Command
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Description
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Modified On
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Abs
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Absolute value. If x is a number, returns |x|. If x is a matrix, returns maximum absolute value among matrix elements, unless x is vector in which case the euclidean norm is returned. If x is a string, returns the length of the string.
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8/9/2002
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Arctan
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Inverse Tangent. Returns the inverse tangent of x.
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8/17/1999
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ASSIGNED_SEED
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If ASSIGNED_SEED is set, then it is fed to the standard random number generator seed function. Can be used to replicate simulation results.
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1/19/2000
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Beta
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The 'Beta'function. Beta(x,y)=Gamma(x)Gamma(y)/Gamma(x+y).
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8/17/1999
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BranchCount
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When applied to a tree variable, returns the number of internal branches in the tree.
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1/19/2000
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BranchLength
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'BranchLength' returns the expected number of substitution along a given branch using the model and parameter value currently attached to the branch. The value of 0 is returned for undefined cases.
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5/11/2000
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BranchName
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Returns a string containing the name of an internal node of the tree.
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5/11/2000
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CChi2
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The cumulative Chi squared distribution. CChi2(x,n) = P{t<x}, where t is a random variable with the Chi-squared n degrees of freedom distribution.
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5/11/2000
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CGammaDist
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The cumulative gamma distribution. CGammaDist(x,a,b) = P{t<x}, where t has gamma distribution with the shape parameter a, and the 'mean' parameter b.
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5/11/2000
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Columns
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The number of columns function. Returns the number of columns in a matrix.
|
8/17/1999
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Cos
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The cosine function.
|
8/17/1999
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Erf
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The error function. Erf(x)=2/Sqrt(Pi) Integral{0,x,Exp[-t^2]dt}
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8/17/1999
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Exp
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The exponential function. Returns both numeric and matrix exponentials.
|
8/17/1999
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Format
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Format is used to print a floating point number with a specified number of places of precision. The function returns a string containing the appropriate representation of the number. 'width' is the total length of the number string, 'places' is the number of decimal places to be printed. Format (x,width,places) is equivalent to sprintf ("%width.placesf",x);
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5/11/2000
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Gamma
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The gamma function. Gamma[a] = Integral{0,Infinity, Exp[-x] x^(a-1)dx};
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8/17/1999
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GammaDist
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The gamma distrufunction. GammaDist[x,a,b] = b^a/Gamma(a) Exp[-bx] x^(a-1).
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8/17/1999
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IBeta
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The incomplete beta function. IBeta[x,p,q] = Integral{0,x, Gamma[p+q]/Gamma[p]Gamma[q] t^(p-1) (1-t)^(q-1)};
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6/6/2001
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IGamma
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The incomplete gamma function. IGamma[a,x] = Integral{0,x, Exp[-t] t^(a-1)dt};
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5/10/2000
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InvChi2
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The inverse Chi squared distribution. InvChi2(r,n) = x, such that P(t<x)=r where t is a random variable distributed as Chi-squared with n degrees of freedom.
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8/9/2002
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Inverse
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The matrix inverse function.
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8/17/1999
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Log
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The natural (base 'eÕ) logarithm function.
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8/17/1999
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LUDecompose
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The LU matrix decomposition function. Any non-degenerate square matrix can be 'uniqely'decomposed into the product of a lower triangular with an upper triangular matrices.
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8/20/2002
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LUSolve
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Solves systems of the form LUx = b. Performs a double back substitution to solve a system of linear equations.
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8/20/2002
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Max
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Returns the maximum of its arguments.
|
6/6/2001
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Min
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Returns the minimum of its arguments.
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6/6/2001
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PSTreeString
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Returns a string containing a post script rendering of the tree. The length of the branches can be scaled on any model parameter (if it is defined for all branches), or left unscaled (all branches have equal length). The command also takes a page size parameter.
|
8/14/2002
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Random
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The random number generation function. Returns a random number of from a uniform distribution over [a,b].
|
8/17/1999
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RerootTree
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Returns a string containing the Newick style string of the tree rerooted at a specified branch.
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8/20/2002
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Rows
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The number of rows function. Returns the number of rows in a matrix. Can also be used to count the number of objects of a given kind.
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8/9/2002
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Sin
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The sine function.
|
8/17/1999
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Sqrt
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The square root function.
|
8/17/1999
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Tan
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The tangent function.
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8/17/1999
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TEXTreeString
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Returns a string containing a LaTEX picture description of the tree. The length of the branches can be scaled on any model parameter (if it is defined for all branches), or left unscaled (all branches have equal length).
|
8/14/2002
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Time
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The timer function. Returns the value of the system timer in seconds.
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5/11/2000
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TipCount
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When applied to a tree variable, returns the number of tips(leaves) in the tree.
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1/19/2000
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TipName
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Returns a string containing the name of a tip of the tree.
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5/11/2000
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Transpose
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The matrix transpose function. Returns the transpose of a matrix.
|
8/17/1999
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ZCDF
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Cumulative distribution function of the standard normal random variable
ZCDF(x) = P{N(0,1)<x}
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8/9/2002
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