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.

Author
Karline Soetaert <karline.soetaert@nioz.nl>, Thomas Petzoldt <thomas.petzoldt@tu-dresden.de>
Date of publication
2016-09-08 10:09:45
Maintainer
Karline Soetaert <karline.soetaert@nioz.nl>
License
GPL (>= 2)
Version
1.3.5

View on R-Forge

Man pages

collin
Estimates the Collinearity of Parameter Sets
cross2long
Convert a dataset in wide (crosstab) format to long...
FME
A Flexible Modelling Environment for Inverse Modelling,...
gaussianWeights
A kernel average smoother function to weigh residuals...
Grid
Grid Distribution
Latinhyper
Latin Hypercube Sampling
modCost
Calculates the Discrepancy of a Model Solution with...
modCRL
Monte Carlo Analysis
modFit
Constrained Fitting of a Model to Data
modMCMC
Constrained Markov Chain Monte Carlo
Norm
Normal Random Distribution
obsplot
Plot Method for observed data
pseudoOptim
Pseudo-random Search Optimisation Algorithm of Price (1977)
sensFun
Local Sensitivity Analysis
sensRange
Sensitivity Ranges of a Timeseries or 1-D Variables
Unif
Uniform Random Distribution

Files in this package

FME/.Rinstignore
FME/DESCRIPTION
FME/NAMESPACE
FME/R
FME/R/Grid.R
FME/R/Latinhyper.R
FME/R/Norm.R
FME/R/Unif.R
FME/R/collin.R
FME/R/cross2long.R
FME/R/gaussianWeights.R
FME/R/modCRL.R
FME/R/modCost.R
FME/R/modFit.R
FME/R/modMCMC.R
FME/R/obsplot.R
FME/R/pseudoOptim.R
FME/R/sensFun.R
FME/R/sensRange.R
FME/R/ultilities.R
FME/build
FME/build/vignette.rds
FME/inst
FME/inst/CITATION
FME/inst/doc
FME/inst/doc/FME.R
FME/inst/doc/FME.Rnw
FME/inst/doc/FME.pdf
FME/inst/doc/FMEdyna.R
FME/inst/doc/FMEdyna.Rnw
FME/inst/doc/FMEdyna.pdf
FME/inst/doc/FMEmcmc.R
FME/inst/doc/FMEmcmc.Rnw
FME/inst/doc/FMEmcmc.pdf
FME/inst/doc/FMEother.R
FME/inst/doc/FMEother.Rnw
FME/inst/doc/FMEother.pdf
FME/inst/doc/FMEsteady.R
FME/inst/doc/FMEsteady.Rnw
FME/inst/doc/FMEsteady.pdf
FME/inst/doc/examples
FME/inst/doc/examples/ABrun.R
FME/inst/doc/examples/BODO2_FME.R
FME/inst/doc/examples/Logist.R
FME/inst/doc/examples/Monod.R
FME/inst/doc/examples/O2profile_FME.R
FME/inst/doc/examples/Omexdia_FME.R
FME/inst/doc/examples/bact_FME.R
FME/inst/doc/examples/banana.R
FME/inst/doc/examples/ccl4rmodel_FME.R
FME/inst/doc/examples/modFit_with_simecol.R
FME/man
FME/man/FME.Rd
FME/man/Grid.Rd
FME/man/Latinhyper.Rd
FME/man/Norm.Rd
FME/man/Unif.Rd
FME/man/collin.Rd
FME/man/cross2long.Rd
FME/man/gaussianWeights.Rd
FME/man/modCRL.Rd
FME/man/modCost.Rd
FME/man/modFit.Rd
FME/man/modMCMC.Rd
FME/man/obsplot.Rd
FME/man/pseudoOptim.Rd
FME/man/sensFun.Rd
FME/man/sensRange.Rd
FME/src
FME/src/mod.f
FME/vignettes
FME/vignettes/FME-HIV.pdf
FME/vignettes/FME.Rnw
FME/vignettes/FMEdyna.Rnw
FME/vignettes/FMEmcmc.Rnw
FME/vignettes/FMEother.Rnw
FME/vignettes/FMEsteady.Rnw
FME/vignettes/mcmc.Rdata
FME/vignettes/vignettes.bib