dMod: Dynamic Modeling and Parameter Estimation in ODE Models

Share:

The framework provides functions to generate ODEs of reaction networks, parameter transformations, observation functions, residual functions, etc. The framework follows the paradigm that derivative information should be used for optimization whenever possible. Therefore, all major functions produce and can handle expressions for symbolic derivatives.

Author
Daniel Kaschek
Date of publication
2016-09-30 10:47:59
Maintainer
Daniel Kaschek <daniel.kaschek@physik.uni-freiburg.de>
License
GPL (>= 2)
Version
0.3.2

View on CRAN

Man pages

addReaction
Add reaction to reaction table
as.data.frame.eqnlist
Coerce equation list into a data frame
as.eqnvec
Coerce to an equation vector
as.objlist
Generate objective list from numeric vector
as.parframe
Coerce object to a parameter frame
as.parvec.parframe
Select a parameter vector from a parameter frame.
attrs
Select attributes.
blockdiagSymb
Embed two matrices into one blockdiagonal matrix
combine
Combine several data.frames by rowbind
compare
Compare two objects and return differences
conservedQuantities
Determine conserved quantites by finding the kernel of the...
constraintL2
Soft L2 constraint on parameters
controls
List, get and set controls for different functions
coordTransform
Coordinate transformation for data frames
createExample
Open a unit test template.
datalist
Generate a datalist object
datapointL2
L2 objective function for validation data point
detectFreeCores
Detect number of free cores (on UNIX)
dot
Symbolic time derivative of equation vector given an equation...
eqnlist
Generate eqnlist object
eqnvec
Generate equation vector object
exmpextr
Extract an example from a unit test file.
expand.grid.alt
Alternative version of expand.grid
extractExamples
Extract example from unit tests.
fitErrorModel
Fit an error model
forcingsSymb
Return some useful forcing functions as strings
format.eqnvec
Encode equation vector in format with sufficient spaces
funC0
Evaluation of algebraic expressions defined by characters
getCoefficients
Get coefficients from a character
getConditions
Extract the conditions of an object
getDerivs
Extract the derivatives of an object
getFluxes
Generate list of fluxes from equation list
getParameters
Extract the parameters of an object
getReactions
Generate a table of reactions (data.frame) from an equation...
ggopen
Open last plot in external pdf viewer
lbind
Bind named list of data.frames into one data.frame
load.parlist
Construct fitlist from temporary files.
loadTemplate
Load a template file in the editor
long2wide
Translate long to wide format (inverse of wide2long.matrix)
lsdMod
Print list of dMod objects in .GlobalEnv
mssample
Generate sample for multi-start fit
mstrust
Non-Linear Optimization, multi start
nll
Compute the negative log-likelihood
normL2
L2 norm between data and model prediction
nullZ
Find integer-null space of matrix A
objframe
Objective frame
objlist
Generate objective list
obsfn
Observation function
odemodel
Generate the model objects for use in Xs (models with...
P
Generate a parameter transformation function
parfn
Parameter transformation function
parframe
Generate a paramter frame
parlist
Parameter list
parvec
Parameter vector
Pexpl
Parameter transformation
Pimpl
Parameter transformation (implicit)
plotArray
Plot an array of model predictions for a list of parameters
plotCombined
Plot a list of model predictions and a list of data points in...
plotData
Plot a list data points
plot.datalist
Plot a list data points
plotFluxes
Plot Fluxes given a list of flux Equations
plot.parlist
Plot a parameter list.
plotPars
Plot parameter values for a fitlist
plotPaths
Profile likelihood: plot of the parameter paths.
plotPrediction
Plot a list of model predictions
plotProfile
Profile likelihood plot
plotValues
Plotting objective values of a collection of fits
plus-.datalist
Direct sum of datasets
plus-.fn
Direct sum of functions
plus-.objfn
Direct sum of objective functions
plus-.objlist
Add two lists element by element
prdfn
Prediction function
prdframe
Prediction frame
prdlist
Prediction list
print0
Print object and its "default" attributes only.
print.eqnlist
Print or pander equation list
print.eqnvec
Print equation vector
print.parfn
Pretty printing parameter transformations
print.parvec
Pretty printing for a parameter vector
priorL2
L2 objective function for prior value
profile
Profile-likelihood (PL) computation
progressBar
Progress bar
python.version.request
Check if rPython comes with the correct Python version
python.version.rpython
Get the Python version to which rPython is linked
python.version.sys
Check which Python versions are installed on the system
quasiSteadyStates
Reduce the ODE system by means of a quasi steady-state...
reduceReplicates
Reduce replicated measurements to mean and standard deviation
repWithNames
Named repititions
res
Compare data and model prediction by computing residuals
resolveRecurrence
Place top elements into bottom elemens
rref
Transform matrix A into reduced row echelon form this...
runbg
Run an R expression in the background (only on UNIX)
runbg.install
Remote install dMod to a ssh-reachable host
scale_color_dMod
Standard dMod color palette
scale_fill_dMod
Standard dMod color scheme
stat.parlist
Gather statistics of a fitlist
steadyStates
Calculate analytical steady states
strelide
Elide character vector
strpad
Pad string to desired width
submatrix
Submatrix of a matrix returning ALWAYS a matrix
subset.eqnlist
subset of an equation list
summary.eqnvec
Summary of an equation vector
symmetryDetection
Search for symmetries in the loaded model
theme_dMod
Standard plotting theme of dMod
times-.fn
Concatenation of functions
wide2long
Translate wide output format (e.g. from ode) into long format
wide2long.data.frame
Translate wide output format (e.g. from ode) into long format
wide2long.list
Translate wide output format (e.g. from ode) into long format
wide2long.matrix
Translate wide output format (e.g. from ode) into long format
write.eqnlist
Write equation list into a csv file
wrss
Compute the weighted residual sum of squares
Xd
Model prediction function from data.frame
Xf
Model prediction function for ODE models without...
Xs
Model prediction function for ODE models.
Xt
Generate a prediction function that returns times
Y
Observation functions.

