Update docs and clean up pkgdown site

biodiverse · Feb 9, 2025 · d652d38 · d652d38
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -14,3 +14,4 @@ README.Rmd
 ^vignettes/colext.Rmd.orig
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^pkgdown$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: unmarked
 Version: 1.5.0
-Date: 2025-02-07
+Date: 2025-02-09
 Type: Package
 Title: Models for Data from Unmarked Animals
 Authors@R: c(

diff --git a/NEWS.md b/NEWS.md
@@ -6,7 +6,6 @@
 * Improve and standardize documentation for these methods
 * More tests for these methods
 * Use reformulas package instead of lme4 for random effects formula handling
-* Deprecate imputeMissing function
 * Fix likelihood bug in goccu when primary periods were missing
 * Fix bug in occuMulti getP method
 

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -15,20 +15,19 @@ reference:
       - occu
       - goccu
       - colext
-      - occuFP
+      - occuComm
       - occuMS
       - occuMulti
       - occuPEN
+      - occuFP
       - occuTTD
       - occuCOP
   - title: Abundance models
     contents:
       - occuRN
       - pcount
       - distsamp
-      - IDS
       - multinomPois
-      - pcount.spHDS
       - gpcount
       - gmultmix
       - gdistsamp
@@ -37,27 +36,37 @@ reference:
       - distsampOpen
       - multmixOpen
       - nmixTTD
-  - title: Model diagnostics
+      - IDS
+      - pcount.spHDS
+  - title: Study design
     contents:
-      - fitted,unmarkedFit-method
-      - parboot
-      - nonparboot,unmarkedFit-method
-      - residuals,unmarkedFit-method
+      - simulate,unmarkedFrame-method
       - powerAnalysis
-      - simulate,unmarkedFit-method
-      - vif
-  - title: Model selection
+  - title: Model criticism
     contents:
+      - vif
+      - fitted,unmarkedFit-method
+      - residuals,unmarkedFit-method
       - fitList
-      - modSel
       - crossVal,unmarkedFit-method
+      - modSel
+      - simulate,unmarkedFit-method
+      - parboot
+      - nonparboot,unmarkedFit-method
+  - title: Model results
+    contents:
+      - predict,unmarkedFit-method
+      - ranef
+      - bup
+      - posteriorSamples,unmarkedRanef-method
+      - plotEffects
+      - randomTerms
+      - sigma
   - title: Organize data
     contents:
-      - unmarkedFrame
-      - unmarkedFrame-class
-      - unmarkedMultFrame
       - unmarkedFrameDS
       - unmarkedFrameOccu
+      - unmarkedFrameOccuComm
       - unmarkedFrameOccuFP
       - unmarkedFrameOccuMulti
       - unmarkedFramePCount
@@ -74,19 +83,7 @@ reference:
       - unmarkedFrameGOccu
       - unmarkedFrameMMO
       - unmarkedFrameDSO
-  - title: Model results
-    contents:
-      - coef,unmarkedFit-method
-      - predict,unmarkedFit-method
-      - linearComb
-      - backTransform
-      - ranef
-      - bup
-      - posteriorSamples,unmarkedRanef-method
-      - projected
-      - plotEffects
-      - randomTerms
-      - sigma
+      - unmarkedMultFrame
   - title: Datasets
     contents:
       - birds
@@ -105,6 +102,9 @@ reference:
       - Switzerland
   - title: internal
     contents:
+      - unmarkedFrame
+      - linearComb
+      - backTransform
       - SE-methods
       - SSE
       - computeMPLElambda
@@ -121,7 +121,7 @@ reference:
       - occuPEN_CV
       - optimizePenalty-methods
       - getFP-methods
-      - getP-methods
+      - getP
       - imputeMissing
       - lambda2psi
       - makePiFuns
@@ -137,3 +137,9 @@ reference:
       - sight2perpdist
       - predict,unmarkedFitOccuMulti-method
       - predict,unmarkedFitOccuMS-method
+      - unmarkedFit-class
+      - unmarkedFrame-class
+      - coef-methods
+      - richness
+      - unmarkedModSel-class
+      - unmarkedRanef-class
diff --git a/man/bup.Rd b/man/bup.Rd
@@ -0,0 +1,31 @@
+\name{bup}
+\alias{bup}
+\alias{bup,unmarkedRanef-method}
+
+\title{Extract Best Unbiased Predictors (BUPs) of latent variables from \code{ranef} output}
+
+\description{
+  Extract Best Unbiased Predictors (BUPs) of latent variables such as 
+  occupancy or abundance from a \code{unmarkedRanef} object produced by the
+  \code{ranef} function. Either the posterior mean or median can be requested.
+}
+
+\usage{
+\S4method{bup}{unmarkedRanef}(object, stat = c("mean", "mode"), ...)
+}
+
+\arguments{
+  \item{object}{A \code{unmarkedRanef} object, the output of a call to \code{ranef}.}
+  \item{stat}{The statistic to calculate from the posterior, either mean or mode.}
+  \item{...}{Other arguments, currently ignored} 
+}
+
+\value{
+  A vector of length M for single-season models, where M is the number of sites.
+  A matrix MxT for multi-season models, where T is the number of primary periods.
+  Values in the vector or matrix are the BUPs (occupancy or abundance states).
+}
+
+\seealso{
+\code{\link{ranef}}, \code{\link{unmarkedRanef-class}}
+}
diff --git a/man/crossVal.Rd b/man/crossVal.Rd
@@ -8,7 +8,7 @@
 \alias{show,unmarkedCrossVal-method}
 \alias{show,unmarkedCrossValList-method}
 
