Nonlinear Mixed Effects Models in Population PK/PD, Estimation Routines

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Documentation for package ‘nlmixr2est’ version 7.0.2

• DESCRIPTION file.
• Package NEWS.

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A B C E F G I L M N O P Q R S T U V Y misc

-- A --

aaaCranNlmixrThreads	This function is to set the number of threads to 2
addCwres	Add CWRES
addNpde	NPDE calculation for nlmixr2
addTable	Add table information to nlmixr2 fit object without tables
agqControl	Control options for the agq estimation method
assertNlmixrFit	Assert that this is a nlmixr2 fit object
assertNlmixrFitData	Assert that this is a nlmixr2 fit data object
augPred.nlmixr2FitData	Augmented Prediction for nlmixr2 fit

-- B --

bobyqaControl	Control for bobyqa estimation method in nlmixr2
boxCox	Cox Box, Yeo Johnson and inverse transformation

-- C --

cholSE

Generalized Cholesky Matrix Decomposition

-- E --

emviControl

Control for the variational inference methods emvi and fbvi in nlmixr2

-- F --

fbviControl	Control for the fbvi (full-Bayes variational inference) method
foceControl	Control options for the foce estimation method
foceiControl	Control Options for FOCEi
foceiLikLoad	Load a general FOCE-family likelihood into memory
foceiLikRun	Evaluate a loaded general FOCE-family likelihood at supplied etas
foceiLikUnload	Unload the general FOCE-family likelihood from memory
focepControl	Control options for the focep (FOCE+) estimation method
foControl	Control options for the FO estimation method
foiControl	Control options foir the FOI estimation method
formatMinWidth	Format numeric values to minimize the printing width

-- G --

getOfvType	Set/get Objective function type for a nlmixr2 object
getValidNlmixrControl	Get valid nlmixr control object
getValidNlmixrCtl	Get valid nlmixr control object
getValidNlmixrCtl.agq	Get valid nlmixr control object
getValidNlmixrCtl.agqf	Get valid nlmixr control object
getValidNlmixrCtl.bfgs	Get valid nlmixr control object
getValidNlmixrCtl.bobyqa	Get valid nlmixr control object
getValidNlmixrCtl.brent	Get valid nlmixr control object
getValidNlmixrCtl.cg	Get valid nlmixr control object
getValidNlmixrCtl.default	Get valid nlmixr control object
getValidNlmixrCtl.emvi	Get valid nlmixr control object
getValidNlmixrCtl.fbvi	Get valid nlmixr control object
getValidNlmixrCtl.fo	Get valid nlmixr control object
getValidNlmixrCtl.foce	Get valid nlmixr control object
getValidNlmixrCtl.focef	Get valid nlmixr control object
getValidNlmixrCtl.focei	Get valid nlmixr control object
getValidNlmixrCtl.foceif	Get valid nlmixr control object
getValidNlmixrCtl.focep	Get valid nlmixr control object
getValidNlmixrCtl.focepf	Get valid nlmixr control object
getValidNlmixrCtl.foi	Get valid nlmixr control object
getValidNlmixrCtl.iagq	Get valid nlmixr control object
getValidNlmixrCtl.iagqf	Get valid nlmixr control object
getValidNlmixrCtl.ifoce	Get valid nlmixr control object
getValidNlmixrCtl.ifocef	Get valid nlmixr control object
getValidNlmixrCtl.ifocei	Get valid nlmixr control object
getValidNlmixrCtl.ifoceif	Get valid nlmixr control object
getValidNlmixrCtl.ifocep	Get valid nlmixr control object
getValidNlmixrCtl.ifocepf	Get valid nlmixr control object
getValidNlmixrCtl.ilaplace	Get valid nlmixr control object
getValidNlmixrCtl.imp	Get valid nlmixr control object
getValidNlmixrCtl.impmap	Get valid nlmixr control object
getValidNlmixrCtl.inpag	Get valid nlmixr control object
getValidNlmixrCtl.inpb	Get valid nlmixr control object
getValidNlmixrCtl.laplace	Get valid nlmixr control object
getValidNlmixrCtl.lbfgsb	Get valid nlmixr control object
getValidNlmixrCtl.lbfgsb3c	Get valid nlmixr control object
getValidNlmixrCtl.magq	Get valid nlmixr control object
getValidNlmixrCtl.magqf	Get valid nlmixr control object
getValidNlmixrCtl.mfoce	Get valid nlmixr control object
getValidNlmixrCtl.mfocef	Get valid nlmixr control object
getValidNlmixrCtl.mfocei	Get valid nlmixr control object
getValidNlmixrCtl.mfoceif	Get valid nlmixr control object
getValidNlmixrCtl.mfocep	Get valid nlmixr control object
getValidNlmixrCtl.mfocepf	Get valid nlmixr control object
getValidNlmixrCtl.mlaplace	Get valid nlmixr control object
getValidNlmixrCtl.mnpag	Get valid nlmixr control object
getValidNlmixrCtl.mnpb	Get valid nlmixr control object
getValidNlmixrCtl.n1qn1	Get valid nlmixr control object
getValidNlmixrCtl.neldermead	Get valid nlmixr control object
getValidNlmixrCtl.newuoa	Get valid nlmixr control object
getValidNlmixrCtl.nlm	Get valid nlmixr control object
getValidNlmixrCtl.nlme	Get valid nlmixr control object
getValidNlmixrCtl.nlminb	Get valid nlmixr control object
getValidNlmixrCtl.nls	Get valid nlmixr control object
getValidNlmixrCtl.npag	Get valid nlmixr control object
getValidNlmixrCtl.npb	Get valid nlmixr control object
getValidNlmixrCtl.optim	Get valid nlmixr control object
getValidNlmixrCtl.posthoc	Get valid nlmixr control object
getValidNlmixrCtl.predict	Get valid nlmixr control object
getValidNlmixrCtl.qrpem	Get valid nlmixr control object
getValidNlmixrCtl.rxSolve	Get valid nlmixr control object
getValidNlmixrCtl.saem	Get valid nlmixr control object
getValidNlmixrCtl.sann	Get valid nlmixr control object
getValidNlmixrCtl.simulate	Get valid nlmixr control object
getValidNlmixrCtl.simulation	Get valid nlmixr control object
getValidNlmixrCtl.tableControl	Get valid nlmixr control object
getValidNlmixrCtl.uobyqa	Get valid nlmixr control object
getValidNlmixrCtl.vae	Get valid nlmixr control object

