In my previous post on this topic, I discussed two techniques for finding the combination of mixture distribution parameters that have the lowest log likelihood, direct search and the mixdist package for R. I suggested that direct search of the parameter space allowed the effects of outliers in my data to be identified more clearly. I have done additional work since that time, comparing direct search and the mixdist package. As a result of this work, I have concluded that direct search is much more effective at finding the optimal combination of parameter values.

Mixdist returned parameter values that consistently produced higher log likelihoods than I found using direct search. The differences were substantial. I can not fully explain the observed differences, but the differences were also consistent among all of my data sets.

Direct search of the parameter space is obviously not the most convenient approach. My model involved only two lognormal distributions with a total of five parameters. Direct search of the optimal parameters for more complex mixture models may not be feasible, as the number of parameter value combinations that need to be searched is too large. For simple mixture models, however, the direct search may be preferable.

The following code is the very simple program that I wrote for R to find the lowest log likelihood and corresponding parameter values. The program was written specifically for a mixture model of two lognormal distributions. The parameter value search space included the range of likely values of log mean of fish vertebra height and the log standard deviation of fish vertebrae height in both of the two distributions. I am not a professional programmer, as you will see, so any suggestions for improving and extending the code will be greatly appreciated.

#vcdata is a list of the data for which the parameter estimates and likelihood will be calculated

vcdata<-c(…your data here…)

#pvec provides the sequence of values for the proportion of vertebrae in the mode of smaller (net-caught) fish over which the program loops.

pvec=seq(0.10, 0.99, by=0.015)

#mean1vec provides the sequence of values for the log mean of vertebra height in the mode of smaller (net-caught) fish over which the program loops.

mean1vec = seq(0.80, 1.20, by = 0.03)

#sd1vec provides the sequence of values for the log standard deviation of vertebra height in the mode of smaller (net-caught) fish over which the program loops.

sd1vec=seq(0.02, 0.44, by=0.03)

#mean2vec provides the sequence of values for the log mean of vertebra height in the mode of larger (hook- or spear-caught) fish over which the program loops.

mean2vec=seq(1.25, 1.70, by=0.03)

#sd2vec provides the sequence of values for the log standard deviation of vertebra height in the mode of larger (hook- or spear-caught) fish over which the program loops.

sd2vec=seq(0.02, 0.44, by=0.03)

#loglike is the negative log likelihood, which is calculated for each combination of parameter values.

loglike=100000

#p stores the parameter value for the proportion of vertebrae in the mode of smaller (net-caught) fish.

p=0

#mean1 stores the parameter value for the log mean of vertebra height in the mode of smaller (net-caught) fish.

mean1=0

#sd1 stores the parameter value for the log standard deviation of vertebra height in the mode of smaller (net-caught) fish.

sd1=0

#mean2 stores the parameter value for the log mean of vertebra height in the mode of larger (hook- or spear-caught) fish.

mean2=0

#sd2 stores the parameter value for the log standard deviation of vertebra height in the mode of larger (hook- or spear-caught) fish.

sd2=0

#the result data frame returns the value of the log likelihood at a particular combination of parameter values

result<-data.frame(loglike, p, mean1, sd1, mean2, sd2)

#the finalresult data frame stores the log likelihood and parameter values for the combination of parameter values that returns a log likelihood that is smaller than all other log likelihoods generated.

#looping over the combination of parameter values

finalresult<-data.frame(loglike, p, mean1, sd1, mean2, sd2)

for (j in 1:length(mean1vec)) {

for (k in 1:length(pvec)) {

for (m in 1:length(sd1vec)) {

for (n in 1:length(mean2vec)){

for (q in 1:length(sd2vec)){

#the following function returns the negative log likelihood value at a particular combination of parameter values

L= -sum(log(pvec[k]*(dlnorm(vcdata, meanlog=mean1vec[j], sdlog=sd1vec[m]))+(1-pvec[k])*(dlnorm(vcdata, meanlog=mean2vec[n], sdlog=sd2vec[q]))))

result$loglike=L

result$p=pvec[k]

result$mean1=mean1vec[j]

result$sd1=sd1vec[m]

result$mean2=mean2vec[n]

result$sd2=sd2vec[q]

#the following comparison stores the lowest log likelihood and the corresponding combination of parameter values seen up to this point

if (L<finalresult$loglike) finalresult=result

}

}

}

}

}

finalresult

When I employed the direct search, I ran it twice for each data set. The first time, I looped over a wider range of parameter values. The sequence of parameter values searched within each variable was spaced sufficiently far apart so the direct search would not bog down. The one exception was the proportion of fish vertebrae in each mode. For this variable, the step-size between the values of proportion for which I calculated the log likelihood was fairly small from the start. Experience with my data sets showed that this variable had the biggest effect on the log likelihood.

The second time that I ran the direct search for each data set, I focused on a narrower range of parameter values. The range of parameter values that I searched centered around the values found in the initial run. The sequence of values searched within each variable was spaced closer together in the second run.

Additional code, of course, needs to be written in order to determine the standard errors of the parameter estimates.

© Scott Pletka and *Mathematical Tools, Archaeological Problems*, 2009.

Tags: archaeology, mathematical modeling in archaeology, maximum likelihood, mixture models, statistics in archaeology

## Leave a Reply