**************************************************
*                                                *
* Created  : 2006-02-16                          *
* Author   : Fredrik Tegenfeldt, CERN            *
* Modified : 2006-11-07                          *
*            Major revision.                     *
*                                                *
**************************************************

This is a short version of a 'manual'. The intention is to include this in the doxygen
documentation with somewhat more fancy layout.

The contents for now is:

I    Installation
II   Tools
III  Input options, polelim
IV   Input options, polecov
V    Example, polelim
VI   Example, polecov
VII  Scripts
VIII Known issues



I. INSTALLATION
==============

1. untar file. The files will be created in current directory.

tar -xzvf polelib.tgz

2. compile

make

3. to run the code, you need to make the library available.
   This can be done by copying libPole++.so to /usr/lib or similar (need to be root).
   Otherwise, you can add the current directory to the library path:

	setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:.

   or in bash:

	export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:.

   Now it should be possible to run polelim or polecov.

4. To clean up:

make clean


II. TOOLS
==========

1. polelim:   limit calculator
2. polecov:   coverage calculator
3. poleconst: calculates only the likelihood ratio construction in (s_hyp,N) plane
4. polebelt:  calculates the confidence belt

To create these tools, do

   make tools


III. INPUT OPTIONS, POLELIM
============================

The tools polelim, poleconst and polebelt all have the same options.
Their options are all defined in the file argsPole.cxx.

Running polelim with option --help yields:

USAGE:

   ./polelim  [-l <int>] [-f <string>] [-V <int>] [--poisnx <int>]
              [--poisnm <int>] [--poismax <float>] [--poismin <float>]
              [--bkgintn <int>] [--bkgintscale <float>] [--effintn <int>]
              [--effintscale <float>] [--hstep <float>] [--hmax <float>]
              [--hmin <float>] [--threshprec <float>] [--threshbs <float>]
              [--nmus <float>] [--dmus <float>] [--corr <float>]
              [--bkgscale <float>] [--bkgdist <int>] [--bkgmeas <float>]
              [--bkgsigma <float>] [--effscale <float>] [--effdist <int>]
              [--effmeas <float>] [--effsigma <float>] [--minp <float>]
              [-K] [-m <int>] [--strue <float>] [--cl <float>] [--nobs
              <int>] [--] [-v] [-h]



III.1 Minimum requirements
--------------------------

Pole calculates the confidence interval of a given confidence level from the following information:

* Number of observed events
  --nobs <int>         : default is 1

* Method
  -m or --method <int> : 1 - FHC2 (default), 2 - MBT

* Confidence level
  --cl       <float>   : default is 0.90

* Efficiency
  --effmeas  <float>   : measured mean
  --effdist  <float>   : assumed distribution
  --effsigma <float>   : measured uncertainty

* Background
  --bkgmeas  <float>   : measured mean
  --bkgdist  <float>   : assumed distribution
  --bkgsigma <float>   : measured uncertainty

* Correlation coefficient between eff and bkg:
  --corr     <float>   : is in the range of [-1,1]

The distributions above are:
  0 - none
  1 - poisson
  2 - gauss
  3 - flat
  4 - log normal
  5 - 2d gauss, that is, use --corr; eff and bkg correlated

------------------------------------------------------------------

An alternative way of inputting data is by file. This is not yet well developed.
See the function Pole::exeFromFile().

* Filename
  -f <string>   : data file name - see/modify Pole::exeFromFile()
  -l <int>      : number of lines to read from input file

  If -f is used --nobs, --eff/bkg{meas,dist,sigma} are ignored



III.2 Precision related
-----------------------

There are several other parameters to control the precision of integrals, limit scan etc.

* Integral over aposteriori efficiency distribution:
  --effn     <float    : number of points, default = 21
  --effscale <float>   :  integrate between [ mean-scale*sigma, mean+scale*sigma ]
		         where mean == --effmeas and sigma = --effsigma
		         default = 5.0

* Ditto for background integration:
  --bkgn     <float>   : see above
  --bkgscale <float>   : see above

* Finding s_best - only used when method is FHC2

  --dmus     <float>   : step size in search, usually fine with 0.01
	                 increase or reduce depending on requirements in precision or speed.
  --nmus     <float>   : maximum number of steps - using the given step size, the number of steps is not allowed
                         to be greater than nmus. default = 100

* Search threshholds

  --threshbs    <float> : minimum relative change in hypothesis in the binary search for the limit
                          default = 0.0001
  --threshalpha <float> : minimum relative diff in alpha to required alpha = 1-cl
                          default = 0.0001

  The binary search stops whenever one of the above conditions are met.

