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statsLib.h File Reference
Statistical Fuctions.

Library of statistic functions. More...

#include <fvar.hpp>
#include <admodel.h>
#include <df1b2fun.h>
#include <adrndeff.h>

Go to the source code of this file.

Classes

class  plogisTraits< double >
class  plogisTraits< dvariable >
class  plogisTraits< named_dvariable >
class  vcubic_spline_function_array
 A class for implementin cubic splines. More...

Defines

#define LOGISTIC_HPP

Typedefs

typedef vcubic_spline_function * pvcubic_spline_function

Functions

dvar_matrix ageLengthKey (const dvar_vector &mu, const dvar_vector &sig, const dvector &x)
 Age Length Key.
dmatrix ageLengthKey (const dvector &mu, const dvector &sig, const dvector &x)
 Age Length Key.
dvar_matrix ALK (dvar_vector mu, dvar_vector sig, dvector x)
void bicubic_spline (const dvector &x, const dvector &y, dvar_matrix &knots, dvar_matrix &S)
dvar_vector cubic_spline (const dvar_vector &spline_nodes, const dvar_vector &ip)
dvariable dbeta (const dvariable &x, const double &shape1, const double &shape2)
dvariable dbeta (const dvariable &x, const dvariable &shape1, const dvariable &shape2)
dvariable dbeta (const dvariable &x, const prevariable &shape1, const prevariable &shape2)
dvariable dbinom (const prevariable &x, const double &n, const double &p)
dvariable dbinom (const prevariable &x, const prevariable &n, const double &p)
dvariable dbinom (const prevariable &x, const prevariable &n, const prevariable &p)
dvariable dbinom (const dvar_vector &x, const dvar_vector &n, const dvar_vector &p)
dvariable dbinom (const prevariable &x, const dvar_vector &n, const dvar_vector &p)
dvariable dbinom (const dvar_vector &x, const prevariable &n, const dvar_vector &p)
dvariable dbinom (const dvar_vector &x, const dvar_vector &n, const prevariable &p)
df1b2variable dbinom (const df1b2variable &x, const double &n, const double &p)
df1b2variable dbinom (const df1b2variable &x, const df1b2variable &n, const double &p)
df1b2variable dbinom (const df1b2variable &x, const df1b2variable &n, const df1b2variable &p)
df1b2variable dbinom (const df1b2vector &x, const df1b2vector &n, const df1b2vector &p)
df1b2variable dbinom (const df1b2variable &x, const df1b2vector &n, const df1b2vector &p)
df1b2variable dbinom (const df1b2vector &x, const df1b2variable &n, const df1b2vector &p)
df1b2variable dbinom (const df1b2vector &x, const df1b2vector &n, const df1b2variable &p)
dvariable dgamma (const dvariable &x, const double &a, const double &b)
dvariable dgamma (const dvariable &x, const dvariable &a, const dvariable &b)
dvariable dgamma (const dvector &x, const prevariable &a, const prevariable &b)
dvariable dgamma (const dvector &x, const prevariable &a, const dvar_vector &b)
dvariable dgamma (const dvector &x, const dvar_vector &a, const dvar_vector &b)
dvariable dgamma (const dvector &x, const dvar_vector &a, const prevariable &b)
dvariable dinvgamma (const dvariable &x, const double a, const double b)
dvariable dlnorm (const prevariable &x, const double &mu, const double &std)
dvariable dlnorm (const prevariable &x, const prevariable &mu, const double &std)
dvariable dlnorm (const prevariable &x, const prevariable &mu, const prevariable &std)
dvariable dlnorm (const dvar_vector &x, const double &mu, const double &std)
dvariable dlnorm (const dvar_vector &x, const prevariable &mu, const double &std)
dvariable dlnorm (const dvar_vector &x, const prevariable &mu, const prevariable &std)
dvariable dmultinom (const dvector &x, const dvar_vector &p)
dvariable dmultinom (const dmatrix o, const dvar_matrix &p, dvar_matrix &nu, double &tau2, const double minp)
dvariable dmvlogistic (const dmatrix o, const dvar_matrix &p, dvar_matrix &nu, double &tau2, const double minp)
dvariable dmvlogistic (const dmatrix o, const dvar_matrix &p, double &tau2)
dvariable dnbinom (const double &x, const prevariable &mu, const prevariable &k)
 negative log likelihood of negative binomial with mean=mu and variance = mu + mu^2 /k
df1b2variable dnbinom (const double &x, const df1b2variable &mu, const df1b2variable &k)
 negative log likelihood of negative binomial with mean=mu and variance = mu + mu^2 /k
df1b2variable dnbinom (const dvector &x, const df1b2vector &mu, const df1b2variable &k)
 negative log likelihood of negative binomial with mean=mu and variance = mu + mu^2 /k
df1b2variable dnbinom (const dvector &x, const df1b2vector &mu, const df1b2vector &k)
 negative log likelihood of negative binomial with mean=mu and variance = mu + mu^2 /k
dvariable dnbinom (const dvector &x, const dvar_vector &mu, const prevariable &k)
 negative log likelihood of negative binomial with mean=mu and variance = mu + mu^2 /k
dvariable dnbinom (const dvector &x, const dvar_vector &mu, const dvar_vector &k)
 negative log likelihood of negative binomial with mean=mu and variance = mu + mu^2 /k
dvariable dnbinom_tau (const double &x, const prevariable &mu, const prevariable &tau)
 negative log likelihood of negative binomial with mean and tau
df1b2variable dnbinom_tau (const double &x, const df1b2variable &mu, const df1b2variable &tau)
 negative log likelihood of negative binomial with mean and tau
df1b2variable dnbinom_tau (const dvector &x, const df1b2vector &mu, const df1b2variable &tau)
 negative log likelihood of negative binomial with mean and tau
