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Name Modified Size InfoDownloads / Week
walkthrough.txt 2012-05-07 2.1 kB
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OP685nr_days.nex.txt 2012-05-07 1.3 kB
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OP685nr_days.nex.run2.t 2012-05-07 1.9 MB
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OP685nr_days.nex.run1.t 2012-05-07 1.9 MB
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set1_Shankarappa.txt 2012-05-07 1.7 kB
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set1_Shankarappa.tree 2012-05-07 4.5 kB
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phyloTempoBayes.R 2012-02-24 14.4 kB
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README.txt 2012-02-23 1.5 kB
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phyloTempo.R 2012-02-20 22.2 kB
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temporalClusteringFunction.R 2012-02-20 11.4 kB
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Totals: 10 Items   3.9 MB 0 
DATA FORMATS

1. Tree data (treeFile): NEWICK format for all scripts (except for phyloTempoBayes.R script which requires NEXUS tree files from MrBayes)
2. Temporal data (dataFile): TAB-DELIMITED TEXT file. The file must contain at least two columns named "taxaId" and "timeNum". Each row of the file contains the name of the taxon (taxaId) and the corresponding sampling time in any numerical scale (timeNum) for all taxa present in the tree file. The order is not important.


SCRIPTS

phyloTempo.R: the main script with graphical and text file output. The user has to insert the treeFile and dataFile names in the very first lines of the script, and specify the number of tree randomizations.

temporalClusteringFunction.R: this script calculates only the TC statistic with a specified number of randomization, using the following syntax
variable <- temporalClustering (treeFile, dataFile, boot, picture)
The boot parameter corresponds to the number of tree randomizations.
A value of zero or less in the boot parameter forces the program to report the raw number of changes.
The picture parameter is a boolean value and if TRUE draws a the ancestral character tree on the screen.

phyloTempoBayes.R: takes NEXUS tree files and temporal data files as input (to be specified in the very first lines of the script) and calculates the temporal clustering statistic, the root-to-tip-distance with time correlation, and the staircaseness for a specified number of trees. An output file is written in tab-delimited format.
Source: README.txt, updated 2012-02-23