-- I --

iagqControl	Control options for the iagq estimation method
iBoxCox	Cox Box, Yeo Johnson and inverse transformation
ifoceControl	Control options for the ifoce estimation method
ifoceiControl	Control options for the ifocei estimation method
ifocepControl	Control options for the ifocep (IRLS FOCE+) estimation method
ilaplaceControl	Control options for the ilaplace estimation method
impControl	Control for the imp (importance-sampling EM without MAP search) method
impmapControl	Control options for the impmap (importance-sampling EM) estimation method
iterPrintControl	Control iteration-time print formatting
iYeoJohnson	Cox Box, Yeo Johnson and inverse transformation

-- L --

laplaceControl	Control options for the Laplace estimation method
lbfgsb3cControl	Control for lbfgsb3c estimation method in nlmixr2

-- M --

magqControl	Control options for the magq estimation method
mfoceControl	Control options for the mfoce estimation method
mfoceiControl	Control options for the mfocei estimation method
mfocepControl	Control options for the mfocep (mu-referenced FOCE+) estimation method
mlaplaceControl	Control options for the mlaplace estimation method

-- N --

n1qn1Control	Control for n1qn1 estimation method in nlmixr2
newuoaControl	Control for newuoa estimation method in nlmixr2
nlmControl	nlmixr2 defaults controls for nlm
nlmeControl	Control Values for nlme Fit with extra options for nlmixr
nlminbControl	nlmixr2 nlminb defaults
nlmixr	nlmixr2 fits population PK and PKPD non-linear mixed effects models.
nlmixr2	nlmixr2 fits population PK and PKPD non-linear mixed effects models.
nlmixr2.function	nlmixr2 fits population PK and PKPD non-linear mixed effects models.
nlmixr2.nlmixr2FitCore	nlmixr2 fits population PK and PKPD non-linear mixed effects models.
nlmixr2.nlmixr2FitCoreSilent	nlmixr2 fits population PK and PKPD non-linear mixed effects models.
nlmixr2.nlmixr2FitData	nlmixr2 fits population PK and PKPD non-linear mixed effects models.
nlmixr2.rxUi	nlmixr2 fits population PK and PKPD non-linear mixed effects models.
nlmixr2AllEst	Show all the current estimation methods
nlmixr2AllEstType	Tagged list of the available nlmixr2 estimation methods
nlmixr2AugPredSolve	Augmented Prediction for nlmixr2 fit
nlmixr2CreateOutputFromUi	Create nlmixr output from the UI
nlmixr2Est	Generic for nlmixr2 estimation methods
nlmixr2Est.agq	Generic for nlmixr2 estimation methods
nlmixr2Est.agqf	Generic for nlmixr2 estimation methods
nlmixr2Est.bfgs	Generic for nlmixr2 estimation methods
nlmixr2Est.bobyqa	Generic for nlmixr2 estimation methods
nlmixr2Est.brent	Generic for nlmixr2 estimation methods
nlmixr2Est.cg	Generic for nlmixr2 estimation methods
nlmixr2Est.default	Generic for nlmixr2 estimation methods
nlmixr2Est.emvi	Generic for nlmixr2 estimation methods
nlmixr2Est.fbvi	Generic for nlmixr2 estimation methods
nlmixr2Est.fo	Generic for nlmixr2 estimation methods
nlmixr2Est.foce	Generic for nlmixr2 estimation methods
nlmixr2Est.focef	Generic for nlmixr2 estimation methods
nlmixr2Est.focei	Generic for nlmixr2 estimation methods
nlmixr2Est.foceif	Generic for nlmixr2 estimation methods
nlmixr2Est.focep	Generic for nlmixr2 estimation methods
nlmixr2Est.focepf	Generic for nlmixr2 estimation methods
nlmixr2Est.foi	Generic for nlmixr2 estimation methods
nlmixr2Est.iagq	Generic for nlmixr2 estimation methods
nlmixr2Est.iagqf	Generic for nlmixr2 estimation methods
nlmixr2Est.ifoce	Generic for nlmixr2 estimation methods
nlmixr2Est.ifocef	Generic for nlmixr2 estimation methods
nlmixr2Est.ifocei	Generic for nlmixr2 estimation methods
nlmixr2Est.ifoceif	Generic for nlmixr2 estimation methods
nlmixr2Est.ifocep	Generic for nlmixr2 estimation methods
nlmixr2Est.ifocepf	Generic for nlmixr2 estimation methods
nlmixr2Est.ilaplace	Generic for nlmixr2 estimation methods
