Directories
¶
| Path | Synopsis |
|---|---|
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PGS is a tool for simulations of biogeographic data using spherical diffusion and dynamic geography.
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PGS is a tool for simulations of biogeographic data using spherical diffusion and dynamic geography. |
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cmpcmd
Package cmpcmd implements a command to compare two reconstructions.
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Package cmpcmd implements a command to compare two reconstructions. |
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freq
Package freq implements a command to calculate pixel frequencies from a simulation or inference output.
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Package freq implements a command to calculate pixel frequencies from a simulation or inference output. |
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infer
Package infer implements a command to reads simulated data and infer the parameters using maximum likelihood.
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Package infer implements a command to reads simulated data and infer the parameters using maximum likelihood. |
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sim
Package sim implements a command to simulate a phylogenetic tree and its biogeographic data.
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Package sim implements a command to simulate a phylogenetic tree and its biogeographic data. |
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unrot
Package unrot implements a command to rotate a reconstruction from past to present coordinates.
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Package unrot implements a command to rotate a reconstruction from past to present coordinates. |
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PhyGeo is a tool for phylogenetic biogeography analysis.
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PhyGeo is a tool for phylogenetic biogeography analysis. |
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diff
Package diff is a metapackage for commands that dealt with the biogeographic inference using a diffusion model.
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Package diff is a metapackage for commands that dealt with the biogeographic inference using a diffusion model. |
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diff/freq
Package freq implements a command to calculate pixel frequencies from the stochastic mapping output.
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Package freq implements a command to calculate pixel frequencies from the stochastic mapping output. |
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diff/integrate
Package integrate implements a numerical integration of the likelihood curve for a diffusion model.
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Package integrate implements a numerical integration of the likelihood curve for a diffusion model. |
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diff/like
Package like implements a command to perform a biogeographic reconstruction using likelihood.
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Package like implements a command to perform a biogeographic reconstruction using likelihood. |
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diff/mapcmd
Package mapcmd implements a command to draw range reconstructions from pixel probability files.
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Package mapcmd implements a command to draw range reconstructions from pixel probability files. |
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diff/ml
Package ml implements a command to search for the maximum likelihood estimation of a biogeographic reconstruction.
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Package ml implements a command to search for the maximum likelihood estimation of a biogeographic reconstruction. |
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diff/particles
Package particles implements a command to run a stochastic mapping from a down-pass reconstruction.
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Package particles implements a command to run a stochastic mapping from a down-pass reconstruction. |
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diff/speed
Package speed implements a command to measure the speed and distance traveled in a reconstruction.
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Package speed implements a command to measure the speed and distance traveled in a reconstruction. |
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geo
Package geo is a metapackage for commands that dealt with paleogeographic reconstruction models.
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Package geo is a metapackage for commands that dealt with paleogeographic reconstruction models. |
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geo/add
Package add implements a command to add a paleogeographic reconstruction model to a PhyGeo project.
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Package add implements a command to add a paleogeographic reconstruction model to a PhyGeo project. |
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geo/prior
Package prior implements a command to manage pixel priors defined for a project.
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Package prior implements a command to manage pixel priors defined for a project. |
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prj
Package prj implements a command to print the basic information of a project.
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Package prj implements a command to print the basic information of a project. |
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rangecmd
Package rangecmd is a metapackage for commands that dealt with taxon distribution ranges.
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Package rangecmd is a metapackage for commands that dealt with taxon distribution ranges. |
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rangecmd/add
Package add implements a command to add taxon ranges to a PhyGeo project.
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Package add implements a command to add taxon ranges to a PhyGeo project. |
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rangecmd/kde
Package kde implements a command to estimate the range distributions using a kernel density estimator.
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Package kde implements a command to estimate the range distributions using a kernel density estimator. |
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rangecmd/mapcmd
Package mapcmd implements a command to draw the geographic range of the taxa in a PhyGeo project with defined distribution ranges.
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Package mapcmd implements a command to draw the geographic range of the taxa in a PhyGeo project with defined distribution ranges. |
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rangecmd/remove
Package remove implements a command to remove range distribution records not present on a tree.
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Package remove implements a command to remove range distribution records not present on a tree. |
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rangecmd/rotate
Package rotate implements a command to rotate the point records of a phygeo project.
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Package rotate implements a command to rotate the point records of a phygeo project. |
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rangecmd/taxa
Package terms implements a command to print the list of taxa in a PhyGeo project with defined distribution ranges.
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Package terms implements a command to print the list of taxa in a PhyGeo project with defined distribution ranges. |
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tree
Package tree is a metapackage for commands that dealt with phylogenetic trees.
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Package tree is a metapackage for commands that dealt with phylogenetic trees. |
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tree/add
Package add implements a command to add trees to a PhyGeo project.
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Package add implements a command to add trees to a PhyGeo project. |
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tree/draw
Package draw implements a command to draw trees in a phygeo project as SVG files.
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Package draw implements a command to draw trees in a phygeo project as SVG files. |
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tree/list
Package list implements a command to print the list of trees in a phygeo project.
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Package list implements a command to print the list of trees in a phygeo project. |
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tree/remove
Package remove implements a command to remove tree terminals from a PhyGeo project without defined distribution ranges.
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Package remove implements a command to remove tree terminals from a PhyGeo project without defined distribution ranges. |
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tree/terms
Package terms implements a command to print the list of the terminals in the trees of a PhyGeo project.
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Package terms implements a command to print the list of the terminals in the trees of a PhyGeo project. |
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