Logistic Regression

gistfile1.r

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# Calculates the maximum likelihood estimates of a logistic regression model
#
# fmla : model formula
# x : a [n x p] dataframe with the data. Factors should be coded accordingly
#
# OUTPUT
# beta : the estimated regression coefficients
# vcov : the variane-covariance matrix
# ll : -2ln L (deviance)
#
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# Author : Thomas Debray
# Version : 22 dec 2011
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mle.logreg = function(fmla, data)
{
    # Define the negative log likelihood function
    logl <- function(theta,x,y){
      y <- y
      x <- as.matrix(x)
      beta <- theta[1:ncol(x)]

      # Use the log-likelihood of the Bernouilli distribution, where p is
      # defined as the logistic transformation of a linear combination
      # of predictors, according to logit(p)=(x%*%beta)
      loglik <- sum(-y*log(1 + exp(-(x%*%beta))) - (1-y)*log(1 + exp(x%*%beta)))
      return(-loglik)
    }

    # Prepare the data
    outcome = rownames(attr(terms(fmla),"factors"))[1]
    dfrTmp = model.frame(data)
    x = as.matrix(model.matrix(fmla, data=dfrTmp))
    y = as.matrix(data[,match(outcome,colnames(data))])

    # Define initial values for the parameters
    theta.start = rep(0,(dim(x)[2]))
    names(theta.start) = colnames(x)

    # Calculate the maximum likelihood
    mle = optim(theta.start,logl,x=x,y=y,hessian=F)

    # Obtain regression coefficients
    beta = mle$par
 
    # Calculate the Information matrix
    # The variance of a Bernouilli distribution is given by p(1-p)
    p = 1/(1+exp(-x%*%beta))
    V = array(0,dim=c(dim(x)[1],dim(x)[1]))
    diag(V) = p*(1-p) 
    IB = t(x)%*%V%*%x 
 
    # Return estimates
    out = list(beta=beta,vcov=solve(IB),dev=2*mle$value)
}
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