df1b2variable dnbinom_tau (const dvector &x, const df1b2vector &mu, const df1b2vector &tau)
 negative log likelihood of negative binomial with mean and tau
dvariable dnbinom_tau (const dvector &x, const dvar_vector &mu, const prevariable &tau)
 negative log likelihood of negative binomial with mean and tau
dvariable dnbinom_tau (const dvector &x, const dvar_vector &mu, const dvar_vector &tau)
 negative log likelihood of negative binomial with mean and tau
dvariable dnorm (const prevariable &x, const double &mu, const double &std)
dvariable dnorm (const dvar_vector &x, const double &mu, const double &std)
dvariable dnorm (const prevariable &x, const double &mu, const double &std, bool bLog)
dvariable dnorm (const dvector &x, const prevariable &mu, const prevariable &std)
dvariable dnorm (const dvector &x, const prevariable &mu, const prevariable &std, bool dLog)
dvariable dnorm (const dvar_vector &residual, const prevariable &std)
dvariable dnorm (const dvar_vector &residual, const double &std)
dvariable dnorm (const dvar_vector &residual, const dvector &std)
dvariable dnorm (const dvar_vector &residual, const dvar_vector std)
dvariable dnorm (const dvar_vector &residual)
dvariable dnorm (const dmatrix &obs, const dvar_matrix &pred)
df1b2variable dnorm (const df1b2variable &x, const double &mu, const double &std)
df1b2variable dnorm (const df1b2variable &x, const double &mu, const double &std, bool bLog)
df1b2variable dnorm (const df1b2variable &x, const df1b2variable &mu, const df1b2variable &std, bool bLog)
df1b2variable dnorm (const df1b2vector &x, const df1b2variable &mu, const df1b2variable &std, bool dLog)
dvariable dpois (const double &k, const prevariable &lambda)
dvariable dpois (const prevariable &k, const prevariable &lambda)
dvariable dstudent_t (const dvar_vector &residual, const dvar_vector &df)
dvariable dunif (const dvariable &x, const double min, const double max)
df1b2variable dzinbinom (const double &x, const df1b2variable &mu, const df1b2variable &k, const df1b2variable &p)
 ecologically parametarized negative binomial with zero inflation
dvariable dzinbinom (const double &x, const prevariable &mu, const prevariable &k, const prevariable &p)
 ecologically parametarized negative binomial with zero inflation
df1b2variable dzinbinom (const dvector &x, const df1b2vector &mu, const df1b2variable &k, const df1b2variable &p)
 ecologically parametarized negative binomial with zero inflation
df1b2variable dzinbinom (const dvector &x, const df1b2vector &mu, const df1b2vector &k, const df1b2variable &p)
 ecologically parametarized negative binomial with zero inflation
dvariable dzinbinom (const dvector &x, const dvar_vector &mu, const prevariable &k, const prevariable &p)
 ecologically parametarized negative binomial with zero inflation
dvariable dzinbinom (const dvector &x, const dvar_vector &mu, const dvar_vector &k, const prevariable &p)
 ecologically parametarized negative binomial with zero inflation
df1b2variable dzinbinom (const dvector &x, const df1b2vector &mu, const df1b2variable &k, const df1b2vector &p)
 now p is a vector///
df1b2variable dzinbinom (const dvector &x, const df1b2vector &mu, const df1b2vector &k, const df1b2vector &p)
 ecologically parametarized negative binomial with zero inflation
dvariable dzinbinom (const dvector &x, const dvar_vector &mu, const prevariable &k, const dvar_vector &p)
 ecologically parametarized negative binomial with zero inflation
dvariable dzinbinom (const dvector &x, const dvar_vector &mu, const dvar_vector &k, const dvar_vector &p)
 ecologically parametarized negative binomial with zero inflation
dvar_vector eplogis (const dvar_vector &x, const dvariable &alpha, const dvariable &beta, const dvariable &gamma)
dvector eplogis (const dvector &x, const double &alpha, const double &beta, const double &gamma)
void fill (const dmatrix &_d, const dvector &_v)
void fill (const dvar_matrix &_d, const dvar_vector &_v)
double get_ft (const double &ct, const double &m, const dvector &va, const dvector &ba)
dvector get_ft (dvector &ct, const double &m, const dmatrix &V, const dvector &ba)
 Solving the Baranov catch equation for multiple fleets.
dvector get_ft (dvector &ct, const double &m, const dmatrix &V, const dvector &na, const dvector &wa)
 Solving the Baranov catch equation for multiple fleets.
dvariable multifan (const dmatrix oprop, const dvar_matrix &pprop, const int &Nsamp)
dvariable multifan (const int &n, const dmatrix obs, const dvar_matrix pred, double &nef)
dvariable multifan (const double &s, const dvector obsQ, const dvar_vector &preQ, double &nmle)
double neff (const dvector &obs, const dvar_vector &pred)
dvector pearson_residuals (long m, dvector obs_p, dvector pred_p)
template<typename T , typename T1 >
plogisTraits< T >::plogisT plogis (const T1 &x, const T &location, const T &scale)
dvector rmvlogistic (const dvector &p, const double &tau2, const int &seed)
dvar_matrix splie2 (const dvector &_x1a, const dvector &_x2a, const dvar_matrix &_ya)
dvariable splin2 (const dvector &_x1a, const dvector &_x2a, const dvar_matrix _ya, dvar_matrix &_y2a, const double &x1, const double &x2)
dvar_vector spline (const dvector &_x, const dvar_vector &_y, double yp1, double ypn)
 Cubic spline interpolation.
dvariable splint (const dvector &_xa, const dvar_vector &_ya, const dvar_vector &_y2a, double x)
 Cubic spline interpolation.

