template: Create cpp template to get started.
In TMB: Template Model Builder: A General Random Effect Tool Inspired by 'ADMB'

template

R Documentation

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<Type>	vector
DATA_MATRIX(name)	matrix<Type>	matrix
DATA_SCALAR(name)	Type	numeric(1)
DATA_INTEGER(name)	int	integer(1)
DATA_FACTOR(name)	vector<int>	factor
DATA_IVECTOR(name)	vector<int>	integer
DATA_SPARSE_MATRIX(name)	Eigen::SparseMatrix<Type>	dgTMatrix
DATA_ARRAY(name)	array<Type>	array
PARAMETER_MATRIX(name)	matrix<Type>	matrix
PARAMETER_VECTOR(name)	vector<Type>	vector
PARAMETER_ARRAY(name)	array<Type>	array
PARAMETER(name)	Type	numeric(1)

Basic calculations:

Template Syntax	Explanation
REPORT(x)	Report x back to R
ADREPORT(x)	Report x back to R with derivatives
vector<Type> v(n1);	R equivalent of v=numeric(n1)
matrix<Type> m(n1,n2);	R equivalent of m=matrix(0,n1,n2)
array<Type> 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