Klaus Schliep

Klaus Schliep

11 packages on CRAN

kknn

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Weighted k-Nearest Neighbors for Classification, Regression and Clustering.

phangorn

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Package contains methods for estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation. Allows to compare trees, models selection and offers visualizations for trees and split networks.

adegenet

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Toolset for the exploration of genetic and genomic data. Adegenet provides formal (S4) classes for storing and handling various genetic data, including genetic markers with varying ploidy and hierarchical population structure ('genind' class), alleles counts by populations ('genpop'), and genome-wide SNP data ('genlight'). It also implements original multivariate methods (DAPC, sPCA), graphics, statistical tests, simulation tools, distance and similarity measures, and several spatial methods. A range of both empirical and simulated datasets is also provided to illustrate various methods.

ape

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Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.

apex

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Toolkit for the analysis of multiple gene data. Apex implements the new S4 classes 'multidna', 'multiphyDat' and associated methods to handle aligned DNA sequences from multiple genes.

laser

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laser implements maximum likelihood methods based on the birth-death process to test whether diversification rates have changed over time and whether rates vary among lineages.

pegas

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Functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, including from VCF files, and for the analysis of population nucleotide sequences and micro-satellites including coalescent analyses, linkage disequilibrium, population structure (Fst, Amova) and equilibrium (HWE), haplotype networks, minimum spanning tree and network, and median-joining networks.

RADami

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Implements import, export, manipulation, visualization, and downstream (post-clustering) analysis of RADseq data, integrating with the 'pyRAD' package by Deren Eaton.

rWind

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Tools for download and manage surface wind and sea currents data from the Global Forecasting System <https://www.ncdc.noaa.gov/data-access/model-data/model-datasets/global-forcast-system-gfs> and to compute connectivity between locations.

rwty

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Implements various tests, visualizations, and metrics for diagnosing convergence of MCMC chains in phylogenetics. It implements and automates many of the functions of the AWTY package in the R environment.

TreeSearch

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Searches for phylogenetic trees that are optimal using a user-defined criterion. Implements Profile Parsimony (Faith and Trueman, 2001) <doi:10.1080/10635150118627>, and Successive Approximations (Farris, 1969) <doi:10.2307/2412182>. Handles inapplicable data using the algorithm of Brazeau, Guillerme and Smith (2019) <doi:10.1093/sysbio/syy083>.