* Probability threshhold

  --minp        <float> : minimum probability p(n|H) considered when calculating the belt
                          automatically set depending on the selected CL

* Poisson table; for speed, the poisson table is tabulated for a range of N and mean values.
  This only makes sense if many points are to be caclulated.
  When reading the table, 2nd order derivative corrections are applied.

  --poisnx      <int>   : maximum N
                          default = 200
  --poisnm      <int>   : number of mean values
                          default = 100000
  --poismin     <float> : minimum mean
                          default = 0.0
  --poismax     <float> : maximum mean
                          default = 100.0

  NOTE: if large N or mean values are used, it might fail due to limited memory.

  -K                    : do not tabulate poisson - rarely needed but can be good to check that the
                          poisson table is accurate enough

III.3 Various options
---------------------

  -V or --verbose <int> : verbose mode; mainly for debugging. Output may be confusing...

  -v or --version       : print version

  -h or --help          : print help


III.4 Extras - NOT USED WHEN CALCULATING LIMITS
-----------------------------------------------

* Confidence belt construct.
  Relevant when calculating the construct or belt (polebelt and poleconst tools).

  --hstep <float> : hypothesis step size
  --hmin  <float> : minimum
  --hmax  <float> : maximum


The following options are now obsolete:

--strue


IV. INPUT OPTIONS, POLECOV
===========================

Running polecov --help gives:

USAGE: 

   ./polecov  [--poisnx <int>] [--poisnm <int>] [--poismax <float>]
              [--poismin <float>] [--bkgn <int>] [--bscale <float>] [--effn
              <int>] [--effscale <float>] [--hstep <float>] [--hmax
              <float>] [--hmin <float>] [--threshalpha <float>] [--threshbs
              <float>] [--nmus <float>] [--dmus <float>] [--corr <float>]
              [--bkgstep <float>] [--bkgmax <float>] [--bkgmin <float>]
              [--bkgsigma <float>] [--bkgdist <int>] [--effstep <float>]
              [--effmax <float>] [--effmin <float>] [--effsigma <float>]
              [--effdist <int>] [--sstep <float>] [--smax <float>] [--smin
              <float>] [-P <int>] [-V <int>] [--dump <string>] [--minp
              <float>] [-S] [-C] [-K] [-m <int>] [--cl <float>] [--rseedofs
              <int>] [--rseed <int>] [--nloops <int>] [--] [-v] [-h]



polecov calculates the coverage over a given range of parameters.
It accepts largely the same arguments as for polelim.
The specifics for polecov are described below.

*The program can scan over:

1. true signal
   --smin   : min signal
   --smax   : max signal
   --sstep  : step size

2. efficiency:
   --emin, --emax, --estep
   --effdist: distribution (not scanable...)

3. background
   --bmin, --bmax, --bstep, --bkgdist

Number of loops

   --nloops : number of MC experiments (default = 1), usually 1000 is enough, increase the number for increased precision

Random number generator

  --rseed    :  set the random number seed; if not set, a seed is set based on the time
  --rseedofs :  seed offset (not really used)

It is possible to fix the N(obs) in each experiment:

   -S or --fixsig

Control the usage of tabulated poisson:

   -K or --notab  : do not use the table

Verbosity:

   -P or --verbpol : set verbosity level for the pole part

   -V or --verbcov : ditto for the coverage

Statistics:

   --dump   :  dump file prefix

   -C,  --stats : collect statistics - will take longer time since it will always calculate the full limits

* The output

For each point calculated a line is printed as follows:

 DATA: <s(true)>    <eff>  <sigma(eff)>  <bkg> <sigma(bkg)>  <corr>  <coverage> <coverage uncertainty>  <number of loops done>  <max n(loops)>  <time in ms>

From the logfile, a tabulated file can be obtained using the following:

 grep "DATA:" <logfile> | cut -d ":" -f 2 > output.dat

The coverage can then be plotted using, e.g, gnuplot.