-\title{Cross-validation methods for fitted unmarked models and fit lists}
+\title{Cross-validation methods for fitted \code{unmarked} models and fit lists}
 
 \description{Test predictive accuracy of fitted models using several 
   cross-validation approaches. The dataset is divided by site only into folds or

diff --git a/man/fitList.Rd b/man/fitList.Rd
@@ -1,6 +1,6 @@
 \name{fitList}
 \alias{fitList}
-\title{constructor of unmarkedFitList objects}
+\title{Create a list of fitted \code{unmarked} models}
 \usage{fitList(..., fits, autoNames=c("object", "formula"))}
 \description{Organize models for model selection or model-averaged prediction.}
 \arguments{

diff --git a/man/goccu.Rd b/man/goccu.Rd
@@ -1,7 +1,7 @@
 \name{goccu}
 \alias{goccu}
 \title{
-Fit multi-scale occupancy models
+Fit the multi-scale occupancy model of Nichols et al. (2008)
 }
 \description{
 Fit multi-scale occupancy models as described in Nichols et al. (2008) to

diff --git a/man/modSel.Rd b/man/modSel.Rd
@@ -1,13 +1,8 @@
 \name{modSel}
-\title{Model selection results from an unmarkedFitList}
+\title{Model selection on a list of \code{unmarked} model fits}
 \description{Model selection results from an unmarkedFitList}
 \alias{modSel}
-\alias{modSel-methods}
-\alias{unmarkedModSel-class}
-\alias{show,unmarkedModSel-method}
-\alias{summary,unmarkedModSel-method}
-\alias{coef,unmarkedModSel-method}
-\alias{SE,unmarkedModSel-method}
+
 \arguments{
 	\item{object}{an object of class "unmarkedFitList" created by the function
 	  \code{\link{fitList}}.}
@@ -17,20 +12,17 @@
 	      }
 }
 \value{
-A S4 object with the following slots
-	\item{Full}{data.frame with formula, estimates, standard errors and model 
-		selection information. Converge is optim convergence code. CondNum is
-		model condition number. n is the number of sites. delta is delta AIC.
-		cumltvWt is cumulative AIC weight.
-        Rsq is Nagelkerke's (1991) R-squared index, which is only returned when 
-        the nullmod argument is specified. }
-	\item{Names}{matrix referencing column names of estimates (row 1) and 
-	   standard errors (row 2).}
+  An object of class \code{unmarkedModSel}.
 }
+
 \note{Two requirements exist to conduct AIC-based model-selection and model-averaging in unmarked. First, the data objects (ie, unmarkedFrames) must be identical among fitted models. Second, the response matrix must be identical among fitted models after missing values have been removed. This means that if a response value was removed in one model due to missingness, it needs to be removed from all models.
 } 
+
+\seealso{\code{\link{unmarkedModSel-class}}}
+
 \references{Nagelkerke, N.J.D. (2004) A Note on a General Definition of the 
 	Coefficient of Determination. \emph{Biometrika} 78, pp. 691-692.}
+
 \author{Richard Chandler \email{[email protected]}}
 \examples{
 data(linetran)

