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stephenslab

mashr:Multivariate Adaptive Shrinkage

Implements the multivariate adaptive shrinkage (mash) method of Urbut et al (2019) <DOI:10.1038/s41588-018-0268-8> for estimating and testing large numbers of effects in many conditions (or many outcomes). Mash takes an empirical Bayes approach to testing and effect estimation; it estimates patterns of similarity among conditions, then exploits these patterns to improve accuracy of the effect estimates. The core linear algebra is implemented in C++ for fast model fitting and posterior computation.

Maintained by Peter Carbonetto. Last updated 5 months ago.

openblasgslcppopenmp

91 stars 11.04 score 624 scripts 3 dependents

murrayefford

secr:Spatially Explicit Capture-Recapture

Functions to estimate the density and size of a spatially distributed animal population sampled with an array of passive detectors, such as traps, or by searching polygons or transects. Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.

Maintained by Murray Efford. Last updated 4 days ago.

cpp

3 stars 10.06 score 410 scripts 5 dependents

r-forge

CHNOSZ:Thermodynamic Calculations and Diagrams for Geochemistry

An integrated set of tools for thermodynamic calculations in aqueous geochemistry and geobiochemistry. Functions are provided for writing balanced reactions to form species from user-selected basis species and for calculating the standard molal properties of species and reactions, including the standard Gibbs energy and equilibrium constant. Calculations of the non-equilibrium chemical affinity and equilibrium chemical activity of species can be portrayed on diagrams as a function of temperature, pressure, or activity of basis species; in two dimensions, this gives a maximum affinity or predominance diagram. The diagrams have formatted chemical formulas and axis labels, and water stability limits can be added to Eh-pH, oxygen fugacity- temperature, and other diagrams with a redox variable. The package has been developed to handle common calculations in aqueous geochemistry, such as solubility due to complexation of metal ions, mineral buffers of redox or pH, and changing the basis species across a diagram ("mosaic diagrams"). CHNOSZ also implements a group additivity algorithm for the standard thermodynamic properties of proteins.

Maintained by Jeffrey Dick. Last updated 22 days ago.

fortran

9.46 score 238 scripts 4 dependents

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