* Special features

1. Process signal handling:

   SIGINT (ctrl-c) : stops the program and prints out the latest result
   SIGUSR1         : prints out a "STATUS:" line which has the same contents as "DATA:"

2. Run time estimations:

   After a certain time, the code will print out a time estimation based on the performance so far.
   This estimation is rather a lower limit as the time per point varies with the values of the parameters.


V. EXAMPLE POLELIM
===================

* Running the polelim with default parameters:


---------------------------------------------------------------------
--- Tabulating pdf <Poisson>
--- N(X)       = 201
---   min      = 0
---   max      = 200
--- N(mean)    = 100000
---   min      = 0
---   max      = 100
--- N(sigma)   = 1
---   min      = 0
---   max      = 0
---------------------------------------------------------------------
--- Tabulating ... be patient
--- Tabulating DONE!

================ P O L E ==================
 1.0 - conf. level  : 0.1
 N observed         : 1
----------------------------------------------
 Coverage friendly  : No
 True signal        : 1
----------------------------------------------
 Efficiency meas    : 1
 Efficiency sigma   : 0.2
 Efficiency dist    : Gauss
 Efficiency scale   : 1
----------------------------------------------
 Background meas    : 0
 Background sigma   : 0
 Background dist    : None
 Background scale   : 1
----------------------------------------------
 Bkg-Eff correlation: 0
----------------------------------------------
 Int. eff. min      : 0
 Int. eff. max      : 2
 Int. eff. N pts    : 21
----------------------------------------------
 Int. bkg. min      : 0
 Int. bkg. max      : 0
 Int. bkg. N pts    : 1
----------------------------------------------
 Binary search thr. : 0.0001
 1-CL threshold     : 0.0001
 Min prob in belt   : 0.001
----------------------------------------------
 *Test hyp. min     : 0
 *Test hyp. max     : 35
 *Test hyp. step    : 0.01
----------------------------------------------
 Step mu_best       : 0.002
 Max N, mu_best     : 100
----------------------------------------------
 Method             : FHC2
----------------------------------------------
 Verbosity          : 0
----------------------------------------------
 Parameters prefixed with a * above are not
 relevant for limit calculations.
==============================================

*--------------------------------------------------*
* Precision of lower limit = 0.000007
*              upper limit = 0.002139
*
* Limits = [ 0.105591, 4.639010 ]
*--------------------------------------------------*


* Fixed efficiency, gaussian backgound:

./polelim --effdist 0 --bkgdist 2 --bkgmeas 2 --bkgsigma 0.5 --nobs 4

 => [0.00,6.94]

* Very large N(obs)

./polelim --nobs 30

 => Used to fail in previous versions. Due to the binary search approach, this does not fail anymore.
 => [ 17.81, 47.66 ]


VI. EXAMPLE POLECOV
====================

* Running polecov with default settings:


---------------------------------------------------------------------
--- Tabulating pdf <Poisson>
--- N(X)       = 201
---   min      = 0
---   max      = 200
--- N(mean)    = 100000
---   min      = 0
---   max      = 100
--- N(sigma)   = 1
---   min      = 0
---   max      = 0
---------------------------------------------------------------------
--- Tabulating ... be patient
--- Tabulating DONE!

==============C O V E R A G E=================
 Random seed        : 1162916891
 Number of loops    : 1
 Collect statistics : No
----------------------------------------------
 Signal min         : 1
 Signal max         : 1
 Signal step        : 0
 Signal N           : 1
 Signal fixed       : No
----------------------------------------------
 Efficiency min     : 1
 Efficiency max     : 1
 Efficiency step    : 0
 Efficiency sigma   : 0.2
 Efficiency dist    : Gauss
----------------------------------------------
 Background min     : 0
 Background max     : 0
 Background step    : 0
 Background sigma   : 0
 Background dist    : None
----------------------------------------------
 Correlated bkg,eff : No
==============================================
Start of run: 07/11/2006 17:28:12
#==================================================================================================================
#     Signal    |     Efficiency       |      Background       |      Coverage         |    Loops    |    Time
#               | mean        sigma    |  mean        sigma    |  mean        sigma    | done    max |    [ms]
#==================================================================================================================
COVERAGE: 1.000000    1.000000    0.200000    0.000000    0.000000    1.000000    0.000000    1    1      10.00
>>>Limit calculation failure rate: 0

End of run: 07/11/2006 17:28:12


* Scanning several parameters:

> ./polecov --smin 1.0 --smax 5.0 --sstep 1.0 --dmus 0.1 --nloops 1000

---------------------------------------------------------------------
--- Tabulating pdf <Poisson>
--- N(X)       = 201
---   min      = 0
---   max      = 200
--- N(mean)    = 100000
---   min      = 0
---   max      = 100
--- N(sigma)   = 1
---   min      = 0
---   max      = 0
---------------------------------------------------------------------
--- Tabulating ... be patient
--- Tabulating DONE!

