https://sourceforge.net/p/synapomorphy/home/Home/Recent changes to HomeenWed, 23 May 2012 11:18:50 -0000https://sourceforge.net/p/synapomorphy/home/Home/<pre>--- v51 +++ v52 @@ -134,7 +134,7 @@ - **Our manuscript:** - - Turjak, M., Trontelj, P. A method for measuring support for synapomorphy using characterstate distributions on phylogenetic trees. [Cladistics][1], In Press. + - Turjak, M., Trontelj, P. 2012. A method for measuring support for synapomorphy using characterstate distributions on phylogenetic trees. [Cladistics][1], DOI: 10.1111/j.1096-0031.2012.00403.x The script is free to use under a GNU [GPLv3 license][10].<br /> </pre>Martin TurjakWed, 23 May 2012 11:18:50 -0000https://sourceforge.net6ad1d26abe2aa3dae114801e3c4649766e336e1ahttps://sourceforge.net/p/synapomorphy/home/Home/<pre>--- v50 +++ v51 @@ -80,7 +80,8 @@ ~~~~~ # - +The full documentation and method description will be made available shortly. + Download R Script and Example Files ----------------------------------- </pre>Martin TurjakWed, 23 May 2012 11:16:45 -0000https://sourceforge.nete588a047c2837b7fb424e7be36c56c703c396311https://sourceforge.net/p/synapomorphy/home/Home/<pre>--- v49 +++ v50 @@ -133,7 +133,7 @@ - **Our manuscript:** - - Turjak, M., Trontelj, P. A method for measuring support for synapomorphy using characterstate distributions on phylogenetic trees. \[Cladistics][1]\, In Press. + - Turjak, M., Trontelj, P. A method for measuring support for synapomorphy using characterstate distributions on phylogenetic trees. [Cladistics][1], In Press. The script is free to use under a GNU [GPLv3 license][10].<br /> </pre>Martin TurjakThu, 10 May 2012 08:46:39 -0000https://sourceforge.net357279422990fa51806a4ce31170eea971085104https://sourceforge.net/p/synapomorphy/home/Home/<pre>--- v48 +++ v49 @@ -4,95 +4,95 @@  -An R script written by Martin Turjak, implementing a newly developed method for evaluating synapomorphy on phylogenetic trees. The method is described in detail in our manuscript **Measuring Synapomorphy: A Hennigian Method for Evaluating Character State Distributions on Phylogenetic Trees** (accepted for publication in [Cladistics][1]) and all details will be made available here at the time of publication. - - +An R script written by Martin Turjak, implementing a newly developed method for evaluating synapomorphy on phylogenetic trees. The method is described in detail in our manuscript **A method for measuring support for synapomorphy using characterstate distributions on phylogenetic trees** (accepted for publication in [Cladistics][1]) and all details will be made available here at the time of publication. + + Introduction ------------ In our manuscript we propose a method that quantifies the pattern of character state distribution over a cladogram and as such is free of any transformational model. We define the condition for a fully synapomorphic character state as a character state shared by all of the clade’s terminal taxa and at the same time completely absent from all terminal taxa outside that clade. The extent to which this condition is not violated serves to quantify the probability of synapomorphy. This probability is calculated as a combination of relative character state frequencies within and outside the clade based on the hierarchical structure of the cladogram. It corresponds to the probability of randomly selecting two terminals that share the same character state within the clade and at the same time differ from all outside terminals. The Method - Documentation -------------------------- Setup and use. - Download the R script from the link below. Set the working directory to the directory containing the script file and run the script file using folowing command in the R console: ~~~~~ > source("Syn.R") ~~~~~ # The script uses functions included in the ape package. So make sure ape is installed prior to using the Syn script. If everything loads right you should see a welcome message and you will be asked to enter the tree file: ~~~~~ Please enter your tree file: ~~~~~ # Enter the path (realtive or absolute) to your tree file (in newick format). In next steps we will use the sample files provided with the script as if they have been saved directly into the working directory. If the tree file loads successfully you will see this message: ~~~~~ > tree_1.nwk Tree "tree_1.nwk" has been loaded successfuly. Please enter your data file: ~~~~~ # Enter the path to your data file - see sample files for correct formating. ~~~~~ > data_1.txt Data file "data_1.txt" has been loaded successfuly. ~~~~~ # The results of the