Displays some benchmarking statistics on CarthaGene and the Heap.

The `cgstat` command is invoked either as:

`cgstat`*Options*`cgstat`*LOD-Threshold*

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.

*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.

- 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.

# we load a dataset CG> dsload Data/bc.cg {1 f2 backcross 20 208 /homes/thomas/carthagene/test/Data/bc.cg} #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 = -135.41, log-e-likelihood = -311.80 -------: Data Set Number 1 : Markers Distance Cumulative Distance Theta 2pt Pos Id name Haldane Haldane Kosambi (%%age) LOD 1 2 MS2 0.6 cM 0.6 cM 0.6 cM 0.6 %% 47.6 2 3 MS3 5.8 cM 6.4 cM 5.5 cM 5.5 %% 35.1 3 4 MS4 3.6 cM 10.1 cM 3.5 cM 3.5 %% 21.1 4 5 MS5 3.7 cM 13.8 cM 3.6 cM 3.6 %% 15.4 5 6 MS6 1.6 cM 15.4 cM 1.6 cM 1.6 %% 17.3 6 7 MS7 6.7 cM 22.1 cM 6.3 cM 6.3 %% 35.1 7 8 MS8 2.5 cM 24.6 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 = -135.41 log-e-likelihood = -311.80 Total CPU Time (secondes): 0.01 Number of calls to EM: 28 # of maps within -136.410765: 1 Current best LogLike is -135.410765 and worst is -159.395426 Reliability Threshold = 1e+100 Tolerance Threshold1 = 0.1 Tolerance Threshold2 = 0.001 {1 0.010000 1 0.000000 0.010000 1 28}

Thomas Schiex 2009-10-27