emaxsim {clinDR}R Documentation

Simulate Emax maximum likelihood estimation

Description

Simulate dose response data and apply 4- or 3- parameter Emax MLE estimation. For binary data, the model is fit on the logit scale and then back-transformed. When MLE estimation fails, models with fewer parameters (including models linear in their parameters) are substituted. Summaries of estimation performance are returned for further analyses. An MCP-MOD test is also performed for each simulated data set.

Usage

emaxsim(
	nsim, 
	genObj, 
	modType=3,
	binary=FALSE,
	seed=12357,
	nproc = parallel::detectCores(),
	negEmax=FALSE,
	ed50contr=NULL,
	lambdacontr=NULL,
	testMods=NULL,
	idmax=length(doselev), 
	iparm=NA,
	ed50cutoff=2.5*max(doselev), 
	ed50lowcutoff=doselev[2]/1000,
	switchMod= TRUE,
	truncLambda=6,
	description="")

Arguments

nsim

Number of simulation replications

genObj

Object containing inputs and function to create simulated data sets. These objects are created by special constructor functions; the current choices are FixedMean and RandEmax.

modType

When modType=4, the fitting begins with the 4 parameter model. If estimation fails or modType=3, the 3-parameter estimation is applied. If it fails, a best-fitting model linear in its parameters is selected.

binary

When specified, the Emax model is fit on the logit scale, and then the results are back-transformed to proportions.

seed

Seed for random number generator used to create data.

nproc

The number of processors to use in parallel computation of the simulations, which are divided into equal-sized computational blocks. When nproc=1 a single local processor.

negEmax

When TRUE, the intended effect is assumed to be negative.

ed50contr

A vector of ED50 values for creating a global null test using the MCP-MOD package DoseFinding based on Emax model-based contrasts. The default is 3 contrasts: the mid-point between pbo and the lowest dose, the mid-point between the 2 highest doses, and the median of the dose levels. When there are <=4 doses including pbo, the median-based contrast is excluded.

lambdacontr

Hill parameters matched to the ed50contr. The default value is 1 for each contrast model.

testMods

The model object for a MCP-MOD test created by Mods from package DoseFinding. If specified, the other contrast inputs are ignored. The Mods call should use the unique sorted dose levels. The direction of the trend should be specificed in the call to Mods. The negEmax is stored for use by support functions, but it does not determine the direction of the effect when testMods is specified. The validity of testMods is not checked.

idmax

Index of the default dose group for comparison to placebo. Most analysis functions allow other dose groups to be specified. The default is the index of the highest dose.

iparm

Starting values for the Emax fit. If unspecified, starting values are computed. The order of the variables is (log(ED50),Emax,E0) or (log(ED50),lambda,Emax,E0). Note the transformation of ED50.

ed50cutoff

The upper limit for the ED50 parameter estimates.The default is large enough to ensure a near linear fit to the data from an Emax model.

ed50lowcutoff

Lower allowed limit for the ED50 estimates.

switchMod

If switchMod is TRUE, the algorithm substitutes a simpler model if (1) convergence is not achieved, (2) the information matrix is not positive definite at the converged values, (3) the ED50 estimates are outside the cutoff bounds. If switchMod is F, only conditions (1) or (2) cause a simpler model to be used.

truncLambda

When modType=4 and the converged estimate of the Hill parameter lambda exceeds truncLambda, the model fit is judged unstable and discarded. Set truncLambda=Inf for no truncation. Four parameter model fits are also discarded when lambda is less than 0.1.

description

Optional text describing the simulation setting that is stored with the simulation output.

Details

Continuous data can be simulated from any dose response curve with homogeneous normally distributed residuals. The estimation procedure starts with ML estimation of a 4- or 3- parameter Emax model depending on modType. If modType=3 or 4-parameter estimation fails, a 3 parameter Emax model is fit by maximum likelihood non-linear least squares. If 1) nls fails to converge for a 3 parameter Emax model, 2) the ED50 estimate is <=0, or 3) the ED50 estimate exceeds ed50cutoff, a linear, log-linear (offset of 1.0), or scaled exponental (exp(dose/max(dose))), is fit using simple linear least squares estimation. The model selected has the smallest residual SS.