calculation for the first apomorphic character state will be plotted as numeric values on the nodes of the tree. The data and tree will stay loaded. If you want to plot another character state fom the same dataset you can use this command (Nu = integer index of character state): ~~~~~ > Syn(Nu) ~~~~~ # To display the whole list of character states and their indexes use: ~~~~~ > ChStates Index ChState 1 1 0 2 2 1 ~~~~~ # If you want to know which data is currenty loaded you can use: ~~~~~ > curData() Tree: tree_1.nwk Data: data_1.txt ~~~~~ #  Download R Script and Example Files ----------------------------------- **Script: [Syn.R][2]** The script is free to use under a GNU [GPLv3 license][10].<br /> The code can be viewed here: [Code: Syn.R][9] ###### Example files: ###### - Sample tree: [tree_1.nwk][3] - Sample data: [data_1.txt][4] ~~~~~ @@ -100,19 +100,19 @@ ~~~~~ # ###### Used in manuscript: ###### - _Niphargus_ tree: [niph_tree.nwk][5] (see Fišer et al., 2008) - _Niphargus_ data: [niph_data.txt][6] (see Fišer et al., 2008) ~~~~~ \[character state 12 marked with "e" is the elegans-valachicus morphotype used in manuscript\] ~~~~~ # - Sarcopterygian tree: [sarco_tree.nwk][7] - Sarcopterygian data: [sarco_data.txt][8] ~~~~~ \[the sarco_tree.nwk file contains 2 trees - uncomment the one you want to load\] ~~~~~ @@ -121,19 +121,19 @@ ~~~~~ # References ---------- - **The _Niphargus_ example:** - Fišer, C., Sket, B., Trontelj, P. 2008. A phylogenetic perspective on 160 years of troubled taxonomy of _Niphargus_ (Crustacea: Amphipoda). Zool. Scr. 37, 665-680. - **The R Project:** - R Development Core Team 2008. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org. - **Our manuscript:** - - Turjak, M., Trontelj, P. Measuring Synapomorphy: A Hennigian Method for Evaluating Character State Distributions on Phylogenetic Trees. \[Submitted to [Cladistics][1]\] + - Turjak, M., Trontelj, P. A method for measuring support for synapomorphy using characterstate distributions on phylogenetic trees. \[Cladistics][1]\, In Press. The script is free to use under a GNU [GPLv3 license][10].<br /> </pre>Martin TurjakThu, 10 May 2012 08:45:30 -0000https://sourceforge.net1a6ee26d968749e059e27e8ebfda500ac6de1df4https://sourceforge.net/p/synapomorphy/home/Home/<pre>--- v47 +++ v48 @@ -4,97 +4,95 @@  -An R script written by Martin Turjak, implementing a newly developed method for evaluating synapomorphy on phylogenetic trees. The method is described in detail in our manuscript **Measuring Synapomorphy: A Hennigian Method for Evaluating Character State Distributions on Phylogenetic Trees** (currently submitted for consideration to [Cladistics][1]) and all details will be made available here at the time of publication. - - - - - +An R script written by Martin Turjak, implementing a newly developed method for evaluating synapomorphy on phylogenetic trees. The method is described in detail in our manuscript **Measuring Synapomorphy: A Hennigian Method for Evaluating Character State Distributions on Phylogenetic Trees** (accepted for publication in [Cladistics][1]) and all details will be made available here at the time of publication. + + Introduction ------------ In our manuscript we propose a method that quantifies the pattern of character state distribution over a cladogram and as such is free of any transformational model. We define the condition for a fully synapomorphic character state as a character state shared by all of the clade’s terminal taxa and at the same time completely absent from all terminal taxa outside that clade. The extent to which this condition is not violated serves to quantify the probability of synapomorphy. This probability is calculated as a combination of relative character state frequencies within and outside the clade based on the hierarchical structure of the cladogram. It corresponds to the probability of randomly selecting two terminals that share the same character state within the clade and at the same time differ from all outside terminals. + The Method - Documentation -------------------------- Setup and use. - Download the R script from the link below. Set the working directory to the directory containing the script file and run the script file using folowing command in the R console: ~~~~~ > source("Syn.R") ~~~~~ # The script uses functions included in the ape package. So make sure ape is installed prior to using the Syn script. If everything loads right you should see a welcome message and you will be asked to enter the tree file: ~~~~~ Please enter your tree file: ~~~~~ # Enter the path (realtive or absolute) to your tree file (in newick format). In next steps we will use the sample files provided with the script as if they have been saved directly into the working directory. If the tree file loads successfully you will see this message: ~~~~~ > tree_1.nwk Tree "tree_1.nwk" has been loaded successfuly. Please enter your data file: ~~~~~ # Enter the path to your data file - see sample files for correct formating. ~~~~~ > data_1.txt Data file "data_1.txt" has been loaded successfuly. ~~~~~ # The results of the calculation for the first apomorphic character state will be plotted as numeric values on the nodes of the tree. The data and tree will stay loaded. If you want to plot another character state fom the same dataset you can use this command (Nu = integer index of character state): ~~~~~ > Syn(Nu) ~~~~~ # To display the whole list of character states and their indexes use: ~~~~~ > ChStates Index ChState 1 1 0 2 2 1 ~~~~~ # If you want to know which data is currenty loaded you can use: ~~~~~ > curData() Tree: tree_1.nwk Data: data_1.txt ~~~~~ #  Download R Script and Example Files ----------------------------------- **Script: [Syn.R][2]** The script is free to use under a GNU [GPLv3 license][10].<br /> The code can be viewed here: [Code: Syn.R][9] ###### Example files: ###### - Sample tree: [tree_1.nwk][3] - Sample data: [data_1.txt][4] ~~~~~ @@ -102,19 +100,19 @@ ~~~~~ # ###### Used in manuscript: ###### - _Niphargus_ tree: [niph_tree.nwk][5] (see Fišer et al., 2008) - _Niphargus_ data: [niph_data.txt][6] (see Fišer et al., 2008) ~~~~~ \[character state 12 marked with "e" is the elegans-valachicus morphotype used in manuscript\] ~~~~~ # - Sarcopterygian tree: [sarco_tree.nwk][7] - Sarcopterygian data: [sarco_data.txt][8] ~~~~~ \[the sarco_tree.nwk file contains 2 trees - uncomment the one you want to load\] ~~~~~ @@ -123,21 +121,20 @@ ~~~~~ # References ---------- - **The _Niphargus_ example:** - Fišer, C., Sket, B., Trontelj, P. 2008. A phylogenetic perspective on 160 years of troubled taxonomy of _Niphargus_ (Crustacea: Amphipoda). Zool. Scr. 37, 665-680. - **The R Project:** - R Development Core Team 2008. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org. - **Our manuscript:** - Turjak, M., Trontelj, P. Measuring Synapomorphy: A Hennigian Method for Evaluating Character State Distributions on Phylogenetic Trees. \[Submitted to [Cladistics][1]\] - The script is free to use under a GNU [GPLv3 license][10].<br /> The code can be viewed here: [Code: Syn.R][9] </pre>Martin TurjakThu, 10 May 2012 08:39:49 -0000https://sourceforge.netf807f539ad59990c7af81278d09d6f2817d4c25dhttps://sourceforge.net/p/synapomorphy/home/Home/<pre>--- v46 +++ v47 @@ -131,7 +131,7 @@ - **The R Project:** - - R Development Core Team (2008). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org. + - R Development Core Team 2008. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org. - **Our manuscript:** </pre>Martin TurjakWed, 19 Oct 2011 20:00:17 -0000https://sourceforge.nete5676ab5e92d452aa2c4c5c77ce563d864263f39https://sourceforge.net/p/synapomorphy/home/Home/<pre>--- v45 +++ v46 @@ -156,4 +156,4 @@ Contact ------- -<martin.turjak@gmail.com> +[martin.turjak@gmail.com](mailto:martin.turjak@gmail.com) </pre>Martin TurjakWed, 19 Oct 2011 14:56:32 -0000https://sourceforge.neta02eb719d88e4916479a512378af92529977a317https://sourceforge.net/p/synapomorphy/home/Home/<pre>--- v44 +++ v45 @@ -152,3 +152,8 @@ [8]: http://sourceforge.net/projects/synapomorphy/files/Examples/sarco_data.txt/download [9]: http://sourceforge.net/p/synapomorphy/home/Code%3A%20Syn.R/ [10]: http://www.opensource.org/licenses/gpl-3.0.html + +Contact +------- + +<martin.turjak@gmail.com> </pre>Martin TurjakWed, 19 Oct 2011 14:51:25 -0000https://sourceforge.netd9752788c3357eaee0907deee2e9f86000777a2fhttps://sourceforge.net/p/synapomorphy/home/Home/<pre>--- v43 +++ v44 @@ -87,8 +87,6 @@ Download R Script and Example Files ----------------------------------- -[[download_button]] - **Script: [Syn.R][2]** The script is free to use under a GNU [GPLv3 license][10].<br /> </pre>Martin TurjakWed, 19 Oct 2011 14:43:52 -0000https://sourceforge.net3d4294ef41e1b6dad6efb746b4a7c22f7d4a26afhttps://sourceforge.net/p/synapomorphy/home/Home/<pre>--- v42 +++ v43 @@ -87,6 +87,8 @@ Download R Script and Example Files ----------------------------------- +[[download_button]] + **Script: [Syn.R][2]** The script is free to use under a GNU [GPLv3 license][10].<br /> </pre>Martin TurjakWed, 19 Oct 2011 14:43:16 -0000https://sourceforge.net0d180e44bf12e18bc7ed1011e15bf0fc95659e91