Don't export unused unmarkedFrame functionmethods_doc_updates

11 files changed, 16 insertions, 114 deletions

diff --git a/NAMESPACE b/NAMESPACE
index 894646c..e92ab9e 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -52,7 +52,7 @@ exportMethods(backTransform, coef, confint, fitted, getData,
 S3method("print", "unmarkedPostSamples")
 
 # Constructors
-export(unmarkedEstimate, fitList, unmarkedFrame,
+export(unmarkedEstimate, fitList,
     unmarkedFrameOccu, unmarkedFrameOccuFP, unmarkedFramePCount, unmarkedFrameMPois,
     unmarkedFrameDS, unmarkedMultFrame, unmarkedFrameGMM,
     unmarkedFramePCO, unmarkedFrameGDS, unmarkedFrameGPC, unmarkedFrameOccuMulti,
diff --git a/man/formatDistData.Rd b/man/formatDistData.Rd
index f5aaa83..df304a9 100644
--- a/man/formatDistData.Rd
+++ b/man/formatDistData.Rd
@@ -36,7 +36,8 @@ levels for all the transects surveyed, not just those with >=1
 detection. Likewise, if transects were visited more than once, the
 factor containing the occasion numbers should include levels for all
 occasions. See the example for how to add levels to a factor.}
-\seealso{\code{\link{distsamp}}, \code{\link{unmarkedFrame}}}
+\seealso{\code{\link{distsamp}}, \code{\link{gdistsamp}}, 
+  \code{\link{unmarkedFrameDS}}, \code{\link{unmarkedFrameGDS}}}
 \examples{
 # Create a data.frame containing distances of animals detected
 # along 4 transects.
diff --git a/man/occu.Rd b/man/occu.Rd
index ad104b8..c68e00b 100644
--- a/man/occu.Rd
+++ b/man/occu.Rd
@@ -38,8 +38,8 @@
 
 \details{
 
-See \code{\link{unmarkedFrame}} and \code{\link{unmarkedFrameOccu}} for a
-description of how to supply data to the \code{data} argument.
+See \code{\link{unmarkedFrameOccu}} for a description of how to supply data to the 
+\code{data} argument.
 
 \code{occu} fits the standard occupancy model based on zero-inflated
 binomial models (MacKenzie et al. 2006, Royle and Dorazio
diff --git a/man/occuCOP.Rd b/man/occuCOP.Rd
index 7549ca3..30446f7 100644
--- a/man/occuCOP.Rd
+++ b/man/occuCOP.Rd
@@ -47,7 +47,7 @@ occuCOP(data,
 
 \details{
   
-  See \code{\link{unmarkedFrameOccuCOP}} for a description of how to supply data to the \code{data} argument. See \code{\link{unmarkedFrame}} for a more general documentation of \code{unmarkedFrame} objects for the different models implemented in \pkg{unmarked}.
+  See \code{\link{unmarkedFrameOccuCOP}} for a description of how to supply data to the \code{data} argument.
   
   \subsection{The COP occupancy model}{
     
diff --git a/man/occuFP.Rd b/man/occuFP.Rd
index daadb4e..a21299b 100644
--- a/man/occuFP.Rd
+++ b/man/occuFP.Rd
@@ -32,8 +32,7 @@ false positive detections.}
 
 \details{
 
-See \code{\link{unmarkedFrame}} and \code{\link{unmarkedFrameOccuFP}} for a
-description of how to supply data to the \code{data} argument.
+See \code{\link{unmarkedFrameOccuFP}} for a description of how to supply data to the \code{data} argument.
 
 \code{occuFP} fits an extension of the standard single-season occupancy model (MacKenzie et al. 2002), which allows
 false positive detections. The occupancy status of a site is the same way as with the \code{\link{occu}} function, where stateformula
diff --git a/man/occuMS.Rd b/man/occuMS.Rd
index 5796527..bbae576 100644
--- a/man/occuMS.Rd
+++ b/man/occuMS.Rd
@@ -136,8 +136,8 @@ of staying in the same state between seasons can be obtained via subtraction.
 See \code{umf@phiOrder$multinomial} for the correct order matching the number
 of states in your dataset.
 
