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shape - Functions for Plotting Graphical Shapes, Colors

Functions for plotting graphical shapes such as ellipses, circles, cylinders, arrows, ...

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11.04 score 1.6k dependents 1.0k scripts 226k downloads

plot3D - Plotting Multi-Dimensional Data

Functions for viewing 2-D and 3-D data, including perspective plots, slice plots, surface plots, scatter plots, etc. Includes data sets from oceanography.

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9.89 score 3 stars 81 dependents 3.9k scripts 14k downloads

rootSolve - Nonlinear Root Finding, Equilibrium and Steady-State Analysis of Ordinary Differential Equations

Routines to find the root of nonlinear functions, and to perform steady-state and equilibrium analysis of ordinary differential equations (ODE). Includes routines that: (1) generate gradient and jacobian matrices (full and banded), (2) find roots of non-linear equations by the 'Newton-Raphson' method, (3) estimate steady-state conditions of a system of (differential) equations in full, banded or sparse form, using the 'Newton-Raphson' method, or by dynamically running, (4) solve the steady-state conditions for uni-and multicomponent 1-D, 2-D, and 3-D partial differential equations, that have been converted to ordinary differential equations by numerical differencing (using the method-of-lines approach). Includes fortran code.

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9.82 score 1 stars 254 dependents 1.8k scripts 49k downloads

diagram - Functions for Visualising Simple Graphs (Networks), Plotting Flow Diagrams

Visualises simple graphs (networks) based on a transition matrix, utilities to plot flow diagrams, visualising webs, electrical networks, etc. Support for the book "A practical guide to ecological modelling - using R as a simulation platform" by Karline Soetaert and Peter M.J. Herman (2009), Springer. and the book "Solving Differential Equations in R" by Karline Soetaert, Jeff Cash and Francesca Mazzia (2012), Springer. Includes demo(flowchart), demo(plotmat), demo(plotweb).

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9.26 score 549 dependents 778 scripts 143k downloads

FME - A Flexible Modelling Environment for Inverse Modelling, Sensitivity, Identifiability and Monte Carlo Analysis

Provides functions to help in fitting models to data, to perform Monte Carlo, sensitivity and identifiability analysis. It is intended to work with models be written as a set of differential equations that are solved either by an integration routine from package 'deSolve', or a steady-state solver from package 'rootSolve'. However, the methods can also be used with other types of functions.

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8.95 score 7 dependents 451 scripts 6.2k downloads

limSolve - Solving Linear Inverse Models

Functions that (1) find the minimum/maximum of a linear or quadratic function: min or max (f(x)), where f(x) = ||Ax-b||^2 or f(x) = sum(a_i*x_i) subject to equality constraints Ex=f and/or inequality constraints Gx>=h, (2) sample an underdetermined- or overdetermined system Ex=f subject to Gx>=h, and if applicable Ax~=b, (3) solve a linear system Ax=B for the unknown x. It includes banded and tridiagonal linear systems.

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openblas

8.33 score 16 dependents 219 scripts 5.1k downloads

ReacTran - Reactive Transport Modelling in 1d, 2d and 3d

Routines for developing models that describe reaction and advective-diffusive transport in one, two or three dimensions. Includes transport routines in porous media, in estuaries, and in bodies with variable shape.

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4.63 score 6 stars 59 scripts 395 downloads

marelac - Tools for Aquatic Sciences

Datasets, constants, conversion factors, and utilities for 'MArine', 'Riverine', 'Estuarine', 'LAcustrine' and 'Coastal' science. The package contains among others: (1) chemical and physical constants and datasets, e.g. atomic weights, gas constants, the earths bathymetry; (2) conversion factors (e.g. gram to mol to liter, barometric units, temperature, salinity); (3) physical functions, e.g. to estimate concentrations of conservative substances, gas transfer and diffusion coefficients, the Coriolis force and gravity; (4) thermophysical properties of the seawater, as from the UNESCO polynomial or from the more recent derivation based on a Gibbs function.

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4.57 score 1 stars 3 dependents 138 scripts 401 downloads

OceanView - Visualisation of Oceanographic Data and Model Output

Functions for transforming and viewing 2-D and 3-D (oceanographic) data and model output.

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4.13 score 67 scripts 352 downloads

plot3Drgl - Plotting Multi-Dimensional Data - Using 'rgl'

The 'rgl' implementation of plot3D functions.

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4.11 score 5 dependents 257 scripts 3.4k downloads

NetIndices - Estimating Network Indices, Including Trophic Structure of Foodwebs in R

Given a network (e.g. a food web), estimates several network indices. These include: Ascendency network indices, Direct and indirect dependencies, Effective measures, Environ network indices, General network indices, Pathway analysis, Network uncertainty indices and constraint efficiencies and the trophic level and omnivory indices of food webs.

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3.95 score 2 dependents 147 scripts 266 downloads

AquaEnv - Integrated Development Toolbox for Aquatic Chemical Model Generation

Toolbox for the experimental aquatic chemist, focused on acidification and CO2 air-water exchange. It contains all elements to model the pH, the related CO2 air-water exchange, and aquatic acid-base chemistry for an arbitrary marine, estuarine or freshwater system. It contains a suite of tools for sensitivity analysis, visualisation, modelling of chemical batches, and can be used to build dynamic models of aquatic systems. As from version 1.0-4, it also contains functions to calculate the buffer factors.

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2.54 score 35 scripts 288 downloads

ecolMod - "A Practical Guide to Ecological Modelling - Using R as a Simulation Platform"

Figures, data sets and examples from the book "A practical guide to ecological modelling - using R as a simulation platform" by Karline Soetaert and Peter MJ Herman (2009). Springer. All figures from chapter x can be generated by "demo(chapx)", where x = 1 to 11. The R-scripts of the model examples discussed in the book are in subdirectory "examples", ordered per chapter. Solutions to model projects are in the same subdirectories.

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2.00 score 1 stars 8 scripts 246 downloads