NAME

       mcmc_analysis - Analysis of the MCMC

SYNOPSIS

       mcmc_analysis [OPTIONS] MCMC-data ...

DESCRIPTION

       This  program  reads  MCMC  output,  from  one or several files, from programs in the BEEP package. It is
       important that the same columns are present in each input file.

       Input format:
         Output from MCMC iterations on the format
               <likelihood> <tab> <iter> <tab> <params>
            where
               <likelihood> is the logarithm of the likelihood in float format
               <tab>        is tab whitespace separating the fields
               <iter>       is an integer for the ordinal of the iteration
               <params>     is a list of fields separated by semicolons containing
                            the parameters of the MCMC.

            The MCMC params are typed and given names by the first line in the file,
            which is on the format
               # L <tab> N <tab> [<name>(<type>)]+
            The names ought to be unique, but do not have to be. The <type> is one
            of
               float
               logfloat
               integer
               tree
               orthologypairs
            and used to infer how to parse and analyze the rest of the lines.

       Output format:
         A report on the MCMC run, with posterior estimates of the parameters.

OPTIONS

       -b [FLOAT|INT]
              The percentage (0 <= x <1), or the number of (x is integer >= 1) of the input to be  discarded  as
              burnin. Default: 0.1.

       -p STRING
              Plot the parameter named <string>. Output is two columns, the iteration number and the parameter's
              value in the iteration.

       -i STRING
              Ignore the named parameter. See header line in MCMC output for column names. You can name  several
              columns  at  once using a comma-delimited format, (e.g. -i Length,Name). No spaces allowed between
              column names.

       -t     Output LaTex for the analysis.

       -l     Count and report the number of samples in the input file.

       -mp NT The maximum number of points to plot.

       -sp    Explicitly indicate points in plots.

       -coda  Output file for the CODA package in R

       -codatrees
              Same as -coda, but includes tree parameters. Each tree is  output  as  an  integer  ID  (order  of
              visitation   in   chain,   1,2,...).   Make   sure   to  use  -i  to  hide  any  trees  containing
              lengths/times/rates.

       -P     Parallel chains. This implies that several files of (parallel) samples are listed.

URL

       The prime-phylo home page: http://prime.sbc.su.se

SEE ALSO

       primeDTLSR(1),  primeGSRf(1),  primeGEM(1),  chainsaw(1),  reconcile(1),  reroot(1),   tree2leafnames(1),
       treesize(1)