### Re: [R-sig-eco] The final result of TWINSPAN

On 14/04/11 10:37 AM, Yong Zhang 2010202...@njau.edu.cn wrote: Dear all, I conducted the two-way indicator species analysis using TWINSPAN program, and following is the final result: 0111 00011011 011000111 01001001 I have to certify my analysis, I want to classify the above 24 sampling sites into 3 major groups based on 7 biotic metrics. The name of my 24 samples could be site1 to site24, from the left to the right, and I set the cut levels 0, 2, 5, 10, 20, the maximum level of divisions: 6, and maximum group size for division:3 . Now, my question is whether my setting is correct? And how should I classify these sites into 3 groups accoding to this final result? Dear Yong Zhang, This is not an R issue, because there is no TWINSPAN in R. However, the answer to your question is that strictly speaking you cannot group your data into three major groups with TWINSPAN. TWINSPAN is a bisection method so that first division gives you two groups, and second splits each of these into two groups so that the next choice is to have four groups. However, in this case one of the groups was so small (3 plots were split off from other in the first division, and then these were split into groups of 2 plots and 1 plot) that you probably can ignore the second division of the small group. If your goal was as vague as wanting to classify 24 sites into 3 major groups you could do better than use TWINSPAN: what's the problem with proper classification methods in R? Moreover, have you checked that your biotic metrics suit to the pseudospecies cut level concept of TWINSPAN? Cheers, jari oksanen ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology

### Re: [R-sig-eco] The final result of TWINSPAN

Dear Yong, This *is* a list about R. Your question has *nothing* to do with R. Please ask such questions elsewhere, like the ORDNEWS list. On Thu, 2011-04-14 at 15:37 +0800, Yong Zhang wrote: snip / I conducted the two-way indicator species analysis using TWINSPAN program, and following is the final result: Being painfully aware of the output TWINSPAN generates, I'm certain this isn't all that TWINSPAN output, but I presume it is the binary indicator for the groups/splits from the output? 0111 00011011 011000111 01001001 I have to certify my analysis, I want to classify the above 24 sampling sites into 3 major groups based on 7 biotic metrics. The name of my 24 samples could be site1 to site24, from the left to the right, and I set the cut levels 0, 2, 5, 10, 20, the maximum level of divisions: 6, and maximum group size for division:3 . Then you are out of luck, without using some other means of pruning back divisions. TWINSPAN implements a binary split process, and without other intervention you get 0, 2, 4, 8, 16 groups etc. You /can/ post-process the results of TWINSPAN using another DOS application to merge lower nodes of certain, specific branches into higher nodes to get different numbers of groups than 2, 4, 8, ..., but I forget the name of this DOS application at the moment - I used to teach a computer class using this so I have the details somewhere so will see if I can hunt those old notes out. My interpretation of the above would be that you could just ignore the split that cuts the 3 extreme right samples into two groups so you have groups consisting of the first 11 samples, the next 10 in another group, and the final 3 samples in a group. But that is without seeing any of the other output, so I don't know if the CA clustering technique used is doing silly things splitting your main group of samples - i.e. are there samples close to the origin but on opposite sides that are similar to one another but which have been pushed into separate groups? Hopefully the above helps, but please direct further and future requests for help with non-R applications to more appropriate lists. G Now, my question is whether my setting is correct? And how should I classify these sites into 3 groups accoding to this final result? Thanks in advance for your time and suggestion. Kind wishes, Yong 2011-04-14 ZHANG Yong Lab of aquatic insects stream ecology Dept.of Entonology, Nanjing Agricultural University Nanjing, 210095,China Phone number: (+86) -25-84395241 E-mail:2010202...@njau.edu.cn ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology