Fix simulation with random effects for distsamp and multinomPois, fixes #235

2 files changed, 10 insertions, 10 deletions

diff --git a/R/simulate.R b/R/simulate.R
index 7868948..7793820 100644
--- a/R/simulate.R
+++ b/R/simulate.R
@@ -66,7 +66,7 @@ setMethod("simulate", "character",
   coefs <- check_coefs(coefs, fit, formulas)
   coefs <- generate_random_effects(coefs, fit, formulas)
   fit <- replace_estimates(fit, coefs)
-  ysims <- simulate(fit, nsim)
+  ysims <- suppressWarnings(simulate(fit, nsim))
   umf <- fit@data
   # fix this
   umfs <- lapply(ysims, function(x){
@@ -533,5 +533,5 @@ setMethod("simulate_fit", "unmarkedFitGDR",
   gdistremoval(lambdaformula=formulas$lambda, phiformula=formulas$phi,
                removalformula=formulas$rem, distanceformula=formulas$dist,
                data=umf, keyfun=keyfun, output=output, unitsOut=unitsOut,
-               mixture=mixture, K=K, se=FALSE, control=list(maxit=1))
+               mixture=mixture, K=K, se=FALSE, control=list(maxit=1), method='L-BFGS-B')
 })
diff --git a/R/unmarkedFit.R b/R/unmarkedFit.R
index 0a8d107..6557b9d 100644
--- a/R/unmarkedFit.R
+++ b/R/unmarkedFit.R
@@ -1631,13 +1631,13 @@ setMethod("getP", "unmarkedFitDS",
     umf <- object@data
     designMats <- getDesign(umf, formula, na.rm = na.rm)
     y <- designMats$y
-    V <- designMats$V
+    V <- cbind(designMats$V, designMats$Z_det)
     V.offset <- designMats$V.offset
     if (is.null(V.offset))
         V.offset <- rep(0, nrow(V))
     M <- nrow(y)
     J <- ncol(y)
-    ppars <- coef(object, type = "det")
+    ppars <- coef(object, type = "det", fixedOnly=FALSE)
     db <- umf@dist.breaks
     w <- diff(db)
     survey <- umf@survey
@@ -1902,13 +1902,13 @@ setMethod("getP", "unmarkedFitMPois", function(object, na.rm = TRUE)
     umf <- object@data
     designMats <- getDesign(umf, formula, na.rm = na.rm)
     y <- designMats$y
-    V <- designMats$V
+    V <- as.matrix(cbind(designMats$V, designMats$Z_det))
     V.offset <- designMats$V.offset
     if (is.null(V.offset))
         V.offset <- rep(0, nrow(V))
     M <- nrow(y)
     J <- obsNum(umf) #ncol(y)
-    ppars <- coef(object, type = "det")
+    ppars <- coef(object, type = "det", fixedOnly=FALSE)
     p <- plogis(V %*% ppars + V.offset)
     p <- matrix(p, M, J, byrow = TRUE)
     pi <- do.call(piFun, list(p = p))
@@ -2063,13 +2063,13 @@ setMethod("simulate", "unmarkedFitDS",
     w <- diff(db)
     designMats <- getDesign(umf, formula, na.rm = na.rm)
     y <- designMats$y
-    X <- designMats$X
+    X <- as.matrix(cbind(designMats$X, designMats$Z_state))
     X.offset <- designMats$X.offset
     if (is.null(X.offset))
         X.offset <- rep(0, nrow(X))
     M <- nrow(y)
     J <- ncol(y)
-    lamParms <- coef(object, type = "state")
+    lamParms <- coef(object, type = "state", fixedOnly=FALSE)
     lambda <- drop(exp(X %*% lamParms + X.offset))
     if(identical(object@output, "density")) {
         switch(umf@survey,
@@ -2342,14 +2342,14 @@ setMethod("simulate", "unmarkedFitMPois",
     umf <- object@data
     designMats <- getDesign(umf, formula, na.rm = na.rm)
     y <- designMats$y
-    X <- designMats$X
+    X <- as.matrix(cbind(designMats$X, designMats$Z_state))
     X.offset <- designMats$X.offset
     if (is.null(X.offset)) {
         X.offset <- rep(0, nrow(X))
         }
     M <- nrow(y)
     J <- ncol(y)
-    lamParms <- coef(object, type = "state")
+    lamParms <- coef(object, type = "state", fixedOnly=FALSE)
     lam <- as.numeric(exp(X %*% lamParms + X.offset))
     lamvec <- rep(lam, each = J)
     pivec <- as.vector(t(getP(object, na.rm = na.rm)))