Fix CRAN issues

19 files changed, 177 insertions, 76 deletions

diff --git a/man/coef-ubmsFit-method.Rd b/man/coef-ubmsFit-method.Rd
new file mode 100644
index 0000000..59feff6
--- /dev/null
+++ b/man/coef-ubmsFit-method.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ubmsFit-methods.R
+\name{coef,ubmsFit-method}
+\alias{coef,ubmsFit-method}
+\title{Extract Coefficient Values From a ubmsFit Model}
+\usage{
+\S4method{coef}{ubmsFit}(object, ...)
+}
+\arguments{
+\item{object}{A \code{ubmsFit} model}
+
+\item{...}{Currently ignored}
+}
+\value{
+A vector of coefficient values for all submodels.
+}
+\description{
+Extract Coefficient Values From a ubmsFit Model
+}
diff --git a/man/getY-ubmsFit-method.Rd b/man/getY-ubmsFit-method.Rd
new file mode 100644
index 0000000..12a3588
--- /dev/null
+++ b/man/getY-ubmsFit-method.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ubmsFit-methods.R
+\name{getY,ubmsFit-method}
+\alias{getY,ubmsFit-method}
+\title{Extract y, the Response Variable, From a ubmsFit Model}
+\usage{
+\S4method{getY}{ubmsFit}(object)
+}
+\arguments{
+\item{object}{A \code{ubmsFit} model}
+}
+\value{
+A matrix containing the response variable \code{y}.
+}
+\description{
+Extract y, the Response Variable, From a ubmsFit Model
+}
diff --git a/man/names-ubmsFit-method.Rd b/man/names-ubmsFit-method.Rd
new file mode 100644
index 0000000..3a99fd9
--- /dev/null
+++ b/man/names-ubmsFit-method.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ubmsFit-methods.R
+\name{names,ubmsFit-method}
+\alias{names,ubmsFit-method}
+\title{Get Parameter Names From a ubmsFit Model}
+\usage{
+\S4method{names}{ubmsFit}(x)
+}
+\arguments{
+\item{x}{A \code{ubmsFit} model}
+}
+\value{
+A character vector of parameter names.
+}
+\description{
+Get Parameter Names From a ubmsFit Model
+}
diff --git a/man/names-ubmsFitList-method.Rd b/man/names-ubmsFitList-method.Rd
new file mode 100644
index 0000000..8550afa
--- /dev/null
+++ b/man/names-ubmsFitList-method.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ubmsFitList-methods.R
+\name{names,ubmsFitList-method}
+\alias{names,ubmsFitList-method}
+\title{Get Names of Models in a ubmsFitList}
+\usage{
+\S4method{names}{ubmsFitList}(x)
+}
+\arguments{
+\item{x}{A \code{ubmsFitList} object}
+}
+\value{
+A character vector of model names.
+}
+\description{
+Get Names of Models in a ubmsFitList
+}
diff --git a/man/nsamples-ubmsFit-method.Rd b/man/nsamples-ubmsFit-method.Rd
new file mode 100644
index 0000000..bcc2ecc
--- /dev/null
+++ b/man/nsamples-ubmsFit-method.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ubmsFit-methods.R
+\name{nsamples,ubmsFit-method}
+\alias{nsamples,ubmsFit-method}
+\title{Get number of Posterior Samples Stored in a ubmsFit Model}
+\usage{
+\S4method{nsamples}{ubmsFit}(object, ...)
+}
+\arguments{
+\item{object}{A \code{ubmsFit} model}
+
+\item{...}{Currently ignored}
+}
+\value{
+An integer representing the number of posterior samples
+}
+\description{
+Get number of Posterior Samples Stored in a ubmsFit Model
+}
diff --git a/man/plot-ubmsFit-ANY-method.Rd b/man/plot-ubmsFit-ANY-method.Rd
new file mode 100644
index 0000000..392c019
--- /dev/null
+++ b/man/plot-ubmsFit-ANY-method.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ubmsFit-methods.R
+\name{plot,ubmsFit,ANY-method}
+\alias{plot,ubmsFit,ANY-method}
+\title{Plot Residuals For All Submodels in a ubmsFit Model}
+\usage{
+\S4method{plot}{ubmsFit,ANY}(x, y, ...)
+}
+\arguments{
+\item{x}{A \code{ubmsFit} model}
+
+\item{y}{Currently ignored}
+
+\item{...}{Currently ignored}
+}
+\value{
+A plot object of class \code{gtable} with one panel per submodel.
+}
+\description{
+Plot Residuals For All Submodels in a ubmsFit Model
+}
diff --git a/man/stan_colext.Rd b/man/stan_colext.Rd
index 533adb5..8ebd17c 100644
--- a/man/stan_colext.Rd
+++ b/man/stan_colext.Rd
@@ -36,7 +36,7 @@ This function fits the dynamic occupancy model of
 MacKenzie et al. (2003).
 }
 \examples{
-\dontrun{
+\donttest{
 data(frogs)
 umf <- formatMult(masspcru)
 umf@y[umf@y > 1] <- 1 #convert counts to presence/absence
diff --git a/man/stan_distsamp.Rd b/man/stan_distsamp.Rd
index fb67769..78aee4c 100644
--- a/man/stan_distsamp.Rd
+++ b/man/stan_distsamp.Rd
@@ -54,7 +54,7 @@ Values of `dist.breaks` in the `unmarkedFrameDS` should be as small
 }
 
