Guide to adding a distribution

Background

RTMBdist provides additional probability distributions that work inside RTMB::MakeTape for automatic differentiation (AD). RTMB records a computation tape by operator overloading: every arithmetic operation on an advector is intercepted. All code must therefore be plain R arithmetic — anything that drops below R to compiled C++ is invisible to the tape. This is why built-in distributions such as dgamma must be called as RTMB::dgamma, not stats::dgamma, and why @import RTMB is needed whenever a function uses mathematical operations (exp, log, sqrt, etc.).

Every density function must support three modes:

Plain R evaluation — standard use outside of RTMB.
AD tape recording — called with an advector; gradients must flow.
Simulation and OSA residuals — called with a simref or osa object.

What to implement

At minimum, provide a density (d<dist>) and a random-number generator (r<dist>). A CDF (p<dist>) and quantile function (q<dist>) are strongly preferred; they are required for OSA residuals and quantile-based tests. All four functions must be pure R arithmetic.

Naming conventions

Follow the d/p/q/r prefix convention. Spell out distribution names rather than abbreviating — gompertz, invgamma, laplace — unless the name becomes unwieldy. Reparameterised variants take a 2 suffix: beta2, gamma2.

Files to create or modify

File	What to do
`R/<dist>.R`	implement `d`, `p`, `q`, `r` functions
`tests/testthat/test-<dist>.R`	add standard tests
`vignettes/distlist.Rmd`	add one bullet in alphabetical order

Implementing the density function

dfoo <- function(x, theta1, theta2 = 1, log = FALSE) {

  # 1. Validate inputs — skip during AD recording
  if (!ad_context()) {
    args <- as.list(environment())
    simulation_check(args)           # catches likelihood written in wrong order
    if (any(theta1 <= 0)) stop("theta1 must be positive")
  }

  # 2. Simulation and OSA escapes
  if (inherits(x, "simref"))
    return(dGenericSim("dfoo", x = x, theta1 = theta1, theta2 = theta2, log = log))
  if (inherits(x, "osa"))
    return(dGenericOSA("dfoo", x = x, theta1 = theta1, theta2 = theta2, log = log))

  # 3. Log-density
  logdens <- ...

  if (log) return(logdens)
  exp(logdens)
}

A few rules:

Always compute in log space and only call exp() at the very end.
The string passed to dGenericSim/dGenericOSA must exactly match the function name, because RTMB uses it to look up the corresponding p<dist> or r<dist>.
Parameter validation and simulation_check must be inside the if (!ad_context()) guard — they would fail or give wrong results on advector inputs.

Implementing the CDF

pfoo <- function(q, theta1, theta2 = 1, lower.tail = TRUE, log.p = FALSE) {
  if (!ad_context()) {
    if (any(theta1 <= 0)) stop("theta1 must be positive")
  }

  p <- ...   # compute CDF using RTMB:: functions where needed

  if (!lower.tail) p <- 1 - p
  if (log.p) p <- log(p)
  p
}

No simulation_check is needed in p<dist>. Apply lower.tail and log.p at the end, in that order.

Implementing the quantile function

qfoo <- function(p, theta1, theta2 = 1, lower.tail = TRUE, log.p = FALSE) {
  if (!ad_context()) {
    if (any(theta1 <= 0)) stop("theta1 must be positive")
  }

  if (log.p) p <- exp(p)          # undo transformations first ...
  if (!lower.tail) p <- 1 - p     # ... in the reverse order of pfoo

  ...   # compute quantile
}

Implementing the RNG

rfoo <- function(n, theta1, theta2 = 1) {
  if (any(theta1 <= 0)) stop("theta1 must be positive")
  ...
}

The RNG is never called during AD, so no ad_context() guard is needed. Two common approaches:

Inversion: qfoo(runif(n), theta1, theta2) — works whenever q<dist> exists.
Direct formula: use a known relationship to a base distribution, e.g. log(1 + rexp(n, rate = eta)) / b for the Gompertz distribution.

Numerical stability

Prefer numerically stable forms whenever the argument may be close to zero:

Instead of	Write
`exp(x) - 1`	`expm1(x)`
`log(1 + x)`	`log1p(x)`
`1 - exp(-x)`	`-expm1(-x)`
`x^2`, `x^3`	`x * x`, `x * x * x`
`x^a` (non-integer exponent)	`exp(a * log(x))`

Avoid expressions that produce 0 * (-Inf) — this evaluates to NaN and kills the gradient. Common fixes:

Add a small offset before taking a log: log(x + .Machine$double.xmin).
Clamp a log term that can hit -Inf at a boundary: as.finite(log(...)).