-See \code{\link{unmarkedFrame}} and \code{\link{unmarkedFrameOccuMS}} for a
-description of how to supply data to the \code{data} argument.
+See \code{\link{unmarkedFrameOccuMS}} for a description of how to supply data 
+to the \code{data} argument.
 }
 
 \value{unmarkedFitOccuMS object describing the model fit.}
diff --git a/man/occuMulti.Rd b/man/occuMulti.Rd
index 826f163..7dc33cc 100644
--- a/man/occuMulti.Rd
+++ b/man/occuMulti.Rd
@@ -34,8 +34,8 @@
 
 \details{
 
-See \code{\link{unmarkedFrame}} and \code{\link{unmarkedFrameOccuMulti}} for a
-description of how to supply data to the \code{data} argument.
+See \code{\link{unmarkedFrameOccuMulti}} for a description of how to supply data 
+to the \code{data} argument.
 
 \code{occuMulti} fits the multispecies occupancy model from Rota et al. (2016),
 for two or more interacting species.
diff --git a/man/occuPEN.Rd b/man/occuPEN.Rd
index 7e14c20..2ebcd1d 100644
--- a/man/occuPEN.Rd
+++ b/man/occuPEN.Rd
@@ -30,8 +30,8 @@
 
 \details{
 
-See \code{\link{unmarkedFrame}} and \code{\link{unmarkedFrameOccu}} for a
-description of how to supply data to the \code{data} argument.
+See \code{\link{unmarkedFrameOccu}} for a description of how to supply data to 
+the \code{data} argument.
 
 \code{occuPEN} fits the standard occupancy model based on
 zero-inflated binomial models (MacKenzie et al. 2006, Royle and
diff --git a/man/occuPEN_CV.Rd b/man/occuPEN_CV.Rd
index d73ccbb..e9a063f 100644
--- a/man/occuPEN_CV.Rd
+++ b/man/occuPEN_CV.Rd
@@ -38,8 +38,8 @@ k-fold cross-validation to choose the penalty weight.}
 
 \details{
 
-See \code{\link{unmarkedFrame}} and \code{\link{unmarkedFrameOccu}} for a
-description of how to supply data to the \code{data} argument.
+See \code{\link{unmarkedFrameOccu}} for a description of how to supply data to 
+the \code{data} argument.
 
 This function wraps k-fold cross-validation around \code{occuPEN_CV}
 for the "Bayes" and "Ridge" penalties of Hutchinson et al. (2015). The
diff --git a/man/unmarked-package.Rd b/man/unmarked-package.Rd
index c0595a3..2c0f9e0 100644
--- a/man/unmarked-package.Rd
+++ b/man/unmarked-package.Rd
@@ -75,8 +75,7 @@ and apparent survival.
 a formal S4 class called an unmarkedFrame, which has child classes
 for each model type. This allows metadata (eg as distance interval cut
 points, measurement units, etc...) to be stored with the response and
-covariate data. See \code{\link{unmarkedFrame}} for a detailed
-description of unmarkedFrames and how to create them.
+covariate data.
 