Detailed Description

Library of statistic functions.

Remarks:
This library contains declaratioins for numerous statistical functions that can be used in ADMB TPL files.
Author:
Steve Martell, Chris Grandin, Mollie Brooks
Date:
12/14/2011

Definition in file statsLib.h.

Define Documentation

#define LOGISTIC_HPP

Definition at line 107 of file statsLib.h.

Typedef Documentation

typedef vcubic_spline_function* pvcubic_spline_function

Definition at line 261 of file statsLib.h.

Function Documentation

dmatrix ageLengthKey ( const dvector &  mu,
const dvector &  sig,
const dvector &  x 
)

Age Length Key.

Author:
Steven James Dean Martell UBC Fisheries Centre
Date:
2011-06-28
Parameters:
muis the mean length-at-age
sigis the std in mean length-at-age
xis the vector of break points for the length bins
Returns:
dmatrix containing the probability of length(x) for a given age(a)
See also:

Definition at line 79 of file alk.cpp.

dvar_matrix ALK ( dvar_vector  mu,
dvar_vector  sig,
dvector  x 
)

Definition at line 105 of file alk.cpp.

void bicubic_spline ( const dvector &  x,
const dvector &  y,
dvar_matrix &  knots,
dvar_matrix &  S 
)

Definition at line 107 of file vcubicspline.cpp.

dvar_vector cubic_spline ( const dvar_vector &  spline_nodes,
const dvar_vector &  ip 
)
dvariable dbeta ( const dvariable &  x,
const double &  shape1,
const double &  shape2 
)
Author:
Steven Martell
Parameters:
shape1= a parameter (a > 0)
shape2= b parameter (b > 0)
Remarks:
x must greater than 0 and less than 1. The mean is given by a/(a+b) and the variance ab/((a+b)^2(a+b+1)).

The log density function is implemented as:

\[ -\ln(\Gamma(a+b)) +\ln(\Gamma(a)) + \ln(\Gamma(b))-(a-1)\ln(x)-(b-1)\ln(1-x) \]

Definition at line 37 of file dbeta.cpp.

dvariable dbeta ( const dvariable &  x,
const dvariable &  shape1,
const dvariable &  shape2 
)

Definition at line 58 of file dbeta.cpp.

dvariable dbeta ( const dvariable &  x,
const prevariable &  shape1,
const prevariable &  shape2 
)

Definition at line 79 of file dbeta.cpp.

dvariable dbinom ( const prevariable &  x,
const double &  n,
const double &  p 
)
Author:
Steven James Dean Martell
Date:
2011-06-21
Parameters:
xnumber of sucesses
nis the number of trials
pis the binomial probability
Returns:
returns the negative loglikelihood of the normal distribution
See also:

Definition at line 39 of file dbinom.cpp.

dvariable dbinom ( const prevariable &  x,
const prevariable &  n,
const double &  p 
)
Author:
Steven James Dean Martell
Date:
2011-06-21
Parameters:
xnumber of sucesses
nis the number of trials
pis the binomial probability
Returns:
returns the negative loglikelihood of the normal distribution
See also:

Definition at line 63 of file dbinom.cpp.

dvariable dbinom ( const prevariable &  x,
const prevariable &  n,
const prevariable &  p 
)
Author:
Steven James Dean Martell
Date:
2011-06-21
Parameters:
xnumber of sucesses
nis the number of trials
pis the binomial probability
Returns:
returns the negative loglikelihood of the normal distribution
See also:

Definition at line 86 of file dbinom.cpp.

dvariable dbinom ( const dvar_vector &  x,
const dvar_vector &  n,
const dvar_vector &  p 
)
Author:
Steven James Dean Martell
Date:
2011-06-21
Parameters:
xis a vector of the number of sucesses
nis vector for the number of trials
pis a vector for the binomial probability
Returns:
returns the negative loglikelihood of the normal distribution
See also:

Definition at line 110 of file dbinom.cpp.

dvariable dbinom ( const prevariable &  x,
const dvar_vector &  n,
const dvar_vector &  p 
)

Definition at line 134 of file dbinom.cpp.

dvariable dbinom ( const dvar_vector &  x,
const prevariable &  n,
const dvar_vector &  p 
)

Definition at line 157 of file dbinom.cpp.

dvariable dbinom ( const dvar_vector &  x,
const dvar_vector &  n,
const prevariable &  p 
)

Definition at line 180 of file dbinom.cpp.

df1b2variable dbinom ( const df1b2variable &  x,
const double &  n,
const double &  p 
)

Definition at line 203 of file dbinom.cpp.

df1b2variable dbinom ( const df1b2variable &  x,
const df1b2variable &  n,
const double &  p 
)
Author:
Steven James Dean Martell
Date:
2011-06-21
Parameters:
xnumber of sucesses
nis the number of trials
pis the binomial probability
Returns:
returns the negative loglikelihood of the normal distribution
See also:

Definition at line 227 of file dbinom.cpp.

df1b2variable dbinom ( const df1b2variable &  x,
const df1b2variable &  n,
const df1b2variable &  p 
)
Author:
Steven James Dean Martell
Date:
2011-06-21
Parameters:
xnumber of sucesses
nis the number of trials
pis the binomial probability
Returns:
returns the negative loglikelihood of the normal distribution
See also:

Definition at line 250 of file dbinom.cpp.