Conditional logic

Never branch on the value of x inside the tape with plain if/else or ifelse — the condition is not recorded and the gradient will be wrong. Use the smooth indicator helpers from aaa_utils.R instead:

Helper	Meaning
`iszero(x)`	1 if x == 0, else 0
`isnonzero(x)`	1 if x != 0, else 0
`ispos(x)`	1 if x >= 0, else 0
`isneg(x)`	1 if x < 0, else 0

These are defined as pure arithmetic and propagate gradients correctly. Look distributions already implemented to see how to use this.

Zero-inflated distributions

Two utility functions handle the mixture in a tape-compatible way:

log_zi(x, logdens, zeroprob) — continuous ZI: point mass at 0, density for x > 0.
log_zi_discrete(x, logdens, zeroprob) — discrete ZI: adds inflation mass on top of the PMF at 0.

Typical usage:

logdens <- RTMB::dgamma(x + .Machine$double.xmin, shape = shape, scale = scale, log = TRUE)
logdens <- log_zi(x, logdens, zeroprob)

The eps offset prevents log(0) before log_zi has a chance to zero out the weight.

Reparameterised variants

Transform parameters at the top and delegate to the base function:

dfoo2 <- function(x, mean, sd, log = FALSE) {
  if (!ad_context()) { ... }
  if (inherits(x, "simref")) return(dGenericSim("dfoo2", ...))
  if (inherits(x, "osa"))    return(dGenericOSA("dfoo2", ...))

  shape <- mean * mean / (sd * sd)
  scale <- sd * sd / mean
  dfoo(x, shape = shape, scale = scale, log = log)
}

Do not skip the simulation_check and simref/osa escapes just because the base function also has them.

Documentation

Use the @name / NULL trick to attach the shared Roxygen block to a dummy object and give each function @rdname:

#' Foo distribution
#'
#' Density, distribution function, quantile function, and random generation
#' for the Foo distribution.
#'
#' @details
#' The Foo distribution with parameter \eqn{\theta > 0} has density
#' \deqn{f(x;\,\theta) = \theta e^{-\theta x}, \quad x \ge 0.}
#'
#' @param x,q vector of quantiles
#' @param p vector of probabilities
#' @param n number of random values to return
#' @param theta positive rate parameter
#' @param log,log.p logical; if \code{TRUE}, probabilities/densities are
#'   returned as \eqn{\log(p)}.
#' @param lower.tail logical; if \code{TRUE} (default), probabilities are
#'   \eqn{P[X \le x]}, otherwise \eqn{P[X > x]}.
#' @references \url{https://en.wikipedia.org/wiki/...}
#' @return \code{dfoo} gives the density, \code{pfoo} gives the distribution
#'   function, \code{qfoo} gives the quantile function, and \code{rfoo}
#'   generates random deviates.
#' @examples
#' x <- rfoo(1, theta = 2)
#' d <- dfoo(x, theta = 2)
#' p <- pfoo(x, theta = 2)
#' q <- qfoo(p, theta = 2)
#' @name foo
NULL

#' @rdname foo
#' @export
#' @import RTMB
dfoo <- function(x, theta, log = FALSE) { ... }

Write the \deqn{} in clean mathematical form — not the numerically stable implementation. Use @import RTMB on every function that uses arithmetic or mathematical operations. Use @importFrom stats r<base> in the RNG for the base sampler.

Tests

Place tests in tests/testthat/test-<dist>.R. Use two parameter combinations and always include an AD gradient check.

Continuous distribution:

test_that("foo passes standard distribution checks (theta=1)", {
  check_continuous_dist(dfoo, pfoo, qfoo,
    xs = c(0.2, 0.5, 1, 2),
    lower = 0, upper = Inf,
    theta = 1)
})

test_that("foo passes standard distribution checks (theta=3)", {
  check_continuous_dist(dfoo, pfoo, qfoo,
    xs = c(0.1, 0.4, 0.8, 1.5),
    lower = 0, upper = Inf,
    theta = 3)
})

test_that("foo AD gradient has no NaN", {
  check_ad_gradient(dfoo, rfoo, theta = 1)
})

Choose xs so that pfoo(xs) stays well away from 0 and 1 — the q(p(x)) round-trip returns Inf or -Inf when the CDF saturates in double precision.

Other helpers for different distribution types:

Type	Helper
Continuous	`check_continuous_dist`
Continuous without quantile function	`check_continuous_dist(..., qfun = NULL)`
Zero-inflated continuous	`check_zeroinfl_dist`
Mixed/inflated (ZI+OI etc.)	`check_inflated_dist`
Discrete	`check_discrete_dist`

Vignette entry

Add one bullet to vignettes/distlist.Rmd in the correct section (Continuous / Discrete / Multivariate) in alphabetical order:

* [`foo(theta)`](../reference/foo.html): Foo distribution parameterised by rate `theta`