examinedata: examinedata plots the yearly distributions of catch and...
In haddonm/rforcpue: Functions to Assist With The Analysis of CPUE Data

examinedata

R Documentation

examinedata plots the yearly distributions of catch and effort from 'x'

Description

examinedata plots the yearly distributions of the number of records, the catch, the effort, and the geometric mean cpue by year for the data in the fishery dependent data in the data.frame x. It also tabulates these values. Each of these are stored either as .csv or .png files 'in rundir'. It also logs these files in resfile, which opens the possibility of displaying all results in a local webpage under a tab labelled 'yeardata'. The 'rundir', 'resfile', and 'runname' should be the same as those used by makehtml to prepare a directory and 'resfile' to store the files to be used to make a local webpage of results.

Usage

examinedata(
  x,
  catch = "catch",
  labcatch = "catch",
  effort = "hours",
  labeffort = "effort",
  cpue = "cpue",
  labcpue = "cpue",
  LnCE = "LnCE",
  labLcpue = "log(cpue)",
  year = "year",
  spsname = "",
  rundir = "",
  runname = "",
  plotnum = c(1, 1),
  wid = 6,
  hgt = 5,
  xlimit = rep(NA, 12),
  category = "yeardata"
)

Arguments

`x`	the data.frame of fishery dependent data
`catch`	the name used to identify the catch factor of the species
`labcatch`	the axis label for catch
`effort`	the name used to identify the effort factor of the species
`labeffort`	the axis label for effort
`cpue`	the name used to identify the cpue factor of the species
`labcpue`	the axis label for cpue
`LnCE`	column name of log(cpue) in x, default='LnCE'
`labLcpue`	the axis label for log(cpue)
`year`	the name used to identify the year factor of the species
`spsname`	the name of the species of interest.
`rundir`	the full path of the results directory into which the plot files and the .csv files for the tables are to be stored.
`runname`	the name of the particular run being made
`plotnum`	the number of rows an columns of plots used, default=c(1,1)
`wid`	the width of each plot, default=6
`hgt`	the height of each plot, default=5
`xlimit`	a veector of 12 containing the xlim values, Lbound, Rbound, and inc, for four of the plots. Default is rep(NA,12). For the third plot no inc value is required so set it to zero (it will be ignored)
`category`	default='yeardata' but in case this is called for a subset of data then it can be set to whatever you wish