merge sim_fit fix from master

Merge branch 'master' into staging # Conflicts: # DESCRIPTION
ianjonsen · Apr 29, 2024 · 8bee1c9 · 8bee1c9
2 parents 851f9f8 + 691a06a
commit 8bee1c9
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Showing 2 changed files with 6 additions and 7 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: aniMotum
 Title: Fit Continuous-Time State-Space and Latent Variable Models for Quality Control of Argos Satellite (and Other) Telemetry Data and for Estimating Changes in Animal Movement
 Version: 1.2-05.9001
-Date: 2024-02-26
+Date: 2024-04-29
 Authors@R: 
     c(
       person(given = "Ian",

diff --git a/R/sim_fit.R b/R/sim_fit.R
@@ -124,10 +124,10 @@ sim_fit <-
       mu
     }
   }
-  
+
   ## set up simulation extents
   if(!is.null(grad)) {
-    ex <- ext(grad[[1]])
+    ex <- ext(grad)
   } else {
     ## approx extents of world mercator in km
     ex <- c(-20077.51,20082.49,-19622.54,18437.46) 
@@ -206,8 +206,7 @@ sim_fit <-
 
                  mu1 <- reflect_y(mu1, ex[3:4])
                  if(!is.null(grad)) {
-                   pv <- as.numeric(c(extract(grad[[1]], rbind(mu1))[1],
-                           extract(grad[[2]], rbind(mu1))[1]))
+                   pv <- as.numeric(extract(grad, rbind(mu1)))
 
                    if(all(is.na(pv))) pv <- c(0,0) # unsure why NA's can creep in here
                    mu[i,] <- mu1 + pv * beta
@@ -262,8 +261,8 @@ sim_fit <-
                  mu1 <- wrap_x(mu[i-1,] + dxy, ex[1:2])
                  mu1 <- reflect_y(mu1, ex[3:4])
                  if(!is.null(grad)) {
-                   pv <- as.numeric(c(extract(grad[[1]], rbind(mu1))[1],
-                           extract(grad[[2]], rbind(mu1))[1]))
+                   pv <- as.numeric(extract(grad, rbind(mu1)))
+                   if(all(is.na(pv))) pv <- c(0,0) # unsure why NA's can creep in here
                    mu[i,] <- mu1 + pv * beta
                  } else {
                    mu[i,] <- mu1