saemix (version 0.96.1)

cow.saemix: Evolution of the weight of 560 cows, in SAEM format

Description

cow.saemix contains data from winter wheat experiments.

Usage

cow.saemix

Details

The data used in this example is the evolution of the weight (in kg) of 560 cows. We have 9 or 10 measurements per subject.

We use an exponential growth model for this data: y_ij = A_i (1- B_i exp( - K_i t_ij)) +epsilon_ij

Examples

data(cow.saemix)
saemix.data<-saemixData(name.data=cow.saemix,header=TRUE,name.group=c("cow"), 
  name.predictors=c("time"),name.response=c("weight"), 
  name.covariates=c("birthyear","twin","birthrank"), 
  units=list(x="days",y="kg",covariates=c("yr","-","-")))

growthcow<-function(psi,id,xidep) {
# input:
#   psi : matrix of parameters (3 columns, a, b, k)
#   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
  x<-xidep[,1]
  a<-psi[id,1]
  b<-psi[id,2]
  k<-psi[id,3]
  f<-a*(1-b*exp(-k*x))
  return(f)
}
saemix.model<-saemixModel(model=growthcow,
  description="Exponential growth model", 
  psi0=matrix(c(700,0.9,0.02,0,0,0),ncol=3,byrow=TRUE, 
  dimnames=list(NULL,c("A","B","k"))),transform.par=c(1,1,1),fixed.estim=c(1,1,1), 
  covariate.model=matrix(c(0,0,0),ncol=3,byrow=TRUE), 
  covariance.model=matrix(c(1,0,0,0,1,0,0,0,1),ncol=3,byrow=TRUE), 
  omega.init=matrix(c(1,0,0,0,1,0,0,0,1),ncol=3,byrow=TRUE),error.model="constant")

saemix.options<-list(algorithms=c(1,1,1),nb.chains=1,nbiter.saemix=c(200,100), 
  seed=4526,save=FALSE,save.graphs=FALSE)

# Plotting the data
plot(saemix.data,xlab="Time (day)",ylab="Weight of the cow (kg)")

saemix.fit<-saemix(saemix.model,saemix.data,saemix.options)