Package 'PBSmodelling'

Description

Call the arrows function using relative (0:1) coordinates.

Usage

addArrows(x1, y1, x2, y2, ...)

Arguments

Details

Lines will be drawn from (x1[i],y1[i]) to (x2[i],y2[i])

Author(s)

Jon T. Schnute, Pacific Biological Station, Fisheries and Oceans Canada , Nanaimo BC

See Also

addLabel, addLegend

Examples

local(envir=.PBSmodEnv,expr={
  oldpar = par(no.readonly=TRUE)
  tt=seq(from=-5,to=5,by=0.01)
  plot(sin(tt), cos(tt)*(1-sin(tt)), type="l")
  addArrows(0.2,0.5,0.8,0.5)
  addArrows(0.8,0.95,0.95,0.55, col="#FF0066")
  par(oldpar)
})

Description

Place a label in a plot using relative (0:1) coordinates

Usage

addLabel(x, y, txt, ...)

Arguments

Author(s)

Jon T. Schnute, Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo BC

See Also

addArrows, addLegend

Examples

local(envir=.PBSmodEnv,expr={
  oldpar = par(no.readonly=TRUE)
  resetGraph()
  addLabel(0.75,seq(from=0.9,to=0.1,by=-0.10),c('a','b','c'), col="#0033AA")
  par(oldpar)
})

Description

Place a legend in a plot using relative (0:1) coordinates.

Usage

addLegend(x, y, ...)

Arguments

Author(s)

Jon T. Schnute, Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo BC

See Also

addArrows, addLabel

Examples

local(envir=.PBSmodEnv,expr={
  oldpar = par(no.readonly=TRUE)
  resetGraph()
  n <- sample(1:length(colors()),15); clrs <- colors()[n]
  addLegend(.2,1,fill=clrs,leg=clrs,cex=1.5)
  par(oldpar)
})

Description

Compute Fibonacci numbers using four different methods: 1) iteratively using R code, 2) via the closed function in R code, 3) iteratively in C using the .C function, and 4) iteratively in C using the .Call function.

Usage

calcFib(n, len=1, method="C")

Arguments

Value

Vector of the last len Fibonacci numbers calculated.

Author(s)

Jon T. Schnute, Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo BC

Description

Calculate the geometric mean of a numeric vector, possibly excluding zeroes and/or adding an offset to compensate for zero values.

Usage

calcGM(x, offset = 0, exzero = TRUE)

Arguments

Value

Geometric mean of the modified vector x + offset

Note

NA values are automatically removed from x

Author(s)

Rowan Haigh, Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo BC

Examples

local(envir=.PBSmodEnv,expr={
  calcGM(c(0,1,100))
  calcGM(c(0,1,100),offset=0.01,exzero=FALSE)
})

Description

Minimization based on the R-stat functions nlm, nlminb, and optim. Model parameters are scaled and can be active or not in the minimization.

Usage

calcMin(pvec, func, method="nlm", trace=0, maxit=1000, reltol=1e-8,
        steptol=1e-6, temp=10, repN=0, ...)

Arguments

Details

See optim for details on the following methods: Nelder-Mead, BFGS, CG, L-BFGS-B, and SANN.

Value

A list with components:

Note

Some arguments to calcMin have no effect depending on the method chosen.

Author(s)

Jon T. Schnute, Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo BC

See Also

scalePar, restorePar, calcMin, GT0
In the stats package: nlm, nlminb, and optim.

Examples

local(envir=.PBSmodEnv,expr={
Ufun <- function(P) {
  Linf <- P[1]; K <- P[2]; t0 <- P[3]; obs <- afile$len;
  pred <- Linf * (1 - exp(-K*(afile$age-t0)));
  n <- length(obs); ssq <- sum((obs-pred)^2 );
  return(n*log(ssq)); };

oldpar = par(no.readonly = TRUE)
afile <- data.frame(age=1:16,len=c(7.36,14.3,21.8,27.6,31.5,35.3,39,
  41.1,43.8,45.1,47.4,48.9,50.1,51.7,51.7,54.1));
pvec <- data.frame(val=c(70,0.5,0),min=c(40,0.01,-2),max=c(100,2,2),
  active=c(TRUE,TRUE,TRUE),row.names=c("Linf","K","t0"),
  stringsAsFactors=FALSE);
alist <- calcMin(pvec=pvec,func=Ufun,method="nlm",steptol=1e-4,repN=10);
print(alist[-1]); P <- alist$Pend;
#resetGraph(); 
expandGraph();
xnew <- seq(afile$age[1],afile$age[nrow(afile)],len=100);
ynew <- P[1] * (1 - exp(-P[2]*(xnew-P[3])) );
plot(afile); lines(xnew,ynew,col="red",lwd=2); 
addLabel(.05,.88,paste(paste(c("Linf","K","t0"),round(P,c(2,4,4)),
  sep=" = "),collapse="\n"),adj=0,cex=0.9);
par(oldpar)
})

Description

Count of sampled fish-at-age for quillback rockfish (Sebastes maliger) in Johnstone Strait, British Columbia, from 1984 to 2004.

Usage

data(CCA.qbr)

Format

A matrix with 70 rows (ages) and 14 columns (years). Attributes “syrs” and “cyrs” specify years of survey and commercial data, respectively.

All elements represent sampled counts-at-age in year. Zero-value entries indicate no observations.

Details

Handline surveys for rockfish have been conducted in Johnstone Strait (British Columbia) and adjacent waterways (126$^\circ$37'W to 126$^\circ$53'W, 50$^\circ$32'N to 50$^\circ$39'N) since 1986. Yamanaka and Richards (1993) describe surveys conducted in 1986, 1987, 1988, and 1992. In 2001, the Rockfish Selective Fishery Study (Berry 2001) targeted quillback rockfish Sebastes maliger for experiments on improving survival after capture by hook and line gear. The resulting data subsequently have been incorporated into the survey data series. The most recent survey in 2004 essentially repeated the 1992 survey design. Fish samples from surveys have been supplemented by commercial handline fishery samples taken from a larger region (126$^\circ$35'W to 127$^\circ$39'W, 50$^\circ$32'N to 50$^\circ$59'N) in the years 1984-1985, 1989-1991, 1993, 1996, and 2000 (Schnute and Haigh 2007).

Note

Years 1994, 1997-1999, and 2002-2003 do not have data.

Source

Fisheries and Oceans Canada - GFBio database:
http://www.pac.dfo-mpo.gc.ca/science/species-especes/groundfish-poissonsdesfonds/stats-eng.html

References

Berry, M.D. (2001) Area 12 (Inside) Rockfish Selective Fishery Study. Science Council of British Columbia, Project Number FS00-05.

Schnute, J.T. and Haigh, R. (2007) Compositional analysis of catch curve data with an application to Sebastes maliger. ICES Journal of Marine Science 64, 218–233.

Yamanaka, K.L. and Richards, L.J. (1993) 1992 Research catch and effort data on nearshore reef-fishes in British Columbia Statistical Area 12. Canadian Manuscript Report of Fisheries and Aquatic Sciences 2184, 77 pp.

