Measuring Morphological Diversity and Evolutionary Tempo
Adds polymorphisms to a costmatrix
Adds uncertainties to a costmatrix
Aligns a phylogenetic matrix block
Assign taxa to time bins
Counts the changes in a series of time bins
Phylogenetic character completeness in time-bins
Edge-lengths present in time-bins
Creates a morphological data file from a matrix
Calculate the maximum tree length, g, under parsimony
Calculate the maximum possible tree length, gmax, under parsimony
Calculates a researcher's Kardashian Index
Get distance matrices from a cladistic matrix
Calculate mean pairwise distances
Calculates the parsimony length of a set of phylogenetic tree(s)
Calculate weighted mean pairwise distances
Check cladisticMatrix object for errors
Check a costMatrix object for errors
Check a stateGraph object for errors
Check taxonGroups object for errors
Check timeBins object for errors
Measuring Morphological Diversity and Evolutionary TempoMeasures morph...
Classify a costmatrix character
Collapses matrix to unique character state distributions
Converts an adjacency matrix to a costmatrix
Convert a costmatrix to a minimal state graph
Converts a character state tree to an adjacency matrix
Convert a minimal state graph to a costmatrix
Counts the number of cherries in a tree
Returns node ages for a time-scaled tree
Drop tips from a time-scaled tree
Ancestral Character State Estimation
Estimate ancestral states for a continuous character under squared-cha...
Finds a minimum spanning tree of a costmatrix
Gets descendant edges of an internal node
Find linked edges for a tree
Get edges of minimum spanning tree
Find ancestor
Finds the shortest path between two states in a costmatrix
Finds a minimum spanning tree of a stategraph
Find time bin midpoints
Finds only the unique topologies amongst a set
Fixes a costmatrix that has inconsistent costs
Fixes root.time after taxa have been pruned from a tree
Is a graph connected?
Cladistic matrix class
Costmatrix class
Stategraph class
Taxon groups class
Time bins class
Locates matching positions for sets of brackets in a text string
Make a costmatrix for a given set of states
Make unique text labels
Stochastic Character Map For Dollo Character
Edge matching function
Principal Coordinates on a Cladistic Matrix
Time bin partitioner
Permute all possible polymorphisms for a given set of states
Label treeshapes
Permute all possible uncertainties for a given set of states
Permute all connected graphs
Permute costmatrices
Permute all ways to split a graph
Permute all ways to place n items into m bins
Permute all tip states on a tree
Permute all treeshapes of N tips
Plots character changes on branches
Chronophylomorphospace Plot
Plot stacked ordination spaces
Plot Morphopace
Plot Multiple Morphopaces
Visualize a rate test time series
Visualize a rate test time series
Visualize a rate test time series
Compact display of a cladistic matrix
Compact display of a costmatrix
Compact display of a stategraph
Compact display of taxon groups
Compact display of time bins
Prunes a character matrix of characters or taxa
Reads in a morphological #NEXUS data file
Determine maximum parsimony ancestral state reconstruction(s)
Safe Taxonomic Reduction
Reinsert Safely Removed Taxa Into A Tree
Split adjacency matrix into subgraphs
Discrete character rates across trees, time, and character types
Trims marginal whitespace
Trims a morphological distance matrix
Writes out a morphological #NEXUS data file
Writes out a morphological TNT data file
Measures morphological diversity from discrete character data and estimates evolutionary tempo on phylogenetic trees. Imports morphological data from #NEXUS (Maddison et al. (1997) <doi:10.1093/sysbio/46.4.590>) format with read_nexus_matrix(), and writes to both #NEXUS and TNT format (Goloboff et al. (2008) <doi:10.1111/j.1096-0031.2008.00217.x>). Main functions are test_rates(), which implements AIC and likelihood ratio tests for discrete character rates introduced across Lloyd et al. (2012) <doi:10.1111/j.1558-5646.2011.01460.x>, Brusatte et al. (2014) <doi:10.1016/j.cub.2014.08.034>, Close et al. (2015) <doi:10.1016/j.cub.2015.06.047>, and Lloyd (2016) <doi:10.1111/bij.12746>, and calculate_morphological_distances(), which implements multiple discrete character distance metrics from Gower (1971) <doi:10.2307/2528823>, Wills (1998) <doi:10.1006/bijl.1998.0255>, Lloyd (2016) <doi:10.1111/bij.12746>, and Hopkins and St John (2018) <doi:10.1098/rspb.2018.1784>. This also includes the GED correction from Lehmann et al. (2019) <doi:10.1111/pala.12430>. Multiple functions implement morphospace plots: plot_chronophylomorphospace() implements Sakamoto and Ruta (2012) <doi:10.1371/journal.pone.0039752>, plot_morphospace() implements Wills et al. (1994) <doi:10.1017/S009483730001263X>, plot_changes_on_tree() implements Wang and Lloyd (2016) <doi:10.1098/rspb.2016.0214>, and plot_morphospace_stack() implements Foote (1993) <doi:10.1017/S0094837300015864>. Other functions include safe_taxonomic_reduction(), which implements Wilkinson (1995) <doi:10.1093/sysbio/44.4.501>, map_dollo_changes() implements the Dollo stochastic character mapping of Tarver et al. (2018) <doi:10.1093/gbe/evy096>, and estimate_ancestral_states() implements the ancestral state options of Lloyd (2018) <doi:10.1111/pala.12380>. calculate_tree_length() and reconstruct_ancestral_states() implements the generalised algorithms from Swofford and Maddison (1992; no doi).