Files in this package

dMod
dMod/inst
dMod/inst/examples
dMod/inst/examples/parlist.R
dMod/inst/examples/equations.R
dMod/inst/examples/plotting.R
dMod/inst/examples/parvec.R
dMod/inst/examples/objective.R
dMod/inst/examples/normL2.R
dMod/inst/examples/eqnvec.R
dMod/inst/examples/profiles.R
dMod/inst/examples/odemodel.R
dMod/inst/examples/datalist.R
dMod/inst/examples/prediction.R
dMod/inst/examples/plotArray.R
dMod/inst/examples/sumdatalist.R
dMod/inst/examples/eqnlist.R
dMod/inst/examples/test_blocks.R
dMod/inst/code
dMod/inst/code/readData.py
dMod/inst/code/steadyStates.py
dMod/inst/code/quasiSteadyStates.py
dMod/inst/code/checkPredictions.py
dMod/inst/code/extendObservation.py
dMod/inst/code/functions.py
dMod/inst/code/buildSystem.py
dMod/inst/code/functions_obs.py
dMod/inst/code/symmetryDetection.py
dMod/inst/code/polyClass.py
dMod/inst/templates
dMod/inst/templates/unitTestTemplate.R
dMod/inst/templates/R2CTemplateIE.R
dMod/inst/templates/R2CTemplate.R
dMod/inst/doc
dMod/inst/doc/dMod.R
dMod/inst/doc/dMod.Rmd
dMod/inst/doc/dMod.html
dMod/NAMESPACE
dMod/R
dMod/R/classes.R
dMod/R/toolsWolfgang.R
dMod/R/eqnClass.R
dMod/R/odeClass.R
dMod/R/toolsMarcus.R
dMod/R/prdClass.R
dMod/R/sparseMatrix.R
dMod/R/remoteComputing.R
dMod/R/dMod.R
dMod/R/toolsBeni.R
dMod/R/data.R
dMod/R/statistics.R
dMod/R/plots.R
dMod/R/tools.R
dMod/R/symbolics.R
dMod/R/prediction.R
dMod/R/toolsMirjam.R
dMod/R/objClass.R
dMod/R/testing.R
dMod/R/toolsMalenka.R
dMod/R/toolsDaniel.R
dMod/R/parameters.R
dMod/R/dataClass.R
dMod/R/parClass.R
dMod/vignettes
dMod/vignettes/pnas_data_original.csv
dMod/vignettes/dMod.Rmd
dMod/vignettes/pathway.png
dMod/vignettes/topology.csv
dMod/vignettes/topology_linchain.csv
dMod/vignettes/framework.Rmd
dMod/MD5
dMod/build
dMod/build/vignette.rds
dMod/DESCRIPTION
dMod/man
dMod/man/print0.Rd
dMod/man/parvec.Rd
dMod/man/format.eqnvec.Rd
dMod/man/steadyStates.Rd
dMod/man/prdlist.Rd
dMod/man/progressBar.Rd
dMod/man/print.eqnvec.Rd
dMod/man/addReaction.Rd
dMod/man/constraintL2.Rd
dMod/man/ggopen.Rd
dMod/man/load.parlist.Rd
dMod/man/getConditions.Rd
dMod/man/stat.parlist.Rd
dMod/man/eqnvec.Rd
dMod/man/scale_fill_dMod.Rd
dMod/man/P.Rd
dMod/man/submatrix.Rd
dMod/man/plotProfile.Rd
dMod/man/combine.Rd
