Update extractor methods

5 files changed, 71 insertions, 39 deletions

diff --git a/NAMESPACE b/NAMESPACE
index aea62db..f7baf99 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -42,11 +42,11 @@ exportClasses(unmarkedFit, unmarkedFitOccu, unmarkedFitOccuFP, unmarkedFitDS,
               unmarkedPostSamples, unmarkedPower, unmarkedPowerList)
 
 # Methods
-exportMethods(backTransform, coef, confint, coordinates, fitted, getData,
+exportMethods(backTransform, coef, confint, fitted, getData,
               getP, getFP, getB, getY, head, hessian, linearComb, mle,
               modSel, nllFun, numSites, numY, obsCovs, obsNum, "obsCovs<-",
               obsToY, "obsToY<-", parboot, plot, hist, predict, profile,
-              projection, residuals, sampleSize, SE, show, simulate, siteCovs,
+              residuals, sampleSize, SE, show, simulate, siteCovs,
               "siteCovs<-", summary, update, vcov, yearlySiteCovs,
               "yearlySiteCovs<-", "[", smoothed, projected, nonparboot, logLik,
               LRT, ranef, bup, crossVal, posteriorSamples, sigma, randomTerms, 
@@ -56,7 +56,7 @@ exportMethods(backTransform, coef, confint, coordinates, fitted, getData,
 S3method("print", "unmarkedPostSamples")
 
 # Constructors
-export(unmarkedEstimate, fitList, mapInfo, unmarkedFrame,
+export(unmarkedEstimate, fitList, unmarkedFrame,
     unmarkedFrameOccu, unmarkedFrameOccuFP, unmarkedFramePCount, unmarkedFrameMPois,
     unmarkedFrameDS, unmarkedMultFrame, unmarkedFrameGMM,
     unmarkedFramePCO, unmarkedFrameGDS, unmarkedFrameGPC, unmarkedFrameOccuMulti,
diff --git a/R/unmarkedFrame.R b/R/unmarkedFrame.R
index 48aad33..5e83b76 100644
--- a/R/unmarkedFrame.R
+++ b/R/unmarkedFrame.R
@@ -894,17 +894,6 @@ setGeneric("getY", function(object) standardGeneric("getY"))
 setMethod("getY", "unmarkedFrame", function(object) object@y)
 
 
-setGeneric("coordinates", function(object) standardGeneric("coordinates"))
-setMethod("coordinates", "unmarkedFrame", function(object) {
-    object@mapInfo@coordinates
-})
-
-
-setGeneric("projection", function(object) standardGeneric("projection"))
-setMethod("projection", "unmarkedFrame", function(object) {
-    object@mapInfo@projection
-})
-
 ################################### SUMMARY METHODS ######################
 
