This command allows you to control how the posterior distribution is reported. For rate parameters, it allows you to choose among several popular parameterizations. The report command also allows you to request printing of some model aspects that are usually not reported. For instance, if a node is constrained in the analysis, MrBayes can print the probabilities of the ancestral states at that node. Similarly, if there is rate variation in the model, MrBayes can print the inferred site rates, and if there is omega variation, MrBayes can print the inferred omega (positive selection) values for each codon. In a complex model with several partitions, each partition is controlled separately using the same 'Applyto' mechanism as in the 'Lset' and 'Prset' commands.
Options:
Applyto -- This option allows you to apply the report commands to specific partitions. This command should be the first in the list of commands specified in 'report'.
For example,
report applyto=(1,2) tratio=ratio
report applyto=(3) tratio=dirichlet
would result in the transition and transversion rates of the first and second partitions in the model being reported as a ratio and the transition and transversion rates of the third partition being reported as proportions of the rate sum (the Dirichlet parameterization).
Tratio -- This specifies the report format for the transition and transversion rates of a nucleotide substituion model with nst=2. If 'ratio' is selected, the rates will be reported as a ratio (transition rate/transversion rate). If 'dirichlet' is selected, the transition and transversion rates will instead be reported as proportions of the rate sum. For example, if the transition rate is three times the transversion rate and 'ratio' is selected, this will reported as a single value, '3.0'. If 'dirichlet' is selected instead, the same rates will be reported using two values, '0.75 0.25'. The sum of the Dirichlet values is always 1. Although the Dirichlet format may be unfamiliar to some users, it is more convenient for specifying priors than the ratio format.
Revmat -- This specifies the report format for the substitution rates of a GTR substitution model for nucleutide or amino acid data. If 'ratio' is selected, the rates will be reported scaled to the G-T rate (for nucleotides) or the Y-V rate (for amino acids). If 'dirichlet' is specified instead, the rates are reported as proportions of the rate sum. For instance, assume that the C-T rate is twice the A-G rate and four times the transversion rates, which are equal. If the report format is set to 'ratio', this would be reported as '1.0 2.0 1.0 1.0 4.0 1.0' since the rates are reported in the order rAC, rAG, rAT, rCG, rCT, rGT and scaled relative to the last rate, the G-T rate. If 'dirichlet' is selected instead, the same rates would have been reported as '0.1 0.2 0.1 0.1 0.4 0.1' since the rates are now scaled so that they sum to 1.0. The Dirichlet format is the parameterization used to format used for formulating priors on the rates.
Ratemult -- This specifies the report format used for the rate multiplier of different model partitions. Three formats are available. If 'scaled' is selected, then rates are scaled such that the mean rate per site across partitions is 1.0. If 'ratio' is chosen, the rates are scaled relative to the rate of the first partition. Finally, if 'dirichlet' is chosen, the rates are given as proportions of the rate sum. The latter is the format used when formulating priors on the rate multiplier.
Ancstates -- If this option is set to 'yes', MrBayes will print the probability of the ancestral states at all constrained nodes. Typically, you are interested in the ancestral states of only a few characters and only at one node in the tree. To perform such an analysis, first define and enforce a topology constraint using 'constraint' and 'prset topologypr = constraints (...)'. Then put the character(s) of interest in a separate partition and set MrBayes to report the ancestral states for that partition. For instance, if the characters of interest are in partition 2, use 'report applyto=(2) ancstates=yes' to force MrBayes to print the probability of the ancestral states of those characters at the constrained node to the '.p' file.
Siterates -- If this option is set to 'yes' and the relevant model has rate variation across sites, the mean site rate in the posterior will be reported for each site to the '.p' file.
Possel -- If this option is set to 'yes' and the relevant model has omega variation across sites, the mean omega value for each model site (codon in this case) will be written to the '.p' file.
Current settings:
Parameter Options Current Setting -------------------------------------------------------- Tratio Ratio/Dir Ratio Revmat Ratio/Dir Dirichlet Ratemult Scaled/Ratio/Dir Scaled Ancstates Yes/No No Siterates Yes/No No Possel Yes/No No --------------------------------------------------------