nlmixr2Est.imp	Generic for nlmixr2 estimation methods
nlmixr2Est.impmap	Generic for nlmixr2 estimation methods
nlmixr2Est.inpag	Generic for nlmixr2 estimation methods
nlmixr2Est.inpb	Generic for nlmixr2 estimation methods
nlmixr2Est.laplace	Generic for nlmixr2 estimation methods
nlmixr2Est.lbfgsb	Generic for nlmixr2 estimation methods
nlmixr2Est.lbfgsb3c	Generic for nlmixr2 estimation methods
nlmixr2Est.magq	Generic for nlmixr2 estimation methods
nlmixr2Est.magqf	Generic for nlmixr2 estimation methods
nlmixr2Est.mfoce	Generic for nlmixr2 estimation methods
nlmixr2Est.mfocef	Generic for nlmixr2 estimation methods
nlmixr2Est.mfocei	Generic for nlmixr2 estimation methods
nlmixr2Est.mfoceif	Generic for nlmixr2 estimation methods
nlmixr2Est.mfocep	Generic for nlmixr2 estimation methods
nlmixr2Est.mfocepf	Generic for nlmixr2 estimation methods
nlmixr2Est.mlaplace	Generic for nlmixr2 estimation methods
nlmixr2Est.mnpag	Generic for nlmixr2 estimation methods
nlmixr2Est.mnpb	Generic for nlmixr2 estimation methods
nlmixr2Est.n1qn1	Generic for nlmixr2 estimation methods
nlmixr2Est.neldermead	Generic for nlmixr2 estimation methods
nlmixr2Est.newuoa	Generic for nlmixr2 estimation methods
nlmixr2Est.nlm	Generic for nlmixr2 estimation methods
nlmixr2Est.nlme	Generic for nlmixr2 estimation methods
nlmixr2Est.nlminb	Generic for nlmixr2 estimation methods
nlmixr2Est.nls	Generic for nlmixr2 estimation methods
nlmixr2Est.npag	Generic for nlmixr2 estimation methods
nlmixr2Est.npb	Generic for nlmixr2 estimation methods
nlmixr2Est.optim	Generic for nlmixr2 estimation methods
nlmixr2Est.output	Generic for nlmixr2 estimation methods
nlmixr2Est.posthoc	Generic for nlmixr2 estimation methods
nlmixr2Est.predict	Generic for nlmixr2 estimation methods
nlmixr2Est.qrpem	Generic for nlmixr2 estimation methods
nlmixr2Est.rxSolve	Generic for nlmixr2 estimation methods
nlmixr2Est.saem	Generic for nlmixr2 estimation methods
nlmixr2Est.sann	Generic for nlmixr2 estimation methods
nlmixr2Est.simulate	Generic for nlmixr2 estimation methods
nlmixr2Est.simulation	Generic for nlmixr2 estimation methods
nlmixr2Est.uobyqa	Generic for nlmixr2 estimation methods
nlmixr2Est.vae	Generic for nlmixr2 estimation methods
nlmixr2fix	Try to fix a nlmixr2 fit
nlmixr2Gill83	Get the optimal forward difference interval by Gill83 method
nlmixr2Hess	Calculate Hessian
nlmixr2Keywords	A list and description of the fields in the nlmxir2 object
nlmixr2Logo	Messages the nlmixr2 logo...
nlmixr2NlmeControl	Control Values for nlme Fit with extra options for nlmixr
nlmixr2Validate	Validate nlmixr2
nlmixr2Version	Display nlmixr2's version
nlmixrAddObjectiveFunctionDataFrame	Add objective function data frame to the current objective function
nlmixrAddTiming	Manually add time to a nlmixr2 object
nlmixrCbind	nlmixrCbind
nlmixrClone	Clone nlmixr environment
nlmixrWithTiming	Time a part of a nlmixr operation and add to nlmixr object
nlsControl	nlmixr2 defaults controls for nls
nmNearPD	C++ implementation of Matrix's nearPD
nmObjGetControl	Get control object from fit
nmObjGetControl.agq	Get control object from fit
nmObjGetControl.bobyqa	Get control object from fit
nmObjGetControl.default	Get control object from fit
nmObjGetControl.emvi	Get control object from fit
nmObjGetControl.fbvi	Get control object from fit
nmObjGetControl.fo	Get control object from fit
nmObjGetControl.foce	Get control object from fit
nmObjGetControl.focei	Get control object from fit
nmObjGetControl.focep	Get control object from fit
nmObjGetControl.foi	Get control object from fit
nmObjGetControl.iagq	Get control object from fit
nmObjGetControl.ifoce	Get control object from fit
nmObjGetControl.ifocei	Get control object from fit
nmObjGetControl.ifocep	Get control object from fit
