Command
|
Description
|
Modified On
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ALLOW_BOUNDARY
|
If true (default) then variables are allowed to assume boundary values.
|
8/17/1999
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BRACKETING_PERSISTENCE
|
In conjunction with randomized order bracketing, specifies, how many times, on average each variable will be bracketed. Defualt value is 2.5.
|
8/17/1999
|
CACHE_SUBTREES
|
If true (default) then HyPhy uses a caching scheme to speed up likelihood caclulations. A little less memory is used if caching is turned off.
|
6/7/2001
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CATEGORY_SIMULATION_METHOD
|
Controls how category variables are simulated: 1 - use discrete distibution; 2(default) - when available, use continuous distribution.
|
5/11/2000
|
CLEAR_FILE
|
Used as an argument to FPRINTF, forces the target file to be cleared.
|
1/19/2000
|
COVARIANCE_PRECISION
|
A constant which determines what method is used by CovarianceMatrix in computing the numerical Hessian.
|
8/20/2002
|
DATA_FILE_DEFAULT_WIDTH
|
Controls how dataset filters are printed by fprintf. Specifies the number of sites per line. Default is 50.
|
5/11/2000
|
DATA_FILE_PARTITION_MATRIX
|
A matrix of partition names and specifications from the most recently read NEXUS data file.
|
8/20/2002
|
DATA_FILE_PRINT_FORMAT
|
Controls how dataset filters are printed by fprintf.
|
8/20/2002
|
DATAFILE_TREE
|
Tree string from the most recently read data file.
|
8/20/2002
|
END_OF_FILE
|
Is set to 0 or 1 by FSCANF to indicate whether the last read reached the end of file.
|
8/20/2002
|
GLOBAL_STARTING_POINT
|
Specifies the default initial value for all independent variables during optimization. Default is 0.1.
|
8/20/2002
|
INTEGRATION_PRECISION_FACTOR
|
Designates integration precision used internally for computing cumulative distributions of densities w/o known cumulative distributions formulas. Default is 0.0001.
|
8/17/1999
|
INTERMEDIATE_PRECISION
|
Designates intermediate precision for optimization methods that combine gradient ascent and bracketing.
|
8/20/2002
|
IS_TREE_PRESENT_IN_DATA
|
Was there a tree defined in the last data file read?
|
8/20/2002
|
KEEP_OPTIMAL_ORDER
|
When column optimization is active, this boolean constant allows to keep the optimal order between successive optimizations, meaningful when neither the data nor the tree are changed. Default is false.
|
8/17/1999
|
LAST_FILE_PATH
|
Is set to the last file path returned by a PROMPT_FOR_FILE request. Can be used to access the same file which the user was prompted for at the beginning.
|
1/19/2000
|
LF_CALL_COUNT
|
Contains the number of likelihood function evaluations up to this point.
|
8/20/2002
|
LIKELIHOOD_FUNCTION_OUTPUT
|
Controls how likelihood function is printed by fprintf.
|
8/21/2002
|
LIST_ALL_VARIABLES
|
Passed as an argument to fprintf produces a list of all currently defined variables.
|
8/17/1999
|
MAXIMUM_ITERATIONS_PER_VARIABLE
|
If the optimzation precision could not be reached in MAXIMUM_ITERATIONS_PER_VARIABLE*number of independent variables likelihood function evaluations, the routines return with the best value so far. Default is 100.
|
8/17/1999
|
MESSAGE_LOG
|
The handle to HyPhy messages file which can be passed to fprintf.
|
8/20/2002
|
MESSAGE_LOGGING
|
Toggles writing messages to file 'messages.log' on and off.
|
4/12/2000
|
NEXUS_FILE_TREE_MATRIX
|
A matrix of tree strings and identifiers from the most recently read NEXUS data file.
|
8/20/2002
|
NICETY_LEVEL
|
Controls how cpu-time greedy the application is. Default is 1. Maximum(meaningful) value is 6.
|
8/20/2002
|
OPTIMIZATION_METHOD
|
Specifies the optimization method to utilize.
|
8/20/2002
|
OPTIMIZATION_PRECISION
|
Sets the precision goal for optimization routines. Default is 0.001.
|
1/19/2000
|
OPTIMIZATION_PRECSION_METHOD
|
When OPTIMIZATION_PRECSION_METHOD is 0 (default) the optimization precision objective is applied to the likelihood function value, whereas if it is 1 then all the parameter estimates must meat precision goals.
|
8/17/1999
|
OPTIMIZE_SUMMATION_ORDER
|
When true, pseudo optimal column ordering is used. Default is true.
|
9/5/2002
|
OPTIMIZE_SUMMATION_ORDER_PARTITION
|
Used when pseudo optimal column ordering is active. Specifies the subpartition size for column ordering.
|
9/5/2002
|
PRINT_DIGITS
|
Specifies the number of digits to print for floating point numbers. Default is 8, meaningful values are between 1 and 15.
|
8/20/2002
|
RANDOM_SEED
|
RANDOM_SEED is set to the seed fed to the standard random number generator seed function.
|
8/17/1999
|
RANDOM_STARTING_PERTURBATIONS
|
Used in conjunction with GLOBAL_STARTING_POINT if small (10% in magnitude) random perturbations are desired. Default value is false(0).
|
8/17/1999
|
RELATIVE_PRECISION
|
When RELATIVE_PRECISION is true, the optimization routines use relative error to determine when to return. Default is false.
|
8/17/1999
|
SCREEN_HEIGHT
|
The height in pixels of the display.
|
8/20/2002
|
SCREEN_WIDTH
|
The width in pixels of the display.
|
8/20/2002
|
SKIP_OMISSIONS
|
When true, any data sites which contain characters w/o information (deletions) are omitted from the dataset filters. Default is false.
|
8/17/1999
|
USE_DISTANCES
|
When true (default) distance methods are used (when possible) to get intial parameter value.
|
8/17/1999
|