java.lang.Object
- gov.nih.mipav.model.algorithms.Fastfit

public class Fastfit
extends java.lang.Object

Field Summary

Fields
Modifier and Type	Field	Description
`(package private) int`	`CACHE_SIZE`
`double`	`epsilon`	Original C and MATLAB code from fastfit and lightspeed packages by Tom Minka.
`(package private) static long`	`ix`
`(package private) static long`	`iy`
`(package private) static long`	`iz`
`(package private) static double`	`RandN_previous`
`(package private) static int`	`RandN_usePrevious`

Constructor Summary

Constructors
Constructor Description

Fastfit()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`double`	`BetaRand(double a, double b)`
`long`	`BinoRand(double p, long n)`
`double[][]`	`cholproj(double[][] A, boolean[] isPosDef)`
`double[]`	`col_sum(double[][] x)`
`double`	`di_pochhammer(double x, double n)`
`double`	`di_pochhammer(double x, int n)`
`double`	`digamma(double x)`
`double[]`	`dirichlet_fit(double[] e, double[][] data, double[] ain, double[] bar_p)`
`double[]`	`dirichlet_fit_m(double[][] data, double[] ain, double[] bar_p, int niter)`
`double[]`	`dirichlet_fit_newton(double[] e, double[][] data, double[] ain, double[] bar_p)`
`double[]`	`dirichlet_fit_s(double[][] data, double[] ain, double[] bar_p, int niter)`
`double[]`	`dirichlet_fit_simple(double[] e, double[][] data, double[] ain)`
`double[]`	`dirichlet_logProb(double[] a, double[][] data)`
`double`	`dirichlet_logProb_fast(double[] a, double[] meanlog)`
`double[]`	`dirichlet_moment_match(double[][] p)`
`double[][]`	`dirichlet_sample(double[][] a, int n)`
`double[][]`	`dirichlet_sample_col(double[] acol, int n)`
`void`	`gamma_fit(double[] a, double[] b, double[] x, double s)`
`(package private) double`	`gammaln(double x)`
`(package private) double`	`gammaln2(double x, double d)`
`double`	`GammaRand(double a)`
`void`	`GetSeed(long[] ix_out, long[] iy_out, long[] iz_out)`
`double[]`	`gradient2(double[] a, double[][] data, double[] sdata)`
`double[]`	`hessian_times_gradient(double[] a, double[] g, double lambda)`
`double[]`	`hessian_times_gradient2(double[] a, double[][] data, double[] sdata, double[] g, double lambda)`
`double`	`inv_digamma(double y, int niter)`
`double[][]`	`inv_posdef(double[][] A)`
`double[][]`	`inv_triu(double[][] U)`
`double`	`invnormcdf(double p)`
`double`	`logdet(double[][] A)`
`double[][]`	`logmulexp(double[][] a, double[][] b)`
`double[]`	`logsumexp(double[][] ain, int dim)`
`double[]`	`mvnormpdf(double[][] x, double[][] m, double[][] S, double[][] iS, double[][] V, double[][] iV)`
`double[]`	`mvnormpdfln(double[][] x, double[][] m, double[][] S, double[][] iS, double[][] V, double[][] iV)`
`double`	`normcdf(double x, double m, double s)`
`double`	`normcdfln(double x)`
`double`	`normcdflogit(double x)`
`double`	`pochhammer(double x, double n)`
`double`	`pochhammer(double x, int n)`
`double[]`	`polya_fit(double[][] data, double[] ain)`
`double[]`	`polya_fit_m(double[][] data, double[] ain, double[] weight)`
`double[]`	`polya_fit_ms(double[][] data, double[] ain, double[] weight)`
`double[]`	`polya_fit_s(double[][] data, double[] ain, double[] weight)`
`double[]`	`polya_fit_simple(double[][] data, double[] ain)`
`double[]`	`polya_logProb(double[] a, double[][] data)`
`double[]`	`polya_moment_match(double[][] data)`
`double[][]`	`polya_sample(double[][] a, int[] n)`
`void`	`quad_roots(double[] r1, double[] r2, double a2, double a1, double a0)`
`double`	`Rand()`
`double`	`RandN()`
`double[][]`	`randwishart(double a, int d)`
`void`	`ResetSeed()`
`double[]`	`row_sum(double[][] x)`
`void`	`s_derivatives(double[] g, double[] h, double[] c1, double[] c3, double[] a, double[][] data, double[] sdata, double[] weight)`
`void`	`s_derivatives_c(double[] g, double[] h, double[] c1, double[] c3, double[] a, double[][] data, double[] len, double[] weight)`
