TODO

* Bouts

** TODO Work on MLE (or better) method for modelling mixtures of 3 Poisson
  processes


* Plotting

** DONE Colors should be constant in plotTDR()
   CLOSED: [2016-03-03 Thu 22:17]

Each color should always represent one type of behaviour, regardless of the
number of behaviours shown in each plot.  Whenever panning or zooming, the
number of behaviours shown may be different, so the colors chosen for each
behaviour also change.  This is wrong and confusing to users.

** TODO Embed R graphics in a single widget for plotTDR()

*** Using RGtk2

From the Lawrence and Temple (2010) JSS paper:

#+BEGIN_SRC R
  library(RGtk2)
  
  n <- 5000; backbone <- rnorm(n)
  ma_data <- cbind(backbone + c(rnorm(3 * (n / 4), sd=0.1),
                                rt(n / 4, 80)),
                   backbone + c(rnorm(3 * (n / 4), sd=0.1),
                                rt(n / 4, 80)))
  ma_data <- apply(ma_data, 2, function(col) col - min(col))
  
  win <- gtkWindow(show=FALSE)
  graphics <- gtkDrawingArea()
  slider <- gtkHScale(min=0.1, max=1.0, step=0.1)
  scale_cb <- function(range) {
      par(pty="s")
      plot(ma_data[, 1], ma_data[, 2],
           col=rgb(0, 0, 0, alpha=range$getValue()),
           xlab="Replicate 1", ylab="Replicate 2",
           main="Mock expression data", pch=19)
  }
  gSignalConnect(slider, "value-changed", scale_cb)
  
  vbox <- gtkVBox()
  vbox$packStart(graphics, expand=TRUE, fill=TRUE, padding=0)
  vbox$packStart(slider, expand=TRUE, fill=TRUE, padding=0)
  win$add(vbox)
  win$setDefaultSize(400, 400)
  win$showAll()
  require(cairoDevice)
  asCairoDevice(graphics)
  slider$setValue(0.7)
#+END_SRC

*** Using playwith

Felix Andrews demonstrated a bit:

#+BEGIN_SRC R
  library(playwith)
  library(diveMove)
  
  ## A tool to select a range and store it in a global var.
  
  ## This "callback" is run when the action is activated
  ## (from toolbar, menu, or keyboard shortcut).
  findRange_handler <- function(widget, playState) {
      ## draw rect at drag locations
      rgInfo <- playRectInput(playState)
      if (is.null(rgInfo)) return()
      if (isTRUE(rgInfo$is.click)) return()
      ## store range
      assign("RANGE", rgInfo$coords, globalenv())
      ## annotation call to draw a rect
      rectExpr <- with(rgInfo$coords,
                       call("panel.rect",
                            x[1], y[1], x[2], y[2]))
      playAnnotate(playState, rectExpr, space=rgInfo$space)
      gmessage("Selected range has been stored in object RANGE.")
  }
  
  findRangeTool <- list("FindRange", "gtk-zoom-fit", "Find range",
                         callback=findRange_handler)
  
  utils::example("calibrateDepth", package="diveMove",
                 ask=FALSE, echo=FALSE)
  
  playwith(plotTDR(getTime(divesTDR), getDepth(divesTDR), interact=FALSE),
           tools=list(findRangeTool))
  
#+END_SRC

** DONE Include a control for zoom level in plotTDR()
   CLOSED: [2016-03-03 Thu 22:18]


* Emacs local variables

#+STARTUP: content
#+PROPERTY: results silent
# Local Variables:
# mode: org
# End: