******************** PC-ORD Analysis Wizard ******************** PC-ORD, 6.0 12 Sep 2012, 18:29:10 1. Welcome to the PC-ORD Advisor Wizard. The purpose of the wizard is to help you to decide how to analyze your data, based on a decision tree. You can also use it as a self teaching tool. We attempt to deal only with relatively common data analysis problems that you are likely to encounter with ecological community data. You must have at least a main matrix open to run the wizard. Ready to go? Ans.: Proceed. 2. Where would you like to start? Ans.: Skip to analytical procedures 3. Do you wish to compare existing groups in your data? Ans.: Yes 4. Which kind of comparison do you want to make? You can compare (A) groups of sample units in your main matrix, the groups specified by a categorical variable in your second matrix. Or you can compare (B) two groups of variables from the same sample units, one group of variables in the main matrix and the other group in the second matrix. Ans.: B. Compare groups of variables. 5. Do you wish to seek and define groups of sample units in your data? Ans.: Yes. 6. Do you have an extremely large data set with, for example, 10,000 or more sample units? Ans.: No 7. Do you wish to display row and column dendrograms in relationship to each other in a graphical view of the main matrix? Ans.: Yes 8. Are ALL of the following true? - main matrix contains species abundances or presence-absence - groups are sought along only one strong underlying gradient (or underlying dimension) - ok to implicitly use chi-square distance measure to represent differences between sample units - ok to represent abundances as "pseudospecies" Ans.: No 9. Two-way cluster analysis is recommended. ******************** Operation completed ******************** 12 Sep 2012, 18:38:06 ******************* Two-way Hierarchical Cluster Analysis ******************* PC-ORD, 6.0 12 Sep 2012, 18:38:44 2way CA sorensens Linkage method: FLEXIBLE BETA Distance measure: Sorensen (Bray-Curtis) Total sum of squares: 3785.074 Flexible beta value selected is -0.250 Cluster cycle 1 Combined group 24 into group 3 at level 6.5843E-03 2 Combined group 34 into group 9 at level 2.6584E-02 3 Combined group 27 into group 1 at level 4.9845E-02 4 Combined group 52 into group 22 at level 7.3474E-02 5 Combined group 48 into group 13 at level 9.8165E-02 6 Combined group 45 into group 38 at level 1.2399E-01 7 Combined group 37 into group 3 at level 1.5355E-01 8 Combined group 11 into group 2 at level 1.9437E-01 9 Combined group 29 into group 1 at level 2.3624E-01 10 Combined group 30 into group 3 at level 2.7887E-01 11 Combined group 38 into group 4 at level 3.2489E-01 12 Combined group 28 into group 26 at level 3.7475E-01 13 Combined group 33 into group 21 at level 4.2502E-01 14 Combined group 20 into group 15 at level 4.8057E-01 15 Combined group 10 into group 2 at level 5.4318E-01 16 Combined group 42 into group 5 at level 6.0696E-01 17 Combined group 39 into group 32 at level 6.7482E-01 18 Combined group 8 into group 7 at level 7.4380E-01 19 Combined group 36 into group 5 at level 8.1872E-01 20 Combined group 23 into group 16 at level 8.9776E-01 21 Combined group 50 into group 3 at level 9.7800E-01 22 Combined group 14 into group 13 at level 1.0603E+00 23 Combined group 18 into group 4 at level 1.1451E+00 24 Combined group 26 into group 12 at level 1.2405E+00 25 Combined group 40 into group 1 at level 1.3390E+00 26 Combined group 4 into group 2 at level 1.4394E+00 27 Combined group 16 into group 7 at level 1.5504E+00 28 Combined group 31 into group 22 at level 1.6626E+00 29 Combined group 54 into group 21 at level 1.7901E+00 30 Combined group 46 into group 44 at level 1.9323E+00 31 Combined group 51 into group 22 at level 2.0881E+00 32 Combined group 41 into group 5 at level 2.2571E+00 33 Combined group 47 into group 35 at level 2.4261E+00 34 Combined group 43 into group 12 at level 2.6035E+00 35 Combined group 17 into group 7 at level 2.7828E+00 36 Combined group 3 into group 2 at level 2.9667E+00 37 Combined group 15 into group 6 at level 3.1564E+00 38 Combined group 21 into group 7 at level 3.3574E+00 39 Combined group 49 into group 35 at level 3.5723E+00 40 Combined