`double[][]`	`sample_hist(double[][] p, int[] n)`
`void`	`SetSeed(long new_ix, long new_iy, long new_iz)`
`double`	`slow_di_pochhammer(double x, int n)`
`double`	`slow_pochhammer(double x, int n)`
`double`	`slow_tri_pochhammer(double x, int n)`
`double[][]`	`solve_tril(double[][] T, double[][] b)`
`double[][]`	`solve_tril2(double[][] T, double[][] b)`
`double[][]`	`solve_triu(double[][] T, double[][] b)`
`double[][]`	`solve_triu2(double[][] T, double[][] b)`
`double`	`special_case(double s, double g, double h, double c1, double c3)`
`double[][]`	`sqdist(double[][] p, double[][] q, double[][] A)`
`void`	`test_cholproj()`
`void`	`test_digamma()`
`void`	`test_dirichlet_fit()`
`void`	`test_dirichlet_sample()`
`void`	`test_gamma_fit()`
`void`	`test_gammaln()`
`void`	`test_inv_posdef()`
`void`	`test_logmulexp()`
`void`	`test_logsumexp()`
`void`	`test_normcdf()`
`void`	`test_pochhammer()`
`void`	`test_polya_fit()`
`void`	`test_randgamma()`
`void`	`test_randwishart()`
`void`	`test_solve_tri()`
`void`	`test_trigamma()`
`void`	`test_wishpdf()`
`double`	`tetragamma(double x)`
`double`	`tri_pochhammer(double x, double n)`
`double`	`tri_pochhammer(double x, int n)`
`double`	`trigamma(double x)`
`double`	`wishpdf(double[][] X, double a, double[][] B, boolean inverse)`
`double`	`wishpdf(double X, double a, double B, boolean inverse)`
`double`	`wishpdfln(double[][] Xin, double a, double[][] B, boolean inverse)`
`double`	`wishpdfln(double X, double a, double B, boolean inverse)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail
- epsilon
```
public double epsilon
```
  Original C and MATLAB code from fastfit and lightspeed packages by Tom Minka. Ported to Java by William Gandler Fastfit ======= This toolbox implements efficient maximum-likelihood estimation of various distributions. It utilizes the technique of generalized Newton iteration, described in the following papers: [Beyond Newton's method](http://tminka.github.io/papers/newton.html) [Estimating a Dirichlet distribution](http://tminka.github.io/papers/dirichlet/) [Estimating a Gamma distribution](http://tminka.github.io/papers/minka-gamma.pdf) This toolbox requires the [Lightspeed toolbox](https://github.com/tminka/lightspeed/), so you will need to install both. See Contents.m for more details. A python port is available at https://github.com/ericsuh/dirichlet Tom Minka Lightspeed matlab toolbox ========================= This library provides: highly optimized versions of mathematical functions such as `normcdf`, set intersection, and `gammaln` efficient random number generators evaluation of common probability densities routines for counting floating-point operations (FLOPS), useful for benchmarking algorithms. utilities such as filename globbing and parsing of variable-length argument lists. graphics functions such as `axis_pct` and `mobile_text` (in the graphics subdirectory). See Contents.m for a table of contents. Tom Minka MIT License Copyright (c) 2017 Tom Minka Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
- ix
```
static long ix
```
- iy
```
static long iy
```
- iz
```
static long iz
```
- RandN_previous
```
static double RandN_previous
```
- RandN_usePrevious
```
static int RandN_usePrevious
```
- CACHE_SIZE
```
int CACHE_SIZE
```

Constructor Detail
- Fastfit
```
public Fastfit()
```

Method Detail

test_digamma
```
public void test_digamma()
```

digamma
```
public double digamma(double x)
```

test_trigamma
```
public void test_trigamma()
```

trigamma
```
public double trigamma(double x)
```

tetragamma

public double tetragamma(double x)

Rand
```
public double Rand()
```

ResetSeed
```
public void ResetSeed()
```

SetSeed

public void SetSeed(long new_ix,
                    long new_iy,
                    long new_iz)