Examples

local(envir=.PBSmodEnv,expr={
  oldpar = par(no.readonly=TRUE)
  # Plot age proportions (blue bubbles = survey data, red = commercial)
  data(CCA.qbr,envir=.PBSmodEnv); clrs=c("cornflowerblue","orangered")
  z <- CCA.qbr; cyr <- attributes(z)$cyrs;
  z <- apply(z,2,function(x){x/sum(x)}); z[,cyr] <- -z[,cyr];
  x <- as.numeric(dimnames(z)[[2]]); xlim <- range(x) + c(-.5,.5);
  y <- as.numeric(dimnames(z)[[1]]); ylim <- range(y) + c(-1,1);
  expandGraph(mgp=c(2,.5,0),las=1)
  plotBubbles(z,xval=x,yval=y,powr=.5,size=0.15,clrs=clrs,
    xlim=xlim,ylim=ylim,xlab="Year",ylab="Age",cex.lab=1.5)
  addLegend(.5,1,bty="n",pch=1,cex=1.2,col=clrs,
    legend=c("Survey","Commercial"),horiz=TRUE,xjust=.5)
  par(oldpar)
})

Description

Prompts the user to choose one string item from a list of choices displayed in a GUI, then sets a specified variable in a target GUI.

Usage

chooseWinVal(choice, varname, winname="window")

Arguments

Details

chooseWinVal activates a setWinVal command through an onClose function created by the getChoice command and modified by chooseWinVal.

Value

No value is returned directly. The choice is written to the PBS options workspace, accessible through
getPBSoptions("getChoice"). Also set in PBS options is the window name from which the choice was activated.

Note

Microsoft Windows users may experience difficulties switching focus between the R console and GUI windows. The latter frequently disappear from the screen and need to be reselected (either clicking on the task bar or pressing <Alt><Tab>. This issue can be resolved by switching from MDI to SDI mode. From the R console menu bar, select <Edit> and <GUI preferences>, then change the value of “single or multiple windows” to SDI.

Author(s)

Rowan Haigh, Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo BC

See Also

getChoice, getWinVal, setWinVal

Examples

## Not run: 
local(envir=.PBSmodEnv,expr={
dfnam <-
  c("airquality","attitude","ChickWeight","faithful","freeny",
  "iris","LifeCycleSavings","longley","morley","Orange",
  "quakes","randu","rock","stackloss","swiss","trees")

wlist <- c(
  "window name=choisir title=\"Test chooseWinVal\"",
  "label text=\"Press <ENTER> in the green entry box
  \nto choose a file, then press <GO>\" sticky=W pady=5",
  "grid 1 3 sticky=W",
  "label text=File: sticky=W",
  "entry name=fnam mode=character width=23 value=\"\" 
  func=chFile entrybg=darkolivegreen1 pady=5",
  "button text=GO bg=green sticky=W func=test",
  "")

chFile <- function(ch=dfnam,fn="fnam") 
  {chooseWinVal(ch,fn,winname="choisir")};

#-- Example 1 GUI test
test <- function() {
  oldpar = par(no.readonly=TRUE); on.exit(par(oldpar))
  getWinVal(winName="choisir",scope="L")
  if (fnam!="" && any(fnam==dfnam)) {
    file <- get(fnam);
    pairs(file,gap=0); }
  else {
    resetGraph(); 
    addLabel(.5,.5,"Press <ENTER> in the green entry box
    \nto choose a file, then press <GO>", col="red",cex=1.5)
  }
}
#-- Example 2 Non-GUI test
#To try the non-GUI version, type 'test2()' on the command line
test2 <- function(fnames=dfnam) {
  oldpar = par(no.readonly=TRUE); on.exit(par(oldpar))
  frame();resetGraph()
  again <- TRUE;
  while (again) {
    fnam <- sample(fnames,1); file <- get(fnam); 
    flds <- names(file);
    xfld <- getChoice(paste("Pick x-field from",fnam),flds,gui=FALSE);
    yfld <- getChoice(paste("Pick y-field from",fnam),flds,gui=FALSE)
    plot(file[,xfld],file[,yfld],xlab=xfld,ylab=yfld,
      pch=16,cex=1.2,col="red");
    again <- getChoice("Plot another pair?",gui=FALSE)
  }
}
require(PBSmodelling)
createWin(wlist,astext=TRUE); test();
})

## End(Not run)

Description

Launches a new window which contains an interface for deleting junk files associated with a prefix and a set of suffixes (e.g., PBSadmb project) from the working directory.

Usage

cleanProj(prefix, suffix, files)

Arguments

Details

All arguments may contain wildcard characters ("*" to match 0 or more characters, "?" to match any single character).

The GUI includes the following:

Author(s)

Anisa Egeli, Vancouver Island University, Nanaimo BC

Examples

## Not run: 
local(envir=.PBSmodEnv,expr={
  cleanProj(prefix="foo",suffix=c(".a*",".b?",".c","-old.d"),files=c("red","blue"))
})

## End(Not run)

Description

Launches a new window which contains an interface for deleting specified files from the working directory.

Usage

cleanWD(files)

Arguments

Details

All arguments may contain wildcard characters ("*" to match 0 or more characters, "?" to match any single character).

The GUI includes the following:

Author(s)

Rowan Haigh, Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo BC

Examples

## Not run: 
local(envir=.PBSmodEnv,expr={
  cleanWD(c("*.bak","*.tmp","junk*"))
})

## End(Not run)

Description

Generic function to clear all objects from .RData in R

Usage

clearAll(hidden=TRUE, verbose=TRUE, PBSsave=TRUE, pos=".PBSmodEnv")

Arguments

Author(s)

Jon T. Schnute, Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo BC

Description

Disassociate any number of file extensions from commands previously saved with setPBSext.

Usage

clearPBSext(ext)

Arguments

Author(s)

Alex Couture-Beil, Vancouver Island University, Nanaimo BC

See Also

setPBSext, getPBSext, openFile

Description

Clear the R console window or focus on the RGui window using Visual Basic shell scripts.

Usage

clearRcon(os=.Platform$OS.type)
focusRgui(os=.Platform$OS.type)

Arguments

Details

Creates a VB shell script file called clearRcon.vbs or focusRgui.vbs in R's temporary working directory, then executes the script using the shell command.

While clearRcon clears the R console, focusRgui returns the desktop focus back to the RGui window.

These commands will only work on Windows operating platforms, using the system's executable
%SystemRoot%\system32\cscript.exe.

Author(s)

Norm Olsen, Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo BC

See Also

cleanWD, clearPBSext, clearWinVal

Examples

## Not run: 
local(envir=.PBSmodEnv,expr={
  createWin( c("window title=Focus",
    "button text=\"Go to RGui\" width=20 bg=aliceblue func=focusRgui"), astext=T)
})

## End(Not run)

Description

Remove all global variables that share a name in common with any widget variable name defined in
names(getWinVal()). Use this function with caution.

Usage

clearWinVal()

Author(s)

Alex Couture-Beil, Vancouver Island University, Nanaimo BC

See Also

getWinVal

Description

Clip a vector at one or both ends using the specified clip pattern to match.

Usage

clipVector(vec, clip, end=0)

Arguments

Details

If the vector is named, the names are retained. Otherwise, element positions are assigned as the vector's names.

Value

Clipped vector with names.

Author(s)

Rowan Haigh, Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo BC

See Also

createVector

Examples

local(envir=.PBSmodEnv,expr={
  x=c(0,0,0,0,1,1,1,1,0,0)
  print(clipVector(x,0))

  x=c(TRUE,TRUE,FALSE,TRUE)
  print(clipVector(x,TRUE))

  x=c("red","tide","red","red")
  print(clipVector(x,"red",2))
})

Description

Close (destroy) one or more windows made with createWin.

