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

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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
2016-09-09 10:13:37
Maintainer
Karline Soetaert <karline.soetaert@nioz.nl>
License
GPL (>= 2)
Version
1.3.5

View on CRAN

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
FME/inst
FME/inst/CITATION
FME/inst/doc
FME/inst/doc/FMEsteady.R
FME/inst/doc/examples
FME/inst/doc/examples/ABrun.R
FME/inst/doc/examples/Omexdia_FME.R
FME/inst/doc/examples/banana.R
FME/inst/doc/examples/O2profile_FME.R
FME/inst/doc/examples/Logist.R
FME/inst/doc/examples/bact_FME.R
FME/inst/doc/examples/BODO2_FME.R
FME/inst/doc/examples/ccl4rmodel_FME.R
FME/inst/doc/examples/modFit_with_simecol.R
FME/inst/doc/examples/Monod.R
FME/inst/doc/FMEmcmc.pdf
FME/inst/doc/FMEother.pdf
FME/inst/doc/FMEmcmc.R
FME/inst/doc/FMEother.Rnw
FME/inst/doc/FMEsteady.pdf
FME/inst/doc/FMEmcmc.Rnw
FME/inst/doc/FME.Rnw
FME/inst/doc/FMEdyna.R
FME/inst/doc/FMEother.R
FME/inst/doc/FME.pdf
FME/inst/doc/FMEsteady.Rnw
FME/inst/doc/FME.R
FME/inst/doc/FMEdyna.pdf
FME/inst/doc/FMEdyna.Rnw
FME/src
FME/src/mod.f
FME/NAMESPACE
FME/R
FME/R/cross2long.R
FME/R/modCost.R
FME/R/Norm.R
FME/R/gaussianWeights.R
FME/R/ultilities.R
FME/R/collin.R
FME/R/Latinhyper.R
FME/R/Grid.R
FME/R/pseudoOptim.R
FME/R/sensRange.R
FME/R/modMCMC.R
FME/R/modCRL.R
FME/R/sensFun.R
FME/R/obsplot.R
FME/R/Unif.R
FME/R/modFit.R
FME/vignettes
FME/vignettes/FMEother.Rnw
FME/vignettes/FMEmcmc.Rnw
FME/vignettes/FME.Rnw
FME/vignettes/FME-HIV.pdf
FME/vignettes/FMEsteady.Rnw
FME/vignettes/mcmc.Rdata
FME/vignettes/vignettes.bib
FME/vignettes/FMEdyna.Rnw
FME/MD5
FME/build
FME/build/vignette.rds
FME/DESCRIPTION
FME/man
FME/man/collin.Rd
FME/man/pseudoOptim.Rd
FME/man/modFit.Rd
FME/man/gaussianWeights.Rd
FME/man/Latinhyper.Rd
FME/man/Unif.Rd
FME/man/FME.Rd
FME/man/modMCMC.Rd
FME/man/sensFun.Rd
FME/man/modCost.Rd
FME/man/obsplot.Rd
FME/man/Norm.Rd
FME/man/cross2long.Rd
FME/man/modCRL.Rd
FME/man/sensRange.Rd
FME/man/Grid.Rd
FME/.Rinstignore