PD1.saemix: Data simulated according to an Emax response model, in SAEM...

In saemixdevelopment/saemix: Stochastic Approximation Expectation Maximization (SAEM) Algorithm

Description

PD1.saemix contains data from winter wheat experiments.

Usage

PD1.saemix

PD2.saemix

Format

This data frame contains the following columns:

subject:

the site number

dose:

simulated dose.

response:

simulated response.

gender:

gender (0 for male, 1 for female).

Details

These examples were used by P. Girard and F. Mentre for the symposium dedicated to Comparison of Algorithms Using Simulated Data Sets and Blind Analysis, that took place in Lyon, France, September 2004.

The dataset contains 100 individuals, each receiving 3 different doses:(0, 10, 90), (5, 25, 65) or (0, 20, 30). It was assumed that doses were given in a cross-over study with sufficient wash out period to avoid carry over. Responses (y_ij) were simulated with the following pharmacodynamic model:

y_ij = E0_i + D_ij Emax_i/(D_ij + ED50_i) +epsilon_ij

The individual parameters were simulated according to

log (E0_i) = log (E0) + eta_i1 log (Emax_i) = log (Emax) + eta_i2 log (E50_i) = log (E50) + beta w_i + eta_i3

PD1.saemix contains the data simulated with a gender effect, beta=0.3.

PD2.saemix contains the data simulated without a gender effect, beta=0.

Source

Girard P., Mentre F. Comparison of Algorithms Using Simulated Data Sets and Blind Analysis workshop, Lyon, France, September 2004.

Examples

 

data(PD1.saemix)
saemix.data<-saemixData(name.data=PD1.saemix,header=TRUE,name.group=c("subject"),
  name.predictors=c("dose"),name.response=c("response"),
  name.covariates=c("gender"), units=list(x="mg",y="-",covariates=c("-")))

modelemax<-function(psi,id,xidep) {
# input:
#   psi : matrix of parameters (3 columns, E0, Emax, EC50)
#   id : vector of indices 
#   xidep : dependent variables (same nb of rows as length of id)
# returns:
#   a vector of predictions of length equal to length of id
  dose<-xidep[,1]
  e0<-psi[id,1]
  emax<-psi[id,2]
  e50<-psi[id,3]
  f<-e0+emax*dose/(e50+dose)
  return(f)
}

# Plotting the data
plot(saemix.data,main="Simulated data PD1")

# Not run (strict time constraints for CRAN)

# Compare models with and without covariates with LL by Importance Sampling
# SE not computed
model1<-saemixModel(model=modelemax,description="Emax growth model", 
  psi0=matrix(c(20,300,20,0,0,0),ncol=3,byrow=TRUE,dimnames=list(NULL,
  c("E0","Emax","EC50"))), transform.par=c(1,1,1),
  covariate.model=matrix(c(0,0,0), ncol=3,byrow=TRUE),fixed.estim=c(1,1,1))

model2<-saemixModel(model=modelemax,description="Emax growth model", 
  psi0=matrix(c(20,300,20,0,0,0),ncol=3,byrow=TRUE,dimnames=list(NULL, 
  c("E0","Emax","EC50"))), transform.par=c(1,1,1),
  covariate.model=matrix(c(0,0,1), ncol=3,byrow=TRUE),fixed.estim=c(1,1,1))

saemix.options<-list(algorithms=c(0,1,1),nb.chains=3,seed=765754, 
  nbiter.saemix=c(500,300),save=FALSE,save.graphs=FALSE)

# Not run (strict time constraints for CRAN)
# fit1<-saemix(model1,saemix.data,saemix.options)
# fit2<-saemix(model2,saemix.data,saemix.options)
# wstat<-(-2)*(fit1["results"]["ll.is"]-fit2["results"]["ll.is"])

# cat("LRT test for covariate effect on EC50: p-value=",1-pchisq(wstat,1),"\n")

saemixdevelopment/saemix documentation built on May 27, 2020, 1:56 p.m.