dMod: Dynamic Modeling and Parameter Estimation in ODE Models

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.

Install the latest version of this package by entering the following in R:
install.packages("dMod")
AuthorDaniel Kaschek
Date of publication2016-09-30 10:47:59
MaintainerDaniel Kaschek <daniel.kaschek@physik.uni-freiburg.de>
LicenseGPL (>= 2)
Version0.3.2

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.

Functions

addReaction Man page
as.data.frame.eqnlist Man page
as.datalist Man page
as.datalist.data.frame Man page
as.datalist.list Man page
as.eqnlist Man page
as.eqnlist.data.frame Man page
as.eqnvec Man page
as.eqnvec.character Man page
as.eqnvec.eqnlist Man page
as.objlist Man page
as.parframe Man page
as.parframe.parlist Man page
as.parlist Man page
as.parvec Man page
as.parvec.numeric Man page
as.parvec.parframe Man page
as.prdlist Man page
as.prdlist.list Man page
attrs Man page
blockdiagSymb Man page
combine Man page
compare Man page
compare.character Man page
compare.data.frame Man page
compare.eqnvec Man page
compare.list Man page
conservedQuantities Man page
constraintL2 Man page
controls Man page
controls<- Man page
controls<-.fn Man page
controls.fn Man page
controls<-.objfn Man page
controls.objfn Man page
coordTransform Man page
c.parlist Man page
c.parvec Man page
createExample Man page
datalist Man page
+.datalist Man page
datapointL2 Man page
detectFreeCores Man page
dot Man page
eqnlist Man page
eqnvec Man page
exmpextr Man page
expand.grid.alt Man page
extractExamples Man page
fitErrorModel Man page
*.fn Man page
+.fn Man page
forcingsSymb Man page
format.eqnvec Man page
funC0 Man page
getCoefficients Man page
getConditions Man page
getConditions.fn Man page
getConditions.list Man page
getDerivs Man page
getDerivs.list Man page
getDerivs.objlist Man page
getDerivs.parvec Man page
getDerivs.prdframe Man page
getDerivs.prdlist Man page
getFluxes Man page
getParameters Man page
getParameters.fn Man page
getParameters.odemodel Man page
getParameters.parvec Man page
getParameters.prdframe Man page
getParameters.prdlist Man page
getReactions Man page
ggopen Man page
is.eqnlist Man page
is.eqnvec Man page
lbind Man page
load.parlist Man page
loadTemplate Man page
long2wide Man page
lsdMod Man page
mssample Man page
mstrust Man page
nll Man page
normL2 Man page
nullZ Man page
+.objfn Man page
objframe Man page
objlist Man page
+.objlist Man page
obsfn Man page
odemodel Man page
P Man page
parfn Man page
parframe Man page
[.parframe Man page
parlist Man page
parvec Man page
[.parvec Man page
Pexpl Man page
Pimpl Man page
plotArray Man page
plotCombined Man page
plotData Man page
plot.datalist Man page
plotFluxes Man page
plot.parlist Man page
plotPars Man page
plotPaths Man page
plot.prdframe Man page
plot.prdlist Man page
plotPrediction Man page
plotProfile Man page
plotValues Man page
prdfn Man page
prdframe Man page
prdlist Man page
print0 Man page
print.eqnlist Man page
print.eqnvec Man page
print.parfn Man page
print.parvec Man page
priorL2 Man page
prodfn Man page
profile Man page
progressBar Man page
python.version.request Man page
python.version.rpython Man page
python.version.sys Man page
quasiSteadyStates Man page
reduceReplicates Man page
repWithNames Man page
res Man page
resolveRecurrence Man page
rref Man page
runbg Man page
runbg.install Man page
scale_color_dMod Man page
scale_fill_dMod Man page
stat.parlist Man page
steadyStates Man page
strelide Man page
strpad Man page
submatrix Man page
subset.eqnlist Man page
subset.parframe Man page
sumdatalist Man page
sumfn Man page
summary.eqnvec Man page
summary.parlist Man page
sumobjfn Man page
sumobjlist Man page
symmetryDetection Man page
theme_dMod Man page
wide2long Man page
wide2long.data.frame Man page
wide2long.list Man page
wide2long.matrix Man page
write.eqnlist Man page
wrss Man page
Xd Man page
Xf Man page
Xs Man page
Xt Man page
Y Man page

Files

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

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