- model
the distribution to fit to the data. Choices are: 'IP', 'P', 'ZIP', 'G', 'ZIG', 'L', 'ZIL', 'W', 'ZIW', 'GP', 'ZIGP', 'LP', 'ZILP', 'WP', 'ZIWP' (case insensitive). No default.
- data
a vector of data to fit the distribution to. Count data for the count models, continuous data for the continuous distributions.
- mean
a vector of mean values over which to calculate the likelihood. Must be a matrix with number of columns equal to the number of datapoints for the IP model only, since using the IP model each datapoint has an independant mean (this is effectively a shortcut for repeating the likelihood function for each datapoint). Mean is required for the IP, (ZI)P, (ZI)L, and (ZI)L models. Otherwise ignored (with a warning if silent=FALSE).
- variance
a vector of values for variance over which to calculate the likelihood, with length equal to length of mean. Required for the (ZI)L, and (ZI)L models. Otherwise ignored (with a warning if silent=FALSE).
- zi
a vector of values for zero-inflation, with length equal to either scale/shape or mean/variance as appropriate. Required for zero-inflated models only; if supplied for other models the appropriate zero-inflated model will be used instead (with a warning if silent=FALSE).
- shape
a vector of values for the shape parameter. Must be of length equal to that of the scale parameter. Required for the (ZI)W, (ZI)WP, (ZI)G, and (ZI)GP models. Otherwise ignored (with a warning if silent=FALSE).
- scale
a vector of values for the scale parameter. Must be of length equal to that of the shape parameter. Required for the (ZI)W, (ZI)WP, (ZI)G, and (ZI)GP models. Otherwise ignored (with a warning if silent=FALSE).
- iterations
the total number of iterative samples for which to calculate the likelihood. If this is smaller than the number of iterations provided for mean/variance/shape/scale, then the chain will be thinned to the number of iterations required (this is useful for the mixture models where integrating the likelihood for each datapoint may take some time). Default is 1000 iterations, or the length of the parameters supplied if this is shorter than 1000.
- log
choose to output the log likelihood (TRUE) or the likelihood (FALSE). Default TRUE.
- silent
should warning messages and progress indicators be supressed? Default FALSE.
- raw.output
output a vector of length equal to the number of iterations representing the likelihood at each iteration if TRUE, or a summary of the results (median and 95 percent confidence interval) if FALSE. Default FALSE.