 \strong{Model Specification:}  \emph{unmarked}'s
 model-fitting functions allow specification of covariates for both the
diff --git a/man/unmarkedFrame.Rd b/man/unmarkedFrame.Rd
deleted file mode 100644
index 21ecca6..0000000
--- a/man/unmarkedFrame.Rd
+++ /dev/null
@@ -1,97 +0,0 @@
-\name{unmarkedFrame}
-\title{Create an unmarkedFrame, or one of its child classes.}
-\alias{unmarkedFrame}
-\usage{unmarkedFrame(y, siteCovs=NULL, obsCovs=NULL, mapInfo, obsToY)}
-\description{Constructor for unmarkedFrames.}
-\arguments{
-  \item{y}{An MxJ matrix of the observed measured data, where M is the
-    number of sites and J is the maximum number of observations per site.}
-  \item{siteCovs}{A \code{\link{data.frame}} of covariates that vary at the
-    site level. This should have M rows and one column per covariate}
-  \item{obsCovs}{Either a named list of \code{\link{data.frame}}s of
-    covariates that vary within sites, or a \code{\link{data.frame}}
-    with MxJ rows in site-major order.}
-  \item{obsToY}{optional matrix specifying relationship between
-    observation-level covariates and response matrix}
-  \item{mapInfo}{geographic coordinate information. Currently ignored.}
-}
-
-\details{
-  unmarkedFrame is the S4 class that holds data structures to be passed
-  to the model-fitting functions in unmarked.
-
-  An unmarkedFrame contains the observations (\code{y}), covariates
-  measured at the observation level (\code{obsCovs}), and covariates
-  measured at the site level (\code{siteCovs}).
-  For a data set with M sites and J observations at each site, y is an
-  M x J matrix. \code{obsCovs} and \code{siteCovs} are both data frames
-  (see \link{data.frame}).  \code{siteCovs} has M rows so that each row
-  contains the covariates for the corresponding sites.
-  \code{obsCovs} has M*obsNum rows so that each covariates is ordered by
-  site first, then observation number.  Missing values are coded with
-  \code{NA} in any of y, siteCovs, or obsCovs.
-
-  Additionally, unmarkedFrames contain metadata: obsToY, mapInfo.
-  obsToY is a matrix describing relationship between response matrix and
-  observation-level covariates. Generally this does not need to be
-  supplied by the user; however, it may be needed when using
-  \code{\link{multinomPois}}. For example, double observer sampling, y
-  has 3 columns corresponding the observer 1, observer 2, and both, but
-  there were only two independent observations.
-  In this situation, y has 3 columns, but obsToY must be specified.
-
-  Several child classes of \code{unmarkedFrame} require addional
-  metadata. For example, \code{unmarkedFrameDS} is used to organize
-  distsance sampling data for the \code{\link{distsamp}} function, and
-  it has arguments dist.breaks, tlength, survey, and unitsIn, which
-  specify the distance interval cut points, transect lengths, "line" or
-  "point" transect, and units of measure, respectively.
-
-  All site-level covariates are automatically copied to obsCovs so that
-  site level covariates are available at the observation level.
-}
-
-\value{an unmarkedFrame object}
-
-\seealso{\code{\link{unmarkedFrame-methods}}}
-
-\examples{
-
-# Set up data for pcount()
-data(mallard)
-mallardUMF <- unmarkedFramePCount(mallard.y, siteCovs = mallard.site,
-	obsCovs = mallard.obs)
-summary(mallardUMF)
-
-
-# Set up data for occu()
-data(frogs)
-pferUMF <- unmarkedFrameOccu(pfer.bin)
-
-
-# Set up data for distsamp()
-data(linetran)
-ltUMF <- with(linetran, {
-	unmarkedFrameDS(y = cbind(dc1, dc2, dc3, dc4),
-	siteCovs = data.frame(Length, area, habitat),
-	dist.breaks = c(0, 5, 10, 15, 20),
-	tlength = linetran$Length * 1000, survey = "line", unitsIn = "m")
-	})
-summary(ltUMF)
-
-
-# Set up data for multinomPois()
-data(ovendata)
-ovenFrame <- unmarkedFrameMPois(ovendata.list$data,
-	siteCovs=as.data.frame(scale(ovendata.list$covariates[,-1])),
-	type = "removal")
-summary(ovenFrame)
-
-
-\dontrun{
-# Set up data for colext()
-frogUMF <- formatMult(masspcru)
-summary(frogUMF)
-}
-
-}