R/rforcpue.R

In haddonm/rforcpue: Functions to Assist With The Analysis of CPUE Data

#' @title rforcpue a set of functions to assist with CPUE standardization
#'
#' @description The rforcpue package provides numerous functions to assist
#'     with the standardization of fisheries CPUE data. There are three
#'     types of functions 1) analytical functions that assist with
#'     cpue standardizations, 2) plotting functions that can be used to
#'     illustrate the results of the standardizations, and 3) utility
#'     functions that assist with data manipulations, and other activities
#'     that occur when conducting standardizations.
#'
#' @section Analytical functions:
#' \describe{
#'   \item{coef.outce}{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{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.outce}{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 rforcpue
#' @keywords internal
"_PACKAGE"
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#' @import graphics
#' @import codeutils
#' @import makehtml
#' @importFrom hplot addlnorm addnorm categoryplot expandmatrix
#' @importFrom hplot histyear inthist linept makepolygon newplot panel.hist
#' @importFrom hplot parset parsyn pickbound plot1 plotnull plotprep plotxyy
#' @importFrom hplot RGB setplot uphist xyplotyear yearBubble
#' @importFrom grDevices png rgb dev.cur dev.new dev.off
#' @importFrom stats anova as.formula dnorm lm median qnorm qqline qqnorm
#' @importFrom stats quantile sd loess ccf coef
#' @importFrom utils data read.csv str tail write.table
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