During a MCMC analysis, MrBayes prints the sampled parameter values to a tab-delimited text file. This file has the extension ".p". The command 'Sump' summarizes the information in the parameter file. By default, the name of the parameter file is assumed to be the name of the last matrix-containing nexus file, but with a '.p' extension. You can set 'Sump' to summarize the information in any other parameter file by setting the 'filename' option to the appropriate file name. The 'Sump' command does not require a matrix to be read in first. When you invoke the 'Sump' command, three items are output: (1) a generation plot of the likelihood values; (2) estimates of the marginal likelihood of the model; and (3) a table with the mean, variance, and 95 percent credible interval for the sampled parameters. Each of these items can be switched on or off using the options 'Plot', 'Marglike', and 'Table'. By default, all three items are output but only to the screen. If output to a file is also desired, set 'Printtofile' to 'Yes'. The name of the output file is specified by setting the 'Outputname' option. When a new matrix is read in or when the 'Mcmc' output filename or 'Sump' input filename is changed, the 'Sump' outputname is changed as well. If you want to output to another file than the default, make sure you specify the outputname every time you invoke 'Sump'. If the specified outputfile already exists, you will be prompted about whether you like to overwrite it or append to it. This behavior can be altered using 'Set nowarn=yes'; see the help for the 'Set' command. When running 'Sump' you typically want to discard a specified number of samples from the beginning of the chain as the burnin. Note that the 'Burnin' value of the 'Sump' command is set separately from the 'Burnin' values of the 'Sumt' and 'Mcmc' commands. That is, if you issue
sump burnin = 4000
sumt burnin = 2000
sump
the burnin of the last 'Sump' command is 4000 and not 2000. The burnin values are reset to 0 every time a new matrix is read in. Similarly, 'Plot', 'Marglike' and 'Table' are all set to 'Yes' and 'Printtofile' to 'No' (the default values) when a new matrix is processed. If you have run several independent MCMC analyses, you may want to summarize and compare the samples from each of these runs. To do this, set 'Nruns' to the number of runs you want to compare and make sure that the '.p' files are named using the MrBayes convention (<filename>.run1.p, <filename>.run2.p, etc). When you run several independent analyses simultaneously in MrBayes, the 'Nruns' and 'Filename' options are automatically set such that 'Sump' will summarize all the resulting output files.
Options:
Burnin -- Determines the number of samples that will be discarded from the input file before calculating summary statistics. If there are several input files, the same number of samples will be discarded from each. Note that the burnin is set separately for the 'sump', 'sumt', and 'mcmc' commands.
Nruns -- Determines how many '.p' files from independent analyses that will be summarized. If Nruns > 1 then the names of the files are derived from 'Filename' by adding '.run1.p', '.run2.p', etc. If Nruns=1, then the single filename is obtained by adding '.p' to the 'Filename'.
Filename -- The name of the file to be summarized. This is the base of the file name to which endings are added according to the current setting of the 'Nruns' parameter. If 'Nruns' is 1, then only '.p' is added to the file name. Otherwise, the endings will be '.run1.p', '.run2.p', etc.
Printtofile -- Determines whether results will be printed to file.
Outputname -- Name of the file to which 'sump' results will be printed if 'Printtofile' is set to YES.
Plot -- Determines whether a likelihood plot should be output.
Marglike -- Determines whether estimates of marginal model likelihoods should be calculated. The marginal model likelihoods are useful in Bayesian model testing.
Table -- Determines whether the table summarizing the parameter value samples should be output.
Current settings:
Parameter Options Current Setting -------------------------------------------------------- Burnin <number> 0 Nruns <number> 1 Filename <name> temp.p<.p> Filename <name> temp.p<.run<i>.p> Printtofile Yes/No No Outputname <name> temp.p.stat Plot Yes/No Yes Marglike Yes/No Yes Table Yes/No Yes --------------------------------------------------------