coastline docs: in line with s4

R/adp.R

@@ -6,10 +6,6 @@ setMethod(f="initialize",
               if (!missing(u)) .Object@data$u <- u
               if (!missing(a)) .Object@data$a <- a 
               if (!missing(q)) .Object@data$q <- q
-              ## FIXME: more here
-              ## names(adp$data)
-              ## [1] "v" "a" "q" "bottomRange" "bottomVelocity" "distance" "time"          
-              ## [8] "pressure" "temperature" "salinity" "depth" "heading" "pitch" "roll"          
               .Object@metadata$filename <- if (missing(filename)) "" else filename
               .Object@processingLog$time=c(.Object@processingLog$time, Sys.time())
               .Object@processingLog$value=c(.Object@processingLog$value, "create 'ctd' object")
@@ -19,10 +15,8 @@ setMethod(f="initialize",
 setMethod(f="[[",
           signature="adp",
           definition=function(x, i, j, drop) {
-              ## 'j' can be for times, as in OCE
-              ##if (!missing(j)) cat("j=", j, "*****\n")
-              i <- match.arg(i, c("u1", "u2", "u3","u4","latitude","longitude"))
-              if (i == "u1") return(x@data$v[,,1])
+              if (i == "filename") return(x@metadata$filename)
+              else if (i == "u1") return(x@data$v[,,1])
               else if (i == "u2") return(x@data$v[,,2])
               else if (i == "u3") return(x@data$v[,,3])
               else if (i == "u4") return(x@data$v[,,4])
@@ -35,19 +29,27 @@ setMethod(f="[[",
               else stop("cannot access \"", i, "\"") # cannot get here
           })
 
-##setMethod(f="[[",
-##          signature="adp",
-##          definition=function(x, i, j, drop) {
-##              ## 'j' can be for times, as in OCE
-##              ##if (!missing(j)) cat("j=", j, "*****\n")
-##              i <- match.arg(i, c("time", "u1", "u2", "u3"))
-##              if (i == "time") return(x@data$time)
-##              else if (i == "u1") return(x@data$v[,1])
-##              else if (i == "u2") return(x@data$v[,2])
-##              else if (i == "u3") return(x@data$v[,3])
-##              else stop("cannot access \"", i, "\"") # cannot get here
-##          })
-
+setMethod(f="show",
+          signature="adp",
+          definition=function(object) {
+              filename <- object[["filename"]]
+              if (is.null(filename) || filename == "")
+                  cat("ADP has column data\n", sep="")
+              else
+                  cat("ADP from file '", object[["filename"]], "' has column data\n", sep="")
+              names <- names(object@data)
+              ncol <- length(names)
+              for (i in 1:ncol) {
+                  cat(vectorShow(object@data[[i]], paste("  ", names[i])))
+                  dim <- dim(object@data[[i]])
+                  if (!is.null(dim)) {
+                      if (length(dim) == 2)
+                          cat("      (actually, the above is a matrix of dimension ", dim[1], " by ", dim[2], ")\n", sep="")
+                      else if (length(dim) == 3)
+                          cat("      (actually, the above is a matrix of dimension ", dim[1], " by ", dim[2], " by ", dim[3], ")\n", sep="")
+                  }
+              }
+          })
 
 
 head.adp <- function(x, n = 6L, ...)

R/adv.R

@@ -14,11 +14,8 @@ setMethod(f="initialize",
 setMethod(f="[[",
           signature="adv",
           definition=function(x, i, j, drop) {
-              ## 'j' can be for times, as in OCE
-              ##if (!missing(j)) cat("j=", j, "*****\n")
-              print(i)
-              i <- match.arg(i, c("time", "u1", "u2", "u3", "heading", "pitch", "roll"))
-              if (i == "time") return(x@data$time)
+              if (i == "filename") return(x@metadata$filename)
+              else if (i == "time") return(x@data$time)
               else if (i == "u1") return(x@data$v[,1])
               else if (i == "u2") return(x@data$v[,2])
               else if (i == "u3") return(x@data$v[,3])
@@ -39,6 +36,28 @@ setMethod(f="[[",
               } else stop("cannot access \"", i, "\"") # cannot get here
           })
 
