gadget3 (version 0.14-0)

aab_env: Gadget3 global environment

Description

Functions available to any gadget3 model

ADREPORT

TMB's ADREPORT function. See sdreport documentation

as_integer

C++ compatible equivalent to as.integer

as.numeric

R as.numeric or TMB asDouble

assert_msg

C++/R function that ensures expression is true, or stops model.

assert_msg(x > 0, "x must be positive")

avoid_zero

Adds small value to input to ensure output is never zero avoid_zero_vec is identical to avoid_zero, and is only present for backward compatibility.

bounded / bounded_vec

Ensures x is within limits b & a.

If x positive, return a. If x negative, b. If x -10..10, smoothly transition from b to a

bounded_vec(x, 200, 100)

g3_matrix_vec

Apply matrix transformation tf to vector vec, return resultant vector.

g3_matrix_vec(tf, vec)

lgamma_vec

Vector equivalent of lgamma

logspace_add

TMB's logspace_add, essentially a differentiable version of pmax.

normalize_vec

Divide vector a by it's sum, i.e. so it now sums to 1. If vector is all-zero, return an all-zero vector instead.

nvl

Return first non-null argument. NB: No C++ implementation.

print_array

Utility to pretty-print array ar

ratio_add_pop

Sum orig_vec & new_vec according to ratio of orig_amount & new_amount

nonconform_add / nonconform_mult / nonconform_div / nonconform_div_avz

Scalar sum/multiply/divide 2 non-conforming arrays, by treating the latter as a vector and repeating as many times as required. Results will be structured identically to the first array.

nonconform_div_avz(x, y) is equivalent to nonconform_div(x, avoid_zero_vec(y))

REPORT

TMB's REPORT function.

REprintf

Equivalent of RCpp REprintf

Rprintf

Equivalent of RCpp Rprintf

Details

g3_env is the top-level environment that any gadget3 model uses, populated with utility functions.

NB: Several functions have _vec variants. Due to TMB limitations these should be used when you have a vector not scalar input.

Examples

## avoid_zero
g3_eval(quote( c( avoid_zero(0), avoid_zero(10) ) ))
g3_eval(quote( avoid_zero(0:5) ))

## bounded / bounded_vec
curve(g3_eval(quote( bounded(x, 200, 100) ), x = x), -100, 100)

## logspace_add
curve(g3_eval(quote( logspace_add(x, 10) ), x = x), 0, 40)

## normalize_vec
g3_eval(quote( normalize_vec(c( 4, 4, 8, 2 )) ))

## nonconform_mult
g3_eval(quote( nonconform_mult(
    array(seq(0, 4*5*6), dim = c(4,5,6)),
    c(1e1, 1e2, 1e3, 1e4)) ))

## nonconform_div_avz
g3_eval(quote( nonconform_div_avz(
    array(seq(0, 4*5*6), dim = c(4,5,6)),
    c(1e1, 1e2, 0, 1e4)) ))
g3_eval(quote( nonconform_div(
    array(seq(0, 4*5*6), dim = c(4,5,6)),
    avoid_zero(c(1e1, 1e2, 0, 1e4))) ))