Binary data are handled similarly using maximum likelihood implemented with the nlm function. The models are fit on the logit scale and then back-transformed for estimation of dose response. Reduced linear models are selected based on the corresponding likelihood deviance.

MCP-MOD tests are created from contrasts based on the Emax function using the DoseFinding package. Different ED50 and lambda (Hill) parameters can be specified to form the contrasts. A contrast matrix output from the DoseFinding package can be specified instead, allowing for other contrast choices.

Value

A list is returned with class(emaxsim) containing:

description

User description of simulation

binary

Binary response data.

modType

User supplied starting Emax model

genObj

List object with data and function used to generate study data

pop

Matrix with rows containing population parameters for each simulation. Type of parameter depends on constructor function generating study data.

popSD

Vector containing the population SD used to generate continuous data. NULL for binary data.

init

Matrix with rows containing the starting Emax parameters for each simulation

est4

Matrix with 4 parmameter Emax fit. NA if failed to converge or modType=3

est3

Matrix with 3 parmameter Emax fit. NA if failed to converge or 4-parameter estimation was successful.

estA

Matrix with alternative parameter estimates. NA if Emax model fit successfully

vc

Variance-covariance matrix for the estimated parameters stored as a vector for each simulation. The vc vector stored has 16,9, or 4 elements depending on fitType (with NA values on the end if elements are unused).

residSD

The residual SD based on the selected model.

fitType

Character vector with "4", "3", "L", "LL", or "E" for 4-Emax, 3-Emax, linear, log-linear, or exponential when an alternative model is selected.

pVal

The nsim p-values from the global null test. The p-values are 1-sided computed using MCP-Mod.

selContrast

The index of the test contrast producing the smallest p-value.

testMods

Object of class Mods from R package DoseFinding that defines the contrasts used in MCP-MOD testing. The functions can be plotted with DoseFinding loaded.

negEmax

User input stored for subsequent reference.

ed50cutoff

Upper allowed limit for ED50 estimates

ed50lowcutoff

Lower allowed limit for the ED50 estimates.

switchMod

If switchMod is TRUE, the algorithm substitutes a simpler model if (1) convergence is not achieved, (2) the information matrix is not positive definite at the converged values, (3) the ED50 estimates are outside the cutoff bounds. If switchMod is F, only conditions (1) or (2) cause a simpler model to be used.

negC

negC=TRUE if the primary fit (from modType) yielded a ED50 estimate < ED50 lower limit.

bigC

bigC=TRUE if the primary fit (from modType) yielded an ED50> ED50 upper limit.

predpop

Matrix with population means for each dose group

mv

Matrix with rows containing dose group sample means

sdv

Matrix with rows containing dose group sample SD

fitpredv

Matrix with rows containing dose groups means estimated from the model

sepredv

Matrix with rows containing SE for fitpredv

sedifv

Matrix with rows containing SE for model-based differences with placebo

rseed

Starting random number seed for each simulated data set set that can be assigned to .Random.seed. To reproduce the data, the random number generator must also be changed to RNGkind("L'Ecuyer-CMRG").

idmax

Index of default dose group for comparison to placebo (e.g., for plotting Z-statistics).

Author(s)

Neal Thomas

See Also

print.emaxsim, summary.emaxsim, plot.emaxsim, coef.emaxsim, sigma.emaxsim, vcov.emaxsim, predict.emaxsim, emaxfun

Examples


## Not run: 
## emaxsim changes the random number seed
nsim<-50
idmax<-5
doselev<-c(0,5,25,50,100)
n<-c(78,81,81,81,77)
Ndose<-length(doselev)

### population parameters for simulation
e0<-2.465375 
ed50<-67.481113 

dtarget<-100
diftarget<-2.464592
emax<-solveEmax(diftarget,dtarget,log(ed50),1,e0)

sdy<-7.967897
pop<-c(log(ed50),emax,e0)    
meanlev<-emaxfun(doselev,pop)  

###FixedMean is specialized constructor function for emaxsim
gen<-FixedMean(n,doselev,meanlev,sdy)  

D1 <- emaxsim(nsim,gen,modType=3)
summary(D1,testalph=0.05)

D4 <- emaxsim(nsim,gen,modType=4)
summary(D4,testalph=0.05)

## End(Not run)


[Package clinDR version 2.3.5 Index]