the title or the label is not shown. When specified by character, the string is used as the title or the label.
gray	When TRUE, a plot will be a grayscale image.
area_color	Specify a color palette of a plot.
border	When TRUE, each area in a plot will be surrounded by border.
border_color	Specify a color palette for the border.
font	Font in a plot. The default is "Meiryo" for Windows and "Hiragino Kaku Gothic Pro W3" for the other OS.

Value

A ggplot2::ggplot plot.

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