occuRN ranef gets K automatically

biodiverse · Sep 18, 2024 · dd14d5f · dd14d5f
1 parent 6572a2f
commit dd14d5f
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Showing 3 changed files with 11 additions and 6 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: unmarked
-Version: 1.4.3.9002
-Date: 2024-09-16
+Version: 1.4.3.9003
+Date: 2024-09-18
 Type: Package
 Title: Models for Data from Unmarked Animals
 Authors@R: c(

diff --git a/R/ranef.R b/R/ranef.R
@@ -680,10 +680,15 @@ setMethod("ranef_internal", "unmarkedFitOccuMulti", function(object, ...){
 
 
 setMethod("ranef_internal", "unmarkedFitOccuRN", function(object, ...){
-    K <- list(...)$K
-    if(is.null(K)) {
+
+    if(methods::.hasSlot(object, "K")){
+      K <- object@K
+    } else {
+      K <- list(...)$K
+      if(is.null(K)) {
         warning("You did not specify K, the maximum value of N, so it was set to 50")
         K <- 50
+      }
     }
     lam <- predict(object, type="state", level=NULL, na.rm=FALSE)$Predicted # Too slow
     R <- length(lam)

diff --git a/tests/testthat/test_occuRN.R b/tests/testthat/test_occuRN.R
@@ -45,7 +45,7 @@ test_that("occuRN can fit models",{
   expect_equal(dim(res), dim(woodthrushUMF@y))
   expect_equal(res[1,1], 0.73757, tol=1e-4)
 
-  r <- ranef(fm_C, K=10)
+  r <- ranef(fm_C)
   expect_equal(dim(r@post), c(50,11,1))
   expect_equal(bup(r)[1:4], c(5.1059,5.6125,3.2689,5.6125), tol=1e-4)
 
@@ -126,7 +126,7 @@ test_that("occuRN can handle NAs",{
   expect_true(is.na(ft[1,1])) # missing obs cov
   expect_true(all(!is.na(ft[2,]))) # missing site cov
 
-  r <- ranef(fm_na, K=30)
+  r <- ranef(fm_na)
   expect_equal(nrow(r@post), numSites(fm_na@data))
   expect_true(all(is.na(r@post[1:2,,1])))
 })