GetSeed

public void GetSeed(long[] ix_out,
                    long[] iy_out,
                    long[] iz_out)

RandN
```
public double RandN()
```

test_randgamma
```
public void test_randgamma()
```

GammaRand
```
public double GammaRand(double a)
```

BetaRand

public double BetaRand(double a,
                       double b)

BinoRand

public long BinoRand(double p,
                     long n)

logdet

public double logdet(double[][] A)

test_randwishart
```
public void test_randwishart()
```

randwishart

public double[][] randwishart(double a,
                              int d)

test_logsumexp
```
public void test_logsumexp()
```

logsumexp

public double[] logsumexp(double[][] ain,
                          int dim)

test_logmulexp
```
public void test_logmulexp()
```

logmulexp

public double[][] logmulexp(double[][] a,
                            double[][] b)

test_normcdf
```
public void test_normcdf()
```

normcdf

public double normcdf(double x,
                      double m,
                      double s)

normcdfln
```
public double normcdfln(double x)
```

normcdflogit

public double normcdflogit(double x)

test_cholproj
```
public void test_cholproj()
```

cholproj

public double[][] cholproj(double[][] A,
                           boolean[] isPosDef)

gammaln2

double gammaln2(double x,
                double d)

test_gammaln
```
public void test_gammaln()
```

gammaln
```
double gammaln(double x)
```

wishpdfln

public double wishpdfln(double X,
                        double a,
                        double B,
                        boolean inverse)

wishpdfln

public double wishpdfln(double[][] Xin,
                        double a,
                        double[][] B,
                        boolean inverse)

test_wishpdf
```
public void test_wishpdf()
```

wishpdf

public double wishpdf(double X,
                      double a,
                      double B,
                      boolean inverse)

wishpdf

public double wishpdf(double[][] X,
                      double a,
                      double[][] B,
                      boolean inverse)

test_pochhammer
```
public void test_pochhammer()
```

pochhammer

public double pochhammer(double x,
                         double n)

pochhammer

public double pochhammer(double x,
                         int n)

slow_pochhammer

public double slow_pochhammer(double x,
                              int n)

di_pochhammer

public double di_pochhammer(double x,
                            double n)

di_pochhammer

public double di_pochhammer(double x,
                            int n)

slow_di_pochhammer

public double slow_di_pochhammer(double x,
                                 int n)

tri_pochhammer

public double tri_pochhammer(double x,
                             double n)

tri_pochhammer

public double tri_pochhammer(double x,
                             int n)

slow_tri_pochhammer

public double slow_tri_pochhammer(double x,
                                  int n)

solve_tril

public double[][] solve_tril(double[][] T,
                             double[][] b)

solve_tril2

public double[][] solve_tril2(double[][] T,
                              double[][] b)

test_solve_tri
```
public void test_solve_tri()
```

solve_triu

public double[][] solve_triu(double[][] T,
                             double[][] b)

solve_triu2

public double[][] solve_triu2(double[][] T,
                              double[][] b)

inv_triu

public double[][] inv_triu(double[][] U)

test_inv_posdef
```
public void test_inv_posdef()
```

inv_posdef

public double[][] inv_posdef(double[][] A)

invnormcdf

public double invnormcdf(double p)

col_sum

public double[] col_sum(double[][] x)

row_sum

public double[] row_sum(double[][] x)

mvnormpdf

public double[] mvnormpdf(double[][] x,
                          double[][] m,
                          double[][] S,
                          double[][] iS,
                          double[][] V,
                          double[][] iV)

mvnormpdfln

public double[] mvnormpdfln(double[][] x,
                            double[][] m,
                            double[][] S,
                            double[][] iS,
                            double[][] V,
                            double[][] iV)

sqdist

public double[][] sqdist(double[][] p,
                         double[][] q,
                         double[][] A)

test_dirichlet_sample
```
public void test_dirichlet_sample()
```

dirichlet_sample

public double[][] dirichlet_sample(double[][] a,
                                   int n)

dirichlet_sample_col

public double[][] dirichlet_sample_col(double[] acol,
                                       int n)

dirichlet_moment_match

public double[] dirichlet_moment_match(double[][] p)

dirichlet_fit_s

public double[] dirichlet_fit_s(double[][] data,
                                double[] ain,
                                double[] bar_p,
                                int niter)

dirichlet_logProb

public double[] dirichlet_logProb(double[] a,
                                  double[][] data)