nmObjGetControl.ilaplace	Get control object from fit
nmObjGetControl.imp	Get control object from fit
nmObjGetControl.impmap	Get control object from fit
nmObjGetControl.inpag	Get control object from fit
nmObjGetControl.inpb	Get control object from fit
nmObjGetControl.laplace	Get control object from fit
nmObjGetControl.lbfgsb3c	Get control object from fit
nmObjGetControl.magq	Get control object from fit
nmObjGetControl.mfoce	Get control object from fit
nmObjGetControl.mfocei	Get control object from fit
nmObjGetControl.mfocep	Get control object from fit
nmObjGetControl.mlaplace	Get control object from fit
nmObjGetControl.mnpag	Get control object from fit
nmObjGetControl.mnpb	Get control object from fit
nmObjGetControl.n1qn1	Get control object from fit
nmObjGetControl.newuoa	Get control object from fit
nmObjGetControl.nlm	Get control object from fit
nmObjGetControl.nlme	Get control object from fit
nmObjGetControl.nlminb	Get control object from fit
nmObjGetControl.nls	Get control object from fit
nmObjGetControl.npag	Get control object from fit
nmObjGetControl.npb	Get control object from fit
nmObjGetControl.optim	Get control object from fit
nmObjGetControl.posthoc	Get control object from fit
nmObjGetControl.qrpem	Get control object from fit
nmObjGetControl.saem	Get control object from fit
nmObjGetControl.uobyqa	Get control object from fit
nmObjGetControl.vae	Get control object from fit
nmObjGetEstimationModel	Get the estimation model for a fit object depending on the object type
nmObjGetEstimationModel.default	Get the ipred model for a fit object depending on the object type
nmObjGetEstimationModel.saem	Get the ipred model for a fit object depending on the object type
nmObjGetFoceiControl	Method for getting focei compatible control object from nlmixr object
nmObjGetFoceiControl.agq	Method for getting focei compatible control object from nlmixr object
nmObjGetFoceiControl.default	Method for getting focei compatible control object from nlmixr object
nmObjGetFoceiControl.foce	Method for getting focei compatible control object from nlmixr object
nmObjGetFoceiControl.focep	Method for getting focei compatible control object from nlmixr object
nmObjGetFoceiControl.iagq	Method for getting focei compatible control object from nlmixr object
nmObjGetFoceiControl.ifoce	Method for getting focei compatible control object from nlmixr object
nmObjGetFoceiControl.ifocei	Method for getting focei compatible control object from nlmixr object
nmObjGetFoceiControl.ifocep	Method for getting focei compatible control object from nlmixr object
nmObjGetFoceiControl.ilaplace	Method for getting focei compatible control object from nlmixr object
nmObjGetFoceiControl.imp	Method for getting focei compatible control object from nlmixr object
nmObjGetFoceiControl.impmap	Method for getting focei compatible control object from nlmixr object
nmObjGetFoceiControl.inpag	Method for getting focei compatible control object from nlmixr object
nmObjGetFoceiControl.inpb	Method for getting focei compatible control object from nlmixr object
nmObjGetFoceiControl.laplace	Method for getting focei compatible control object from nlmixr object
nmObjGetFoceiControl.magq	Method for getting focei compatible control object from nlmixr object
nmObjGetFoceiControl.mfoce	Method for getting focei compatible control object from nlmixr object
nmObjGetFoceiControl.mfocei	Method for getting focei compatible control object from nlmixr object
nmObjGetFoceiControl.mfocep	Method for getting focei compatible control object from nlmixr object
nmObjGetFoceiControl.mlaplace	Method for getting focei compatible control object from nlmixr object
nmObjGetFoceiControl.mnpag	Method for getting focei compatible control object from nlmixr object
nmObjGetFoceiControl.mnpb	Method for getting focei compatible control object from nlmixr object