 \examples{
-\dontrun{
+\donttest{
 data(issj)
 #Note use of km instead of m for distance breaks
 jayUMF <- unmarkedFrameDS(y=as.matrix(issj[,1:3]),
diff --git a/man/stan_multinomPois.Rd b/man/stan_multinomPois.Rd
index b05cfe0..d975aeb 100644
--- a/man/stan_multinomPois.Rd
+++ b/man/stan_multinomPois.Rd
@@ -23,7 +23,7 @@ This function fits the multinomial-Poisson mixture model, useful for
 data collected via survey methods such as removal or double observer sampling.
 }
 \examples{
-\dontrun{
+\donttest{
 data(ovendata)
 ovenFrame <- unmarkedFrameMPois(ovendata.list$data,
                                 siteCovs=ovendata.list$covariates,
diff --git a/man/stan_occu.Rd b/man/stan_occu.Rd
index b350d37..c14b9c7 100644
--- a/man/stan_occu.Rd
+++ b/man/stan_occu.Rd
@@ -23,7 +23,7 @@ This function fits the single season occupancy model of
 MacKenzie et al. (2002).
 }
 \examples{
-\dontrun{
+\donttest{
 data(frogs)
 pferUMF <- unmarkedFrameOccu(pfer.bin)
 
diff --git a/man/stan_occuRN.Rd b/man/stan_occuRN.Rd
index 7c67d13..b81e352 100644
--- a/man/stan_occuRN.Rd
+++ b/man/stan_occuRN.Rd
@@ -28,7 +28,7 @@ probability of detection of the species to the number of individuals
 available for detection at each site.
 }
 \examples{
-\dontrun{
+\donttest{
 data(birds)
 woodthrushUMF <- unmarkedFrameOccu(woodthrush.bin)
 #Add a site covariate
diff --git a/man/stan_occuTTD.Rd b/man/stan_occuTTD.Rd
index 0a8007d..213fee6 100644
--- a/man/stan_occuTTD.Rd
+++ b/man/stan_occuTTD.Rd
@@ -50,7 +50,7 @@ Fit time-to-detection occupancy models of Garrard et al.
 or Weibull distribution.
 }
 \examples{
-\dontrun{
+\donttest{
 #Simulate data
 N <- 500; J <- 1
 scovs <- data.frame(elev=c(scale(runif(N, 0,100))),
diff --git a/man/stan_pcount.Rd b/man/stan_pcount.Rd
index 788e0b7..3894b88 100644
--- a/man/stan_pcount.Rd
+++ b/man/stan_pcount.Rd
@@ -29,7 +29,7 @@ This function fits the single season N-mixture model of
 Royle et al. (2004).
 }
 \examples{
-\dontrun{
+\donttest{
 data(mallard)
 mallardUMF <- unmarkedFramePCount(mallard.y, siteCovs=mallard.site)
 
