README.md

In NZRLIC/RLPlots: Graphical outputs for New Zealand rock lobster stock assessment

RLPlots

RLPlots is an R package for plotting rock lobster (RL) stock assessment outputs and management proceedure evaluations (MPEs). Plotting functions are available for MPD fits, Markov chain Monte Carlo (MCMC) and some other plots.

Installation

RLPlots can be installed from R using

install.packages("devtools")
devtools::install_github("NZRLIC/RLPlots")

To install the devtools package requires Rtools, which is available from

https://cran.r-project.org/bin/windows/Rtools/

Using RLPlots

Once RLPlots has been installed it can be loaded in R using

library(RLPlots)

MPDs

Plotting of MPDs can be done using, for example

MPD.All(stock = "CRA1")

MCMCs

Plotting of MCMCs can be done using

MCMC.All(stock = "CRA1", source.dir = ".")

Plotting multiple MCMC chais on a single plot can be done using

Multichain.All(stock = "CRA1", source.dir = c("chain1/", "chain2/"))

The snail trail plot can be done using

Snail(stock = "CRA1", source.dir = ".")

MPEs

To plot MPE rules and results you must first read in the data before plotting

dat <- read.sims.sum(source.dir = ".")
# To plot all rules
MPE_rules(control.pars = dat[,13:22], target.dir = ".")
MPE_rules(control.pars = dat[irule,13:22], current.cpue = 1.48, target.dir = ".")
mpeview(dat = dat, stock = "CRA1", point.col = "par5", target.dir = ".",
        pars = c("avI_med","AvComm_med","P<Bref","AAV_med"),
        axis.labels = list(x = "CPUE", y = c("Commercial catch (tonnes)","P<Bref","%AAV")))

Developer commandments

• Thou shalt use four-space indentation
• Thou shalt place parentheses below function/loop/if statements
• Thou shalt use spaces between equal signs
• Thou shalt use a space after a comma
• Thou shalt use comments within a function
• Thou shalt fill out the doxygen header for each function
• Thou shalt test thy code

For example

#' Doxygen header function name
#'
#' Description
#'
#' @author Who
#' @param var1 a variable
#' @param var1 another variable
#' @return stuff
#' @export
#'
func <- function(var1 = 1, var2 = 2)
{
    # An example
    if (var1 == 1) stuff <- do_something(var1)
    # Or
    if (var2 != 3)
    {
        stuff <- do_something(var2)
    }
    return(stuff)
}

NZRLIC/RLPlots documentation built on May 7, 2019, 6:05 p.m.