Fix fitted with certain Dail-Madsen models, fixes #278

rbchan · Apr 1, 2024 · 1815977 · 1815977
1 parent 5b2b00e
commit 1815977
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Showing 2 changed files with 16 additions and 3 deletions.
diff --git a/R/unmarkedFit.R b/R/unmarkedFit.R
@@ -559,7 +559,7 @@ setMethod("fitted", "unmarkedFitDailMadsen",
     if(is.null(Xom.offset)) Xom.offset <- rep(0, M*(T-1))
     if(is.null(Xiota.offset)) Xiota.offset <- rep(0, M*(T-1))
 
-    lambda <- exp(Xlam %*% coef(object, 'lambda') + Xlam.offset)
+    lambda <- as.vector(exp(Xlam %*% coef(object, 'lambda') + Xlam.offset))
     if(identical(mixture, "ZIP")) {
         psi <- plogis(coef(object, type="psi"))
         lambda <- (1-psi)*lambda
@@ -618,7 +618,7 @@ setMethod("fitted", "unmarkedFitDailMadsen",
                 N[i,t] <- N[i,t-1]*exp(gamma[i,t-1]*(1-N[i,t-1]/omega[i,t-1]))+
                     iota[i, t-1]
             else if(identical(dynamics, "gompertz"))
-                N[i,1] <- N[i,t-1] * exp(gamma[i,t-1]*(1-log(N[i,t-1]+1)/
+                N[i,t] <- N[i,t-1] * exp(gamma[i,t-1]*(1-log(N[i,t-1]+1)/
                   log(omega[i,t-1]+1))) + iota[i, t-1]
             else
                 N[i,t] <- N[i,t-1] * omega[i,t-1] + gamma[i,t-1]
@@ -633,7 +633,7 @@ setMethod("fitted", "unmarkedFitDailMadsen",
                         N[i, t] <- N[i, t] * exp(gamma[i, t-1] * (1 - N[i,t] /
                             omega[i,t-1]))+ iota[i, t-1]
                     else if(identical(dynamics, "gompertz"))
-                        N[i, 1] <- N[i, t] * exp(gamma[i, t-1] * (1 -
+                        N[i, t] <- N[i, t] * exp(gamma[i, t-1] * (1 -
                             log(N[i, t]+1) / log(omega[i, t-1] + 1))) +
                             iota[i, t-1]
                     else

diff --git a/tests/testthat/test_pcountOpen.R b/tests/testthat/test_pcountOpen.R
@@ -353,11 +353,24 @@ test_that("pcountOpen can fit models with various dynamics",{
                        c(1.2131713,  0.7301736,  1.1949289),
                        tolerance=1e-5)
 
+    # issue #278
+    ft2 <- fitted(m2)
+    expect_equal(dim(ft2), c(20,5)) 
+
     m3 <- pcountOpen(~1, ~1, ~1, ~1, umf, K=20, dynamics="trend")
     expect_equivalent(coef(m3),
                        c(1.67211946, -0.06534021, 0.18287762),
                        tolerance=1e-5)
 
+    m4 <- pcountOpen(~1, ~1, ~1, ~1, umf, K=20, dynamics="gompertz")
+    expect_equivalent(coef(m3),
+                       c(1.67211946, -0.06534021, 0.18287762),
+                       tolerance=1e-5)
+
+    # issue #278
+    ft4 <- fitted(m4)
+    expect_true(all(!is.na(ft4)))
+
 })