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Seems that both Jari and Dave spent considerable effort trying to implement the method into R, but seems like there is some problem which is not easy to crack.
From my experience and I guess also from experience of many others, not only vegetation ecologists , TWINSPAN does sometimes give rather nice and ecologically meaningful results, since it is based on cutting the data along the main compositional gradients. But it seems to me that this method for some reason never gained so much popularity like TWINSPAN did, mostly perhaps due to its sensitivity to outlying samples which will be separated first into one-item clusters.
The way I used is somewhat clumsy, but it seems to work. I used the twinspan. I created R package twinspanR , which includes twinspan. For details how to install the library from GitHub see the Readme. Some more examples how to use twinspan package will be hopefully made soon available on my website for analysis of community ecology data in R.
Some further details how it works. The executable file, twinspan. There is also tw. Then, I create file tw. All calculations are done using original twinspan. PUN file. The twinspan. Hill, compiled cca in by Stephan M. Hennekens into twinspan. The version of twinspan. In fact, there are at least four different versions of TWINSPAN recently used for analysis, and in certain circumstances they differ in the results how they classify the samples when I have time, I will elaborate this topic further.
Unfortunately, the presence of twinspan. For now, the channel for distribution of this package is GitHub, and it will perhaps remain there until some other solution will show up. Hi David, it is nice to see Twinspan finally implemented in R! Congratulations for your especially useful site! Cheers, Attila.
Hi Attila, Thanks for a nice comment! The package is far from ready, but is somewhat functional — there is still couple of things needed to be finished, like plotting the dendrogram, or printing the indicator values for individual splits.
Hope to finish these once. I will be happy, if you use it, if you give me a feedback — especially about things which are not working in a way advertised in the package. Apologies for previous question. Indeed, this is only one reason — the package is in the developmental stage, and was a kind of experiment — hope to finish in future when I have more time, if I see it can be useful. Thanks for you reply. Are you planning on making it mac friendly at some point?
I will see if I can find someone with R on a windows machine. Congratulations and thank you for your efforts. And if not, do you have any tips as to how I might most efficiently extract and organize the relevant information from the output provided? So far the best guess is to extract the hierarchy from the output and draw it somewhere externally. If you use standard Twinspan, just print the two-way sorted table, and at the bottom of the table you will find the sequence determining the hierarchy, e.
Hi David, Thanks for your comments. So it seems exporting and manual construction is the way to go if I want to create the dendrogram itself. Although I guess I can actually review the hierarchical group structure quite easily in a piecemeal fashion by interrogating the binary matrix with site labels , which would serve my current analytical desires just fine…. The reason for my guess is that twinspanR is using twinspan. But there are some differences between twinspan. I did some testing, though not really comprehensively, but seems like each version is giving slightly different results in non standard parametric settings.
It does help quite a bit. I checked my repositories an I do not have Github. What do I do? To install the twinspanR library, first install library devtools, and then twinspanR: install.
I have encountered an error with twinspanR. Sometimes when I go to use it, I get an error that reads:. Is this something you have encountered before? I have looked over the source code and cannot exactly figure out what this means. My guess is that there is something happening between the creation of the empty matrix group01 and the empty list tw. I have sent, in an email, an example data set that has been acting up on me, though it is not the only one.
I think I found the bug, thanks for sending the data. The easiest way to fix is to avoid the spaces at all. I modified the twinspanR library function twinspan — I released the twinspanR version v0.
Can you check whether it works with the v0. When I tried, looks ok, no error. That works perfectly. I even had made modifications to print the output from certain functions and was very confused because it seemed to be working internally. Great, happy that it works. Frist of all, thank you so much! Hope I can use the twinspanR in mac someday. Am I doing something wrong or are my settings wrong? Do you have any idea how I can solve this?
Sorry, I overlooked this comment, now I see you posted it already in May, sorry for that! I guess the reply is already not relevant for you, but could be for others running into the same problem.
From the error message you posted it seems like a problem with R package dependencies, not really twinspanR package. If you observe similar error messages, just install the problematic library manually as the betapart library above e. Hi, David, There are some wrong when I install package twinspanR.
Your help is badly needed! Thank you! Please download and install Rtools 3. Hi, sorry for late reply. This problem happens because the package rioja no more contains the function write. CEP, needed by twinspanR package. Dear Dr. Zeleny Thanks for creating this package. I fail to use this package.
I wondering if you could take valuble comments to slove the problem? Hi Naghmeh, Installing betapart and geometry was an old problem, I think this is not an issue any more. But current problem is that the riojaExtra library needs to be installed from GitHub directly.
Hope it works, David. After doing this I still get trouble as I still get an error message below These packages have more recent versions available. Which would you like to update? Hi Bukombe, this is just a warning that newer version of vegan, one of the packages required by twinspanR, has a newer version available.
If you run into this, simply press 1 to update. Alternatively, you can in R studio update the vegan package manually. Remember that to update vegan, you need to restart R to make sure that it is not loaded otherwise it will break the package structure due to the dynamic library loaded. Then, use command line to write remove. Hope it helps, David. I have a problem similar to Wangya Han. There are some wrong when I install package riojaExtra.
The description of this problem is as follows. By the way, my R version is 3. Anyway, I have to thank you for your help. Your sincerely, Linda. From the error message, it seems to me that the problem is on the side of your computer. I guess the problem may be that the R is unable to install the package into the folder which contains Chinese characters in the path.
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