From 3cbec00794c30fa626a2ef731215a29600b2af8c Mon Sep 17 00:00:00 2001
From: Christopher Paciorek <paciorek@stat.berkeley.edu>
Date: Sun, 13 Oct 2024 14:04:57 -0700
Subject: [PATCH] Turn off AD warnings for `is.na`.

---
 R/dBetaBinom.R  | 4 ++++
 R/dCJS.R        | 6 ++++++
 R/dNmixtureAD.R | 6 ++++++
 R/dOcc.R        | 4 ++++
 R/utils.R       | 4 ++++
 5 files changed, 24 insertions(+)

diff --git a/R/dBetaBinom.R b/R/dBetaBinom.R
index 0c76153..2563f3f 100644
--- a/R/dBetaBinom.R
+++ b/R/dBetaBinom.R
@@ -68,6 +68,8 @@ nimBetaFun <- nimbleFunction(
     returnType(double(0))
   }, buildDerivs=list(run=list()))
 
+nimbleOptions(doADerrorTraps = FALSE)
+
 #' @rdname dBetaBinom
 #' @export
 dBetaBinom_v <- nimbleFunction(
@@ -124,6 +126,8 @@ dBetaBinom_s <- nimbleFunction(
   buildDerivs = list(run=list(ignore = c('i','xi')))
 )
 
+nimbleOptions(doADerrorTraps = TRUE)
+
 #' @rdname dBetaBinom
 #' @export
 #' @importFrom stats rbeta
diff --git a/R/dCJS.R b/R/dCJS.R
index f3eb973..c69de9f 100644
--- a/R/dCJS.R
+++ b/R/dCJS.R
@@ -145,6 +145,10 @@
 
 NULL
 
+## Turn off warnings about use of `is.na` in deriv-enabled nimbleFunction.
+
+nimbleOptions(doADerrorTraps = FALSE)
+
 #' @rdname dCJS
 #' @export
 dCJS_ss <- nimbleFunction(
@@ -342,6 +346,8 @@ dCJS_vv <- nimbleFunction(
   }, buildDerivs = list(run = list(ignore = c('i', "xt", "t")))
 )
 
+nimbleOptions(doADerrorTraps = TRUE)
+
 #' @rdname dCJS
 #' @export
 rCJS_ss <- nimbleFunction(
diff --git a/R/dNmixtureAD.R b/R/dNmixtureAD.R
index beb70eb..c8449c1 100644
--- a/R/dNmixtureAD.R
+++ b/R/dNmixtureAD.R
@@ -61,6 +61,9 @@
 
 ##### Regular N-mixture #####
 NULL
+
+nimbleOptions(doADerrorTraps = FALSE)
+
 #' @rdname dNmixtureAD
 #' @export
 dNmixtureAD_v <- nimbleFunction(
@@ -553,6 +556,9 @@ dNmixtureAD_BBNB_oneObs <- nimbleFunction(
   }, buildDerivs=list(run=list())
 )
 
+nimbleOptions(doADerrorTraps = TRUE)
+
+
 ##### rNmixtureAD extensions #####
 NULL
 #' @rdname dNmixtureAD
diff --git a/R/dOcc.R b/R/dOcc.R
index 672c34d..d9628ae 100644
--- a/R/dOcc.R
+++ b/R/dOcc.R
@@ -127,6 +127,8 @@
 #' Occ_model$calculate()
 #' # Use the model for a variety of other purposes...
 
+nimbleOptions(doADerrorTraps = FALSE)
+
 #' @export
 #' @rdname dOcc
 dOcc_s <- nimbleFunction(
@@ -178,6 +180,8 @@ dOcc_v <- nimbleFunction(
   }, buildDerivs = list(run = list(ignore = c("i", "xi")))
 )
 
+nimbleOptions(doADerrorTraps = TRUE)
+
 #' @export
 #' @rdname dOcc
 
diff --git a/R/utils.R b/R/utils.R
index 3ce140b..8d66f57 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -92,6 +92,8 @@ nimNmixPois_logFac <- nimbleFunction(
     returnType(double())
   }, buildDerivs = list(run = list()))
 
+nimbleOptions(doADerrorTraps = FALSE)
+
 #' @rdname dNmixture_steps
 #' @importFrom stats dpois
 #' @export
@@ -322,3 +324,5 @@ dNmixture_BBNB_steps <- nimbleFunction(
   },
   buildDerivs = list(run = list(ignore = c("i","j","xj")))
 )
+
+nimbleOptions(doADerrorTraps = TRUE)