Toni Cebrián

In the past if you wanted to do some Bayesian Modelling using a Gibbs sampler you had to rely on Winbugs but it isn’t open source and it only runs in Windows. The JAGS project started as a full feature alternative for the Linux platform. Here are some instructions for getting started

First install the required dependencies. In my Ubuntu 11.04, is something like:

sudo apt-get install gfortran liblapack-dev libltdl-dev r-base-core

For Ubuntu 11.04 you have to install JAGS from sources, but it seems that this version will be packaged in the next Ubuntu release. Download the software from here and install.

tar xvfz JAGS-3.1.0.tar.gz
cd JAGS-3.1.0
./configure
make
sudo make install

Now fire R and install the interface package rjags

$ R
...
> install.package("rjags",dependencies=TRUE)

Now let's do something interesting (although pretty simple). Let's assume we have a stream of 1s and 0s with an unknown proportion of each one. From R we can generate such distribution with the command

> points <- floor(runif(1000)+.4)

that generates a distribution with roughly 40% of 1s and 60% of 0s. So, our stream consists of a sequence of 0s and 1s generated using the uniform(phi) distribution where the phi parameter equals 0.4.

If we don't know this parameter and we try to learn it, we can assume that this parameter has prior uniform in the range [0,1] and thus the model that describes this scenario in the Winbugs language is

model
{
    phi ~ dunif(0,1);
    y ~ dbin(phi,N);
}

In this model N and y are known, so we provide this information in order to estimate our unknown parameter phi. We create the model and query the resulting parameter distribution:

> result <- list(y=sum(points), N=1000)
> result
$y
[1] 393

$N
[1] 1000

> library(rjags)
Loading required package: coda
Loading required package: lattice
linking to JAGS 3.1.0
module basemod loaded
module bugs loaded
> myModel <- jags.model("model.dat", result)
Compiling model graph
   Resolving undeclared variables
   Allocating nodes
   Graph Size: 5

Initializing model

> update(myModel, 1000)
  |**************************************************| 100%
> x <- jags.samples(myModel, c('phi'), 1000)
  |**************************************************| 100%
> x
$phi
mcarray:
[1] 0.3932681

Marginalizing over: iteration(1000),chain(1) 

>

So the inferred value of phi is 0.3932. One interesting thing in Bayesian statistics is that it does not estimate points, but probabilistic distributions over the parameters. We can see how the phi parameter was estimated by examining the Monte Carlo Chain and the distribution of the generated values during the simulation

> chain <- as.mcmc.list(x$phi)
> plot(chain)

Where we can see that the values for phi in the chain were centered around the 0.4, the true parameter value.

Fire a terminal, fire another terminal and tail some logs, open your browser and point to the web page you are developing, open your IDE and open three or four tabs with the code you suspect is causing the bug, put some breakpoints, alt-tab to the first terminal start your system under test, connect your debugging IDE to your system, perform some operations to your browser, catch the breakpoint, switch back and forth the code tabs, etc… This daily routine common to most developers, involves grabbing the mouse, arranging some windows, and switching context continuously. This creates a cognitive overload and a lack of productivity because developers are doing tasks not directly related to the task at hand.

This is the reason I don’t use Gnome any more and I’ve switched to Xmonad a tiling window manager that can be controlled almost exclusively with the keyboard. With this fully configurable window manager, I can move, resize, minimize, arrange, customize all the visible windows, move windows between workspaces, all with my hands not leaving the keyboard.The only thing I have not been able to accomplish is having the UrgentHook working for Skype. The Linux version of Skype fails to set the WM_URGENT X11 event when a new chat opens, and if I’m not in that workspace I don’t get any notification besides the bell. Still thinking about a good workaround, any ideas?

