Merge pull request #25 from hmecology/ranef_updates

Consolidate `ranef` methods

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: unmarked
-Version: 1.4.1.9016
-Date: 2024-08-21
+Version: 1.4.1.9017
+Date: 2024-08-22
 Type: Package
 Title: Models for Data from Unmarked Animals
 Authors@R: c(
@@ -47,12 +47,13 @@ LazyData: yes
 Collate: 'classes.R' 'unmarkedEstimate.R' 'unmarkedFrame.R'
     'unmarkedFit.R' 'utils.R' 'getDesign.R'
     'fitted.R' 'residuals.R' 'update.R' 'simulate.R' 'nonparboot.R' 'getP.R'
+    'ranef.R' 'posteriorSamples.R'
     'colext.R' 'distsamp.R'
     'multinomPois.R' 'occu.R' 'occuRN.R' 'occuMulti.R' 'pcount.R' 'gmultmix.R'
     'pcountOpen.R' 'gdistsamp.R' 'unmarkedFitList.R' 'unmarkedLinComb.R'
-    'ranef.R' 'parboot.R' 'occuFP.R' 'gpcount.R' 'occuPEN.R' 'pcount.spHDS.R'
+    'parboot.R' 'occuFP.R' 'gpcount.R' 'occuPEN.R' 'pcount.spHDS.R'
     'occuMS.R' 'occuTTD.R' 'distsampOpen.R' 'multmixOpen.R' 
-    'unmarkedCrossVal.R' 'piFun.R' 'vif.R' 'makePiFun.R' 'posteriorSamples.R'
+    'unmarkedCrossVal.R' 'piFun.R' 'vif.R' 'makePiFun.R'
     'nmixTTD.R'
     'gdistremoval.R'
     'plotEffects.R'

R/IDS.R

@@ -596,8 +596,8 @@ setMethod("nonparboot_internal", "unmarkedFitIDS",
    stop("Not currently supported for unmarkedFitIDS", call.=FALSE)
 })
 
-setMethod("ranef", "unmarkedFitIDS",
-    function(object, B = 0, keepOldSamples = TRUE, ...)
+setMethod("ranef_internal", "unmarkedFitIDS",
+    function(object, ...)
 {
    stop("Not currently supported for unmarkedFitIDS", call.=FALSE)
 })

R/gdistremoval.R

@@ -595,7 +595,7 @@ setMethod("residuals_internal", "unmarkedFitGDR", function(object){
 
 # ranef
 
-setMethod("ranef", "unmarkedFitGDR", function(object){
+setMethod("ranef_internal", "unmarkedFitGDR", function(object, ...){
 
   M <- numSites(object@data)
   T <- object@data@numPrimary

R/goccu.R

@@ -208,7 +208,7 @@ setMethod("fitted_internal", "unmarkedFitGOccu", function(object){
 
 
 # based on ranef for GPC
-setMethod("ranef", "unmarkedFitGOccu", function(object, ...){
+setMethod("ranef_internal", "unmarkedFitGOccu", function(object, ...){
 
   M <- numSites(object@data)
   JT <- obsNum(object@data)

R/occuCOP.R

@@ -458,7 +458,7 @@ setMethod("nonparboot_internal", "unmarkedFitOccuCOP",
 
 
 ## ranef ----
-setMethod("ranef", "unmarkedFitOccuCOP", function(object, ...) {
+setMethod("ranef_internal", "unmarkedFitOccuCOP", function(object, ...) {
   # Sites removed (srm) and sites kept (sk)
   srm <- object@sitesRemoved
   if (length(srm) > 0) {

R/posteriorSamples.R

@@ -19,6 +19,7 @@ setMethod("posteriorSamples", "unmarkedRanef", function(object, nsims=100, ...)
   out <- array(NA, c(N, T, nsims))
 
   for (n in 1:N){
+    if(any(is.na(object@post[n,,]))) next
     for (t in 1:T){
         out[n, t, ] <- sample(0:(K-1), nsims, replace=TRUE,
                               prob=object@post[n,,t])