Usage

closeWin(name)

Arguments

Author(s)

Alex Couture-Beil, Vancouver Island University, Nanaimo BC

See Also

createWin

Description

This function provides an alternative to using R's SHLIB command to compile C code into a shared library object.

Usage

compileC(file, lib="", options="", logWindow=TRUE, logFile=TRUE)

Arguments

Details

If lib="", it will take the same name as file (with a different extension).

If an object with the same name has already been dynamically loaded in R, it will be unloaded automatically for recompilation.

The name of the log file, if created, uses the string value from lib concatenated with ".log".

Author(s)

Anisa Egeli, Vancouver Island University, Nanaimo BC

See Also

loadC

Examples

## Not run: 
local(envir=.PBSmodEnv,expr={
  cwd = getwd()
  edir <- system.file("examples", package = "PBSmodelling" )
  file.copy(paste(edir,"fib.c",sep="/"), tempdir(), overwrite=TRUE)
  setwd(tempdir())
  compileC("fib.c", lib="myLib", options="myObj.o", logWindow=FALSE)
  print(list.files())
  setwd(cwd)
})

## End(Not run)

Description

Convert a window description file (ASCII markup file) to an equivalent window description list. The output list (an ASCII file containing R-source code) is complete, i.e., all default values have been added.

Usage

compileDescription(descFile, outFile)

Arguments

Details

The window description file descFile is converted to a list, which is then converted to R code, and saved to outFile.

Author(s)

Alex Couture-Beil, Vancouver Island University, Nanaimo BC

See Also

parseWinFile, createWin

Description

Convert slashes in a string from ‘⁠/⁠’ to ‘⁠\\⁠’ if the operating system is ‘⁠windows⁠’. Do the reverse if the OS is ‘⁠unix⁠’.

Usage

convSlashes(expr, os=.Platform$OS.type, addQuotes=FALSE)

Arguments

Value

Returns the input string modified to have the appropriate slashes for the specified operating system.

Author(s)

Rowan Haigh, Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo BC

Description

Create a basic window containing a vector and a submit button. This provides a quick way to create a window without the need for a window description file.

Usage

createVector(vec, vectorLabels=NULL, func="", 
    windowname="vectorwindow", env=NULL)

Arguments

Author(s)

Alex Couture-Beil, Vancouver Island University, Nanaimo BC

See Also

createWin

Examples

## Not run: 
local(envir=.PBSmodEnv,expr={
#user defined function which is called on new data  
drawLiss <- function() {
  oldpar = par(no.readonly=TRUE); on.exit(par(oldpar))
  getWinVal(scope="L");
  tt <- 2*pi*(0:k)/k; x <- sin(2*pi*m*tt); y <- sin(2*pi*(n*tt+phi));
  plot(x,y,type="p"); invisible(NULL); };

#create the vector window
createVector(c(m=2, n=3, phi=0, k=1000), func="drawLiss",
  vectorLabels=c("x cycles","y cycles", "y phase", "points"));
})

## End(Not run)

Description

Create a GUI window with widgets using instructions from a Window Description File (aka mark-up file) .

Usage

createWin( fname, astext=FALSE, env=NULL )

Arguments

Details

Generally, the markup file contains a single widget per line. However, widgets can span multiple lines by including a backslash ('\') character at the end of a line, prompting the suppression of the newline character.

For more details on widget types and markup file, see “PBSModelling-UG.pdf” in the R directory
.../library/PBSmodelling/doc.

It is possible to use a Window Description List produced by compileDescription rather than a file name for fname.

Another alternative is to pass a vector of characters to fname and set astext=T. This vector represents the file contents where each element is equivalent to a new line in the window description file.

Note

Microsoft Windows users may experience difficulties switching focus between the R console and GUI windows. The latter frequently disappear from the screen and need to be reselected (either clicking on the task bar or pressing <Alt><Tab>. This issue can be resolved by switching from MDI to SDI mode. From the R console menu bar, select <Edit> and <GUI preferences>, then change the value of “single or multiple windows” to SDI.

Author(s)

Alex Couture-Beil, Vancouver Island University, Nanaimo BC

See Also

parseWinFile, getWinVal, setWinVal

closeWin, compileDescription, createVector

initHistory for an example of using astext=TRUE

environment

Examples

## Not run: 
# See file .../library/PBSmodelling/testWidgets/LissWin.txt
# Calculate and draw the Lissajous figure
local(envir=.PBSmodEnv,expr={
  drawLiss <- function() {
    oldpar = par(no.readonly=TRUE); on.exit(par(oldpar))
    getWinVal(scope="L"); ti=2*pi*(0:k)/k;
    x=sin(2*pi*m*ti);     y=sin(2*pi*(n*ti+phi));
    plot(x,y,type=ptype); invisible(NULL); };
  createWin(system.file("testWidgets/LissWin.txt",package="PBSmodelling"));
})

############################################################
# Environment example:
# function in global
local(envir=.PBSmodEnv,expr={
  hello <- function() {
    stop( "I shouldn't be called" )
  }

newNameGreeter <- function( name ) {
  # method to display window
  greet <- function() {
    createWin(c("button \"Say hello\" func=hello"), astext=TRUE,
      env=parent.env(environment()))
  }
  # hello method will refer to the name in this local scope
  hello <- function() {
    cat( "Hello", name, "\n" )
  }
  # return functions which the user can call directly
  return( list( greet=greet, hello=hello ) )
}
alex <- newNameGreeter( "Alex" )
jon  <- newNameGreeter( "Jon" )

alex$hello() # prints hello Alex
jon$hello()  # prints hello Jon
alex$greet() # creates a GUI with a button, which will print "hello Alex" when pushed
})

## End(Not run)

Description

This function allows a GUI creator to specify widget names that correspond to names in PBS options. These widgets can then be used to load and set PBS options using getGUIoptions and setGUIoptions.

Usage

declareGUIoptions(newOptions)

Arguments

Details

declareGUIoptions is typically called in a GUI initialization function. The option names are remembered and used for the functions getGUIoptions, setGUIoptions, and promptSave.

Author(s)

Anisa Egeli, Vancouver Island University, Nanaimo BC

See Also

getGUIoptions, setGUIoptions, promptWriteOptions

Examples

## Not run: 
local(envir=.PBSmodEnv,expr={
  declareGUIoptions("editor")
})

## End(Not run)

Description

Executes the action expression formulated by the user and written as an ‘⁠action⁠’ by a widget.

Usage

doAction(act)

Arguments

Details

If act is missing, doAction looks for it in the action directory of the window's widget directory in .PBSmod. This action can be accessed through getWinAct()[1].

Due to parsing complications, the expression act translates various symbols.
The function translates:

1. The back tick character ‘⁠`⁠’ to a double quote ‘⁠"⁠’ character. For example,

"openFile(paste(getWinVal()$prefix,`.tpl`,sep=``))"

2. Underscore period ‘⁠_.⁠’ to four back slashes and one period ‘⁠\\\\.⁠’. For example,

"poop=strsplit(`some.thing.else`,split=`_.`)"

Value

Invisibly returns the string expression expr.