df1b2variable dbinom ( const df1b2vector &  x,
const df1b2vector &  n,
const df1b2vector &  p 
)
Author:
Steven James Dean Martell
Date:
2011-06-21
Parameters:
xis a vector of the number of sucesses
nis vector for the number of trials
pis a vector for the binomial probability
Returns:
returns the negative loglikelihood of the normal distribution
See also:

Definition at line 274 of file dbinom.cpp.

df1b2variable dbinom ( const df1b2variable &  x,
const df1b2vector &  n,
const df1b2vector &  p 
)

Definition at line 298 of file dbinom.cpp.

df1b2variable dbinom ( const df1b2vector &  x,
const df1b2variable &  n,
const df1b2vector &  p 
)

Definition at line 321 of file dbinom.cpp.

df1b2variable dbinom ( const df1b2vector &  x,
const df1b2vector &  n,
const df1b2variable &  p 
)

Definition at line 344 of file dbinom.cpp.

dvariable dgamma ( const dvariable &  x,
const double &  a,
const double &  b 
)
Date:
2/28/2011
Author:
Steven Martell
Parameters:
xis the quantile and must be greater than 0.
ais the shape parameter and must be positive.
bis the rate parameter and must be positive.
Returns:
a dvariable object
See also:

Definition at line 37 of file dgamma.cpp.

dvariable dgamma ( const dvariable &  x,
const dvariable &  a,
const dvariable &  b 
)
Date:
2/28/2011
Author:
Steven Martell
Parameters:
xis the quantile and must be greater than 0.
ais the shape parameter and must be positive.
bis the rate parameter and must be positive.
Returns:
a dvariable object
See also:

Definition at line 66 of file dgamma.cpp.

dvariable dgamma ( const dvector &  x,
const prevariable &  a,
const prevariable &  b 
)
Date:
8/1/2011
Author:
Mollie Brooks
Parameters:
xis the quantile and must be greater than 0.
ais the shape parameter and must be positive.
bis the rate parameter and must be positive.
Returns:
a dvariable object $ \Sigma_i (-a \ln(b)+\ln(\Gamma(a))-(a-1)\ln(x_i)+b x_i) $
See also:

Definition at line 97 of file dgamma.cpp.

dvariable dgamma ( const dvector &  x,
const prevariable &  a,
const dvar_vector &  b 
)
Date:
8/1/2011
Author:
Mollie Brooks
Parameters:
xis the quantile and must be greater than 0.
ais the shape parameter and must be positive.
bis the rate parameter and must be positive.
Returns:
a dvariable object $ \Sigma_i (-a \ln(b_i)+\ln(\Gamma(a))-(a-1)\ln(x_i)+b_i x_i) $
See also:

Definition at line 129 of file dgamma.cpp.

dvariable dgamma ( const dvector &  x,
const dvar_vector &  a,
const dvar_vector &  b 
)
Date:
8/1/2011
Author:
Mollie Brooks
Parameters:
xis the quantile and must be greater than 0.
ais the shape parameter and must be positive.
bis the rate parameter and must be positive.
Returns:
a dvariable object $ \Sigma_i (-a_i \ln(b_i)+\ln(\Gamma(a_i))-(a_i-1)\ln(x_i)+b_i x_i) $
See also:

Definition at line 163 of file dgamma.cpp.

dvariable dgamma ( const dvector &  x,
const dvar_vector &  a,
const prevariable &  b 
)
Date:
8/1/2011
Author:
Mollie Brooks
Parameters:
xis the quantile and must be greater than 0.
ais the shape parameter and must be positive.
bis the rate parameter and must be positive.
Returns:
a dvariable object $ \Sigma_i (-a_i \ln(b)+\ln(\Gamma(a_i))-(a_i-1)\ln(x_i)+b x_i) $
See also:

Definition at line 197 of file dgamma.cpp.

dvariable dinvgamma ( const dvariable &  x,
const double  a,
const double  b 
)

Definition at line 16 of file dinvgamma.cpp.

dvariable dlnorm ( const prevariable &  x,
const double &  mu,
const double &  std 
)
Author:
Steven James Dean Martell
Date:
2011-06-21
Parameters:
xa differentiable variable
muis a double precision log mean
stda double precision log standard deviation
Returns:
returns the negative loglikelihood of the lognormal distribution
See also:

Definition at line 36 of file dlnorm.cpp.