+setMethod(f="show",
+          signature="adv",
+          definition=function(object) {
+              filename <- object[["filename"]]
+              if (is.null(filename) || filename == "")
+                  cat("ADV has column data\n", sep="")
+              else
+                  cat("ADV from file '", object[["filename"]], "' has column data\n", sep="")
+              names <- names(object@data)
+              ncol <- length(names)
+              for (i in 1:ncol) {
+                  cat(vectorShow(object@data[[i]], paste("  ", names[i])))
+                  dim <- dim(object@data[[i]])
+                  if (!is.null(dim)) {
+                      if (length(dim) == 2)
+                          cat("      (actually, the above is a matrix of dimension ", dim[1], " by ", dim[2], ")\n", sep="")
+                      else if (length(dim) == 3)
+                          cat("      (actually, the above is a matrix of dimension ", dim[1], " by ", dim[2], " by ", dim[3], ")\n", sep="")
+                  }
+              }
+          })
+
 read.adv <- function(file, from=1, to, by=1, tz=getOption("oceTz"),
                      type=c("nortek", "sontek", "sontek.adr", "sontek.text"),
                      header=TRUE,

R/cm.R

@@ -7,6 +7,48 @@ setMethod(f="initialize",
               return(.Object)
           })
 
+setMethod(f="[[",
+          signature="cm",
+          definition=function(x, i, j, drop) {
+              if (i %in% names(x@metadata)) return(x@metadata[[i]])
+              else if (i %in% names(x@data)) return(x@data[[i]])
+              else stop("cannot access \"", i, "\"")
+          })
+
+setMethod(f="[[<-",
+          signature="cm",
+          definition=function(x, i, j, value) { # FIXME: use j for e.g. times
+              if (i %in% names(x@metadata)) x@metadata[[i]] <- value
+              else if (i %in% names(x@data)) x@data[[i]] <- value
+              else stop("there is no item named \"", i, "\" in this cm object")
+              ##validObject(x)
+              invisible(x)
+          })
+
+setMethod(f="show",
+          signature="cm",
+          definition=function(object) {
+              filename <- object[["filename"]]
+              if (is.null(filename) || filename == "")
+                  cat("CM has column data\n", sep="")
+              else
+                  cat("CM from file '", object[["filename"]], "' has column data\n", sep="")
+              names <- names(object@data)
+              ncol <- length(names)
+              for (i in 1:ncol) {
+                  cat(vectorShow(object@data[[i]], paste("  ", names[i])))
+                  dim <- dim(object@data[[i]])
+                  if (!is.null(dim)) {
+                      if (length(dim) == 2)
+                          cat("      (actually, the above is a matrix of dimension ", dim[1], " by ", dim[2], ")\n", sep="")
+                      else if (length(dim) == 3)
+                          cat("      (actually, the above is a matrix of dimension ", dim[1], " by ", dim[2], " by ", dim[3], ")\n", sep="")
+                  }
+              }
+          })
+
+
+
 
 ## cm.R current-meter support (interocean S4)
 read.cm <- function(file, from=1, to, by=1, tz=getOption("oceTz"),

R/coastline.R

@@ -13,15 +13,54 @@ setMethod(f="initialize",
 setMethod(f="[[",
           signature="coastline",
           definition=function(x, i, j, drop) {
-              ## 'j' can be for times, as in OCE
-              ##if (!missing(j)) cat("j=", j, "*****\n")
-              i <- match.arg(i, c("latitude", "longitude"))
               if (i == "latitude") x@data$latitude
               else if (i == "longitude") x@data$longitude
+              else if (i == "filename") x@metadata$filename
               else NULL
           })
-#
-#
+
+setMethod(f="[[<-",
+          signature="coastline",
+          definition=function(x, i, j, value) { # FIXME: use j for e.g. times
+              if (i %in% names(x@metadata)) x@metadata[[i]] <- value
+              else if (i %in% names(x@data)) x@data[[i]] <- value
+              else stop("there is no item named \"", i, "\" in this coastline object")
+              validObject(x)
+              invisible(x)
+          })
+
+setValidity("coastline",
+            function(object) {
+                if (inherits(object, "coastline")) {
+                    ndata <- length(object@data)
+                    lengths <- vector("numeric", ndata)
+                    for (i in 1:ndata)
+                        lengths[i] <- length(object@data[[i]])
+                    if (var(lengths) != 0) {
+                        cat("lengths of data elements are unequal\n")
+                        return(FALSE)
+                    } else
+                        return(TRUE)
+                }
+            })
+
+
+
+setMethod(f="show",
+          signature="coastline",
+          definition=function(object) {
+              filename <- object[["filename"]]
+              if (is.null(filename) || filename == "")
+                  cat("Coastline has column data\n", sep="")
+              else
+                  cat("Coastline from file '", object[["filename"]], "' has column data\n", sep="")
+              names <- names(object@data)
+              ncol <- length(names)
+              for (i in 1:ncol) {
+                  cat(vectorShow(object@data[[i]], paste("  ", names[i])))
+              }
+          })
+
 as.coastline <- function(latitude, longitude)
 {
     n <- length(latitude)

