Turboveg For Windows
Powered by Redmine © 2006-2019 Jean-Philippe Lang Redmine © 2006-2019 Jean-Philippe Lang.
0## Modified TWINSPAN on traditional Ellenberg's Danube meadow dataset, ## projected on DCA and compared with original classification into ## three vegetation types made by tabular sorting: library (twinspanR ) library (vegan ) data (danube )res. ↓.Hi Attila,Thanks for a nice comment! I was working on TWINSPAN in R last Christmas, because I just suddently realized the way how it can be done in R and just wanted to try it – and looks like it works. 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.Have a nice day!David. ↓.Hi Sapphire,you are right, the package is only on GitHub, and this is perhaps not going to change any time soon – the problem is that the twinspanR library can be used only under Windows (due to it’s internal dependencies, since the TWINSPAN algorithm is calculated externally using twinspan.exe program), so it cannot be uploaded into CRAN (which requires multiplatform usability of packages). 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. CRAN is not a good place for packages under development, while GitHub is.Cheers!David. ↓.Hi Sapphire,To write a Twinspan package which can be used across platforms would be great, but currently I don’t plan to do it – it’s different story than my simple solution (to wrap twinspan.exe file and send data into and back). The most recent attempt to rewrite twinspan into R I know is from Dave Roberts, but his solution differs from “genuine” TWINSPAN of Mark Hill, so the results will be more or less different.
I also heard somewhere that Jari Oksanen tried to port the original Fortran library into R, but didn’t succeed for some reason, but may be if he has motivation, he may give it a try again. That’s it, sorry for that 🙂David. ↓.Hi Kieran,Unfortunately there is no plotting function in the twinspanR package so far, I haven’t found a handy way how to make it. 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 0-1 sequence determining the hierarchy, e.g.:tw.res. ↓. kieranHi David,Thanks for your comments.
I'm pretty much sure, some of you or maybe all of you have been searching for the working method on how to with downloaded all those shit IMVU credits hack, IMVU credits generator, but none of them even work. Usually some of them just a virus, isn't it? It can generate and s and send it directly to your account in less that 10 minutes! 
Sounds great, huh?
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.Anyways, thanks again for sorting a quick and easy TWINSPAN option(s) for R and for your subsequent help!All the best,Kieran. ↓.Hi Noah,My guess is that the convergence criteria are the same as in Hill & Šmilauer 2005. The reason for my guess is that twinspanR is using twinspan.exe library, which is currently used in JUICE software, and as I know, Petr Šmilauer couple of years ago was fixing this file, since it gave unstable classification results. But there are some differences between twinspan.exe and Hill & Šmilauer’s Windows program, since the later implements also other tweaks by ter Braak and Birks (I guess), which are not implemented in twinspan.exe (this has different evolution – it comes from original Hill’s fortan-based twinspan, and was originally maintained by Stephan Hennekens for his Megatab software).I did some testing, though not really comprehensively, but seems like each version is giving slightly different results (in non standard parametric settings). Problem is that only the original Hill’s algorithm is somewhat properly described (in his report from 1979, which is unfortunately hard to get), the later changes are actually not properly described anywhere.Not sure if this helpsDavid.
↓. Noah DellDavid,I have encountered an error with twinspanR. Sometimes when I go to use it, I get an error that reads:“Error in groups01,1 = cut(tw.temp1,level=1)-1: number of items to replace is not a multiple of replacement length”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.temp and the the reference to tw.temp1, and I presume it is happening in the call to twinspan0.Thanks in advance,Noah.
↓.Hi Noah,I think I found the bug, thanks for sending the data. The problem is actually with row names in your community matrix – the rownames should not contain the white spaces, this will cause trouble in ‘cut.tw’ function. The easiest way to fix is to avoid the spaces at all. I modified the twinspanR library (function twinspan) – I released the twinspanR version v0.16 into GitHub which – in case that the rownames contain spaces will convert it into syntactically valid names using ‘make.names’ function (replace spaces with dots).Can you check whether it works with the v0.16 version and let me know? When I tried, looks ok, no error.CheersDavid. ↓.Great, happy that it works. Thanks for feedback, it’s great to know that somebody is actually really using that 🙂 This library is just my sentiment, once during Christmas I just by the way found a way how to put twinspan.exe into R folder and tailor all those algorithms to feed it by data and take data out, and cannot get rid of the excitements that it may be actually “twinspan in R” until it was finished.
Turboveg For Windows 10
What bugs me most at this moment is that there is not good plot function for the dendrogram, I want to add, but it’s a bit complexCheers!David. ↓. Jolien DHiThank you for creating this package, but I don’t seem to be able to install it. ↓. david Post authorHi Jolien,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.
Looks like ‘betapart’ package cannot load the dependency ‘geometry’, for reason I cannot see. Could you try to install ‘betapart’ package first, i.e. Typeinstall.packages (‘betapart’)and then run the twinspanR installation again? If you observe similar error messages, just install the problematic library manually as the betapart library above (e.g. Install manually the library ‘geometry’, which was causing the problem in your case).David. ↓.
Wangya HanHi, David,There are some wrong when I install package twinspanR. Your help is badly needed!
↓. NaghmehDear Dr. ZelenyThanks for creating this package. But I can’t use twinspanR library.I used this steps for install:install.packages (‘devtools’)devtools::installgithub(“zdealveindy/twinspanR”)library (twinspanR)Error in library(twinspanR): there is no package called ‘twinspanR’then I read commnts in this page. You sugessted that install ” betapart” and ” geometry” but after install these. I fail to use this package.
I wondering if you could take valuble comments to slove the problem?Sincerely.
Turboveg For Windows 8
@@ -1,10 +1,19 @@Package: twinspanRType: PackageTitle: TWo-way INdicator SPecies ANalysis (and its modified version) in R.Version: 0. 15Date: 2016- 02-26Version: 0.
16Date: 2016- 05-18Author: David Zeleny, Petr Smilauer, Stephan M. Hennekens & Mark O. HillMaintainer: David Zeleny Description: This R library is an R wrapper with added functionality (written by D. Zeleny) around twinspan.exe file. The source code for twinspan.exe is based on TWINSPAN algorithm introduced by Mark O. Hill; original FORTRAN code was compiled into twinspan.exe by Stephan M. Hennekens for the usi with his program MEGATAB (part of Turboveg), with later added modifications by Petr Smilauer (for program JUICE).Depends: vegan, rioja, betapartDescription: This R library is an R wrapper with added functionality (written byD.
Turboveg For Windows Vista
Zeleny) around twinspan.exe file. The source code for twinspan.exe is basedon TWINSPAN algorithm introduced by Mark O. Hill; original FORTRAN code wascompiled into twinspan.exe by Stephan M. Hennekens for the usi with his programMEGATAB (part of Turboveg), with later added modifications by Petr Smilauer (forprogram JUICE).Depends:vegan,rioja,betapartLicense: GPL-2RoxygenNote: 5.0.1.