nmObjGetFoceiControl.nlme	Method for getting focei compatible control object from nlmixr object
nmObjGetFoceiControl.npag	Method for getting focei compatible control object from nlmixr object
nmObjGetFoceiControl.npb	Method for getting focei compatible control object from nlmixr object
nmObjGetFoceiControl.posthoc	Method for getting focei compatible control object from nlmixr object
nmObjGetFoceiControl.qrpem	Method for getting focei compatible control object from nlmixr object
nmObjGetFoceiControl.saem	Method for getting focei compatible control object from nlmixr object
nmObjGetIpredModel	Get the ipred model for a fit object depending on the object type
nmObjGetIpredModel.default	Get the ipred model for a fit object depending on the object type
nmObjGetIpredModel.saem	Get the ipred model for a fit object depending on the object type
nmObjGetPredOnly	Get the pred-only model for a fit depending on the object type
nmObjGetPredOnly.default	Get the pred-only model for a fit depending on the object type
nmObjGetPredOnly.saem	Get the pred-only model for a fit depending on the object type
nmObjHandleControlObject	Handle the control object
nmObjHandleControlObject.agqControl	Handle the control object
nmObjHandleControlObject.bobyqaControl	Handle the control object
nmObjHandleControlObject.default	Handle the control object
nmObjHandleControlObject.emviControl	Handle the control object
nmObjHandleControlObject.foceControl	Handle the control object
nmObjHandleControlObject.foceiControl	Handle the control object
nmObjHandleControlObject.focepControl	Handle the control object
nmObjHandleControlObject.foControl	Handle the control object
nmObjHandleControlObject.foiControl	Handle the control object
nmObjHandleControlObject.iagqControl	Handle the control object
nmObjHandleControlObject.ifoceControl	Handle the control object
nmObjHandleControlObject.ifoceiControl	Handle the control object
nmObjHandleControlObject.ifocepControl	Handle the control object
nmObjHandleControlObject.ilaplaceControl	Handle the control object
nmObjHandleControlObject.impmapControl	Handle the control object
nmObjHandleControlObject.laplaceControl	Handle the control object
nmObjHandleControlObject.lbfgsb3cControl	Handle the control object
nmObjHandleControlObject.magqControl	Handle the control object
nmObjHandleControlObject.mfoceControl	Handle the control object
nmObjHandleControlObject.mfoceiControl	Handle the control object
nmObjHandleControlObject.mfocepControl	Handle the control object
nmObjHandleControlObject.mlaplaceControl	Handle the control object
nmObjHandleControlObject.n1qn1Control	Handle the control object
nmObjHandleControlObject.newuoaControl	Handle the control object
nmObjHandleControlObject.nlmControl	Handle the control object
nmObjHandleControlObject.nlmeControl	Handle the control object
nmObjHandleControlObject.nlminbControl	Handle the control object
nmObjHandleControlObject.nlsControl	Handle the control object
nmObjHandleControlObject.optimControl	Handle the control object
nmObjHandleControlObject.posthocControl	Handle the control object
nmObjHandleControlObject.saemControl	Handle the control object
nmObjHandleControlObject.uobyqaControl	Handle the control object
nmObjHandleControlObject.vaeControl	Handle the control object
nmObjHandleModelObject	Handle Model Object
nmObjHandleModelObject.default	Handle Model Object
nmObjHandleModelObject.foceiModelList	Handle Model Object
nmObjHandleModelObject.saemModelList	Handle Model Object
nmObjUiSetCompressed	Set if the nlmixr2 object will return a compressed ui
nmsimplex	Nelder-Mead simplex search
nmTest	Validate nlmixr2
npagControl	Control for the npag (nonparametric adaptive grid) method
npbControl	Control for the npb (nonparametric Bayes) method

