Random Tanglegram Partitions

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Documentation for package ‘Rtapas’ version 1.2

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amphipod amph_trem dataset
amphipod_1000tr amph_trem dataset
amph_trem amph_trem dataset
am_matrix amph_trem dataset
assoc_mat Create an host-symbiont association matrix
CPtr Nuclear and chloroplast dataset of orchids
CP_500tr Nuclear and chloroplast dataset of orchids
geo_D Geodesic distance between trees
gini_ci Plot the confidence intervals of Gini coefficient
gini_RSV The Gini coefficient adjusted for negative attributes (Raffinetti, Siletti, & Vernizzi, 2015)
linkf_CI Confidence intervals for the frequency of host-symbiont association
link_freq Frequency of host-symbiont association
max_cong Algortihm for maximizing congruence between two phylogenies
max_incong Algortihm for maximizing incongruence between two phylogenies
np_matrix Nuclear and chloroplast dataset of orchids
NUCtr Nuclear and chloroplast dataset of orchids
NUC_500tr Nuclear and chloroplast dataset of orchids
nuc_cp Nuclear and chloroplast dataset of orchids
one2one_f Maximum number of unique one-to-one association over a number of runs
paco_ss Procrustes Approach to Cophylogeny (PACo) of the host and symbiont configurations
paraF Test of host-symbiont coevolution
pp_treesPACo_cong Nuclear and chloroplast dataset of orchids
pp_treesPACo_incong Nuclear and chloroplast dataset of orchids
prob_statistic Frequencies of the associations for the posterior probability trees
tangle_gram Tanglegram of the host-symbiont frequencies
trematode amph_trem dataset
trematode_1000tr amph_trem dataset
trimHS_maxC Trims the H-S association matrix maximizing the congruence
trimHS_maxI Trims the H-S association matrix maximizing the incongruence