Computation:
Load the utility, Commonness_and_Rarity.exe’, and both inputs i.e. ‘Observed Matrix –
Input.txt’ and ‘Generated Matrices - Input’ on your computer.
1.
2.
3.
4.
Run the utility (exe file).
Load a matrix (Files, Load Observed Matrix).
Load the set of generated matrices (Files, Load Generated Matrices)
Press ‘Setting’ item in the main menu; Check ‘Show’ if you need to see the matrices
during the computation; Check ‘Step by Step’ if you need to see each of the generated
matrices separately. The setting have to be confirmed in any case (even if you want
nothing to change on the panel).
5. Confirm your setting by pressing the ‘Save the Setting’ button.
6. Run the computation (Computations, Run the Computation). You will be asked for
creating the output file.
There are some files that appear on your disk in the file with the running utility during
computation. Their extensions are ‘$$$’. If you fail terminate the computation properly,
you can simply delete them. The ‘end’ item in the main menu is recommended to
terminate the utility.
Input I (an Observed Matrix)
0
0
0
0
0
0
0
0
0
0
0
1
2
3
4
5
6
7
0
1
1
0
1
1
0
1
0
0
2
1
0
1
0
1
0
1
0
3
0
1
1
1
1
1
1
0
4
0
1
0
0
0
0
0
0
5
1
0
0
1
0
0
0
First column are codes used for another analyses. They are not of any use here. Use ‘0’ for all
rows, please.
Second column are codes of the species. They are 1-7 in the case.
The description of the data file is missing in the case (see the other utilities on the wiki page
you loaded the files from)
First raw is an Y coordinate of a plot. In case of transect it is zero.
Third raw is an X coordinate of plot. In case of transect it is a rank of the point of the transect.
Cells of the matrix are abundances (they can be just incidences for this computation).
Input II (The simulated Matrices)
The input is identical to the output from the utility ‘matrices_generator.exe’.
The first number is compulsory; it shows the number of rows (species in the case) of each
consecutive matrix in the file (radku bez hlavicky=rows without a headline); (The text after
the number is just information, can be modified deliberately)
7 radku bez hlavicky
0
0
0
0
0
1
0
1
0
0
2
0
0
3
0
0
4
0
0
5
0
0
6
0
0
7
0
0
0
0
0
0
1
0
1
0
0
2
0
0
3
1
0
4
0
0
5
0
0
6
0
0
7
1
0
0
0
0
0
1
0
1
0
0
2
0
0
3
1
0
4
0
0
5
0
0
6
0
0
7
0
0
0
0
0
0
1
0
1
0
0
2
0
0
3
0
0
4
0
0
5
0
0
6
0
0
7
0
0
0
0
0
0
1
0
1
0
0
2
0
0
3
0
0
4
0
0
5
0
0
2
0
0
1
0
1
1
0
0
2
0
0
0
0
1
0
0
0
2
0
0
0
0
1
0
0
0
2
0
0
0
0
1
1
0
0
2
0
0
1
0
0
0
3
1
1
0
1
0
1
1
0
3
1
1
0
1
0
1
1
0
3
1
1
0
1
1
1
1
0
3
1
1
0
1
0
1
1
0
3
0
0
0
0
1
0
4
0
0
0
0
0
0
1
0
4
0
0
0
0
1
1
0
0
4
0
0
0
1
1
1
1
0
4
0
0
1
1
1
0
1
0
4
1
1
0
1
1
0
5
1
1
1
1
1
1
1
0
5
1
1
1
1
1
1
1
0
5
1
1
1
1
0
1
1
0
5
1
1
1
1
1
1
1
0
5
0
1
1
1
1
0
0
6
7
0
0
1
1
1
0
1
1
0
1
Output
The output is a table comprising the following list of items (labeled according to the paper)
Simulation
Focal Species
Occupancy
Sum of D_j
r-Nestedness
D_s
Max D_s
Correlation
Max Correlation
rNestedness Sim
rNestedness Obs
D_s Sim
D_s Obs
Correlation Sim
Correlation Obs
Numerator Sim
Numerator Obs