The hardware and bandwidth for this mirror is donated by dogado GmbH, the Webhosting and Full Service-Cloud Provider. Check out our Wordpress Tutorial.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]dogado.de.

Rtapas

We introduce Rtapas (v1.1.1), an R package to perform Random Tanglegram Partitions (Balbuena et al. 2020). Rtapas applies a given global-fit method to random partial tanglegrams of a fixed size to identify the associations, terminals, and nodes that maximize phylogenetic congruence. Incorporates ParaFit (Legendre et al. 2002), geodesic distances (GD) (Schardl et al. 2008) and PACo (Balbuena et al. 2013) as global-fit methods to implement Random TaPas. Rtapas further enhances the usability and implementation of Random TaPas by including functions (i) to facilitate the prior processing of association data between taxa, (ii) to estimate, in a set of probability trees, the statistic of a given global-fit method, (iii) to estimate the (in)congruence metrics of the individual host-symbiont associations, and (iv) to compute either conventional (G) or normalized (G*) (Raffinetti et al. 2015) characterizing the distribution of such metrics.

Installation

You can install the development version of Rtapas from GitHub with:

# install.packages("devtools")
devtools::install_github("mllaberia/Rtapas")

Example

This is a basic example which shows you how to solve a common problem:

library(Rtapas)
data(nuc_pc)
N = 1e+2  # we recommend using 1e+4.
n = n = round(sum(np_matrix)*0.2)
NPc <- max_cong(np_matrix, NUCtr, CPtr, n, N, method = "paco",
               symmetric = FALSE, ei.correct = "sqrt.D",
               percentile = 0.01, res.fq = FALSE,
               strat = "parallel", cl = 10)

tangle_gram(NUCtr, CPtr, np_matrix, NPc, colscale = "sequential", 
            colgrad = c("darkorchid4", "gold"), nbreaks = 50, node.tag = TRUE, 
            cexpt = 1.2, link.lwd = 1, link.lty = 1, fsize = 0.75, pts = FALSE,
            ftype ="i")

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.