dirichlet_fit_m

public double[] dirichlet_fit_m(double[][] data,
                                double[] ain,
                                double[] bar_p,
                                int niter)

inv_digamma

public double inv_digamma(double y,
                          int niter)

dirichlet_logProb_fast

public double dirichlet_logProb_fast(double[] a,
                                     double[] meanlog)

test_dirichlet_fit
```
public void test_dirichlet_fit()
```

dirichlet_fit

public double[] dirichlet_fit(double[] e,
                              double[][] data,
                              double[] ain,
                              double[] bar_p)

dirichlet_fit_simple

public double[] dirichlet_fit_simple(double[] e,
                                     double[][] data,
                                     double[] ain)

dirichlet_fit_newton

public double[] dirichlet_fit_newton(double[] e,
                                     double[][] data,
                                     double[] ain,
                                     double[] bar_p)

hessian_times_gradient

public double[] hessian_times_gradient(double[] a,
                                       double[] g,
                                       double lambda)

test_gamma_fit
```
public void test_gamma_fit()
```

gamma_fit

public void gamma_fit(double[] a,
                      double[] b,
                      double[] x,
                      double s)

polya_moment_match

public double[] polya_moment_match(double[][] data)

polya_logProb

public double[] polya_logProb(double[] a,
                              double[][] data)

gradient2

public double[] gradient2(double[] a,
                          double[][] data,
                          double[] sdata)

hessian_times_gradient2

public double[] hessian_times_gradient2(double[] a,
                                        double[][] data,
                                        double[] sdata,
                                        double[] g,
                                        double lambda)

polya_fit

public double[] polya_fit(double[][] data,
                          double[] ain)

polya_fit_simple

public double[] polya_fit_simple(double[][] data,
                                 double[] ain)

polya_fit_m

public double[] polya_fit_m(double[][] data,
                            double[] ain,
                            double[] weight)

quad_roots

public void quad_roots(double[] r1,
                       double[] r2,
                       double a2,
                       double a1,
                       double a0)

special_case

public double special_case(double s,
                           double g,
                           double h,
                           double c1,
                           double c3)

s_derivatives_c

public void s_derivatives_c(double[] g,
                            double[] h,
                            double[] c1,
                            double[] c3,
                            double[] a,
                            double[][] data,
                            double[] len,
                            double[] weight)

s_derivatives

public void s_derivatives(double[] g,
                          double[] h,
                          double[] c1,
                          double[] c3,
                          double[] a,
                          double[][] data,
                          double[] sdata,
                          double[] weight)

polya_fit_s

public double[] polya_fit_s(double[][] data,
                            double[] ain,
                            double[] weight)

polya_fit_ms

public double[] polya_fit_ms(double[][] data,
                             double[] ain,
                             double[] weight)

polya_sample

public double[][] polya_sample(double[][] a,
                               int[] n)

sample_hist

public double[][] sample_hist(double[][] p,
                              int[] n)

test_polya_fit
```
public void test_polya_fit()
```

Class Fastfit

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

epsilon

ix

iy

iz

RandN_previous

RandN_usePrevious

CACHE_SIZE

Constructor Detail

Fastfit

Method Detail

test_digamma

digamma

test_trigamma

trigamma

tetragamma

Rand

ResetSeed

SetSeed

GetSeed

RandN

test_randgamma

GammaRand

BetaRand

BinoRand

logdet

test_randwishart

randwishart

test_logsumexp

logsumexp

test_logmulexp

logmulexp

test_normcdf

normcdf

normcdfln

normcdflogit

test_cholproj

cholproj

gammaln2

test_gammaln

gammaln

wishpdfln

wishpdfln

test_wishpdf

wishpdf

wishpdf

test_pochhammer

pochhammer

pochhammer

slow_pochhammer

di_pochhammer

di_pochhammer

slow_di_pochhammer

tri_pochhammer

tri_pochhammer

slow_tri_pochhammer

solve_tril

solve_tril2

test_solve_tri

solve_triu

solve_triu2

inv_triu

test_inv_posdef

inv_posdef

invnormcdf

col_sum

row_sum

mvnormpdf

mvnormpdfln

sqdist

test_dirichlet_sample

dirichlet_sample

dirichlet_sample_col

dirichlet_moment_match

dirichlet_fit_s