Author(s)

Rowan Haigh, Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo BC

See Also

createWin, evalCall, getWinAct

Examples

## Not run: 
local(envir=.PBSmodEnv,expr={
  createWin("button text=\"list objects\" func=doAction action=print(ls(all.names=TRUE))",
    astext=TRUE)
})

## End(Not run)

Description

Various dot C-support functions used by PBSmodelling code internally.

Usage

.libName(lib="")
.guiSource()
.guiCompileC()
.guiDyn()
.cleanLoadC()
.loadCRunComparison()

Arguments

Details

Value

Varied lists and other objects to facilitate GUI manipulation.

Author(s)

Anisa Egeli, Software Developer, Alumnus of Vancouver Island University, Nanaimo BC

Maintainer: Rowan Haigh, Program Head – Offshore Rockfish
Pacific Biological Station (PBS), Fisheries & Oceans Canada (DFO), Nanaimo BC
locus opus: Remote office, Vancouver BC
Last modified Rd: 2024-11-04

See Also

loadC, compileC

Description

Various dot-convert functions used by PBSmodelling code internally.

Usage

.convertMatrixListToDataFrame(mList, colName="Y", rowNames="X")
.convertMatrixListToMatrix(mList)
.convertMode(x, mode)
.convertOldGridToNewGrid(grid)
.convertParamStrToList(x, fname="", line.start=0, line.end=0, sourcefile=list())
.convertParamStrToVector(x, fname="", line=0)
.convertVecToArray(x, d, byright=FALSE, byrow=TRUE)

Arguments

Details

Various convert functions used by PBSmodelling code.

.convertMatrixListToMatrix – Convert a list into an N-dim array

.convertMatrixListToDataFrame – Convert a list into a data frame

.convertMode – Convert a variable into a mode without showing any warnings (deprecated?)

.convertOldGridToNewGrid – Convert old style (where grid has a grid$.widgets[[i]][[j]] data structure) to new format: list( grid, child, child, ..., child ); this function should never be used by new code (hopefuly it will be removed one day)

.convertParamStrToList – Convert a given string of values seperated by spaces into a list while preserving space and escaped quotes within quotes (kindof – the value must still be stripped depending if its a single string, or vector of strings)

.convertParamStrToVector – Convert a string, x, into a vector of elements seperated by whitespace; whitespace can be interupted as values if it is enclosed by quotes; special characters (newline, tab, \, ', ") must be escaped with \

.convertVecToArray – Convert a vector to an array

Author(s)

Alex Couture-Beil, Software Engineer
Earthly Technologies, Victoria BC

Maintainer: Rowan Haigh, Program Head – Offshore Rockfish
Pacific Biological Station (PBS), Fisheries & Oceans Canada (DFO), Nanaimo BC
locus opus: Remote office, Vancouver BC
Last modified Rd: 2024-10-30

See Also

In PBSmodelling:
.createWidget.data, .createWidget.history, .createWidget.matrix, .extractVar, .getParamFromStr, .readList.P.convertData, .superobject.saveValues

Description

Various dot-create functions used by PBSmodelling code internally.

Usage

.createTkFont(fontstr)
.createWidget(tk, widgetList, winName)
.createWidget.button(tk, widgetList, winName)
.createWidget.check(tk, widgetList, winName)
.createWidget.data(tk, widgetList, winName)
.createWidget.droplist(tk, widgetList, winName)
.createWidget.entry(tk, widgetList, winName)
.createWidget.grid(tk, widgetList, winName)
.createWidget.image(tk, widgetList, winName)
.createWidget.include(tk, widgetList, winName)
.createWidget.label(tk, widgetList, winName)
.createWidget.matrix(tk, widgetList, winName)
.createWidget.notebook(tk, widgetList, winName)
.createWidget.null(tk, widgetList, winName)
.createWidget.object(tk, widgetList, winName, userObject=NULL )
.createWidget.object.scrolling(tk, widgetList, winName)
.createWidget.progressbar(tk, widgetList, winName)
.createWidget.radio(tk, widgetList, winName)
.createWidget.slide(tk, widgetList, winName)
.createWidget.slideplus(tk, widgetList, winName)
.createWidget.spinbox(tk, widgetList, winName)
.createWidget.table(tk, widgetList, winName)
.createWidget.text(tk, widgetList, winName)
.createWidget.vector(tk, widgetList, winName)

Arguments

Details

Various create functions used by PBSmodelling code.

.createTkFont – create a usable TK font from a given string

.createWidget – Generic function to create most widgets, which calls appropriate
.createWidget.<widgetType>() function

Author(s)

Alex Couture-Beil, Software Engineer, Earthly Technologies, Victoria BC

Maintainer: Rowan Haigh, Program Head – Offshore Rockfish
Pacific Biological Station (PBS), Fisheries & Oceans Canada (DFO), Nanaimo BC
locus opus: Remote office, Vancouver BC
Last modified Rd: 2024-10-31

See Also

In PBSmodelling:
testWidgets, showArgs, .createWidget.history

Description

Various dot functions used by PBSmodelling code internally to support the GUI functions.

Usage

.buildgrid(tk, grid, winName, childWidgets)
.map.add(winName, key, ...)
.map.get(winName, key)
.map.getAll(winName)
.map.init(winName)
.map.set(winName, key, ...)
.setMatrixElement(m, a, ind=NULL)
.getMatrixListSize(m, d=NULL, big=0)
.matrixHelp(matrixList, ind, value)
.autoConvertMode(x)
.extractData(command, action, winName)
.extractFuns(data)
.extractVar(winName)
.getParamFromStr(inputStr, fname="", line.start=0, line.end=0, sourcefile=list(),
	paramOrder=.widgetDefs)
.table.getvalue(winName, widgetName)
.table.setvalue(winName, widgetName, value)
.getValueForWidgetSetup(varname, widget, winName)
.getSimilarColour(col)
.adjustAllColours(tObj)
.do.gui.call(what, args, quote=FALSE, envir=parent.frame()) 
.catError(err, fname, line.start, line.end, sourcefile=list(), errorType="GUI parse error")
.catError2(err, fname, line.start)
.check.object.exists(tk, widget, winName)
.inCollection(haystack, needle)
.packWidgetsIntoGrid(widgets, vertical=TRUE)
.parsegrid(data, nRow, nCol)
.parsemenu(data, nItems)
.PBSdimnameHelper(rownames, colnames, dim)
.searchCollection(haystack, needle)
.setWinValHelper(varname, value, winName)
.stopWidget(err, wid.debug, winName)
.stripComments(x)
.stripSlashes(x, fname="", line.start=0, line.end=0, sourcefile=list())
.stripSlashesVec(x, fname="", line.start=0, line.end=0, sourcefile=list())
.superobject.redraw(winName, widget_name)
.superobject.saveValues(winName, widget_name)
.trimWhiteSpace(x)
.validateWindowDescList(x)
.validateWindowDescWidgets(x)

Arguments

Details

Value

Stuff and such.

Author(s)

Alex Couture-Beil, Software Engineer, Earthly Technologies, Victoria BC

Nicholas M. Boers, Software Engineer, Jobber, Edmonton AB

Maintainer: Rowan Haigh, Program Head – Offshore Rockfish
Pacific Biological Station (PBS), Fisheries & Oceans Canada (DFO), Nanaimo BC
locus opus: Remote office, Vancouver BC
Last modified Rd: 2024-11-01

See Also

dot-create.funs, dot-convert.funs

Description

Various dot functions used by PBSmodelling code internally for the history widget.