Here is a screenshot of xmonad in action with  some applications in it,

If you plan to install Xmonad in your computer, use version 0.10 or superior because it solves some nasty problems with Java applications. In case it is not yet ready for your favourite distribution, follow these instructions. In order to have this configuration working, just write the following 3 files:

• .xsession with the programs you need to start when the session begins (network manager, batery manager, etc…). Put it in your $HOME dir.
• .xmobarrc with the configuration of your handy textual status bar . Put it in your $HOME
• xmonad.hs with the configuration of the window manager itself. Put it under $HOME/.xmonad

xmonad.hs is a pure Haskell file for configuring the window manager, no XML, not another fancy configuration language. Some comments to the configuration file

• lines 23-26, send Thunderbird and Skype to their dedicated workspaces
• line 29, name the workspaces
• lines 32-50, define new key combinations, for navigating the tiling windows, send windows to background and toggle between the tiled arrangement and focusing the whole screen into one window
• lines 52-55, define how I want the windows to be arranged. Basically, create a specific configuration for Skype in its dedicated workspace, and for the rest of workspaces, don’t hide the menu, allow navigation with the cursors and minimize unwanted windows.
• lines 57-77, ensemble the main xmonad window manager with the desired configuration. Spawn the status bar, and append the predefined layouts, keybindings and window hooks. Redefine some keys and fool Java setting the name of the Window Manager to LG3D in order to avoid problems with focus.

import XMonad
import XMonad.Hooks.DynamicLog
import XMonad.Hooks.ICCCMFocus
import XMonad.Hooks.ManageDocks
import XMonad.Util.Run(spawnPipe)
import XMonad.Util.EZConfig(additionalKeys)
import System.IO
import XMonad.Hooks.ManageHelpers
import XMonad.Hooks.UrgencyHook
import XMonad.Hooks.SetWMName
import XMonad.Layout.Minimize
import XMonad.Layout.WindowNavigation
import XMonad.Layout.ToggleLayouts
import XMonad.Layout.IM as IM
import XMonad.Layout.PerWorkspace
import XMonad.Layout.Reflect
import XMonad.Layout.Grid
import Data.Ratio ((%))

import qualified Data.Map as M

-- Send applications to their dedicated Workspace
myManageHook = composeAll
                [ className =? "Skype"         --> doShift "4:skype",
                  className =? "Thunderbird"   --> doShift "2:mail"
                ]

-- Name the workspaces
myWorkspaces = ["1:dev","2:mail","3:web","4:skype","5:media", "6:office"] ++ map show [7..9]

-- Add new Keys
newKeys x = M.union (keys defaultConfig x) (M.fromList (myKeys x))

myKeys conf@(XConfig {XMonad.modMask = modm}) =
              [
              -- Minimize a window
                ((modm, xK_z),               withFocused minimizeWindow)
              , ((modm .|. shiftMask, xK_z), sendMessage RestoreNextMinimizedWin  )
              -- Window navigation with cursors
              , ((modm,                 xK_Right), sendMessage $ Go R)
              , ((modm,                 xK_Left ), sendMessage $ Go L)
              , ((modm,                 xK_Up   ), sendMessage $ Go U)
              , ((modm,                 xK_Down ), sendMessage $ Go D)
              , ((modm .|. controlMask, xK_Right), sendMessage $ Swap R)
              , ((modm .|. controlMask, xK_Left ), sendMessage $ Swap L)
              , ((modm .|. controlMask, xK_Up   ), sendMessage $ Swap U)
              , ((modm .|. controlMask, xK_Down ), sendMessage $ Swap D)
              -- Togle Fullscreen
              , ((modm,                 xK_f    ), sendMessage ToggleLayout)
              ]

-- Define the default layout
skypeLayout = IM.withIM (1%7) (IM.And (ClassName "Skype")  (Role "MainWindow")) Grid
normalLayout = windowNavigation $ minimize $ avoidStruts $ onWorkspace "4:skype" skypeLayout $ layoutHook defaultConfig
myLayout = toggleLayouts (Full) normalLayout

