[phylotastic] TreeTools 2.4.0.9000

Efficient implementations of functions for the creation, modification and analysis of phylogenetic trees. Applications include: generation of trees with specified shapes; tree rearrangement; analysis of tree shape; rooting of trees and extraction of subtrees; calculation and depiction of split support; plotting the position of rogue taxa (Klopfstein & Spasojevic 2019) ; calculation of ancestor-descendant relationships, of 'stemwardness' (Asher & Smith, 2022) , and of tree balance (Mir et al. 2013, Lemant et al. 2022) , ; artificial extinction (Asher & Smith, 2022) ; import and export of trees from Newick, Nexus (Maddison et al. 1997) , and TNT formats; and analysis of splits and cladistic information.

#rstats

Ropendal: Abstract Filesystem access in #Rstats via 'Apache OpenDAL' R/Rust package using #savvy and exporting a C API because i for whatever reason i frequently download terabytes from Google Drive. Async API is heavily by #nanonext. Several time faster than paws for most ops at MinIO baseline

[phylotastic] phangorn 3.0.0.1

Allows for estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation (Schliep 2011). Offers methods for tree comparison, model selection and visualization of phylogenetic networks as described in Schliep et al. (2017).

#rstats

[phylotastic] TreeDist 2.14.0.9001

Implements measures of tree similarity, including information-based generalized Robinson-Foulds distances (Phylogenetic Information Distance, Clustering Information Distance, Matching Split Information Distance; Smith 2020) ; Jaccard-Robinson-Foulds distances (Bocker et al. 2013) , including the Nye et al. (2006) metric ; the Matching Split Distance (Bogdanowicz & Giaro 2012) ; the Hierarchical Mutual Information (Perotti et al. 2015) ; Maximum Agreement Subtree distances; the Kendall-Colijn (2016) distance , and the Nearest Neighbour Interchange (NNI) distance, approximated per Li et al. (1996) . Includes tools for visualizing mappings of tree space (Smith 2022) , for identifying islands of trees (Silva and Wilkinson 2021) , for calculating the median of sets of trees, including the transfer consensus (Takazawa et al. 2026) , and for computing the information content of trees and splits.

#rstats

Really handy: the newsmap package for #rstats helps the RadicalRightResearchRobot to understand topics in abstracts #farright #tbp
https://www.kai-arzheimer.com/identifying-topics-in-research-papers-with-the-newsmap-package-for-r-or-how-the-radical-right-research-robot-became-slightly-less-dumb/