Usage

.createWidget.history(tk, widgetList, winName)
.sortHelper()
.sortHelperActive(hisname)
.sortHelperFile(openfile, savefile)
.sortWidget(d, hisname)
.updateFile()
.updateHistory(hisname)
.updateHistoryButtons(hisname)

Arguments

Details

Various dot functions used by PBSmodelling code to control the history widget.

.createWidget.history – create a history widget

.sortHelper – sort entries in an existing history instance

.updateHistory – update widget values

Author(s)

Alex Couture-Beil, Software Engineer
Earthly Technologies, Victoria BC

Maintainer: Rowan Haigh, Program Head – Offshore Rockfish
Pacific Biological Station (PBS), Fisheries & Oceans Canada (DFO), Nanaimo BC
locus opus: Remote office, Vancouver BC
Last modified Rd: 2024-10-31

See Also

In PBSmodelling:
testWidgets, showArgs

Description

Various dot-list functions used by PBSmodelling code internally.

Usage

.mergeLists(x, y) 
.readList.C(fname)
.readList.P(fname)
.readList.P.convertData(varOptions, varData, fname="", sourcefile=list())
.writeList.P(x, fname="", comments, prefix="")

Arguments

Details

Various dot functions used by PBSmodelling code to control list objects.

.mergeLists – taken from R Curl : merge x and y, if elements match in both x and y, then elements from y are stored (overwriting x's elements).

.readList.C – read ADMB-like input file and create a list; adapted from 'readAD' in PBSawatea.

.readList.P – read list in 'P' format (PBS format).

.readList.P.convertData – helper function to convert data into proper mode.

.writeList.P – saves list x to disk using 'P' format (PBS format).

Author(s)

Alex Couture-Beil, Software Engineer
Earthly Technologies, Victoria BC

Maintainer: Rowan Haigh, Program Head – Offshore Rockfish
Pacific Biological Station (PBS), Fisheries & Oceans Canada (DFO), Nanaimo BC
locus opus: Remote office, Vancouver BC
Last modified Rd: 2024-10-31

See Also

In PBSmodelling:
lisp, packList, readList, unpackList, writeList, .pFormatDefs

Description

An environment set aside for PBSmodelling.

Usage

.PBSmodEnv

Format

A new environment with a .GlobalEnv parent.

Details

The environment is created in 'zzz.r' and is used by PBSmodelling functions 'lisp', 'tget', 'tput', 'tprint', and 'tcall'.

Source

Generated by a call to the base function new.env().

See Also

In PBSmodelling:
lisp, tget, packList,

Examples

lisp(.PBSmodEnv)

Description

Various dot functions used by PBSmodelling code internally to support project functions.

Usage

.doClean()
.doCleanWD()
.getHiddenEnv()
.getHome()
.getPrefix(quiet=FALSE)
.makeCleanVec(vecName, items, rowLen)
.mergeLists2(list1, list2)
.mergeVectors(v1, v2)
.optionsNotUpdated()
.removeFromList(l, items)
.selectCleanBoxes()
.setOption(option, type)
.showLog(logText, fname, noWindow=FALSE, width=80, height=30)
.stripExt(x)
.tryOpen(filename, quiet=FALSE)

Arguments

Details

Value

Varied lists and other objects to facilitate GUI manipulation.

Author(s)

Anisa Egeli, Software Developer, Alumnus of Vancouver Island University, Nanaimo BC

Maintainer: Rowan Haigh, Program Head – Offshore Rockfish
Pacific Biological Station (PBS), Fisheries & Oceans Canada (DFO), Nanaimo BC
locus opus: Remote office, Vancouver BC
Last modified Rd: 2024-11-01

See Also

cleanProj, cleanWD, findPrefix, getGUIoptions, setGUIoptions

Description

Various dot support functions used by PBSmodelling code internally.

Usage

.fibCall(n, len=1)
.fibC(n, len=1)
.fibR(n, len=1)
.fibClosedForm(n, len=1)
.viewPkgDemo()
.dClose()
.dUpdateDesc()
.viewPkgVignette()
.addslashes(x, asvector=FALSE )
.findSquare(nc)
.forceMode(x, mode)
.getArrayPts(d, byright=FALSE, byrow=TRUE)
.initPBSoptions()
.mapArrayToVec(x, d, byright=FALSE)
.tclArrayToVector(str)

Arguments

Details

Value

Varied lists and other objects to facilitate GUI manipulation.

Author(s)

Alex Couture-Beil, Software Engineer, Earthly Technologies, Victoria BC

Maintainer: Rowan Haigh, Program Head – Offshore Rockfish
Pacific Biological Station (PBS), Fisheries & Oceans Canada (DFO), Nanaimo BC
locus opus: Remote office, Vancouver BC
Last modified Rd: 2024-11-04

See Also

calcFib, runDemos, showVignettes, readPBSoptions, runExamples

Description

Various dot-talk functions used by PBSmodelling code internally for 'presentTalk()'.

Usage

.getButton(talk_name, obj)
.getButtons(talk)
.getIndexForSection(talk, section_id)
.getMenus(talk)
.getSectionNames(talk)
.getTalkIndexes(talk)
.nextSlide()
.parseTalkFile(talk_fname)
.presentTalkOpenFile()
.prevSlide()
.sectiondrop()
.setsection()
.slidedrop()
.startSlide(talk)
.updateSlide(talk)

Arguments

Details

Various dot functions used by PBSmodelling code to control the talk GUI for presentations.

.getButton – returns win description for a button for a file or section.

.getButtons – gets widget descriptions for file and section buttons.

.getIndexForSection – get the slide index which corresponds to the first slide in a given section.

.getMenus – get widget description for menus.

.getSectionNames – given a talk, return a vector of all section names.

.getTalkIndexes – retuns a list of 2-element vectors (i,j), where i is the section index, and j is the items index; each element of the list corresponds to a break point.

.parseTalkFile – returns a talk s4 class, given a filename to an xml talk

.presentTalkOpenFile – open files from the win act, and supports multiple files.

Note

The function 'presentTalk' offers a cumbersome system for presenting talking points using R. It is likely superceded by more recent appliances like Shiny.

Author(s)

Alex Couture-Beil, Software Engineer
Earthly Technologies, Victoria BC

Maintainer: Rowan Haigh, Program Head – Offshore Rockfish
Pacific Biological Station (PBS), Fisheries & Oceans Canada (DFO), Nanaimo BC
locus opus: Remote office, Vancouver BC
Last modified Rd: 2024-10-31

See Also

In PBSmodelling:
presentTalk, .tagDefs, .tagOptionChecks

Description

Primary controller of the various widgets in PBSmodelling.

Usage

.widgetDefs
.pFormatDefs
.tagDefs
.tagOptionChecks
.maxActionSize
.regex.complex
.regex.numeric
.regex.logical

Format

List of 25 widgets:

Details

Storage list that specifies characteristics of each widget's arguments.

See Also

testWidgets, showArgs, presentTalk, readList

Examples

str(.widgetDefs,1)

Description

Wrapper dot functions to run existing or temporary functions from a GUI's function call.

Usage

.win.chFile()
.win.chTest()
.win.closeALL()
.win.closeChoice()
.win.closeSDE()
.win.makeChoice()
.win.restoreCWD()
.win.runExHelperQuit()
.win.tcall()
.win.tget()
.win.tprint()

Details

PBSmodelling Windows (Graphical User Interfaces or GUIs) call wrapper functions that call non-GUI functions in the package.