diff --git a/man/nmixTTD.Rd b/man/nmixTTD.Rd
@@ -1,6 +1,6 @@
 \name{nmixTTD}
 \alias{nmixTTD}
-\title{Fit N-mixture Time-to-detection Models}
+\title{Fit the N-mixture Time-to-detection Model of Strebel et al. (2021)}
 
 \usage{nmixTTD(stateformula= ~1, detformula = ~1, data, K=100,
     mixture = c("P","NB"), ttdDist = c("exp", "weibull"), starts, method="BFGS", 

diff --git a/man/occuCOP.Rd b/man/occuCOP.Rd
@@ -4,7 +4,7 @@
 
 \encoding{UTF-8}
 
-\title{Fit the occupancy model using count dta}
+\title{Fit the occupancy model using count data}
 
 \usage{
 occuCOP(data, 

diff --git a/man/occuComm.Rd b/man/occuComm.Rd
@@ -1,7 +1,7 @@
 \name{occuComm}
 \alias{occuComm}
 
-\title{Fit a community occupancy model}
+\title{Fit a community occupancy model with species-level random effects}
 
 \usage{
   occuComm(formula, data, starts, method="BFGS", se=TRUE, ...)

diff --git a/man/occuMS.Rd b/man/occuMS.Rd
@@ -2,7 +2,7 @@
 
 \alias{occuMS}
 
-\title{Fit Single-Season and Dynamic Multi-State Occupancy Models}
+\title{Fit Multi-State Occupancy Models (Nichols et al. 2007, MacKenzie et al. 2009)}
 
 \usage{occuMS(detformulas, psiformulas, phiformulas=NULL, data, 
     parameterization=c("multinomial","condbinom"),

diff --git a/man/occuMulti.Rd b/man/occuMulti.Rd
@@ -2,7 +2,7 @@
 
 \alias{occuMulti}
 
-\title{Fit the Rota et al. (2016) Multi-species Occupancy Model}
+\title{Fit the multi-species occupancy model of Rota et al. (2016)}
 
 \usage{occuMulti(detformulas, stateformulas, data, maxOrder, penalty=0, boot=30, 
        starts, method="BFGS", se=TRUE, engine=c("C","R"), silent=FALSE, ...)}

diff --git a/man/parboot.Rd b/man/parboot.Rd
@@ -4,7 +4,7 @@
 \alias{plot,parboot,missing-method}
 \alias{show,parboot-method}
 
-\title{Parametric bootstrap method for \code{unmarked} models}
+\title{Parametric bootstrap for \code{unmarked} models}
 
