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MLE Estimation of Gamma Distribution Parameters for data with 'zeros'

Not necessarily homework, Bert. There's a generic issue with MLE and rounded data, in that gamma densities may be 0 at the boundary but small numbers are represented as 0, making the log-likelihood -Inf. 

The cleanest way out is to switch to a discretized distribution in the likelihood, so that instead of log(dgamma(0,...)) you use log(pgamma(.005,..) - pgamma(0,...)) == pgamma(.005,..., log=TRUE). (For data rounded to nearest .01, that is). Cruder techniques would be to just add, like, .0025 to all the zeros. 

-pd