-- Main executable
main = do
    xmproc <- spawnPipe "xmobar /home/cebrian/.xmobarrc"
    xmonad $ withUrgencyHook NoUrgencyHook $ defaultConfig
        { manageHook = manageDocks <+> myManageHook <+> manageHook defaultConfig
        , keys = newKeys
        , workspaces = myWorkspaces
        , layoutHook = myLayout
        , logHook = takeTopFocus >> dynamicLogWithPP xmobarPP
                        { ppOutput = hPutStrLn xmproc
                        , ppTitle = xmobarColor "green" "" . shorten 50
                        , ppUrgent = xmobarColor "yellow" "red" . xmobarStrip
                        }
        , modMask = mod4Mask     -- Rebind Mod to the Windows key
        , terminal = "terminator"
        , startupHook = setWMName "LG3D"
        } `additionalKeys`
        [ ((controlMask .|. shiftMask, xK_l), spawn "xscreensaver-command -lock")
        , ((controlMask, xK_Print), spawn "sleep 0.2; scrot -s")
        , ((0, xK_Print), spawn "scrot")
        ]

.xsession

#!/bin/bash

xrdb -merge .Xresources

# Configure xrandr for multiple monitors
# External output may be "VGA" or "VGA-0" or "DVI-0" or "TMDS-1"
EXTERNAL_OUTPUT="VGA-0"
INTERNAL_OUTPUT="LVDS"
# EXTERNAL_LOCATION may be one of: left, right, above, or below
EXTERNAL_LOCATION="left"

# In case I want to have both monitors on
case "$EXTERNAL_LOCATION" in
       left|LEFT)
               EXTERNAL_LOCATION="--left-of $INTERNAL_OUTPUT"
               ;;
       right|RIGHT)
               EXTERNAL_LOCATION="--right-of $INTERNAL_OUTPUT"
               ;;
       top|TOP|above|ABOVE)
               EXTERNAL_LOCATION="--above $INTERNAL_OUTPUT"
               ;;
       bottom|BOTTOM|below|BELOW)
               EXTERNAL_LOCATION="--below $INTERNAL_OUTPUT"
               ;;
       *)
               EXTERNAL_LOCATION="--left-of $INTERNAL_OUTPUT"
               ;;
esac
xrandr | grep $EXTERNAL_OUTPUT | grep " connected "

if [ $? -eq 0 ]; then
    xrandr --output $INTERNAL_OUTPUT --off --output $EXTERNAL_OUTPUT --auto
    # Alternative command in case of trouble:
    # (sleep 2; xrandr --output $INTERNAL_OUTPUT --auto --output $EXTERNAL_OUTPUT --auto $EXTERNAL_LOCATION) &
else
    xrandr --output $INTERNAL_OUTPUT --auto --output $EXTERNAL_OUTPUT --off
fi

trayer --edge top --align right --SetDockType true --SetPartialStrut true --expand true --width 15 --height 12 --transparent true --tint 0x000000 &

xscreensaver -no-splash &

# Allow nautilus to take care of plugin USB drives and Dropbox icons
nautilus --no-desktop -n &

if [ -x /usr/bin/nm-applet ] ; then
   nm-applet --sm-disable &
fi

if [ -x /usr/bin/gnome-power-manager ] ; then
   sleep 1
   gnome-power-manager &
fi

/usr/bin/gnome-volume-control-applet &
dropbox start &

exec /home/cebrian/.cabal/bin/xmonad

.xmobarrc

Config { font = "-*-Fixed-Bold-R-Normal-*-13-*-*-*-*-*-*-*"
       , bgColor = "black"
       , fgColor = "grey"
       , position = TopW L 85
       , commands = [ Run Cpu ["-L","3","-H","50","--normal","green","--high","red"] 10
                    , Run Memory ["-t","Mem: <usedratio>%"] 10
                    , Run Swap [] 10
                    , Run Date "%a %b %_d %Y %H:%M:%S" "date" 10
                    , Run StdinReader
                    ]
       , sepChar = "%"
       , alignSep = "}{"
       , template = "%StdinReader% }{ %cpu% | %memory% * %swap%    <fc=#ee9a00>%date%</fc>"
       }