Chapter 1 Welcolme to r4Casal2

This book demonstrates functionality of the r4Casal2 R package. This is an R package that works with the Casal2 base R-library found here, although it is advised to use the R-library that is included with the Casal2 binary and usermanual you acquired. The Casal2 base R-library is responsible for reading in output and interacting with Casal2 configuration files. The r4Casal2 R package has been built for summarising and visualising objects read in from the base Casal2 R-library.

All functions in this package should be documented using the roxygen syntax with input parameters available using the ? query. For example ?get_fisheries. To get a list of functions and general info on the package you can use library(help="r4Casal2") or see Section 2 for another list

library(r4Casal2)
library(Casal2)
library(knitr)
library(ggplot2)
library(dplyr)
library(reshape2)
library(tidyr)

The core functionality of r4Casal2 are its accessor functions. These are functions that will return a specific object from a range of Casal2 objects in long format that are ggplot, dplyr friendly. Most accessors start with get_ and should be self explanatory. There are some plotting functions, but I have found that I often want to custom ggplots and so mainly have custom plots. The accessors are coded to deal with three types of outpus. These are;

extract.mpd() where Casal2 has been run with default report style. These objects are of class casal2MPD which are set by the Casal2 base function
extract.mpd() where Casal2 has been run with tabular reports casal2 --tabular or casal2 -t. These objects are of class casal2TAB which are set by the Casal2 base function
list this is a list of casal2MPD which is a useful format for comparing MPD runs see Section 5