 \description{Simulate datasets from a fitted model, refit the model, and
   generate a sampling distribution for a user-specified fit-statistic.}

diff --git a/man/pcountOpen.Rd b/man/pcountOpen.Rd
@@ -1,6 +1,6 @@
 \name{pcountOpen}
 \alias{pcountOpen}
-\title{Fit the open N-mixture models of Dail and Madsen and extensions}
+\title{Fit the open N-mixture models of Dail and Madsen (2011) and Hostetler and Chandler (2015)}
 \description{Fit the models of Dail and Madsen (2011) and Hostetler and
 Chandler (in press), which are
 generalized forms of the Royle (2004) N-mixture model for open

diff --git a/man/powerAnalysis.Rd b/man/powerAnalysis.Rd
@@ -4,7 +4,7 @@
 \alias{powerAnalysis,list-method}
 \alias{powerAnalysis,unmarkedFit-method}
 
-\title{Conduct a power analysis for an unmarked model}
+\title{Conduct a power analysis for an \code{unmarked} model}
 
 \description{
 This function uses a simulation-based approach to estimate power for parameters 

diff --git a/man/ranef.Rd b/man/ranef.Rd
@@ -50,6 +50,9 @@ for methods used to manipulate the returned object.
 
 \author{Richard Chandler \email{rbchan@uga.edu}}
 
+\seealso{
+\code{\link{unmarkedRanef-class}}, \code{\link{bup}}
+}
 
 \references{
   Laird, N.M. and T.A. Louis. 1987. Empirical Bayes confidence intervals

diff --git a/man/simulate.Rd b/man/simulate.Rd
@@ -4,7 +4,7 @@
 \alias{simulate,unmarkedFrame-method}
 \alias{simulate,character-method}
 
-\title{Data simulation in unmarked}
+\title{Simulate datasets from any \code{unmarked} model type}
 \description{
 Simulate data from a fitted model, or simulate an entirely new dataset
 from a study design defined by an \code{unmarkedFrame}.

diff --git a/man/unmarkedModSel-class.Rd b/man/unmarkedModSel-class.Rd
@@ -0,0 +1,58 @@
+\name{unmarkedModSel-class}
+\title{unmarkedModSel class and methods}
+\alias{unmarkedModSel-class}
+\alias{show,unmarkedModSel-method}
+\alias{coef,unmarkedModSel-method}
+\alias{SE,unmarkedModSel-method}
+
+\description{The unmarkedModSel class and associated methods}
+
+\section{Slots}{
+  \describe{
+	\item{Full}{data.frame with formula, estimates, standard errors and model 
+		selection information. Converge is optim convergence code. CondNum is
+		model condition number. n is the number of sites. delta is delta AIC.
+		cumltvWt is cumulative AIC weight.
+        Rsq is Nagelkerke's (1991) R-squared index, which is only returned when 
+        the nullmod argument is specified. }
+	\item{Names}{matrix referencing column names of estimates (row 1) and 
+	   standard errors (row 2).}
+  }
+}
+
+\section{Methods}{
+  \describe{
+    \item{show}{Print the AIC model selection table}
+    \item{coef}{Data frame of coefficients from all models in model selection table}
+    \item{SE}{Data frame of coefficient SEs from all models in model selection table}
+  }
+}
+
+\seealso{\code{\link{modSel}}}
+
+\examples{
+data(linetran)
+(dbreaksLine <- c(0, 5, 10, 15, 20)) 
+lengths <- linetran$Length * 1000
+
+ltUMF <- with(linetran, {
+	unmarkedFrameDS(y = cbind(dc1, dc2, dc3, dc4), 
+	siteCovs = data.frame(Length, area, habitat), dist.breaks = dbreaksLine,
+	tlength = lengths, survey = "line", unitsIn = "m")
+	})
+
+fm1 <- distsamp(~ 1 ~1, ltUMF)
+fm2 <- distsamp(~ area ~1, ltUMF)
+fm3 <- distsamp( ~ 1 ~area, ltUMF)
+
+fl <- fitList(Null=fm1, A.=fm2, .A=fm3)
+fl
+
+ms <- modSel(fl, nullmod="Null")
+ms
+
+coef(ms)                            # Estimates only
+SE(ms)                              # Standard errors only
+(toExport <- as(ms, "data.frame"))  # Everything
+
+}