amph_trem: amph_trem dataset

In Rtapas: Random Tanglegram Partitions

amph_trem dataset

Description

Data set of mitochondrial haplotypes of the trematode Coitocaecum parvum (Crowcroft, 1945) and those of its amphipod host, Paracalliope fluviatilis (Thomson, 1879) from several locations in South Island, New Zeland (Largue et al. 2016).

Usage

data(amph_trem)

Format

This data set compresses five objects:

am_matrix

Associations between 17 haplotypes of Coitocaecum parvum and 59 haplotypes of Paracalliope fluviatilis. A binary matrix with 59 rows (amphipod) and 17 variables (trematode).

amphipod

Paracalliope fluviatilis consensus tree. An object of class "phylo" containing a list with the details of the consensus phylogenetic tree (i.e. edges, edges length, nodes, and tips names).

trematode

Coitocaecum parvum consensus tree. An object of class "phylo" containing a list with the details of the phylogenetic tree (i.e. edges, edges length, nodes and tips names).

amphipod_1000tr

1000 Bayesian posterior probability trees of Paracalliope fluviatilis. List of class "multiphylo" containing a 1000 phylogenetic trees with their respective details (i.e. edges, edges length, nodes, and tips names).

trematode_1000tr

1000 Bayesian posterior probability trees of Coitocaecum parvum. List of class "multiphylo" containing a 1000 phylogenetic trees with their respective details (i.e. edges, edges length, nodes, and tips names).

Source

Balbuena J.A., Perez-Escobar O.A., Llopis-Belenguer C., Blasco-Costa I. (2022). User’s Guide Random Tanglegram Partitions V.1.0.0. Zenodo. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.5281/zenodo.6327235")}

References

Lagrue C., Joannes A., Poulin R., Blasco-Costa I. (2016). Genetic structure and host–parasite co‐divergence: evidence for trait‐specific local adaptation. Biological Journal of the Linnean Society. 118:344–358.

Balbuena J.A., Perez-Escobar O.A., Llopis-Belenguer C., Blasco-Costa I. (2022). User’s Guide Random Tanglegram Partitions V.1.0.0. Zenodo. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.5281/zenodo.6327235")}

Rtapas documentation built on June 22, 2024, 10:47 a.m.