From ccdc19729b2fec77e571bae7cfae5fa0d509210a Mon Sep 17 00:00:00 2001
From: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
Date: Thu, 2 May 2024 22:37:47 +0100
Subject: [PATCH] rename argument silent -> strict (#648)

* rename argument silent -> strict

* example requires non-strictness

* re-render docs

* fix typo

Co-authored-by: James Azam <james.azam@lshtm.ac.uk>

---------

Co-authored-by: James Azam <james.azam@lshtm.ac.uk>
---
 R/create.R                      |  2 +-
 R/dist_spec.R                   | 19 ++++++++++---------
 man/discretise.Rd               | 13 +++++++------
 tests/testthat/test-dist_spec.R |  3 ++-
 tests/testthat/test-epinow.R    |  2 +-
 5 files changed, 21 insertions(+), 18 deletions(-)

diff --git a/R/create.R b/R/create.R
index 8f4bbfd31..55be17600 100644
--- a/R/create.R
+++ b/R/create.R
@@ -728,7 +728,7 @@ create_stan_args <- function(stan = stan_opts(),
 create_stan_delays <- function(..., time_points = 1L) {
   delays <- list(...)
   ## discretise
-  delays <- map(list(...), discretise)
+  delays <- map(delays, discretise, strict = FALSE)
   ## convolve where appropriate
   delays <- map(delays, collapse)
   ## apply tolerance
diff --git a/R/dist_spec.R b/R/dist_spec.R
index 8e8ae7362..281fb5a08 100644
--- a/R/dist_spec.R
+++ b/R/dist_spec.R
@@ -406,9 +406,10 @@ max.dist_spec <- function(x, ...) {
 #' (i.e. those with finite support and constant parameters).
 #' @title Discretise a <dist_spec>
 #' @param x A `<dist_spec>`
-#' @param silent Logical; if `TRUE` then any distribution that can't be
-#'   discretised will be returned as is. If `FALSE` then an error will be
-#'   thrown.
+#' @param strict Logical; If `TRUE` (default) an error will be thrown if a
+#' distribution cannot be discretised (e.g., because no finite maximum has been
+#' specified or parameters are uncertain). If `FALSE` then any distribution
+#' that cannot be discretised will be returned as is.
 #' @return A `<dist_spec>` where all distributions with constant parameters are
 #'   nonparametric.
 #' @export
@@ -420,14 +421,14 @@ max.dist_spec <- function(x, ...) {
 #' dist2 <- LogNormal(mean = Normal(3, 0.5), sd = Normal(2, 0.5), max = 20)
 #'
 #' # The maxf the sum of two distributions
-#' discretise(dist1 + dist2)
-discretise <- function(x, silent = TRUE) {
+#' discretise(dist1 + dist2, strict = FALSE)
+discretise <- function(x, strict = TRUE) {
   if (!is(x, "dist_spec")) {
     stop("Can only discretise a <dist_spec>.")
   }
   ## check max
   max_x <- max(x)
-  if (any(is.infinite(max_x)) && !silent) {
+  if (any(is.infinite(max_x)) && strict) {
     stop("Cannot discretise a distribution with infinite support.")
   }
   ## discretise
@@ -445,12 +446,12 @@ discretise <- function(x, silent = TRUE) {
         ))
         z$distribution <- "nonparametric"
         return(z)
-      } else if (silent) {
-        return(y)
-      } else {
+      } else if (strict) {
         stop(
           "Cannot discretise a distribution with uncertain parameters."
         )
+      } else {
+        return(y)
       }
     }
   })
diff --git a/man/discretise.Rd b/man/discretise.Rd
index f6163d29a..a24848ebd 100644
--- a/man/discretise.Rd
+++ b/man/discretise.Rd
@@ -5,16 +5,17 @@
 \alias{discretize}
 \title{Discretise a <dist_spec>}
 \usage{
-discretise(x, silent = TRUE)
+discretise(x, strict = TRUE)
 
-discretize(x, silent = TRUE)
+discretize(x, strict = TRUE)
 }
 \arguments{
 \item{x}{A \verb{<dist_spec>}}
 
-\item{silent}{Logical; if \code{TRUE} then any distribution that can't be
-discretised will be returned as is. If \code{FALSE} then an error will be
-thrown.}
+\item{strict}{Logical; If \code{TRUE} (default) an error will be thrown if a
+distribution cannot be discretised (e.g., because no finite maximum has been
+specified or parameters are uncertain). If if \code{FALSE} then any distribution
+that cannot be discretised will be returned as is.}
 }
 \value{
 A \verb{<dist_spec>} where all distributions with constant parameters are
@@ -35,5 +36,5 @@ dist1 <- Gamma(mean = 5, sd = 1, max = 20)
 dist2 <- LogNormal(mean = Normal(3, 0.5), sd = Normal(2, 0.5), max = 20)
 
 # The maxf the sum of two distributions
-discretise(dist1 + dist2)
+discretise(dist1 + dist2, strict = FALSE)
 }
diff --git a/tests/testthat/test-dist_spec.R b/tests/testthat/test-dist_spec.R
index 8c028a825..992e746a2 100644
--- a/tests/testthat/test-dist_spec.R
+++ b/tests/testthat/test-dist_spec.R
@@ -14,7 +14,8 @@ test_that("dist_spec returns correct output for fixed lognormal distribution", {
 
 test_that("dist_spec returns correct output for uncertain gamma distribution", {
   result <- discretise(
-    Gamma(shape = Normal(3, 0.5), rate = Normal(2, 0.5), max = 19)
+    Gamma(shape = Normal(3, 0.5), rate = Normal(2, 0.5), max = 19),
+    strict = FALSE
   )
   expect_equal(result[[1]]$parameters$shape[[1]]$parameters$mean, 3)
   expect_equal(result[[1]]$parameters$shape[[1]]$parameters$sd, 0.5)
diff --git a/tests/testthat/test-epinow.R b/tests/testthat/test-epinow.R
index 876fdcbba..50264ef18 100644
--- a/tests/testthat/test-epinow.R
+++ b/tests/testthat/test-epinow.R
@@ -28,7 +28,7 @@ test_that("epinow produces expected output when run with default settings", {
         control = list(adapt_delta = 0.8)
       ),
       logs = NULL, verbose = FALSE
-      )
+    )
   )))
 
   expect_equal(names(out), expected_out)