dvariable dlnorm ( const prevariable &  x,
const prevariable &  mu,
const double &  std 
)
Author:
Steven James Dean Martell
Date:
2011-06-21
Parameters:
xa differentiable variable
muis a variable log mean
stda double precision log standard deviation
Returns:
returns the negative loglikelihood of the lognormal distribution
See also:

Definition at line 58 of file dlnorm.cpp.

dvariable dlnorm ( const prevariable &  x,
const prevariable &  mu,
const prevariable &  std 
)
Author:
Steven James Dean Martell
Date:
2011-06-21
Parameters:
xa differentiable variable
muis a variable log mean
stda variable log standard deviation
Returns:
returns the negative loglikelihood of the lognormal distribution
See also:

Definition at line 80 of file dlnorm.cpp.

dvariable dlnorm ( const dvar_vector &  x,
const double &  mu,
const double &  std 
)
Author:
Steven James Dean Martell
Date:
2011-06-21
Parameters:
xa differentiable vector
muis a double precision log mean
stda double precision log standard deviation
Returns:
returns the negative loglikelihood of the lognormal distribution
See also:

Definition at line 102 of file dlnorm.cpp.

dvariable dlnorm ( const dvar_vector &  x,
const prevariable &  mu,
const double &  std 
)
Author:
Steven James Dean Martell
Date:
2011-06-21
Parameters:
xa differentiable vector
muis a prevariable log mean
stda double precision log standard deviation
Returns:
returns the negative loglikelihood of the lognormal distribution
See also:

Definition at line 130 of file dlnorm.cpp.

dvariable dlnorm ( const dvar_vector &  x,
const prevariable &  mu,
const prevariable &  std 
)
Author:
Steven James Dean Martell
Date:
2011-06-21
Parameters:
xa differentiable vector
muis a prevariable log mean
stda prevariable log standard deviation
Returns:
returns the negative loglikelihood of the lognormal distribution
See also:

Definition at line 158 of file dlnorm.cpp.

dvariable dmultinom ( const dvector &  x,
const dvar_vector &  p 
)

Definition at line 15 of file dmultinom.cpp.

dvariable dmultinom ( const dmatrix  o,
const dvar_matrix &  p,
dvar_matrix &  nu,
double &  tau2,
const double  minp 
)

Definition at line 50 of file dmultinom.cpp.

dvariable dmvlogistic ( const dmatrix  o,
const dvar_matrix &  p,
dvar_matrix &  nu,
double &  tau2,
const double  minp 
)

Definition at line 15 of file dmvlogistic.cpp.

dvariable dmvlogistic ( const dmatrix  o,
const dvar_matrix &  p,
double &  tau2 
)

Definition at line 102 of file dmvlogistic.cpp.

dvariable dnorm ( const prevariable &  x,
const double &  mu,
const double &  std 
)
Author:
Steven James Dean Martell
Date:
2011-06-21
Parameters:
xa differentiable variable
muthe mean
stda double precision standard deviation
Returns:
returns the negative loglikelihood of the normal distribution
See also:

Definition at line 46 of file dnorm.cpp.

dvariable dnorm ( const dvar_vector &  x,
const double &  mu,
const double &  std 
)
Author:
Steven James Dean Martell
Date:
2011-06-21
Parameters:
xvariable vector of observations
mua double mean
stda double standard deviation
Returns:
returns the sum of negative loglikelihoods of the normal distribution
See also:

Definition at line 130 of file dnorm.cpp.

dvariable dnorm ( const prevariable &  x,
const double &  mu,
const double &  std,
bool  bLog 
)

Definition at line 59 of file dnorm.cpp.

dvariable dnorm ( const dvector &  x,
const prevariable &  mu,
const prevariable &  std 
)
Author:
Steven James Dean Martell
Date:
2011-06-21
Parameters:
xa vector of observations
mua variable mean
stda variable standard deviation
Returns:
returns the sum of negative loglikelihoods of the normal distribution
See also:

Definition at line 195 of file dnorm.cpp.

dvariable dnorm ( const dvector &  x,
const prevariable &  mu,
const prevariable &  std,
bool  dLog 
)
dvariable dnorm ( const dvar_vector &  residual,
const prevariable &  std 
)
Author:
Steven James Dean Martell
Date:
2011-06-21
Parameters:
residuala variable vector of residuals
stda variable standard deviation
Returns:
returns the sum of negative loglikelihoods of the normal distribution
See also:

Definition at line 259 of file dnorm.cpp.

dvariable dnorm ( const dvar_vector &  residual,
const double &  std 
)
Author:
Steven James Dean Martell
Date:
2011-06-21
Parameters:
residuala variable vector of residuals
stda double standard deviation
Returns:
returns the sum of negative loglikelihoods of the normal distribution
See also:

Definition at line 285 of file dnorm.cpp.

dvariable dnorm ( const dvar_vector &  residual,
const dvector &  std 
)
Author:
Steven James Dean Martell
Date:
2011-06-21
Parameters:
residuala variable vector of residuals
stda vector of standard deviations
Returns:
returns the sum of negative loglikelihoods of the normal distribution
See also:

Definition at line 311 of file dnorm.cpp.

dvariable dnorm ( const dvar_vector &  residual,
const dvar_vector  std 
)
Author:
Steven James Dean Martell
Date:
2011-06-21
Parameters:
residuala variable vector of residuals
stda variable vector of standard deviations
Returns:
returns the sum of negative loglikelihoods of the normal distribution
See also:

Definition at line 382 of file dnorm.cpp.

dvariable dnorm ( const dvar_vector &  residual)
Author:
Steven James Dean Martell
Date:
2011-06-21
Parameters:
residuala variable vector of residuals
Returns:
returns the concentrated likelihood for the normal distribution.
See also:

Definition at line 345 of file dnorm.cpp.

dvariable dnorm ( const dmatrix &  obs,
const dvar_matrix &  pred 
)
Author:
Steven James Dean Martell
Date:
2011-06-21
Parameters:
obsa matrix of observed values
preda variable matrix of predicted values
Returns:
returns the concentrated likelihood for the normal distribution.
See also:

Definition at line 363 of file dnorm.cpp.

df1b2variable dnorm ( const df1b2variable &  x,
const double &  mu,
const double &  std 
)

Definition at line 90 of file dnorm.cpp.

df1b2variable dnorm ( const df1b2variable &  x,
const double &  mu,
const double &  std,
bool  bLog 
)

Definition at line 105 of file dnorm.cpp.

df1b2variable dnorm ( const df1b2variable &  x,
const df1b2variable &  mu,
const df1b2variable &  std,
bool  bLog 
)

Definition at line 75 of file dnorm.cpp.

df1b2variable dnorm ( const df1b2vector &  x,
const df1b2variable &  mu,
const df1b2variable &  std,
bool  dLog 
)
dvariable dpois ( const double &  k,
const prevariable &  lambda 
)
Author:
Steven James Dean Martell UBC Fisheries Centre
Date:
2011-06-24
Parameters:
kobserved number
lambdaepected mean of the distribution
Returns:
returns the negative loglikelihood $ -k \ln( \lambda ) - \lambda + \ln(k)! $
See also:

Definition at line 35 of file dpois.cpp.

dvariable dpois ( const prevariable &  k,
const prevariable &  lambda 
)
Author:
Steven James Dean Martell UBC Fisheries Centre
Date:
2011-06-24
Parameters:
kobserved number
lambdaepected mean of the distribution
Returns:
returns the negative loglikelihood $ -k \ln( \lambda ) - \lambda + \ln(k!) $
See also:

Definition at line 51 of file dpois.cpp.

dvariable dstudent_t ( const dvar_vector &  residual,
const dvar_vector &  df 
)
Author:
Steven James Dean Martell UBC Fisheries Centre
Date:
2011-06-24
Parameters:
residualdvar_vector vector of residual differences
dfdvar_vector for the degrees of freedom
Returns:
returns the negative loglikelihood of the students's-t density function.
See also:

Definition at line 38 of file studentT.cpp.

dvariable dunif ( const dvariable &  x,
const double  min,
const double  max 
)

Definition at line 16 of file dunif.cpp.

dvar_vector eplogis ( const dvar_vector &  x,
const dvariable &  alpha,
const dvariable &  beta,
const dvariable &  gamma 
)

Definition at line 14 of file eplogis.cpp.

dvector eplogis ( const dvector &  x,
const double &  alpha,
const double &  beta,
const double &  gamma 
)