Author(s)

Rowan Haigh, Program Head – Offshore Rockfish
Pacific Biological Station (PBS), Fisheries & Oceans Canada (DFO), Nanaimo BC
locus opus: Offsite, Vancouver BC
Last modified Rd: 2023-10-25

See Also

In PBSmodelling:
getWinAct, getWinVal, runExamples, tget

Description

Draw a linear barplot on the current plot. Fill if desired.

Usage

drawBars(x, y, width, base=0, fill=NULL, ...)

Arguments

Author(s)

Jon T. Schnute, Scientist Emeritus,
Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo BC

Examples

local(envir=.PBSmodEnv,expr={
    if (dev.cur()>1) {
      oldpar=par(no.readonly=TRUE); on.exit(par(oldpar)) }
  plot(0:10,0:10,type="n")
  drawBars(x=1:9,y=9:1,col="deepskyblue4",fill="cyan",lwd=3)
})

Description

Evaluates a function call after resolving potential argument conflicts.

Usage

evalCall(fn, argu, ..., envir = parent.frame(),
    checkdef=FALSE, checkpar=FALSE)

Arguments

Details

This function builds a call to the specified function and executes it. During the build, optional arguments (...) are checked for
(i) duplication with explicit arguments argu: if any are duplicated, the user-supplied arguments supersede the explicit ones;
(ii) availability as usable arguments in fn, fn.default if checkdef=TRUE, and par if checkpar=TRUE.

Value

Invisibly returns the string expression of the function call that is passed to eval(parse(text=expr)).

Note

Sometimes the user may wish to pass arguments into a function to be used by other functions within, but may not want all the arguments to be used, depending on the functions subsequently called. In this case, the user needs to create a list object called dots, which is passed to evalCall.

For instance, if the user passes lwd=4 but only wants this used in a call to lines but not in a call to points, the function might look like this:

myfunc = function(x=seq(0,360,5), ...) {
  pdots = ldots = list(...)
  pdots[["lwd"]] = NULL
  ldots[["col"]] = "cyan"
  xrad = x*pi/180
  plot(sin(xrad),type="n")
  evalCall(lines, argu=list(x=sin(xrad)), dots=ldots, checkpar=TRUE)
  evalCall(points,argu=list(x=sin(xrad)), dots=pdots, checkpar=TRUE)
}
myfunc(lwd=4,pch=20,col=" blue")

Author(s)

Rowan Haigh, Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo BC

See Also

doAction, plotAsp

Examples

local(envir=.PBSmodEnv,expr={
  oldpar = par(no.readonly=TRUE)
  # A user may have a function that calls other functions
  # using specific defaults (e.g., blue triangles)
  #------------------------------------------------------
  pbsfun = function(..., use.evalCall=TRUE) {
    plotAsp(0,0,type="n",xlim=c(-1.5,1.5),ylim=c(-1.5,1.5),
      axes=FALSE, frame.plot=TRUE, xlab="",ylab="")
    if (use.evalCall)
      evalCall(polygon, ...,
        argu=list(x=c(-1,1,0),y=c(1,1,-1), col="dodgerblue", border="grey"))
    else
      polygon(x=c(-1,1,0),y=c(1,1,-1),col="dodgerblue",border="grey",...) 
  }
  par(mfrow=c(2,1))
  pbsfun(lwd=4,use.evalCall=FALSE)
  #------------------------------------------------------
  # But what if the user wants pink triangles?
  pbsfun(col="pink",lwd=4,use.evalCall=TRUE,checkpar=TRUE)
  par(oldpar)
})

# Without 'evalCall' an error occurs due to duplicated arguments
## Not run: pbsfun(col="pink",lwd=4,use.evalCall=FALSE)

Description

Optimize the plotting region(s) by minimizing margins.

Usage

expandGraph(mar=c(4,3,1.2,0.5), mgp=c(1.6,.5,0),...)

Arguments

Author(s)

Jon T. Schnute, Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo BC

See Also

resetGraph

Examples

local(envir=.PBSmodEnv,expr={
  oldpar = par(no.readonly=TRUE)
  expandGraph(mfrow=c(2,1));
  tt=seq(from=-10, to=10, by=0.05);

  plot(tt,sin(tt), xlab="this is the x label",  ylab="this is the y label", 
    main="main title", sub="sometimes there is a \"sub\" title")
  plot(cos(tt),sin(tt*2), xlab="cos(t)", ylab="sin(2 t)", main="main title", 
    sub="sometimes there is a \"sub\" title")
  par(oldpar)
})

Description

Export the current history list.

Usage

exportHistory(hisname="", fname="")

Arguments

Author(s)

Alex Couture-Beil, Vancouver Island University, Nanaimo BC

See Also

importHistory, initHistory

Description

Use all available patterns in pat to search in vec, and return the matched elements in vec.

Usage

findPat(pat, vec)

Arguments

Value

A character vector of all matched strings.

Author(s)

Rowan Haigh, Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo BC

Examples

local(envir=.PBSmodEnv,expr={
  #find all strings with a vowel, or that start with a number
  print(findPat(c("[aeiou]", "^[0-9]"), c("hello", "WORLD", "1over")))
})

Description

Find the prefixes or suffixes of files with a given suffix or prefix in a directory.

Usage

findPrefix(suffix,path=".")
findSuffix(prefix,path=".")

Arguments

Details

The function findPrefix locates all files in a directory that end with one of the provided suffixes; where as findSuffix locates all files that start with the given prefixes.

Value

A character vector of all the prefixes or sufixes of files in the working directory that matched to one of the given suffixes.

Author(s)

Anisa Egeli, Vancouver Island University, Nanaimo BC

Examples

local(envir=.PBSmodEnv,expr={
  edir = system.file("examples", package="PBSmodelling")
  print(findPrefix(suffix=c(".txt", ".r"),path=edir)); cat("\n")

  #or use R's dir for similar functionality
  print(dir(pattern="txt$",path=edir)); cat("\n")
  print(dir(pattern="^[a-h]",path=edir)); cat("\n")
})

Description

Returns the complete filename and path of a program in the PATH environment variable. This is a wrapper for Sys.which, and may be deprecated in the future.

Usage

findProgram( name, includename=FALSE )

Arguments

Value

A string containing the location of the program. NULL is returned if the program is not located.

Author(s)

Alex Couture-Beil, Vancouver Island University, Nanaimo BC

See Also

Sys.which

Examples

local(envir=.PBSmodEnv,expr={
  print(list(
  gcc =     findProgram( "gcc" ),
  notepad = findProgram( "notepad" ),
  R       = findProgram( "R", includename=TRUE ) ))
})

Description

Bring the specified window into focus, and set it as the active window. focusWin will fail to bring the window into focus if it is called from the R console, since the R console returns focus to itself once a function returns. However, it will work if focusWin is called as a result of calling a function from the GUI window. (i.e., pushing a button or any other widget that has a function argument).