R/misc.R

@@ -307,15 +307,15 @@ vectorShow <- function(v, msg, digits=5)
         paste(msg, "(empty vector)\n")
     } else {
         if (is.numeric(v)) {
-            if (n > 6) {
-                vv <- format(v[c(1, 2, 3, n-2, n-1, n)], digits=digits)
-                paste(msg, ": ", vv[1], ", ", vv[2], ", ", vv[3], ", ..., ", vv[4], ", ", vv[5], ", ", vv[6], " (length ", n, ")\n", sep="")
+            if (n > 4) {
+                vv <- format(v[c(1, 2, n-1, n)], digits=digits)
+                paste(msg, ": ", vv[1], ", ", vv[2], ", ..., ", vv[3], ", ", vv[4], " (length ", n, ")\n", sep="")
             } else {
                 paste(msg, ": ", paste(format(v, digits=digits), collapse=", "), "\n", sep="")
             }
         } else {
-            if (n > 6) {
-                paste(msg, ": ", v[1], ", ", v[2], ", ", v[3], ", ..., ", v[n-2], ", ", v[n-1], ", ", v[n], " (length ", n, ")\n", sep="")
+            if (n > 4) {
+                paste(msg, ": ", v[1], ", ", v[2], ", ..., ", v[n-1], ", ", v[n], " (length ", n, ")\n", sep="")
             } else {
                 paste(msg, ": ", paste(v, collapse=", "), "\n", sep="")
             }

man/as.coastline.Rd

@@ -16,11 +16,10 @@ the data have been manipulated.
 
 \value{An object of \code{\link[base]{class}} \code{"coastline"} (for details, see \code{\link{read.coastline}}).}
 
-\seealso{
-You may also use \code{\link{read.coastline}} to read a coastline file.
-Plotting is typically done with \code{\link{plot.coastline}}, although
-it is sufficient to just use \code{plot} for coastline objects.
-}
+\seealso{The documentation for \code{\link{coastline-class}} explains the
+    structure of coastline objects, and also outlines the other functions
+    dealing with them.}
+
 \examples{
 \dontrun{
 d<-read.table("bbasin.dat",header=FALSE) # dataset not provided with oce

man/cm-class.Rd

@@ -4,6 +4,8 @@
 
 \alias{cm-class}
 \alias{[[,cm-method}
+\alias{[[<-,cm-method}
+\alias{show,cm-method}
 
 \title{Class to store current meter data}
 

man/coastline-class.Rd

@@ -4,15 +4,27 @@
 
 \alias{coastline-class}
 \alias{[[,coastline-method}
+\alias{[[<-,coastline-method}
+\alias{show,coastline-method}
 
 \title{Class to store coastline data}
 
 \description{Class to store coastline data, with standard slots \code{metadata}
     (containing \code{fillable} and \code{filename}),  \code{data} (containing
     \code{latitude} and \code{longitude}) and \code{processingLog}.}
 
-\section{Methods}{Data may be accessed as e.g. \code{coastline[["latitude"]]}
-    or \code{coastline[["longitude"]]}.}
+\section{Methods}{
+    \subsection{Extracting values}{Data may be accessed as e.g.
+        \code{ctd[["latitude"]]} or
+        \code{ctd[["longitude"]]}.}
+
+    \subsection{Assigning values}{Latitude may be changed with e.g.
+        \code{ctd[["latitude"]] <- value}, and of course the same can be done
+        for \code{longitude}.}
+
+    \subsection{Overview of contents}{The \code{show} method (e.g.
+        \code{show(coastline)}) displays information about the object.}
+}
 