Definition at line 20 of file eplogis.cpp.

void fill ( const dmatrix &  _d,
const dvector &  _v 
)
Author:
Steven James Dean Martell UBC Fisheries Centre
Date:
2011-07-11
Parameters:
_da data matix that is filled with vector v
_va data vector
See also:

Definition at line 40 of file fill.cpp.

void fill ( const dvar_matrix &  _d,
const dvar_vector &  _v 
)
Author:
Steven James Dean Martell UBC Fisheries Centre
Date:
2011-07-11
Parameters:
_da data matix that is filled with vector v
_va data vector
See also:

Definition at line 75 of file fill.cpp.

double get_ft ( const double &  ct,
const double &  m,
const dvector &  va,
const dvector &  ba 
)
Author:
Steven James Dean Martell UBC Fisheries Centre
Date:
2011-07-12
Parameters:
ctthe observed catch
mthe instantaneous natural mortality rate
vaa vector of age-specific selectivities.
bathe initial numbers or biomass (same units as the catch) at age.
Returns:
ft the instantaneous fishing mortality rate for fully selected (va=1) individuals.
See also:

Definition at line 51 of file baranov.cpp.

dvector get_ft ( dvector &  ct,
const double &  m,
const dmatrix &  V,
const dvector &  ba 
)

Solving the Baranov catch equation for multiple fleets.

Author:
Steven James Dean Martell UBC Fisheries Centre
Date:
2011-07-12
Parameters:
cta vector of observed catch for each fleet.
mthe instantaneous natural mortality rate (age-independent).
Va matrix of age-specific selectivities where each row corresponds to the fleet.
bathe initial numbers or biomass (same units as the catch) at age.
Returns:
ft a vector of instantaneous fishing mortality rate for fully selected (va=1) individuals for each fishing fleet.
See also:

Definition at line 94 of file baranov.cpp.

dvector get_ft ( dvector &  ct,
const double &  m,
const dmatrix &  V,
const dvector &  na,
const dvector &  wa 
)

Solving the Baranov catch equation for multiple fleets.

Author:
Steven James Dean Martell UBC Fisheries Centre
Date:
2011-07-12
Parameters:
cta vector of observed catch for each fleet.
mthe instantaneous natural mortality rate (age-independent).
Va matrix of age-specific selectivities where each row corresponds to the fleet.
naa vector of initial numbers or biomass (same units as the catch) at age.
waa vector of mean weights-at-age
Returns:
ft a vector of instantaneous fishing mortality rate for fully selected (va=1) individuals for each fishing fleet.
See also:

Definition at line 174 of file baranov.cpp.

dvariable multifan ( const dmatrix  oprop,
const dvar_matrix &  pprop,
const int &  Nsamp 
)

Definition at line 14 of file multifan.cpp.

dvariable multifan ( const int &  n,
const dmatrix  obs,
const dvar_matrix  pred,
double &  nef 
)

Definition at line 21 of file multifan.cpp.

dvariable multifan ( const double &  s,
const dvector  obsQ,
const dvar_vector &  preQ,
double &  nmle 
)

Definition at line 31 of file multifan.cpp.

double neff ( const dvector &  obs,
const dvar_vector &  pred 
)

Definition at line 28 of file dmultinom.cpp.

dvector pearson_residuals ( long  m,
dvector  obs_p,
dvector  pred_p 
)

Definition at line 16 of file pearsonresiduals.cpp.

template<typename T , typename T1 >
plogisTraits<T>::plogisT plogis ( const T1 &  x,
const T &  location,
const T &  scale 
) [inline]

Definition at line 133 of file statsLib.h.

dvector rmvlogistic ( const dvector &  p,
const double &  tau2,
const int &  seed 
)

Definition at line 15 of file rmvlogistic.cpp.

dvar_matrix splie2 ( const dvector &  _x1a,
const dvector &  _x2a,
const dvar_matrix &  _ya 
)

Definition at line 257 of file vcubicspline.cpp.

Referenced by bicubic_spline().

dvariable splin2 ( const dvector &  _x1a,
const dvector &  _x2a,
const dvar_matrix  _ya,
dvar_matrix &  _y2a,
const double &  x1,
const double &  x2 
)

Definition at line 289 of file vcubicspline.cpp.

Referenced by bicubic_spline().

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