Usage

focusWin(winName, winVal=TRUE)

Arguments

Author(s)

Alex Couture-Beil, Vancouver Island University, Nanaimo BC

Examples

## Not run: 
local(envir=.PBSmodEnv,expr={
focus <- function() {
  winName <- getWinVal()$select;
  focusWin(winName);
  mess = paste("Calling focusWin(\"", winName, "\")\n",
    "getWinVal()$myvar = ", getWinVal()$myvar, "\n\n", sep="",collapse="")
  cat(mess); invisible()
}
#create three windows named win1, win2, win3
#each having three radio buttons, which are used to change the focus
for(i in 1:3) {
  winDesc <- c(
    paste('window onclose=closeWin name=win',i,' title="Win',i,'"', sep=''),
    paste('entry myvar ', i, sep=''),
    'radio name=select value=win1 text="one" function=focus mode=character',
    'radio name=select value=win2 text="two" function=focus mode=character',
    'radio name=select value=win3 text="three" function=focus mode=character');
  createWin(winDesc, astext=TRUE); };
})

## End(Not run)

Description

Generate a test matrix of random numbers (mu = mean and signa = standard deviation), primarily for plotBubbles.

Usage

genMatrix(m,n,mu=0,sigma=1)

Arguments

Value

An m by n matrix with normally distributed random values.

Author(s)

Jon T. Schnute, Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo BC

See Also

plotBubbles

Examples

local(envir=.PBSmodEnv,expr={
  plotBubbles(genMatrix(20,6))
})

Description

Prompts the user to choose one string item from a list of choices displayed in a GUI. The simplest case getChoice() yields TRUE or FALSE.

Usage

getChoice(choice=c("Yes","No"), question="Make a choice: ",
          winname="getChoice", horizontal=TRUE, radio=FALSE,
          qcolor="blue", gui=FALSE, quiet=FALSE)

Arguments

Details

The user's choice is stored in .PBSmod$options$getChoice (or whatever winname is supplied).

getChoice generates an onClose function that returns focus to the calling window (if applicable) and prints out the choice.

Value

If called from a GUI (gui=TRUE), no value is returned directly. Rather, the choice is written to the PBS options workspace, accessible through getPBSoptions("getChoice") (or whatever winname was supplied).

If called from a command line program (gui=FASLE), the choice is returned directly as a string scalar (e.g., answer <- getChoice(gui=F) ).

Note

Microsoft Windows users may experience difficulties switching focus between the R console and GUI windows. The latter frequently disappear from the screen and need to be reselected (either clicking on the task bar or pressing <Alt><Tab>. This issue can be resolved by switching from MDI to SDI mode. From the R console menu bar, select <Edit> and <GUI preferences>, then change the value of “single or multiple windows” to SDI.

Author(s)

Rowan Haigh, Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo BC

See Also

chooseWinVal, getWinVal, setWinVal

Examples

## Not run: 
#-- Example 1
local(envir=.PBSmodEnv,expr={
  getChoice(c("Fame","Fortune","Health","Beauty","Lunch"),
    "What do you want?",qcolor="red",gui=FALSE)
})

#-- Example 2
local(envir=.PBSmodEnv,expr={
  getChoice(c("Homer Simpson","Wilberforce Humphries","Miss Marple","Gary Numan"),
    "Who`s your idol?",horiz=FALSE,radio=TRUE,gui=FALSE)
})

## End(Not run)

Description

Get the PBS options declared for GUI usage and set their corresponding widget values.

Usage

getGUIoptions()

Details

The options declared using declareGUIoptions are copied from the R environment into widget values. These widgets should have names that match the names of their corresponding options.

Author(s)

Anisa Egeli, Vancouver Island University, Nanaimo BC

See Also

declareGUIoptions, setGUIoptions, promptWriteOptions, readPBSoptions

Examples

## Not run: 
local(envir=.PBSmodEnv,expr={
  getPBSoptions() #loads from default PBSoptions.txt
})

## End(Not run)

Description

Functions to get and set user options within an option class object.

Usage

getOptions(option.object, key)
setOptions(option.object, ...)
.showOptions(object)

Arguments

Value

Value of the option specified by key (if specified) or a list of all options (if missing).

Author(s)

Alex Couture-Beil, Software Engineer, Earthly Technologies, Victoria BC

Maintainer: Rowan Haigh, Program Head – Offshore Rockfish
Pacific Biological Station (PBS), Fisheries & Oceans Canada (DFO), Nanaimo BC
locus opus: Remote office, Vancouver BC
Last modified Rd: 2024-11-04

See Also

See PBSoptions-class for more details and an example that uses PBSmodelling's option management functions.

Description

Functions for retrieving and setting the default file name used by loadOptions and saveOptions.

Usage

getOptionsFileName(option.object)
setOptionsFileName(option.object, name)

Arguments

Value

getOptionsFileName: the default file name

Author(s)

Alex Couture-Beil, Vancouver Island University, Nanaimo BC

See Also

loadOptions, saveOptions
See PBSoptions-class for more details and an example using PBSmodelling's option management functions.

Description

The GUI prefix is used for determining which GUI variables are associated with a user option.

Usage

getOptionsPrefix(option.object)
setOptionsPrefix(option.object, prefix)

Arguments

Value

getOptionsPrefix: a prefix string used to reference GUI variables

Author(s)

Alex Couture-Beil, Vancouver Island University, Nanaimo BC

See Also

See PBSoptions-class for more details and an example using PBSmodelling's option management functions.

Examples

## Not run: 
local(envir=.PBSmodEnv,expr={
  # For the example, the options object is saved to the temporary environment;
  # however, a user would normally create the object in his/her workspace.
  .mypkg <- new( "PBSoptions", filename="my_pkg.txt", 
    initial.options=list(pi=3.14), gui.prefix="opt" )

  #prefix the option "pi" with "opt" to get "optpi"
  createWin( "entry name=optpi", astext = TRUE )

  #the GUI variable "optpi" will be loaded with the option "pi"
  loadOptionsGUI( .mypkg )
})

## End(Not run)

Description

Display all locally defined file extensions and their associated commands, or search for the command associated with a specific file extension ext.

Usage

getPBSext(ext)

Arguments

Value

Command associated with file extension.

Note

These file associations are not saved from one PBS Modelling session to the next unless explicitly saved and loaded (see writePBSoptions and readPBSoptions).

Author(s)

Alex Couture-Beil, Software Engineer
Earthly Technologies, Victoria BC

Maintainer: Rowan Haigh, Program Head – Offshore Rockfish
Pacific Biological Station (PBS), Fisheries & Oceans Canada (DFO), Nanaimo BC
locus opus: Regional Headquarters (RHQ), Vancouver BC
Last modified Rd: 2023-01-05

See Also

In package PBSmodelling:
setPBSext, openFile, clearPBSext

Description

Get a previously defined user option.

Usage

getPBSoptions(option)

Arguments

Value

Value of the specified option, or NULL if the specified option is not found.

Author(s)

Alex Couture-Beil, Vancouver Island University, Nanaimo BC

See Also

getPBSext, readPBSoptions

Description

Get a string vector of actions (latest to earliest).

Usage

getWinAct(winName)

Arguments

Details

When a function is called from a GUI, a string descriptor associated with the action of the function is stored internally (appended to the first position of the action vector). A user can utilize this action as a type of argument for programming purposes. The command getWinAct()[1] yields the latest action.

Value

String vector of recorded actions (latest first).

Author(s)

Alex Couture-Beil, Vancouver Island University, Nanaimo BC

Description

Get a vector of all function names referenced by a window.

Usage

getWinFun(winName)

Arguments

Value

A vector of function names referenced by a window.