-- O --

ofv	Return the objective function
optimControl	nlmixr2 optim defaults

-- P --

posthocControl	Control options for the posthoc estimation method
predict.nlmixr2FitCore	Predict method for nlmixr2 fit core objects
print.saemFit	Print an SAEM model fit summary

-- Q --

qrpemControl

Control for the qrpem (quasi-random parametric EM) estimation method

-- R --

residuals.nlmixr2FitData	Extract residuals from the FOCEI fit
rmEta	Remove an eta from the model

-- S --

saemControl	Control Options for SAEM
setCov	Set the covariance type based on prior calculated covariances
setOfv	Set/get Objective function type for a nlmixr2 object
sqrtm	Return the square root of general square matrix A
summary.saemFit	Print an SAEM model fit summary

-- T --

tableControl

Output table/data.frame options

-- U --

uobyqaControl

Control for uobyqa estimation method in nlmixr2

-- V --

vaeControl	Control for vae (variational autoencoder) estimation method in nlmixr2
vaeCovariates	Covariates explored by the VAE covariate search
vpcSim	VPC simulation

-- Y --

yeoJohnson

Cox Box, Yeo Johnson and inverse transformation

-- misc --

.augPredIpredModel	Augment Prediction for Ipred Model
.nlmFamilyFitGeneric	Shared fit driver for the nlm-family estimation methods
.nlmixr0preProcessCovariatesPresent	Preprocess Covariates needed (or other data items)
.nlmixr0preProcessNpMuExpand	Preprocessing hook: mu-expand non-mu structural fixed-effect thetas for the nonparametric engines, before the rest of the pipeline builds on the ui. Doing it here (rather than mutating the ui mid-setup) keeps the injected pseudo-etas consistent through covariate/mu processing and model compilation. Off when control$muExpand is FALSE.
.nlmixrPreprocessLiteralFix	This literally fixes parameters in the model
.preProcessDataUi	Preprocess the zero omegas
.preProcessLinCmtOde	Translate a mixed 'linCmt()'/ODE model to all-ODEs
.preProcessVaeNonMuTheta	VAE preprocessing hook: inject etas for non-mu-referenced thetas per vaeControl(nonMuTheta=).
.preProcessZeroOmega	Preprocess the zero omegas
.preProcessZeroTheta	Nudge exactly-zero theta initial estimates off zero (FOCEi family)