Executables
Usage
ecovolve(args = "--help", intern = FALSE)
phylocom(args = "help", intern = FALSE)
phylomatic(args = "--help", intern = FALSE)Examples
ecovolve()
#>
#> ======================================================
#>
#> E C O V O L V E
#> PHYLOGENY AND TRAIT SIMULATOR WITH ECOLOGICAL PROCESSES
#> Cam Webb <campbell.webb@yale.edu>
#>
#> ======================================================
#>
#> Usage: ecovolve [-s -e -t -m -c -p -l -d -h]
#>
#> Switches:
#> -s prob of speciation per unit time[0.05]
#> -e prob of extinction per unit time[0.01]
#> -t time units to simulate over [100]
#> -m output mode (2 = LTT; 3 = newick) [3]
#> -c prob envelope for char change, string of 10 ints [3211000000]
#> -l stop simulation after this number of extant lineages [NO]
#> -p output phylogeny pruned only for extant taxa [NO]
#> -d taper character change by exp(-time / INT )
#> -x simulate competition, with trait proximity increasing extinction
#> -h help
#>
#> View it!:
#> $ ecovolve > ecovolve.phylo
#> $ phylocom makenex -f ecovolve.phylo -t ecovolve.traits \
#> -s ecovolve.sample > ecovolve.nex
#> (open and trace character in Mesquite with BLs proportional)
#>
phylocom()
#>
#> ==========================================================
#>
#> P H Y L O C O M
#> PHYLOGENETIC ANALYSIS OF ECOLOGICAL COMMUNITIES
#> AND SPECIES TRAITS, WITH PHYLOGENETIC TOOLS
#> Cam Webb <cwebb@oeb.harvard.edu>,
#> David Ackerly <dackerly@berkeley.edu>,
#> Steve Kembel <skembel@uoregon.edu>
#>
#> ==========================================================
#>
#> Version 4.2. Copyright (c) 2001-2009 Webb, Ackerly and Kembel
#> This program comes with ABSOLUTELY NO WARRANTY. This is free software,
#> and you are welcome to redistribute it under certain conditions;
#> type `phylocom license' for warranty, license and citation information.
#>
#> Usage: phylocom method [ options ]
#>
#> Phylogenetic community structure (intrasample):
#> comstruct: Calculates mean phylogenetic distance and mean nearest
#> taxon phylogenetic distance for each plot and all plots, and
#> compares them to [999] random runs with matrices created by
#> the null model specified by the -m switch.
#> Alter # runs with a second argument.
#> swap: Swaps the input matrix 1000 times using the Independent Swap
#> Algorithm (independent swap) and outputs swapped matrix console.
#> pd: Faith's Phylogenetic diversity; proportion of total branch length.
#> ltt: Prints the number of lineages at fixed divs of total time
#> proportional to no. of tip taxa. Phylo must be
#> ultrametric. [lttr compares with random samples.]
#> nodesig: Tests each node for overabundance of terminal taxa.
#> nodesigl: As nodesig, but output in table form.
#>
#> Phylogenetic community structure (intersample):
#> comdist: Outputs the pairwise distance matrix between plots, based on mean
#> phylogenetic distance of all possible pairs of taxa in one plot
#> to the taxa in the other. [comdistnt uses nearest taxon method.]
#> icomdist: Gives the mean distance from each taxon to taxa in other plots.
#> rao : Calculates Rao's entropy measure
#>
#> Community trait structure:
#> comtrait: Measures of trait value clustering and evenness within samples
#>
#> Phylogenetic trait analysis:
#> aot: Trait analysis algorithms of David Ackerly
#> aotn: Trait analysis algorithms (Nexus output)
#> aotf: Trait analysis algorithms (full output)
#>
#> Misc Phylogeny Tools:
#> phydist: Calculates the simple pairwise matrix of phylogenetic distances.
#> phyvar: Output phylogenetic variance-covariance matrix.
#> agenode: Output the ages of each node, calculated from BLs.
#> ageterm: Output the stem age of terminal taxon.
#> makenex: Convert all data files into a Mesquite-readable Nexus
#> naf: Convert all data files into a node-as-factor table
#> new2nex: Convert the phylo file into a Mesquite-readable Nexus
#> new2fy: Convert the phylo file into a tabular list of nodes
#> bladj: Branch length adjust alg. Needs an 'ages' file.
#> comnode: Find common nodes between two trees of different size.
#> sampleprune: Prunes the phylo for each list of taxa in sample.
#> rndprune: Prunes the phylo [-r n] times, using [-p n] terminals.
#> cleanphy: Prunes `empty' internal nodes (e.g., output from phylomatic)
#> version: Print software version.
#> help: This file
#>
#> Options:
#> -r INT Number of randomizations to use [999].
#> -m INT Swap method to use with comstruct/swap: [2].
#> 0 = Shuffle phylogeny taxa labels.
#> 1 = Sample taxa become random draws from sample pool.
#> 2 = Sample taxa become random draws from phylogeny pool.
#> 3 = Shuffle sample using independent swap.
#> 4 = Shuffle sample using trial swap.
#> -w INT Number of swaps/trials per run (for independent/trial swap) [1000].
#> -b INT Number of burnin swaps/trials (for independent/trial swap) [0].
#> -f filename Use this file as the phylogeny file [phylo].
#> -s filename Use this file as the sample file [sample].
#> -t filename Use this file as the traits file [traits].
#> -p INT Number of taxa to include in pruned tree [5].
#> -n Add default internal node names (aot) or
#> enable null model testing (comdist/comdistnt)
#> -y Output phylogeny in `fy` format (selected functions)
#> -e Suppress output of branch lengths.
#> -a Use the abundances in the sample file (otherwise just pres/abs).
#> -v Verbose output of raw MPD/MNTD values (comstruct).
#>
phylomatic()
#>
#> ======================================================
#>
#> P H Y L O M A T I C
#> Cam Webb <cwebb@oeb.harvard.edu>
#>
#> ======================================================
#>
#> Usage: phylomatic [-t -f -n -h -l]
#>
#> Switches:
#> -t FILENAME use this as the taxa file
#> -f FILENAME use this as the phylo file
#> -n label all nodes with default names
#> -h Help information
#> -y Output a tabular representation of phylogeny
#> -l Convert all chars in taxa file to lowercase
#>