# Random Tanglegram Partitions

## Documentation for package ‘Rtapas’ version 1.2

- DESCRIPTION file
- Package README

## Help Pages

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