r4cpue: Functions to assist with CPUE standardization

#' @title r4cpue a set of functions to assist with CPUE standardization
#'
#' @description The r4cpue package provides two categories of functions
#'     analytical functions that assist with the cpue standardization
#'     plotting functions that illustrate the results of the standardizations.
#'     In addition there are example data sets
#'
#' @section Analytical functions:
#' \describe{
#'   \item{coef.CEout}{S3 function applied to the output of standLM}
#'   \item{dosingle}{conducts a standardization of indat using the
#'       inmodel, that can be generated using makeonemodel}
#'   \item{geomean}{Calculates the bias corrected geometric mean}
#'   \item{getmeans}{Calculates a set of central tendency measures for
#'       nominal CPUE}
#'   \item{makecategorical}{converts a series of variables in a data.frame into
#'       factors}
#'   \item{makemodels}{Given a list of factors this generates a list of
#'       formula for inclusion in glm or standLM}
#'   \item{makeonemodel}{generates a single model for use in dosingle}
#'   \item{scaleCE}{Rescales a vector of CPUE to a mean of 1.0 or of avCE}
#'   \item{standLM}{Uses lm to standardize log-transformed CPUE}
#'   \item{summary.CEout}{an S3 function to summarize a standardization output}
#' }
#' @section Plotting functions:
#' \describe{
#'   \item{addnorm}{fits a normal distribution curve to a given histogram}
#'   \item{diagnosticPlot}{plots some diagnostic details for a standardization}
#'   \item{impactplot}{Plots the influence of each factor}
#'   \item{inthist}{a replacement for the hist function for use with integers}
#'   \item{plotdata}{plots graphs of untransformed and log-transformed data}
#'   \item{plotprep}{defines a base graphics window for use in RStudio}
#'   \item{plotstand}{Plots the optimum model vs the year-only model}
#'   \item{plotstandFY}{The same as plotstand but for Fishing year species}
#'   \item{yearBubble}{Generates a bubbleplot of x against Year}
#' }
#' @section Utility functions:
#' \describe{
#'    \item{addcount}{adds a new column to input data.frame that is a count
#'        of the number of years in which the identified variable, default
#'        'Vessel' occurs each year for each level of the factor}
#'    \item{fishery}{generates vectors of year, catch, effort, and cpue}
#'    \item{getfact}{extracts a given factor from the analysis with its
#'        standard errors and rescaled to a mean of 1.0}
#'    \item{getStand}{extracts the main year paramters from a standLM object
#'        with its StErr and confidence itervals}
#'    \item{properties}{Checks a data.frame for NAs and counts; used for QC}
#'    \item{removeEmpty}{removes empty strings from a vector of strings}
#'    \item{selectdata}{simplifies the selection of data from a data.frame
#'        by depth, years, zones, method, and fishery}
#'    \item{toExcel}{copys the selected vector or matrix to the clipboard
#'        it can be pasted directly into Excel or other software}
#'    \item{yearNA}{counts the NAs in each numeric field in a data.frame}
#'    \item{yearZero}{counts the zeros and NAs in identified fields in a df}
#' }
#' @docType package
#' @name r4cpue
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#' @title sps - a 11603 x 10 data.frame for testing CPUE functions
#'
#' @description sps - a 11603 x 10 data.frame for testing CPUE functions
#'    containing simulated trawl shot CPUE data for the years 2003 - 2014,
#'    including details of year, month, vessel, catch_kg, longitude,
#'    latitude, the depth trawled, a daynight identifier, the effort
#'    in hours, and the zone, the CPUE, and the natural log(CPUE) need
#'    to be added.
#' @format A data frame with 11603 records x 10 variables:
#' \itemize{
#'   \item Year - The year in which fishing takes place
#'   \item Month - The month in which fishing took place
#'   \item Vessel - a code uniquely identifying vessels through time
#'   \item catch_kg - the retained catch of the target species in kg
#'   \item Long - the longitude of the start of the trawl shot
#'   \item Lat - the latitude of the start of the trawl shot
#'   \item Depth - the average depth of trawling in meters
#'   \item DayNight - a code denoting the daynight status D = day, N = night,
#'      M = mixed, and U = unknown
#'   \item Effort - the hours trawled
#'   \item Zone the zone in which trawling occurs 1 - 3
#' }
#' @docType data
#' @name sps
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