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 HYPHY Command Reference:HYPHY Constants

Command Description Modified On
ALLOW_BOUNDARY If true (default) then variables are allowed to assume boundary values. 8/17/1999
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
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

 
Sergei L. Kosakovsky Pond and Spencer V. Muse, 1997-2002