Merge branch 'master' into remove_lme4

rbchan · Jan 30, 2024 · 2fcba4f · 2fcba4f
2 parents 5506119 + 85603a5
commit 2fcba4f
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Showing 42 changed files with 3,669 additions and 37 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -12,3 +12,5 @@ README.Rmd
 ^\.github$
 ^_pkgdown\.yml$
 ^vignettes/colext.Rmd.orig
+^.*\.Rproj$
+^\.Rproj\.user$
diff --git a/.gitignore b/.gitignore
@@ -8,6 +8,7 @@
 *.Rd~
 *.R~
 NAMESPACE~
+.RData
 
 
 # TeX
@@ -28,3 +29,6 @@ bc
 .Rhistory
 symbols.rds
 
+# Rproj
+.Rproj.user
+*.Rproj
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: unmarked
-Version: 1.3.2.9005
-Date: 2023-12-10
+Version: 1.4.1.9001
+Date: 2024-01-23
 Type: Package
 Title: Models for Data from Unmarked Animals
 Authors@R: c(
@@ -12,6 +12,7 @@ Authors@R: c(
     person("Jeff", "Hostetler", role="aut"),
     person("Rebecca", "Hutchinson", role="aut"),
     person("Adam", "Smith", role="aut"),
+    person("Lea", "Pautrel", role="aut"),
     person("Marc", "Kery", role="ctb"),
     person("Mike", "Meredith", role="ctb"),
     person("Auriel", "Fournier", role="ctb"),
@@ -51,12 +52,14 @@ Collate: 'classes.R' 'unmarkedEstimate.R' 'mapInfo.R' 'unmarkedFrame.R'
     'unmarkedCrossVal.R' 'piFun.R' 'vif.R' 'makePiFun.R' 'posteriorSamples.R'
     'nmixTTD.R'
     'gdistremoval.R'
+    'IDS.R'
     'plotEffects.R'
     'mixedModelTools.R'
     'power.R' 
     'simulate.R'
     'predict.R'
     'goccu.R'
+    'occuCOP.R'
     'RcppExports.R'
     'zzz.R'
 LinkingTo: 

diff --git a/NAMESPACE b/NAMESPACE
@@ -7,7 +7,7 @@ importFrom(stats, confint, fitted, coef, vcov, predict, update, profile,
            pnorm, qchisq, qnorm, quantile, rbinom,
            reshape, rmultinom, rnbinom, rpois, runif, sd, uniroot,
            update.formula, sigma)
-importFrom(graphics, plot, hist, abline, axis, lines, points, polygon, segments)
+importFrom(graphics, plot, hist, abline, axis, lines, points, polygon, segments, title)
 importFrom(utils, head, read.csv)
 importFrom(grDevices, devAskNewPage, dev.interactive, palette.colors)
 importFrom(MASS, mvrnorm)
@@ -23,7 +23,8 @@ importFrom(Rcpp, evalCpp)
 export(occu, occuFP, occuRN, pcount, pcountOpen, multinomPois, distsamp,
        colext, gmultmix, gdistsamp, gpcount, occuPEN, occuPEN_CV, occuMulti,
        occuMS, computeMPLElambda, pcount.spHDS, occuTTD, distsampOpen,
-       multmixOpen, nmixTTD, gdistremoval, goccu)
+       multmixOpen, nmixTTD, gdistremoval, goccu, occuCOP, IDS)
+
 export(removalPiFun, doublePiFun)
 export(makeRemPiFun, makeCrPiFun, makeCrPiFunMb, makeCrPiFunMh)
 
@@ -32,7 +33,7 @@ exportClasses(unmarkedFit, unmarkedFitOccu, unmarkedFitOccuFP, unmarkedFitDS,
               unmarkedFitPCount, unmarkedFitMPois, unmarkedFitPCO,
               unmarkedFrameDSO, unmarkedFitDSO,
               unmarkedFrameMMO, unmarkedFitMMO,
-              unmarkedFitOccuMulti,
+              unmarkedFitOccuMulti, unmarkedFitIDS,
               unmarkedFrame, unmarkedFrameOccu, unmarkedFramePCount,
               unmarkedFrameMPois, unmarkedFrameDS, unmarkedMultFrame,
               unmarkedFrameGMM, unmarkedFrameGDS, unmarkedFramePCO,
@@ -50,7 +51,8 @@ exportMethods(backTransform, coef, confint, coordinates, fitted, getData,
               "siteCovs<-", summary, update, vcov, yearlySiteCovs,
               "yearlySiteCovs<-", "[", smoothed, projected, nonparboot, logLik,
               LRT, ranef, bup, crossVal, posteriorSamples, sigma, randomTerms, 
-              optimizePenalty, unmarkedPowerList, plotEffectsData, plotEffects)
+              optimizePenalty, unmarkedPowerList, plotEffectsData, plotEffects,
+              getL)
 
 S3method("print", "unmarkedPostSamples")
 
@@ -60,7 +62,8 @@ export(unmarkedEstimate, fitList, mapInfo, unmarkedFrame,
     unmarkedFrameDS, unmarkedMultFrame, unmarkedFrameGMM,
     unmarkedFramePCO, unmarkedFrameGDS, unmarkedFrameGPC, unmarkedFrameOccuMulti,
     unmarkedFrameOccuMS, unmarkedFrameOccuTTD, unmarkedFrameDSO, 
-    unmarkedFrameMMO, unmarkedFrameGDR, unmarkedFrameGOccu)
+    unmarkedFrameMMO, unmarkedFrameGDR, unmarkedFrameGOccu,
+    unmarkedFrameOccuCOP)
 
 # Formatting
 export(csvToUMF, formatLong, formatWide, formatMult, formatDistData)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,10 @@
+# unmarked 1.4.0
+
+* Added count-data occupancy model (occuCOP)
+* Added multi-scale occupancy model (goccu) 
+* Added ZIP support to gdistsamp, gmultmix, and gpcount
+* Fixed bug in TMB engine for occu that resulted in incorrect detection coefficient estimates when there were many interspersed NAs in the encounter history
+
 # unmarked 1.3.3
 
 * Increase required R version to 4.0