group 53 into group 1 at level 3.8038E+00 41 Combined group 12 into group 5 at level 4.0715E+00 42 Combined group 13 into group 1 at level 4.3497E+00 43 Combined group 44 into group 32 at level 4.6613E+00 44 Combined group 25 into group 22 at level 4.9953E+00 45 Combined group 9 into group 7 at level 5.3514E+00 46 Combined group 5 into group 2 at level 5.7125E+00 47 Combined group 19 into group 1 at level 6.1384E+00 48 Combined group 2 into group 1 at level 6.5718E+00 49 Combined group 35 into group 22 at level 7.0265E+00 50 Combined group 7 into group 6 at level 7.5999E+00 51 Combined group 32 into group 22 at level 8.2461E+00 52 Combined group 22 into group 6 at level 9.0414E+00 53 Combined group 6 into group 1 at level 1.0085E+01 Percent chaining = 2.22 ******************* Part 2. Cluster Analysis of Columns ******************* No relativation applied to columns. Distance measure: Sorensen (Bray-Curtis) Total sum of squares: 5927.828 Flexible beta value selected is -0.250 Cluster cycle 1 Combined group 7 into group 2 at level 0.0000E+00 2 Combined group 26 into group 22 at level 0.0000E+00 3 Combined group 35 into group 34 at level 0.0000E+00 4 Combined group 48 into group 44 at level 0.0000E+00 5 Combined group 44 into group 37 at level 1.2755E-02 6 Combined group 56 into group 8 at level 6.8311E-02 7 Combined group 21 into group 19 at level 1.2387E-01 8 Combined group 29 into group 20 at level 1.7942E-01 9 Combined group 28 into group 27 at level 2.3498E-01 10 Combined group 37 into group 4 at level 2.9472E-01 11 Combined group 47 into group 1 at level 3.5773E-01 12 Combined group 10 into group 2 at level 4.2718E-01 13 Combined group 31 into group 22 at level 4.9662E-01 14 Combined group 46 into group 45 at level 5.9993E-01 15 Combined group 24 into group 4 at level 7.0833E-01 16 Combined group 53 into group 19 at level 8.4166E-01 17 Combined group 55 into group 42 at level 9.8663E-01 18 Combined group 36 into group 27 at level 1.1385E+00 19 Combined group 33 into group 18 at level 1.2928E+00 20 Combined group 52 into group 11 at level 1.4728E+00 21 Combined group 50 into group 1 at level 1.6542E+00 22 Combined group 27 into group 4 at level 1.8451E+00 23 Combined group 12 into group 9 at level 2.0367E+00 24 Combined group 45 into group 25 at level 2.2388E+00 25 Combined group 39 into group 13 at level 2.4562E+00 26 Combined group 19 into group 16 at level 2.6751E+00 27 Combined group 54 into group 15 at level 2.8973E+00 28 Combined group 58 into group 43 at level 3.1196E+00 29 Combined group 30 into group 3 at level 3.3508E+00 30 Combined group 17 into group 13 at level 3.6320E+00 31 Combined group 42 into group 40 at level 3.9204E+00 32 Combined group 49 into group 11 at level 4.2143E+00 33 Combined group 51 into group 23 at level 4.5214E+00 34 Combined group 8 into group 6 at level 4.8464E+00 35 Combined group 18 into group 5 at level 5.1759E+00 36 Combined group 13 into group 1 at level 5.5331E+00 37 Combined group 38 into group 4 at level 5.9075E+00 38 Combined group 57 into group 11 at level 6.2886E+00 39 Combined group 20 into group 16 at level 6.6916E+00 40 Combined group 11 into group 9 at level 7.1209E+00 41 Combined group 40 into group 34 at level 7.5871E+00 42 Combined group 32 into group 3 at level 8.0588E+00 43 Combined group 41 into group 14 at level 8.5588E+00 44 Combined group 23 into group 5 at level 9.0756E+00 45 Combined group 25 into group 15 at level 9.6141E+00 46 Combined group 15 into group 9 at level 1.0168E+01 47 Combined group 14 into group 3 at level 1.0730E+01 48 Combined group 43 into group 2 at level 1.1300E+01 49 Combined group 5 into group 3 at level 1.1911E+01 50 Combined group 6 into group 3 at level 1.2606E+01 51 Combined group 9 into group 1 at level 1.3382E+01 52 Combined group 3 into group 1 at level 1.4195E+01 53 Combined group 34 into group 2 at level 1.5076E+01 54 Combined group 2 into group 1 at level 1.6024E+01 55 Combined group 22 into group 1 at level 1.7025E+01 56 Combined group 16 into group 1 at level 1.8111E+01 57 Combined group 4 into group 1 at level 1.9241E+01 Percent chaining = 7.40 ******************* Two-way clustering analysis completed ******************* 12 Sep 2012, 18:38:44