Package | Description |
---|---|
pal.distance |
Classes for reading and generating distance matrices, including computation
of pairwise distances for sequence data (maximum-likelihood and observed
distances).
|
pal.math |
Classes for math stuff such as optimisation, numerical derivatives, matrix exponentials,
random numbers, special function etc.
|
Modifier and Type | Class | Description |
---|---|---|
class |
SequencePairLikelihood |
computation of the (negative) log-likelihood for a pair of sequences
|
Modifier and Type | Class | Description |
---|---|---|
class |
LineFunction |
converts a multivariate function into a univariate function
|
class |
OrthogonalLineFunction |
converts a multivariate function into a univariate function
by keeping all but one argument constant
|
Modifier and Type | Method | Description |
---|---|---|
double |
UnivariateMinimum.findMinimum(double x,
UnivariateFunction f) |
Find minimum
(first estimate given)
|
double |
UnivariateMinimum.findMinimum(double x,
UnivariateFunction f,
int fracDigits) |
Find minimum
(first estimate given, desired number of fractional digits specified)
|
double |
UnivariateMinimum.findMinimum(UnivariateFunction f) |
Find minimum
(no first estimate given)
|
double |
UnivariateMinimum.findMinimum(UnivariateFunction f,
int fracDigits) |
Find minimum
(no first estimate given, desired number of fractional digits specified)
|
static double |
NumericalDerivative.firstDerivative(UnivariateFunction f,
double x) |
determine first derivative
|
double |
UnivariateMinimum.optimize(double x,
UnivariateFunction f,
double tol) |
The actual optimization routine (Brent's golden section method)
|
double |
UnivariateMinimum.optimize(double x,
UnivariateFunction f,
double tol,
double lowerBound,
double upperBound) |
The actual optimization routine (Brent's golden section method)
|
double |
UnivariateMinimum.optimize(UnivariateFunction f,
double tol) |
The actual optimization routine (Brent's golden section method)
|
double |
UnivariateMinimum.optimize(UnivariateFunction f,
double tol,
double lowerBound,
double upperBound) |
The actual optimization routine (Brent's golden section method)
|
static double |
NumericalDerivative.secondDerivative(UnivariateFunction f,
double x) |
determine second derivative
|