From e5cc9d7132b14c3fe928eb13009b308ec861fc6f Mon Sep 17 00:00:00 2001
From: dochvam <dochvam@gmail.com>
Date: Thu, 20 Feb 2020 10:27:37 -0800
Subject: [PATCH 1/2] fix date, fix DHMM double reg, separate dynamic selection
 of Nmin and Nmax

---
 DESCRIPTION   |  2 +-
 R/dDHMM.R     | 31 -------------------------------
 R/dNmixture.R | 11 +++++++----
 3 files changed, 8 insertions(+), 36 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index f96d095..8dbf61f 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -8,7 +8,7 @@ Authors@R: c(person("Benjamin R.", "Goldstein", role = c("aut", "cre"),
               person("Daniel", "Turek", role = "aut"),
               person("Lauren", "Ponisio", role = "aut"),
               person("Perry", "de Valpine", role = "aut"))
-Date: 2019-09-24
+Date: 2020-02-20
 Description: Common ecological distributions for 'nimble' models in the form of nimbleFunction objects. 
   Includes Cormack-Jolly-Seber, occupancy, dynamic occupancy, hidden Markov, and dynamic hidden Markov models.
   (Jolly (1965) <doi:10.2307/2333826>, Seber (1965) <10.2307/2333827>, Turek et al. (2016) <doi:10.1007/s10651-016-0353-z>).
diff --git a/R/dDHMM.R b/R/dDHMM.R
index af30c35..48c6cb2 100644
--- a/R/dDHMM.R
+++ b/R/dDHMM.R
@@ -330,34 +330,3 @@ rDHMMo <- nimbleFunction(
 #     }
 #     return(ans)
 #   })
-
-
-
-registerDistributions(list(
-  dDHMM = list(
-    BUGSdist = "dDHMM(init, probObs, probTrans, len)",
-    Rdist = "dDHMM(init, probObs, probTrans, len)",
-    discrete = TRUE,
-    types = c('value = double(1)',
-              'init = double(1)',
-              'probObs = double(2)',
-              'probTrans = double(3)',
-              'len = double()'),
-    mixedSizes = TRUE,
-    pqAvail = FALSE))
-  )
-
-registerDistributions(list(
-  dDHMMo = list(
-    BUGSdist = "dDHMMo(init, probObs, probTrans, len)",
-    Rdist = "dDHMMo(init, probObs, probTrans, len)",
-    discrete = TRUE,
-    types = c('value = double(1)',
-              'init = double(1)',
-              'probObs = double(3)',
-              'probTrans = double(3)',
-              'len = double()'),
-    mixedSizes = TRUE,
-    pqAvail = FALSE))
-  )
-
diff --git a/R/dNmixture.R b/R/dNmixture.R
index c817b4c..042b33b 100644
--- a/R/dNmixture.R
+++ b/R/dNmixture.R
@@ -173,11 +173,12 @@ dNmixture_v <- nimbleFunction(
 
     ## For each x, the conditional distribution of (N - x | x) is pois(lambda * (1-p))
     ## We determine the lowest N and highest N at extreme quantiles and sum over those.
-    if (Nmin == -1 & Nmax == -1) {
+    if (Nmin == -1) {
       Nmin <- min(x + qpois(0.00001, lambda * (1 - prob)))
-      Nmax <- max(x + qpois(0.99999, lambda * (1 - prob)))
     }
-    Nmin <- max( max(x), Nmin ) ## set Nmin to at least the largest x
+    if (Nmax == -1) {
+      Nmax <- max(x + qpois(0.99999, lambda * (1 - prob)))
+    }    Nmin <- max( max(x), Nmin ) ## set Nmin to at least the largest x
 
     logProb <- -Inf
     if (Nmax > Nmin) {
@@ -217,8 +218,10 @@ dNmixture_s <- nimbleFunction(
 
     ## For each x, the conditional distribution of (N - x | x) is pois(lambda * (1-p))
     ## We determine the lowest N and highest N at extreme quantiles and sum over those.
-    if (Nmin == -1 & Nmax == -1) {
+    if (Nmin == -1) {
       Nmin <- min(x + qpois(0.00001, lambda * (1 - prob)))
+    }
+    if (Nmax == -1) {
       Nmax <- max(x + qpois(0.99999, lambda * (1 - prob)))
     }
     Nmin <- max( max(x), Nmin ) ## set Nmin to at least the largest x

From 9d65989f318231d07d41b6b524abd3a235783793 Mon Sep 17 00:00:00 2001
From: dochvam <dochvam@gmail.com>
Date: Thu, 20 Feb 2020 10:42:47 -0800
Subject: [PATCH 2/2] Fix syntax glitch in dNmixture

---
 R/dNmixture.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/R/dNmixture.R b/R/dNmixture.R
index 042b33b..932168c 100644
--- a/R/dNmixture.R
+++ b/R/dNmixture.R
@@ -178,7 +178,8 @@ dNmixture_v <- nimbleFunction(
     }
     if (Nmax == -1) {
       Nmax <- max(x + qpois(0.99999, lambda * (1 - prob)))
-    }    Nmin <- max( max(x), Nmin ) ## set Nmin to at least the largest x
+    }
+    Nmin <- max( max(x), Nmin ) ## set Nmin to at least the largest x
 
     logProb <- -Inf
     if (Nmax > Nmin) {