==============C O V E R A G E=================
 Random seed        : 1157036928
 Number of loops    : 1000
 Collect statistics : No
----------------------------------------------
 Signal min         : 1
 Signal max         : 5
 Signal step        : 1
 Signal N           : 5
 Signal fixed       : No
----------------------------------------------
 Efficiency min     : 1
 Efficiency max     : 1
 Efficiency step    : 0
 Efficiency sigma   : 0.2
 Efficiency dist    : Gauss
----------------------------------------------
 Background min     : 0
 Background max     : 0
 Background step    : 0
 Background sigma   : 0
 Background dist    : None
----------------------------------------------
 Correlated bkg,eff : No
==============================================
tart of run: 07/11/2006 17:29:51
#==================================================================================================================
#     Signal    |     Efficiency       |      Background       |      Coverage         |    Loops    |    Time
#               | mean        sigma    |  mean        sigma    |  mean        sigma    | done    max |    [ms]
#==================================================================================================================
COVERAGE: 1.000000    1.000000    0.200000    0.000000    0.000000    0.946000    0.007147    1000    1000      250.00
COVERAGE: 2.000000    1.000000    0.200000    0.000000    0.000000    0.979000    0.004534    1000    1000      490.00
COVERAGE: 3.000000    1.000000    0.200000    0.000000    0.000000    0.944000    0.007271    1000    1000      740.00
COVERAGE: 4.000000    1.000000    0.200000    0.000000    0.000000    0.945000    0.007209    1000    1000      1050.00
COVERAGE: 5.000000    1.000000    0.200000    0.000000    0.000000    0.961000    0.006122    1000    1000      1430.00
>>>Limit calculation failure rate: 0

End of run: 07/11/2006 17:29:55


* A long run first checked with  kill -USR1 <process id>

  polecov --nloops 10000

---------------------------------------------------------------------

 < SAME BEGINNING AS BEFORE>

Estimated end of run: 31/08/2006 17:12:19 ( 0h 0m 23s )

#==================================================================================================================
#     Signal    |     Efficiency       |      Background       |      Coverage         |    Loops    |    Time
#               | mean        sigma    |  mean        sigma    |  mean        sigma    | done    max |    [ms]
#==================================================================================================================
STATUS: 1.000000    0.668974    0.200000    0.000000    0.000000    0.944142    0.003791    3670    10000      8540.00
WARNING (31/08/2006 17:12:08 ) Job aborting (signal = 2 ). Will output data from unfinnished loop.

DATA: 1.000000    1.103927    0.200000    0.000000    0.000000    0.943144    0.003220    5171    10000      12090.00

---------------------------------------------------------------------

The STATUS: line is printed whenever polecov receives a SIGUSR1 signal (eg through kill -USR1 <pid> ).
With a ctrl-c (or kill -2 <pid>) the running is aborted and the current result is printed out.



VII. SCRIPTS
=============

The tools polebelt and poleconst produces output which needs processing for plotting.
A few scripts exists which will do the processing and plotting.

1. log2construct.csh <log file>
   The script processes the log file containing the output from poleconst and produces
   a ROOT readable text file (construct.dat)

2. log2confbelt.csh <log file>
   The script processes the log file containing the output from polebelt and produces
   a ROOT readable text file (confbelt.dat)

3. plotconst.C
   Reads <construct.dat> and plots the likelihood ratio construction in (s_hyp,N) plane

4. plotconfbelt.C
   Reads <confbelt.dat> and plots the confidence belt.
   Takes as arguments (Nobs, lower limit, upper limit).
   If given, the intersection lines are drawn -> useful to verify result.

5. plotprob.C
   Reads <construct.dat> and plots the probability at each point in (s_hyp,N) plane



VIII. KNOWN ISSUES
==================

The previous issues have been fixed.

1. Combined measurements - numerically tricky - does not work now