 
diff --git a/man/unmarkedFrame-class.Rd b/man/unmarkedFrame-class.Rd
index ddcd347..44925b5 100644
--- a/man/unmarkedFrame-class.Rd
+++ b/man/unmarkedFrame-class.Rd
@@ -2,37 +2,17 @@
 \Rdversion{1.1}
 \docType{class}
 \alias{unmarkedFrame-class}
-\alias{coordinates,unmarkedFrame-method}
-\alias{coordinates}
-\alias{coords}
-\alias{getY}
-\alias{getY,unmarkedFrame-method}
 \alias{head,unmarkedFrame-method}
 \alias{hist,unmarkedFrameDS-method}
-\alias{mapInfo}
 \alias{numSites}
 \alias{numSites,unmarkedFrame-method}
 \alias{numY}
 \alias{numY,unmarkedFrame-method}
-\alias{obsCovs,unmarkedFrame-method}
-\alias{obsCovs<-,unmarkedFrame-method}
-\alias{obsCovs}
-\alias{obsCovs<-}
 \alias{obsNum,unmarkedFrame-method}
 \alias{obsNum}
-\alias{obsToY,unmarkedFrame-method}
-\alias{obsToY<-,unmarkedFrame-method}
-\alias{obsToY}
-\alias{obsToY<-}
 \alias{plot,unmarkedFrame,missing-method}
 \alias{plot,unmarkedFrameOccuMulti,missing-method}
 \alias{plot,unmarkedFrameOccuTTD,missing-method}
-\alias{projection,unmarkedFrame-method}
-\alias{projection}
-\alias{siteCovs,unmarkedFrame-method}
-\alias{siteCovs<-,unmarkedFrame-method}
-\alias{siteCovs}
-\alias{siteCovs<-}
 \alias{unmarkedFrameOccu-class}
 \alias{unmarkedFrameOccuMulti-class}
 \alias{unmarkedFrameOccuMS-class}
diff --git a/man/unmarkedFrame-extractors.Rd b/man/unmarkedFrame-extractors.Rd
new file mode 100644
index 0000000..87e6ec1
--- /dev/null
+++ b/man/unmarkedFrame-extractors.Rd
@@ -0,0 +1,68 @@
+\name{unmarkedFrame-extractors}
+\alias{getY}
+\alias{siteCovs}
+\alias{siteCovs<-}
+\alias{obsCovs}
+\alias{obsCovs<-}
+\alias{yearlySiteCovs}
+\alias{yearlySiteCovs<-}
+\alias{obsToY}
+\alias{obsToY<-}
+\alias{getY,unmarkedFrame-method}
+\alias{siteCovs,unmarkedFrame-method}
+\alias{siteCovs<-,unmarkedFrame-method}
+\alias{obsCovs,unmarkedFrame-method}
+\alias{obsCovs<-,unmarkedFrame-method}
+\alias{yearlySiteCovs,unmarkedMultFrame-method}
+\alias{yearlySiteCovs<-,unmarkedMultFrame-method}
+\alias{obsToY,unmarkedFrame-method}
+\alias{obsToY<-,unmarkedFrame-method}
+
+\title{Extract and replace methods for unmarkedFrame components}
+
+\description{Methods for extracting and replacing components of \code{unmarkedFrame}s, 
+  such as the observation data (\code{getY}), site covariates (\code{siteCovs}),
+  and observation covariates (\code{obsCovs}).
+}
+
+\usage{
+\S4method{getY}{unmarkedFrame}(object)
+\S4method{siteCovs}{unmarkedFrame}(object)
+\S4method{obsCovs}{unmarkedFrame}(object, matrices = FALSE)
+\S4method{yearlySiteCovs}{unmarkedMultFrame}(object)
+\S4method{obsToY}{unmarkedFrame}(object)
+}
+
+\arguments{
+	\item{object}{An object of class \code{unmarkedFrame}}
+  \item{matrices}{Logical; if FALSE covariates are returned as a long 
+    data frame (MJ x ncovs). If true, a list of matrices (each M x J).}
+}
+
+\value{
+  A matrix of observation data (\code{getY}), a data frame of covariates 
+  (\code{siteCovs}, \code{obsCovs}, \code{yearlySiteCovs}), or the 
+  \code{obsToY} matrix (\code{obsToY}).
+}
+
+\examples{
+
+data(mallard)
+mallardUMF <- unmarkedFramePCount(mallard.y, siteCovs = mallard.site,
+	obsCovs = mallard.obs)
+
+# Extract the observations
+getY(mallardUMF)
+
+# Extract the observation covariates
+obsCovs(mallardUMF)
+obsCovs(mallardUMF, matrices = TRUE)
+
+# Extract the site covariates
+siteCovs(mallardUMF)
+
+# Replace the existing site covariates
+new_covs <- data.frame(x = rnorm(239))
+siteCovs(mallardUMF) <- new_covs
+siteCovs(mallardUMF)
+}
diff --git a/man/unmarkedMultFrame.Rd b/man/unmarkedMultFrame.Rd
index 97533ee..3984233 100644
--- a/man/unmarkedMultFrame.Rd
+++ b/man/unmarkedMultFrame.Rd
@@ -1,10 +1,5 @@
 \name{unmarkedMultFrame}
-
 \alias{unmarkedMultFrame}
-\alias{yearlySiteCovs}
-\alias{yearlySiteCovs,unmarkedMultFrame-method}
-\alias{yearlySiteCovs<-}
-\alias{yearlySiteCovs<-,unmarkedMultFrame-method}
 \alias{unmarkedFrameGMM}
 \alias{unmarkedFrameGDS}
 \alias{unmarkedFrameGPC}