diff --git a/man/sub-ubmsFit-character-missing-missing-method.Rd b/man/sub-ubmsFit-character-missing-missing-method.Rd
new file mode 100644
index 0000000..36ca045
--- /dev/null
+++ b/man/sub-ubmsFit-character-missing-missing-method.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ubmsFit-methods.R
+\name{[,ubmsFit,character,missing,missing-method}
+\alias{[,ubmsFit,character,missing,missing-method}
+\title{Extract a Submodel from a ubmsFit Model}
+\usage{
+\S4method{[}{ubmsFit,character,missing,missing}(x, i)
+}
+\arguments{
+\item{x}{A \code{ubmsFit} model}
+
+\item{i}{The name of a submodel to extract}
+}
+\value{
+An object of class \code{ubmsSubmodel}.
+}
+\description{
+Extract a Submodel from a ubmsFit Model
+}
diff --git a/man/ubmsSubmodelList-methods.Rd b/man/sub-ubmsSubmodelList-character-missing-missing-method.Rd
index ce8377b..93e049a 100644
--- a/man/ubmsSubmodelList-methods.Rd
+++ b/man/sub-ubmsSubmodelList-character-missing-missing-method.Rd
@@ -1,9 +1,8 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/submodel.R
-\name{ubmsSubmodelList-methods}
-\alias{ubmsSubmodelList-methods}
+\name{[,ubmsSubmodelList,character,missing,missing-method}
 \alias{[,ubmsSubmodelList,character,missing,missing-method}
-\title{Methods for ubmsSubmodelList objects}
+\title{Extract a ubmsSubmodel From a ubmsSubmodelList Object}
 \usage{
 \S4method{[}{ubmsSubmodelList,character,missing,missing}(x, i)
 }
@@ -12,6 +11,9 @@
 
 \item{i}{The name of a submodel}
 }
+\value{
+An object of class \code{ubmsSubmodel}.
+}
 \description{
-Basic methods for ubmsSubmodelList objects
+Extract a ubmsSubmodel From a ubmsSubmodelList Object
 }
diff --git a/man/summary-ubmsFit-method.Rd b/man/summary-ubmsFit-method.Rd
new file mode 100644
index 0000000..e9eca0b
--- /dev/null
+++ b/man/summary-ubmsFit-method.Rd
@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ubmsFit-methods.R
+\name{summary,ubmsFit-method}
+\alias{summary,ubmsFit-method}
+\title{Extract Summary Statistics from a ubmsFit Model}
+\usage{
+\S4method{summary}{ubmsFit}(object, submodel, ...)
+}
+\arguments{
+\item{object}{A \code{ubmsFit} model}
+
+\item{submodel}{Name of submodel to summarize}
+
+\item{...}{Currently ignored}
+}
+\value{
+An object of class \code{data.frame} containing summary statistics
+ for posterior distributions of parameters from the chosen submodel.
+}
+\description{
+Extract Summary Statistics from a ubmsFit Model
+}
diff --git a/man/traceplot-ubmsFit-method.Rd b/man/traceplot-ubmsFit-method.Rd
index 1b55cd4..695e1ec 100644
--- a/man/traceplot-ubmsFit-method.Rd
+++ b/man/traceplot-ubmsFit-method.Rd
@@ -11,6 +11,9 @@
 
