This file provides a list and brief description of all functions
that are defined by PBS Modelling. This list includes both exported
function, which are doccumented in the appropriate Rd files which
are made available through the internal R documentation system.

The following functions and data are exported to users of PBS Modelling.


CCA.qbr.hl              Sampled Counts of Quillback Rockfish (Sebastes
                        maliger) (dataset)
addArrows               Add Arrows to a Plot Using Relative (0:1)
                        Coordinates
addLabel                Add Label to a Plot Using Relative (0:1)
                        Coordinates
addLegend               Add Legend to a Plot Using Relative (0:1)
                        Coordinates
calcFib                 Several Methods to Calculate Fibonacci Numbers
calcGM                  Calculate the Geometric Mean
clearAll                Remove All R Objects
clearWinVal             Remove All Widget Variables
closeWin                Close GUI windows
compareLists            Compares two non-recursive lists
compileDescription      Converts and Saves a Window Description Into a
                        List
createVector            Create a GUI with a Vector Widget
createWin               Create a GUI Window
drawBars                Draw a Linear Barplot on the Current Plot
expandGraph             Expand Plot Area by Adjusting Margins
exportPBShistory        Export Saved History
findPat                 Search a Vector With Multiple Patterns
genMatrix               Generate Test Matrices for plotBubbles
getWinVal               Retreive Widget Values
importPBShistory        Import a history list from a file
initPBShistory          Customized History Widget Functions
openFile                Open Files With Associated Program
pad0                    Pads Numbers with leading zeroes
parseWinFile            Convert Window Description File into a List
pause                   Pause
pickCol                 Display Interactive Colour Selection Palette
plotBubbles             Construct a Bubble Plot from a Matrix
plotCsum                Plots Cumulative Frequency of Data
promptOpenFile          Display Open File Dialog
promptSaveFile          Display Save File Dialog
readList                Read a List From a File
resetGraph              Reset plot par Values
runExamples             Display PBS Modelling Examples
setWinVal               Update Widget Values
show0                   Convert Numbers Into Text With Specified
                        Decimal Places
showArgs                Display Expected Widget Arguments
testCol                 Display Colour Palette
testLty                 Display Line Types
testLwd                 Display Line Widths
testPch                 Display Plotting Symbols
testWidgets             Displays Sample GUIs and Source Code
unpackList              Unpack List Elements Into Variables
view                    Display First n Rows of an Object
writeList               Write a List to a File


The following is a list of all the underlying functions which are called as a 
result of a user calling an exported function.

.autoConvertMode
  converts strings into numerical reposentation

.buildgrid
  used for building a grid with nested widgets as described by window 
  description list

.catError
  used for displaying parsing errors (with line numbers..)

.convertMatrixListToDataFrame
  converts a "matrix list" into a dataframe - matrix list is a list of lists

.convertMatrixListToMatrix
  converts a "matrix list" into a real matrix

.convertPararmStrToList
  extracts arguments (seperated by space) from a single string into a list, 
  preserving keys and values. whitespace in quotes is preserved

.convertPararmStrToVector
  extracts elements (seperated by space) into a vector, preserving spaces in 
  quotes. Keys are not valid, and are intrupted as values

.createTkFont
  creates a TKFont variable based of a PBS styled font string

.createWidget
  looks for .createWidget.xxx where xxx is the widget type
  Different types:
  .createWidget.button .createWidget.check  .createWidget.data 
  .createWidget.entry  .createWidget.grid   .createWidget.history 
  .createWidget.label  .createWidget.matrix .createWidget.null 
  .createWidget.radio  .createWidget.slide  .createWidget.slideplus 
  .createWidget.text   .createWidget.vector

.extractData
  called by TK on button, bind, onchange,... events - which then calls a user 
  function, once pbs.win is updated

.extractFuns
  Old function used for extracting user function names

.extractVar
  converts values from TK into R values (converts mode, merges multiple 
  variables into vector, matrix, dataframe if named accordingly - foo[1], 
  foo[1,2] or foo[1,2]d (d for data))

.flipMatrix
  flips around the data in a matrix to make it as if it was read byrow instead 
  of bycol

.getArguments
  used for documenting widget arguments (ordering and default value)

.getMatrixListSize
  determines size of matrix needed for the matrixList

.getParamFromStr
  parses a string representing a widget into an equivalent list

.getParamOrder
  returns a list defining all widget arguments and default values

.getPBS.win
  returns an up-to-date PBS.win list

.hash
  generates a hash table that is passed by reference

.inCollection
  searches a vector - No longer in use - replaced by .isReallyNull

.initPBSoptions
  called by zzz.r - prepares the openFile config list.

.isReallyNull
  returns if a key really exists in a list

.matrixHelp
  stores elements of a matrix in a "matrix list" (which is dynamic)

.parsegrid
  grids in list representation have a data argument which is a list of lists of 
  widget lists. First list represents each row, 2nd list represents each column, 
  each element of the 2nd list is a widget. This function organizes widgets into 
  this 2d list

.parsemenu
  used to setup menu lists - similar to parsegrid

.PBSdimnameHelper
  used to name matrix and dataframe objects (with given rowNames and colNames)

.searchCollection
  returns the position of a needle in a haystack (or if needle is a shortened 
  (but still unique) needle)

.setMatrixElement
  used by .setMatrixElement to assign elements from "matrix list" to real matrix

.setWinValHelper
  used by setWinVal to set individual widgets

.stopWidget
  displays an error (similar to .catError) but stops and closes window (this is 
  for run-time errors, rather than parse errors)

.stripComments
  removes any trailing comments (indicated by #) unless # is within a quoted 
  string

.stripSlashes
  parses a string as if it was a quoted character string (returns a single 
  string)

.stripSlashesVec
  parses a string as if it contains substrings (returns a vector of strings)

.trimWhiteSpace
  removes leading and trailing whitespace

.validateWindowDescList
  validates a desc list, and fills in any default values.

.validateWindowDescWidgets
  validates a single widget of the DescList

.writeListOut
  used by compileDescription - it should use dput instead

.writeListOut.matrix
  helper which should be replaced with dput

.writeListOut.vec
  helper which should be replaced with dput