dMod/man/as.objlist.Rd
dMod/man/lsdMod.Rd
dMod/man/Xf.Rd
dMod/man/summary.eqnvec.Rd
dMod/man/scale_color_dMod.Rd
dMod/man/datalist.Rd
dMod/man/dot.Rd
dMod/man/normL2.Rd
dMod/man/repWithNames.Rd
dMod/man/Xd.Rd
dMod/man/prdfn.Rd
dMod/man/print.parfn.Rd
dMod/man/reduceReplicates.Rd
dMod/man/wide2long.Rd
dMod/man/nll.Rd
dMod/man/theme_dMod.Rd
dMod/man/exmpextr.Rd
dMod/man/wide2long.matrix.Rd
dMod/man/res.Rd
dMod/man/plotArray.Rd
dMod/man/as.eqnvec.Rd
dMod/man/print.parvec.Rd
dMod/man/nullZ.Rd
dMod/man/plus-.objlist.Rd
dMod/man/getDerivs.Rd
dMod/man/extractExamples.Rd
dMod/man/strpad.Rd
dMod/man/obsfn.Rd
dMod/man/parlist.Rd
dMod/man/priorL2.Rd
dMod/man/controls.Rd
dMod/man/Pexpl.Rd
dMod/man/prdframe.Rd
dMod/man/write.eqnlist.Rd
dMod/man/loadTemplate.Rd
dMod/man/lbind.Rd
dMod/man/coordTransform.Rd
dMod/man/parframe.Rd
dMod/man/plus-.fn.Rd
dMod/man/resolveRecurrence.Rd
dMod/man/mstrust.Rd
dMod/man/getCoefficients.Rd
dMod/man/blockdiagSymb.Rd
dMod/man/objframe.Rd
dMod/man/Xt.Rd
dMod/man/parfn.Rd
dMod/man/wide2long.data.frame.Rd
dMod/man/plot.datalist.Rd
dMod/man/rref.Rd
dMod/man/plus-.datalist.Rd
dMod/man/as.data.frame.eqnlist.Rd
dMod/man/subset.eqnlist.Rd
dMod/man/attrs.Rd
dMod/man/getReactions.Rd
dMod/man/quasiSteadyStates.Rd
dMod/man/expand.grid.alt.Rd
dMod/man/python.version.sys.Rd
dMod/man/compare.Rd
dMod/man/Pimpl.Rd
dMod/man/runbg.install.Rd
dMod/man/Xs.Rd
dMod/man/times-.fn.Rd
dMod/man/python.version.rpython.Rd
dMod/man/odemodel.Rd
dMod/man/getFluxes.Rd
dMod/man/datapointL2.Rd
dMod/man/eqnlist.Rd
dMod/man/as.parvec.parframe.Rd
dMod/man/plotPrediction.Rd
dMod/man/print.eqnlist.Rd
dMod/man/fitErrorModel.Rd
dMod/man/plotFluxes.Rd
dMod/man/getParameters.Rd
dMod/man/as.parframe.Rd
dMod/man/long2wide.Rd
dMod/man/plus-.objfn.Rd
dMod/man/plotPaths.Rd
dMod/man/mssample.Rd
dMod/man/strelide.Rd
dMod/man/createExample.Rd
dMod/man/plotCombined.Rd
dMod/man/wrss.Rd
dMod/man/Y.Rd
dMod/man/profile.Rd
dMod/man/objlist.Rd
dMod/man/plotPars.Rd
dMod/man/plotValues.Rd
dMod/man/runbg.Rd
dMod/man/plot.parlist.Rd
dMod/man/funC0.Rd
dMod/man/python.version.request.Rd
dMod/man/plotData.Rd
dMod/man/detectFreeCores.Rd
dMod/man/wide2long.list.Rd
dMod/man/symmetryDetection.Rd
dMod/man/forcingsSymb.Rd
dMod/man/conservedQuantities.Rd