 \item{...}{Arguments passed to \code{rstan::traceplot}}
 }
+\value{
+A \code{ggplot} object.
+}
 \description{
 Draws traceplots for chains from a \code{ubmsFit} object
 }
diff --git a/man/ubmsFit-methods.Rd b/man/ubmsFit-methods.Rd
deleted file mode 100644
index 73bf103..0000000
--- a/man/ubmsFit-methods.Rd
+++ /dev/null
@@ -1,53 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/ubmsFit-methods.R
-\name{ubmsFit-methods}
-\alias{ubmsFit-methods}
-\alias{coef,ubmsFit-method}
-\alias{plot,ubmsFit,ANY-method}
-\alias{[,ubmsFit,character,missing,missing-method}
-\alias{names,ubmsFit-method}
-\alias{nsamples,ubmsFit-method}
-\alias{summary,ubmsFit-method}
-\alias{getY,ubmsFit-method}
-\title{Methods for ubmsFit objects
-These methods are similar to methods defined for objects of class \code{lm},
-\code{merMod}, \code{stanreg}. The most important methods are documented
-separately. Links to those pages are provided in the \strong{See Also}
-section below.}
-\usage{
-\S4method{coef}{ubmsFit}(object, ...)
-
-\S4method{plot}{ubmsFit,ANY}(x, y, ...)
-
-\S4method{[}{ubmsFit,character,missing,missing}(x, i)
-
-\S4method{names}{ubmsFit}(x)
-
-\S4method{nsamples}{ubmsFit}(object, ...)
-
-\S4method{summary}{ubmsFit}(object, submodel, ...)
-
-\S4method{getY}{ubmsFit}(object)
-}
-\arguments{
-\item{object, x}{A fitted model of class \code{ubmsFit}}
-
-\item{...}{Currently ignored}
-
-\item{y}{Currently ignored}
-
-\item{submodel, i}{A submodel, e.g. \code{"det"} for the detection model}
-}
-\description{
-Methods for ubmsFit objects
-These methods are similar to methods defined for objects of class \code{lm},
-\code{merMod}, \code{stanreg}. The most important methods are documented
-separately. Links to those pages are provided in the \strong{See Also}
-section below.
-}
-\seealso{
-\itemize{
- \item The \code{\link{posterior_predict}} for drawing from the posterior
-   distribution of the observed outcome or unobserved latent state
-}
-}
diff --git a/man/ubmsFitList-methods.Rd b/man/ubmsFitList-extractors.Rd
index 8a8256a..7b3979a 100644
--- a/man/ubmsFitList-methods.Rd
+++ b/man/ubmsFitList-extractors.Rd
@@ -1,19 +1,15 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/ubmsFitList-methods.R
-\name{ubmsFitList-methods}
-\alias{ubmsFitList-methods}
+\name{ubmsFitList-extractors}
+\alias{ubmsFitList-extractors}
 \alias{$,ubmsFitList-method}
-\alias{names,ubmsFitList-method}
 \alias{[[,ubmsFitList,numeric,missing-method}
 \alias{[,ubmsFitList,numeric,missing,missing-method}
-\title{Methods for ubmsFitList objects
-Basic methods for ubmsFitList objects. More complex methods have
-their own documentation pages.}
+\title{Extractors for ubmsFitList objects
+Extract parts of ubmsFitList objects.}
 \usage{
 \S4method{$}{ubmsFitList}(x, name)
 
-\S4method{names}{ubmsFitList}(x)
-
 \S4method{[[}{ubmsFitList,numeric,missing}(x, i)
 
 \S4method{[}{ubmsFitList,numeric,missing,missing}(x, i)
@@ -21,10 +17,12 @@ their own documentation pages.}
 \arguments{
 \item{x}{A list of \code{ubmsFit} models of class \code{ubmsFitList}}
 
-\item{name, i}{A single \code{ubmsFit} model}
+\item{name, i}{The names or indices of \code{ubmsFit} models in the \code{ubmsFitList}}
+}
+\value{
+A \code{ubmsFit} object or list of such objects.
 }
 \description{
-Methods for ubmsFitList objects
-Basic methods for ubmsFitList objects. More complex methods have
-their own documentation pages.
+Extractors for ubmsFitList objects
+Extract parts of ubmsFitList objects.
 }