SIMMAP | morphology stats

Morphology Statistics

Statistics summarizing character histories are reported/saved as the posterior expectation (summary values) or saved to file(s) as individual values. SIMMAP collects summary statistics (e.g., number of changes from 0=>1) for each sampled character history when simulating multiple histories using the Simulate Histories option under the Analysis main menu item. Values are not saved when simulating a single history using the Simulate History option although a running history of the number of changes are stored to be viewed when displaying the trees in the Tree View window. The statistics used for detecting character correlation are dealt with elsewhere in the help documents (see here). The rest of this document is split into two sections: Summary and Individual statistics. Each section describes how to view the results from a morphological analysis within SIMMAP and how to save values to a file(s). Setting up and running a character correlation analysis is dealt with in the help documents on correlated characterss.

IMPORTANT NOTE: Summary values are continuously collected from one experiment to the next so beware that the results are those stored since last cleared from memory. Clear the memory from one run to the next unless it is desired that they are averaged over runs. THIS MAYBE USEFUL when analyzing morphological characters if you wish to report the expectation over a number of prior parameter values.

Summary Values

A morphological character history can be performed for an individual character or the correlation among characters. (For information on performing the analysis using ordered character states see here.) Once an analysis is complete summary statistics can be viewed by selecting the Morphology

Morphology Statistics... option in the Statistics main menu item. This opens the window shown on the right which is displaying the results from the analysis of a two-state character. Each character is displayed by its position in the data file. If character histories have been summarized for a character then a triangle,

, is shown preceding the character (displayed as the site number). Selecting the triangle will turn it down and display the summary data.

The following statistics are collected for morphological data:

Sample size

Bias parameter

Rate parameter

Homoplasy Index

Not implemented - NA

Transformations

State

Dwell times

State

Saving Summary Values

Summary values can be saved in three different ways: (1) Using options in Statistics main menu item; (2) Using options available under the Miscellaneous tab in the Simulate Histories window; and (3) Selecting the Save As button in the Summary statistics windows (see above). Each of these is described briefly. Options 1 and 2 differ from Option 3 by occuring during the analysis. Selecting the former options does not slow down the analysis in any considerable way. Information on the format and data saved is described in the help documents on output files.

To save the results using Option 1 select the Set File to Save History Statistics to... option in Statistics the main menu item. This opens a window allowing you to define the file name and location to save the summary values to. This file is automatically append too until it is redefined. The Save Individual/Summary Histories To... window allows you to activate, or deactivate, saving summary statistics. The default is to NOT save the data. To activate the saving select the appropriate values in the Save Individual/Summary Histories To... window. These options can also be turned on and off in the Simulate Histories window under the Miscellaneous tab.

To save the results using Option 2 open the Simulate Histories window [M] and select Miscellaneous tab. Once selected, select the Set button under the Statistics (both are saved to the same file): heading. As described above, this opens the Save Individual/Summary Histories To... window. Select the file, location, and options as previously described.

Finally, Option 3, is a post-analysis approach. You can select to save the values displayed in the Morphology Stats window shown above. To save the summary values simply select the Save As button in the window. This prompts you to select a name and location for the file.

Individual Values

The following is a table describing the individual statistics saved. Activating these options for morphological data analysis is described below.

Data saved	Availability by analysis
Posterior expectations	All analysis types (see summary values above for a description)
Tree histories (raw data)	All analysis types (see the saving raw data help docs)
Predictive null values	Character correlation

Saving Individual and Other Data

To activate saving different individual statistics one of the options (shown as red numbers in the image to the right) need to be activated by selecting the desired check box. Simply activating a switch will not lead to values being saved. A file needs to defined using the Set buttons to the right of each switch. Once a file is successfully defined the filename will be shown below each switch. Each of these is described briefly,

This option activates saving the summary statistics at the end of an analysis. (If saving individual statistics [2.] is also selected to be saved they will be written to the same file.)
This option activates saving the individual statistics from each realization from a history at the end of an analysis. (If saving summary statistics [1.] is also selected to be saved they will be written to the same file.)
This option will activate saving the tree histories (raw data) to a file. For more information on this option see the help documents on saving raw character histories.
This option will activate saving the null statistics from a predictive distribution test. See the help documents on predictive tests for more information.


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	Page Last Updated: 6 August 2008