No packages match

Deriv - Symbolic Differentiation

R-based solution for symbolic differentiation. It admits user-defined function as well as function substitution in arguments of functions to be differentiated. Some symbolic simplification is part of the work.

Last updated

12.34 score 44 stars 1.2k dependents 401 scripts 351k downloads

rmumps - Wrapper for MUMPS Library

Some basic features of 'MUMPS' (Multifrontal Massively Parallel sparse direct Solver) are wrapped in a class whose methods can be used for sequentially solving a sparse linear system (symmetric or not) with one or many right hand sides (dense or sparse). There is a possibility to do separately symbolic analysis, LU (or LDL^t) factorization and system solving. Third part ordering libraries are included and can be used: 'PORD', 'METIS', 'SCOTCH'. 'MUMPS' method was first described in Amestoy et al. (2001) <doi:10.1137/S0895479899358194> and Amestoy et al. (2006) <doi:10.1016/j.parco.2005.07.004>.

Last updated

openblasfortrancpp

5.23 score 10 stars 2 dependents 19 scripts 781 downloads

bspline - B-Spline Interpolation and Regression

Build and use B-splines for interpolation and regression. In case of regression, equality constraints as well as monotonicity and/or positivity of B-spline weights can be imposed. Moreover, knot positions can be on regular grid or be part of optimized parameters too (in addition to the spline weights). For this end, 'bspline' is able to calculate Jacobian of basis vectors as function of knot positions. User is provided with functions calculating spline values at arbitrary points. These functions can be differentiated and integrated to obtain B-splines calculating derivatives/integrals at any point. B-splines of this package can simultaneously operate on a series of curves sharing the same set of knots. 'bspline' is written with concern about computing performance that's why the basis and Jacobian calculation is implemented in C++. The rest is implemented in R but without notable impact on computing speed.

Last updated

openblascpp

3.78 score 4 stars 1 dependents 1 scripts 306 downloads

nlsic - Non Linear Least Squares with Inequality Constraints

We solve non linear least squares problems with optional equality and/or inequality constraints. Non linear iterations are globalized with back-tracking method. Linear problems are solved by dense QR decomposition from 'LAPACK' which can limit the size of treated problems. On the other side, we avoid condition number degradation which happens in classical quadratic programming approach. Inequality constraints treatment on each non linear iteration is based on 'NNLS' method (by Lawson and Hanson). We provide an original function 'lsi_ln' for solving linear least squares problem with inequality constraints in least norm sens. Thus if Jacobian of the problem is rank deficient a solution still can be provided. However, truncation errors are probable in this case. Equality constraints are treated by using a basis of Null-space. User defined function calculating residuals must return a list having residual vector (not their squared sum) and Jacobian. If Jacobian is not in the returned list, package 'numDeriv' is used to calculated finite difference version of Jacobian. The 'NLSIC' method was fist published in Sokol et al. (2012) <doi:10.1093/bioinformatics/btr716>.

Last updated

3.08 score 1 stars 2 dependents 4 scripts 267 downloads

arrApply - Apply a Function to a Margin of an Array

High performance variant of apply() for a fixed set of functions. Considerable speedup of this implementation is a trade-off for universality: user defined functions cannot be used with this package. However, about 20 most currently employed functions are available for usage. They can be divided in three types: reducing functions (like mean(), sum() etc., giving a scalar when applied to a vector), mapping function (like normalise(), cumsum() etc., giving a vector of the same length as the input vector) and finally, vector reducing function (like diff() which produces result vector of a length different from the length of input vector). Optional or mandatory additional arguments required by some functions (e.g. norm type for norm()) can be passed as named arguments in '...'.

Last updated

openblascpp

2.78 score 2 dependents 9 scripts 319 downloads

dynafluxr - Retrieve Reaction Rate Dynamics from Metabolite Concentration Time Courses

Reaction rate dynamics can be retrieved from metabolite concentration time courses. User has to provide corresponding stoichiometric matrix but not a regulation model (Michaelis-Menten or similar). Instead of solving an ordinary differential equation (ODE) system describing the evolution of concentrations, we use B-splines to catch the concentration and rate dynamics then solve a least square problem on their coefficients with non-negativity (and optionally monotonicity) constraints. Constraints can be also set on initial values of concentration. The package 'dynafluxr' can be used as a library but also as an application with command line interface dynafluxr::cli("-h") or graphical user interface dynafluxr::gui().

Last updated

2.70 score 2 scripts 152 downloads

kvh - Read/Write Files in Key-Value-Hierarchy Format

The format KVH is a lightweight format that can be read/written both by humans and machines. It can be useful in situations where XML or alike formats seem to be an overkill. We provide an ability to parse KVH files in R pretty fast due to 'Rcpp' use.

Last updated

cpp

2.70 score 5 scripts 244 downloads

r2sundials - Wrapper for 'SUNDIALS' Solving ODE and Sensitivity Problem

Wrapper for widely used 'SUNDIALS' software (SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers) and more precisely to its 'CVODES' solver. It is aiming to solve ordinary differential equations (ODE) and optionally pending forward sensitivity problem. The wrapper is made 'R' friendly by allowing to pass custom parameters to user's callback functions. Such functions can be both written in 'R' and in 'C++' ('RcppArmadillo' flavor). In case of 'C++', performance is greatly improved so this option is highly advisable when performance matters. If provided, Jacobian matrix can be calculated either in dense or sparse format. In the latter case 'rmumps' package is used to solve corresponding linear systems. Root finding and pending event management are optional and can be specified as 'R' or 'C++' functions too. This makes them a very flexible tool for controlling the ODE system during the time course simulation. 'SUNDIALS' library was published in Hindmarsh et al. (2005) <doi:10.1145/1089014.1089020>.

Last updated

cpp

2.48 score 3 stars 4 scripts 282 downloads

gmresls - Solve Least Squares with GMRES(k)

Solves a least squares system Ax~=b (dim(A)=(m,n) with m >= n) with a precondition matrix B: BAx=Bb (dim(B)=(n,m)). Implemented method is based on GMRES (Saad, Youcef; Schultz, Martin H. (1986). "GMRES: A Generalized Minimal Residual Algorithm for Solving Nonsymmetric Linear Systems" <doi:10.1137/0907058>) with callback functions, i.e. no explicit A, B or b are required.

Last updated

2.18 score 1 dependents 202 downloads

multbxxc - Auxiliary Routines for Influx Software

Contains auxiliary routines for influx software. This packages is not intended to be used directly. Influx was published here: Sokol et al. (2012) <doi:10.1093/bioinformatics/btr716>.

Last updated

openblascpp

1.70 score 4 scripts 168 downloads