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Matrix - Sparse and Dense Matrix Classes and Methods

A rich hierarchy of sparse and dense matrix classes, including general, symmetric, triangular, and diagonal matrices with numeric, logical, or pattern entries. Efficient methods for operating on such matrices, often wrapping the 'BLAS', 'LAPACK', and 'SuiteSparse' libraries.

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openblas

16.44 score 9.8k dependents 47k scripts 304k downloads

epigrowthfit - Nonlinear Mixed Effects Models of Epidemic Growth

Maximum likelihood estimation of nonlinear mixed effects models of epidemic growth using Template Model Builder ('TMB'). Enables joint estimation for collections of disease incidence time series, including time series that describe multiple epidemic waves. Supports a set of widely used phenomenological models: exponential, logistic, Richards (generalized logistic), subexponential, and Gompertz. Provides methods for interrogating model objects and several auxiliary functions, including one for computing basic reproduction numbers from fitted values of the initial exponential growth rate. Preliminary versions of this software were applied in Ma et al. (2014) <doi:10.1007/s11538-013-9918-2> and in Earn et al. (2020) <doi:10.1073/pnas.2004904117>.

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cppopenmp

5.13 score 10 stars 45 scripts 358 downloads

flint - Fast Library for Number Theory

An R interface to 'FLINT' <https://flintlib.org/>, a C library for number theory. 'FLINT' extends GNU 'MPFR' <https://www.mpfr.org/> and GNU 'MP' <https://gmplib.org/> with support for operations on standard rings (the integers, the integers modulo n, finite fields, the rational, p-adic, real, and complex numbers) as well as matrices and polynomials over rings. 'FLINT' implements midpoint-radius interval arithmetic, also known as ball arithmetic, in the real and complex numbers, enabling computation in arbitrary precision with rigorous propagation of rounding and other errors; see Johansson (2017) <doi:10.1109/TC.2017.2690633>. Finally, 'FLINT' provides ball arithmetic implementations of many special mathematical functions, with high coverage of reference works such as the NIST Digital Library of Mathematical Functions <https://dlmf.nist.gov/>. The R interface defines S4 classes, generic functions, and methods for representation and basic operations as well as plain R functions mirroring and vectorizing entry points in the C library.

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flintmpfr4gmp

4.31 score 24 scripts 469 downloads

fastbeta - Fast Approximation of Time-Varying Infectious Disease Transmission Rates

A fast method for approximating time-varying infectious disease transmission rates from disease incidence time series and other data, based on a discrete time approximation of an SEIR model, as analyzed in Jagan et al. (2020) <doi:10.1371/journal.pcbi.1008124>.

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3.30 score 1 stars 6 scripts 325 downloads