Showing 3 of total 3 results (show query)
grunwaldlab
metacoder:Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data
Reads, plots, and manipulates large taxonomic data sets, like those generated from modern high-throughput sequencing, such as metabarcoding (i.e. amplification metagenomics, 16S metagenomics, etc). It provides a tree-based visualization called "heat trees" used to depict statistics for every taxon in a taxonomy using color and size. It also provides various functions to do common tasks in microbiome bioinformatics on data in the 'taxmap' format defined by the 'taxa' package. The 'metacoder' package is described in the publication by Foster et al. (2017) <doi:10.1371/journal.pcbi.1005404>.
Maintained by Zachary Foster. Last updated 2 months ago.
community-diversityhierarchicalmetabarcodingpcrtaxonomytreescpp
140 stars 9.64 score 328 scripts
bafuentes
rassta:Raster-Based Spatial Stratification Algorithms
Algorithms for the spatial stratification of landscapes, sampling and modeling of spatially-varying phenomena. These algorithms offer a simple framework for the stratification of geographic space based on raster layers representing landscape factors and/or factor scales. The stratification process follows a hierarchical approach, which is based on first level units (i.e., classification units) and second-level units (i.e., stratification units). Nonparametric techniques allow to measure the correspondence between the geographic space and the landscape configuration represented by the units. These correspondence metrics are useful to define sampling schemes and to model the spatial variability of environmental phenomena. The theoretical background of the algorithms and code examples are presented in Fuentes, Dorantes, and Tipton (2021). <doi:10.31223/X50S57>.
Maintained by Bryan A. Fuentes. Last updated 3 years ago.
ecologygeoinformaticshierarchicalmodelingsamplingspatial
16 stars 5.96 score 19 scripts
paulnorthrop
bang:Bayesian Analysis, No Gibbs
Provides functions for the Bayesian analysis of some simple commonly-used models, without using Markov Chain Monte Carlo (MCMC) methods such as Gibbs sampling. The 'rust' package <https://cran.r-project.org/package=rust> is used to simulate a random sample from the required posterior distribution, using the generalized ratio-of-uniforms method. See Wakefield, Gelfand and Smith (1991) <DOI:10.1007/BF01889987> for details. At the moment three conjugate hierarchical models are available: beta-binomial, gamma-Poisson and a 1-way analysis of variance (ANOVA).
Maintained by Paul J. Northrop. Last updated 2 months ago.
anovabayesianbetabinomialgammagibbshierarchicalpoisson
3 stars 5.62 score 35 scripts