cgstat

Displays some benchmarking statistics on CarthaGene and the Heap.

Synopsis:

The cgstat command is invoked either as:

• cgstat Options
• cgstat LOD-Threshold

Description:

The command cgstat displays some basic statistics on the software and the contents of the heap. It reports the total CPU-time consumed, the number of calls to the EM (Expectation/Maximization) algorithm and the number of maps in the heap within LOD-Threshold of the best known map in the heap.

For internal use only: if the data-set loaded is identified as a randomly generated test data-set, further statistics are reported: difference in log-likelihood of the best know map with the log-likelihood of the order used to generate the data, at what cpu-time stamp this map was found and if it is identical to the order used to generate the data.

Arguments:

• Options : -u to obtain the synopsys of the normal use, -h to print a one line description, -H to print a short help.
• LOD-Threshold: maximum difference in loglikelihood with the best known map.

Returns:

a list of these different statistics (some may be unapplicable when the data set used is not a benchmarking random data-set).

• a boolean that indicates whether the best map found is the correct (model) map.
• the total cpu-time used
• the difference of loglikelihood between the best maporder and the ``true'' order.
• the cpu-time stamp of the best known map.
• the number of maps in the heap whose loglikelihood is within LOD-Threshold of the best map.
• the number of EM calls overall.

Example:

   CarthaGene version 1.2-LKH, Copyright (c) 1997-2010 (INRA).

   CarthaGene comes with ABSOLUTELY NO WARRANTY.
   CarthaGene is free software. You are welcome to redistribute it,
   under certain conditions. See the License file for information.

Type 'help' for help.

# we load a dataset
CG> dsload Data/bc.cg
{1 f2 backcross 20 208 /home/tschiex/Dev/carthagene/doc/user/exemple/Data/b...
#compute groups
CG> group 0.1 7
...
#and select group 4
CG> mrkselset [groupget 4]
...
# compute a first map
CG> nicemapd
...
# check the quality of this order
CG> flips 2 0 0
...
#check some statistics and ask for the number of maps within 1 of the optimum
CG> cgstat 1

Map  8 : log10-likelihood =  -129.39, log-e-likelihood =  -297.93
-------:

Data Set Number  1 :

             Markers Distance    Cumulative  Distance   Theta       2pt
Pos  Id name         Haldane     Haldane     Kosambi    (%%age)      LOD

  1   2  MS2           0.6 cM      0.0 cM      0.6 cM     0.6 %     47.6
  2   3  MS3           5.8 cM      0.6 cM      5.5 cM     5.5 %     35.1
  3   4  MS4           3.6 cM      6.4 cM      3.5 cM     3.5 %     21.1
  4   5  MS5           3.7 cM     10.1 cM      3.6 cM     3.6 %     15.4
  5   6  MS6           1.6 cM     13.8 cM      1.6 cM     1.6 %     17.3
  6   7  MS7           6.7 cM     15.4 cM      6.3 cM     6.3 %     35.1
  7   8  MS8           2.5 cM     22.1 cM      2.5 cM     2.5 %      7.4
  8  10 MS10           0.0 cM     24.6 cM      0.0 cM     0.0 %      7.2
  9   9  MS9        ----------              ----------
                      24.6 cM                 23.6 cM


        9 markers, log10-likelihood =  -129.39
                   log-e-likelihood =  -297.93
Total CPU Time (secondes): 0.00
Number of calls to EM: 28
# of maps within -130.390165: 1
Current best LogLike is -129.390165 and worst is -153.374826
Reliability Threshold = 1e+100
Tolerance Threshold1 = 0.1
Tolerance Threshold2 = 0.001
{1 0.000000 1 0.000000 0.000000 1 28}

See also:

• cgrestart (2.8.5)
• heaprint (2.4.4)