TMB (version 1.7.5)

template: Create cpp template to get started.

Description

Create a cpp template to get started.

Usage

template(file = NULL)

Arguments

file

Optional name of cpp file.

Details

This function generates a C++ template with a header and include statement. Here is a brief overview of the C++ syntax used to code the objective function. For a full reference see the Doxygen documentation (more information at the package URL).

Macros to read data and declare parameters:

Template Syntax	C++ type
R type	DATA_VECTOR(name)
vector	vector
DATA_MATRIX(name)	matrix
matrix	DATA_SCALAR(name)
Type	numeric(1)
DATA_INTEGER(name)	int
integer(1)	DATA_FACTOR(name)
vector	factor
DATA_IVECTOR(name)	vector
integer	DATA_SPARSE_MATRIX(name)
Eigen::SparseMatrix	dgTMatrix
DATA_ARRAY(name)	array
array	PARAMETER_MATRIX(name)
matrix	matrix
PARAMETER_VECTOR(name)	vector
vector	PARAMETER_ARRAY(name)
array	array
PARAMETER(name)	Type
numeric(1)	Template Syntax

Basic calculations:

Template Syntax

Explanation

REPORT(x)

Report x back to R

ADREPORT(x)

Report x back to R with derivatives

vector v(n1);

R equivalent of v=numeric(n1)

matrix m(n1,n2);

R equivalent of m=matrix(0,n1,n2)

array a(n1,n2,n3);

R equivalent of a=array(0,c(n1,n2,n3))

v+v,v-v,v*v,v/v

Pointwise binary operations

m*v

Matrix-vector multiply

a.col(i)

R equivalent of a[,,i]

a.col(i).col(j)

R equivalent of a[,j,i]

a(i,j,k)

R equivalent of a[i,j,k]

exp(v)

Pointwise math

m(i,j)

R equivalent of m[i,j]

v.sum()

R equivalent of sum(v)

m.transpose()

R equivalent of t(m)

Some distributions are available as C++ templates with syntax close to R's distributions:

Function header

Distribution

dnbinom2(x,mu,var,int give_log=0)

Negative binomial with mean and variance

dpois(x,lambda,int give_log=0)

Poisson distribution as in R

dlgamma(y,shape,scale,int give_log=0)

log-gamma distribution

dnorm(x,mean,sd,int give_log=0)

Normal distribution as in R

Examples

template()