Author(s)

Alex Couture-Beil, Vancouver Island University, Nanaimo BC

Description

Get a list of variables defined and set by the GUI widgets. An optional argument scope directs the function to create local or global variables based on the list that is returned.

Usage

getWinVal(v=NULL, scope="", asvector=FALSE, winName="")

Arguments

Details

TODO: talk about scope=G/P/L and side effects of overwriting existing variables

Value

A list (or vector) with named components, where names and values are defined by GUI widgets.

Author(s)

Alex Couture-Beil, Vancouver Island University, Nanaimo BC

See Also

parseWinFile, setWinVal, clearWinVal

Description

Display a message prompt with "Yes" and "No" buttons.

Usage

getYes(message, title="Choice", icon="question")

Arguments

Value

Returns TRUE if the "Yes" button is clicked, FALSE if the "No" button is clicked.

Author(s)

Anisa Egeli, Vancouver Island University, Nanaimo BC

See Also

showAlert, getChoice, chooseWinVal

Examples

## Not run: 
local(envir=.PBSmodEnv,expr={
  if(getYes("Print the number 1?"))
    print(1) else print("hallucination")
})

## End(Not run)

Description

Restrict a numeric value x to a positive value using a differentiable function. GT0 stands for “greater than zero”.

Usage

GT0(x,eps=1e-4)

Arguments

Details

   if (x >= eps)..........GT0 = x
   if (0 < x < eps).......GT0 = (eps/2) * (1 + (x/eps)^2)
   if (x <= 0)............GT0 = eps/2
  

Author(s)

Jon T. Schnute, Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo BC

See Also

scalePar, restorePar, calcMin

Examples

local(envir=.PBSmodEnv,expr={
  oldpar = par(no.readonly=TRUE)
  plotGT0 <- function(eps=1,x1=-2,x2=10,n=1000,col="black") {
    x <- seq(x1,x2,len=n); y <- GT0(x,eps);
    lines(x,y,col=col,lwd=2); invisible(list(x=x,y=y)); }

  testGT0 <- function(eps=c(7,5,3,1,.1),x1=-2,x2=10,n=1000) {
    x <- seq(x1,x2,len=n); y <- x;
    plot(x,y,type="l");
    mycol <- c("red","blue","green","brown","violet","orange","pink");
    for (i in 1:length(eps)) 
      plotGT0(eps=eps[i],x1=x1,x2=x2,n=n,col=mycol[i]);
    invisible(); };

  testGT0()
  par(oldpar)
})

Description

Import a history list from file fname, and place it into the history list hisname.

Usage

importHistory(hisname="", fname="", updateHis=TRUE)

Arguments

Author(s)

Alex Couture-Beil, Vancouver Island University, Nanaimo BC

See Also

exportHistory, initHistory

Description

PBS history functions (below) are available to those who would like to use the package's history functionality, without using the pre-defined history widget. These functions allow users to create customized history widgets.

Usage

initHistory(hisname, indexname=NULL, sizename=NULL,
    buttonnames=NULL, modename=NULL, func=NULL, overwrite=TRUE)
rmHistory(hisname="", index="")
addHistory(hisname="")
forwHistory(hisname="")
backHistory(hisname="")
lastHistory(hisname="")
firstHistory(hisname="")
jumpHistory(hisname="", index="")
clearHistory(hisname="")

Arguments

Details

PBS Modelling includes a pre-built history widget designed to collect interesting choices of GUI variables so that they can be redisplayed later, rather like a slide show.

Normally, a user would invoke a history widget simply by including a reference to it in the window description file. However, PBS Modelling includes support functions (above) for customized applications.

To create a customized history, each button must be described separately in the window description file rather than making reference to the history widget.

The history "List" must be initialized before any other functions may be called. The use of a unique history name (hisname) is used to associate a unique history session with the supporting functions.

The indexname and sizename arguments correspond to the given names of entry widgets in the window description file, which will be used to display the current index and total size of the list. The indexname entry widget can also be used by jumpHistory to retrieve a target index.

Author(s)

Alex Couture-Beil, Vancouver Island University, Nanaimo BC

See Also

importHistory, exportHistory

Examples

## Not run: 
# ****** THIS CODE DOES NOT RUN. NEEDS FIXING *****
# Example of creating a custom history widget that saves values 
# whenever the "Plot" button is pressed. The user can tweak the 
# inputs "a", "b", and "points" before each "Plot" and see the 
# "Index" increase. After sufficient archiving, the user can review 
# scenarios using the "Back" and "Next" buttons. 
# A custom history is needed to achieve this functionality since 
# the packages pre-defined history widget does not update plots.

# To start, create a Window Description to be used with createWin 
# using astext=TRUE. P.S. Watch out for special characters which 
# must be "escaped" twice (first for R, then PBSmodelling).

local(envir=.PBSmodEnv,expr={
  oldpar = par(no.readonly=TRUE)

winDesc <- '
  window title="Custom History"
  vector names="a b k" labels="a b points" font="bold" \\
  values="1 1 1000" function=myPlot
  grid 1 3
    button function=myHistoryBack text="<- Back"
    button function=myPlot text="Plot"
    button function=myHistoryForw text="Next ->"
  grid 2 2
    label "Index"
    entry name="myHistoryIndex" width=5
    label "Size"
    entry name="myHistorySize" width=5
'
# Convert text to vector with each line represented as a new element
winDesc <- strsplit(winDesc, "\n")[[1]]

# Custom functions to update plots after restoring history values
myHistoryBack <- function() {
  backHistory("myHistory");
  myPlot(saveVal=FALSE); # show the plot with saved values
}
myHistoryForw <- function() {
  forwHistory("myHistory");
  myPlot(saveVal=FALSE); # show the plot with saved values 
}
myPlot <- function(saveVal=TRUE) {
  # save all data whenever plot is called (directly)
  if (saveVal) addHistory("myHistory");
  getWinVal(scope="L");
  tt <- 2*pi*(0:k)/k;
  x <- (1+sin(a*tt));  y <- cos(tt)*(1+sin(b*tt));
  plot(x, y);
}
  iHistory("myHistory", "myHistoryIndex", "myHistorySize")
  createWin(winDesc, astext=TRUE)
  par(oldpar)
})

## End(Not run)

Description

Identify an object by class, mode, typeof, and attributes.

Usage

isWhat(x)

Arguments

Value

No value is returned. The function prints the object's characteristics on the command line.

Author(s)

Jon T. Schnute, Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo BC

Description

The function lisp returns a vector of character strings giving the names of the objects in .PBSmodEnv. It is only a wrapper for the base function ls.

Usage

lisp(name, pos = .PBSmodEnv, envir = as.environment(pos),
   all.names = TRUE, pattern)

Arguments

Details

See the base function ls for details.

Author(s)

Copyright 1995–2012 R Core Development Team; distributed under GPL 2 or later.

See Also

ls, tget
glob2rx for converting wildcard patterns to regular expressions.

Description

A GUI interface allows users to edit, compile, and embed C functions in the R environment.

Usage

loadC()

Details

The function loadC() launches an interactive GUI that can be used to manage the construction of C functions intended to be called from R. The GUI provides tools to edit, compile, load, and run C functions in the R environment.

The loadC GUI also includes a tool for comparison between the running times and return values of R and C functions. It is assumed that the R and C functions are named prefix.r and prefix.c, respectively, where prefix can be any user-chosen prefix. If an initialization function prefix.init exists, it is called before the start of the comparison.

The GUI controls: