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software [2014/11/09 13:42]
david [Cocktail Determination Key (CoDeK)]
software [2017/10/10 01:19] (current)
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-===== Software/R scripts =====+====== Software/R scripts ​======
 <wrap lo> <wrap lo>
 //The following are software applications (based on [[http://​www.r-project.org|R-project]]) I have written, mostly for analysis of vegetation data. They are in different stage of development,​ but should work without too much struggling. Basically they are R scripts wrapped into "user friendly"​ and clickable TclTk interface, which allows using them without even elementary knowledge of R.// //The following are software applications (based on [[http://​www.r-project.org|R-project]]) I have written, mostly for analysis of vegetation data. They are in different stage of development,​ but should work without too much struggling. Basically they are R scripts wrapped into "user friendly"​ and clickable TclTk interface, which allows using them without even elementary knowledge of R.//
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-==== Modified permutation test for mean Ellenberg indicator values (MoPeT) ====+===== Modified permutation test for mean Ellenberg indicator values (MoPeT) ​=====
   *Calculates modified permutation test of ANOVA, regression and correlation of mean Ellenberg indicator values with other variables, either directly measured (qualitative or quantitative environmental variables) or derived from vegetation data (e.g. species richness, clusters of relevés, ordination axes). The permutation test is based on our paper [[http://​onlinelibrary.wiley.com/​doi/​10.1111/​j.1654-1103.2011.01366.x/​abstract|Zelený & Schaffers (2012)]], pointing out the problem of biased test results when mean Ellenberg indicator values are used in vegetation analyses.   *Calculates modified permutation test of ANOVA, regression and correlation of mean Ellenberg indicator values with other variables, either directly measured (qualitative or quantitative environmental variables) or derived from vegetation data (e.g. species richness, clusters of relevés, ordination axes). The permutation test is based on our paper [[http://​onlinelibrary.wiley.com/​doi/​10.1111/​j.1654-1103.2011.01366.x/​abstract|Zelený & Schaffers (2012)]], pointing out the problem of biased test results when mean Ellenberg indicator values are used in vegetation analyses.
   * [[http://​www.davidzeleny.net/​wiki/​doku.php?​id=eiv:​start|MoPeT website with detail description]]   * [[http://​www.davidzeleny.net/​wiki/​doku.php?​id=eiv:​start|MoPeT website with detail description]]
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-==== Cocktail Determination Key (CoDeK) ====+===== Cocktail Determination Key (CoDeK) ​=====
   * Practical application of Cocktail Determination Key, invented by [[https://​www.researchgate.net/​profile/​Ching-Feng_Li|Ching-Feng Li]] and inspired by Cocktail algorithm introduced by [[http://​www.botanik.uni-halle.de/​mitarbeiterinnen_mitarbeiter/​helge_bruelheide/​|Helge Bruelheide]]. It allows automatic assignment of vegetation plots into predefined vegetation types (supervised classification),​ in case that Cocktail determination key for this vegetation is available in suitable format. We developed CoDeK while working on the paper about Classification of Taiwan forest vegetation ([[http://​onlinelibrary.wiley.com/​doi/​10.1111/​avsc.12025/​abstract|Li et al. 2013]]).   * Practical application of Cocktail Determination Key, invented by [[https://​www.researchgate.net/​profile/​Ching-Feng_Li|Ching-Feng Li]] and inspired by Cocktail algorithm introduced by [[http://​www.botanik.uni-halle.de/​mitarbeiterinnen_mitarbeiter/​helge_bruelheide/​|Helge Bruelheide]]. It allows automatic assignment of vegetation plots into predefined vegetation types (supervised classification),​ in case that Cocktail determination key for this vegetation is available in suitable format. We developed CoDeK while working on the paper about Classification of Taiwan forest vegetation ([[http://​onlinelibrary.wiley.com/​doi/​10.1111/​avsc.12025/​abstract|Li et al. 2013]]).
   * [[http://​www.davidzeleny.net/​wiki/​doku.php/​codek:​start|CoDeK website]]   * [[http://​www.davidzeleny.net/​wiki/​doku.php/​codek:​start|CoDeK website]]
  
-==== JUICE-R scripts ====+===== JUICE-R scripts ​=====
   * JUICE-R is a connection between [[http://​www.sci.muni.cz/​botany/​juice|JUICE]] (program for editing and analysis of vegetation data, written in Visual Basic and developed by Lubomír Tichý) and R-program. The philosophy of this connection is to analyse vegetation data (stored in JUICE) conveniently using R-based applications. The original concept was to create open repository website, where people can share their R scripts written in JUICE-R style. However, up to now we haven'​t really managed to debug this function in JUICE, so it's applicability is limited.   * JUICE-R is a connection between [[http://​www.sci.muni.cz/​botany/​juice|JUICE]] (program for editing and analysis of vegetation data, written in Visual Basic and developed by Lubomír Tichý) and R-program. The philosophy of this connection is to analyse vegetation data (stored in JUICE) conveniently using R-based applications. The original concept was to create open repository website, where people can share their R scripts written in JUICE-R style. However, up to now we haven'​t really managed to debug this function in JUICE, so it's applicability is limited.
   * [[http://​www.sci.muni.cz/​botany/​zeleny/​wiki/​juice-r/​doku.php|JUICE-R website with R scripts for analysis of vegetation data]]   * [[http://​www.sci.muni.cz/​botany/​zeleny/​wiki/​juice-r/​doku.php|JUICE-R website with R scripts for analysis of vegetation data]]