 \author{Dan Kelley}
 \keyword{classes}

man/coastlineHalifax.Rd

@@ -1,15 +1,21 @@
 \name{coastlineHalifax}
+
 \docType{data}
+
 \alias{coastlineHalifax}
+
 \title{Coastline data set, showing Halifax Harbour}
+
 \description{A sample coastline dataset, showing Halifax Harbour.
 The little island at about 44.64N is visible outside the author's window.}
 \usage{data(coastlineHalifax)}
+
 \references{\url{http://www.ngdc.noaa.gov/mgg_coastline/}}
-\seealso{Coastlines may be read with
-\code{\link{read.coastline}}, or created with
-\code{\link{as.coastline}}.  Another
-sample coastline file is \code{\link{coastlineMaritimes}}; see these for details of the data format.   Other coastline datasets provided with
-oce are \code{\link{coastlineMaritimes}} and \code{\link{coastlineWorld}}.}
+
+\seealso{The documentation for \code{\link{coastline-class}} explains the
+    structure of coastline objects, and also outlines the other functions
+    dealing with them.}
+
 \author{Dan Kelley}
+
 \keyword{datasets}

man/coastlineMaritimes.Rd

@@ -1,18 +1,26 @@
 \name{coastlineMaritimes}
+
 \docType{data}
+
 \alias{coastlineMaritimes}
+
 \title{Coastline data set, showing Maritime provinces of Canada}
-\description{A sample coastline dataset, showing Nova Scotia, 
-Prince Edward Island, and part of New Brunswick.
-This is the oce author's stomping ground, and so he feels compelled
-to apologize for the error at the Strait of Canso.}
+
+\description{A sample coastline dataset, showing Nova Scotia, Prince Edward
+    Island, and part of New Brunswick.  This is the oce author's stomping
+    ground, and so he feels compelled to apologize for the error at the Strait
+    of Canso.}
+
 \usage{data(coastlineMaritimes)}
+
 \source{The data were extracted from the the 1:2,000,000 ``World Data Bank II''
-dataset at the NOAA site.}
+    dataset at the NOAA site.}
 \references{\url{http://www.ngdc.noaa.gov/mgg_coastline/index.jsp?llat=43.0&ulat=47.2&llon=-66.8&rlon=-59.5}}
-\seealso{Coastlines may be read with
-\code{\link{read.coastline}}, or created with
-\code{\link{as.coastline}}; see these for details of the data format.  Other coastline datasets provided with
-oce are \code{\link{coastlineHalifax}} and \code{\link{coastlineWorld}}.}
+
+\seealso{The documentation for \code{\link{coastline-class}} explains the
+    structure of coastline objects, and also outlines the other functions
+    dealing with them.}
+
 \author{Dan Kelley}
+
 \keyword{datasets}

man/coastlineSLE.Rd

@@ -1,15 +1,24 @@
 \name{coastlineSLE}
+
 \docType{data}
+
 \alias{coastlineSLE}
+
 \title{Coastline of St Lawrence Estuary}
+
 \description{A sample coastline dataset, showing the St Lawrence Estuary.}
+
 \usage{data(coastlineSLE)}
+
 \source{The data were extracted from the the 1:250,000 ``World Vector Shoreline''
 dataset at the NOAA site.}
+
 \references{\url{http://www.ngdc.noaa.gov/mgg_coastline}}
-\seealso{Coastlines may be read with
-\code{\link{read.coastline}}, or created with
-\code{\link{as.coastline}}; see these for details of the data format.  Other coastline datasets provided with
-oce are \code{\link{coastlineHalifax}} and \code{\link{coastlineWorld}}.}
+
+\seealso{The documentation for \code{\link{coastline-class}} explains the
+    structure of coastline objects, and also outlines the other functions
+    dealing with them.}
+
 \author{Dan Kelley}
+
 \keyword{datasets}

man/coastlineWorld.Rd

@@ -26,10 +26,9 @@
   Creative Commons license
   (\url{http://creativecommons.org/licenses/by-sa/3.0/}).}
 
-\seealso{Coastlines may be read with
-\code{\link{read.coastline}}, or created with
-\code{\link{as.coastline}}; see these for details of the data format.  Other coastline datasets provided with
-oce are \code{\link{coastlineHalifax}} and \code{\link{coastlineMaritimes}}.}
+\seealso{The documentation for \code{\link{coastline-class}} explains the
+    structure of coastline objects, and also outlines the other functions
+    dealing with them.}
 
 \author{Dan Kelley}