Merge branch 'develop' into sf

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: oce
 Type: Package
 Title: Analysis of Oceanographic Data
-Version: 1.1-2
+Version: 1.2-1
 Authors@R: c(
     person(given="Dan", family="Kelley", email="[email protected]", role=c("aut", "cre"), comment=c(ORCID="https://orcid.org/0000-0001-7808-5911")),
     person(given="Clark", family="Richards", email="[email protected]", role=c("aut"), comment=c(ORCID="https://orcid.org/0000-0002-7833-206X")),

NEWS.md

@@ -1,19 +1,24 @@
-1.1-2
-
-* accommodate new ocedata (needed to meet new CRAN dependency rule)
-* add `oceRenameData()` and `oceRenamemetadata()`; deprecate `renameData()`
-* improve axis control for `mapPlot()` and `plot,coastline-method`.
-* remove `addColumn()`, `ctdAddColumn()`, `ctdUpdateHeader()`,
-  `findInOrdered()`, `mapMeridians()`, `mapZones()`, and `oce.as.POSIXlt()`,
-   all of which have been marked as "Deprecated" for the past two CRAN
-   releases.
-* `read.met()` handle the new Environment Canada data format
-* handle upcoming rgdal/R-devel changes
-* `sectionSmooth()` detects grids that extend beyond data range
-* `read.adp.rdi()` trims time vector if it exceeds other data lengths
-* `geodDist()` defaults 2nd location correctly when `alongPath=FALSE`
-* improve vignettes
-* fix itemized-list documentation problem pointed out by Kurt Hornik
+1.2-1
+* FIXME: add changes here
+
+1.2-0
+
+* Address argument doc/code warning that blocked CRAN acceptance.
+* Accommodate new ocedata (needed to meet new CRAN dependency rule).
+* Add `oceRenameData()` and `oceRenamemetadata()`.
+* Deprecate `renameData()`.
+* Improve axis control for `mapPlot()` and `plot,coastline-method`.
+* Remove `addColumn()`, `ctdAddColumn()`, `ctdUpdateHeader()`,
+  `findInOrdered()`, `mapMeridians()`, `mapZones()`, and
+  `oce.as.POSIXlt()`, all of which have been marked as
+  "Deprecated" for the past two CRAN releases.
+* Make `read.met()` handle a new Environment Canada data format.
+* Handle some upcoming rgdal/R-devel changes.
+* Make `sectionSmooth()` detect grids extending beyond data range.
+* Make `read.adp.rdi()` trim time if it longer than other data.
+* Make `geodDist()` handle second location correctly when `alongPath=FALSE`.
+* Improve vignettes.
+* Fix itemized-list documentation problem pointed out by Kurt Hornik.
 
 1.1-1
 
@@ -171,7 +176,7 @@
 * swCSTp() added
 * swConductivity() now swThermalConductivity(); using Caldwell (1974).
 * many sw() functions handle eos="gsw"
-* libary(gsw) replaces teos()
+* library(gsw) replaces teos()
 * curl() added
 * handle new NOAA ascii topography dataset type
 * mapGrid() added
@@ -666,7 +671,7 @@
 * add undriftTime()
 * add tdrPatm()
 * make readTdr() gather serial no. info; show this on plot.pt()
-* switch to recommended verion-number format
+* switch to recommended version-number format
 * remove section.subset(), replaced by subset()
 * improve log items in functions that read and assemble oce objects
     http://code.google.com/p/r-oce/issues/detail?id=38

R/AllClass.R

@@ -281,7 +281,7 @@ setClass("satellite", contains="oce") # both amsr and landsat stem from this
 #'
 #' @param x a basic [oce-class] object,
 #' but not from any subclass that derive from this base, because
-#' subclases have their own plot methods, e.g. calling `plot()` on a
+#' subclasses have their own plot methods, e.g. calling `plot()` on a
 #' [ctd-class] object dispatches to [plot,ctd-method()].
 #'
 #' @param y Ignored; only present here because S4 object for generic `plot`

R/adp.R

@@ -228,7 +228,7 @@
 #' @family things related to adp data
 setClass("adp", contains="oce")
 
-#' ADP (acoustic-doppler profiler) dataset
+#' Sample adp (acoustic-doppler profiler) dataset
 #'
 #' This is degraded subsample of measurements that were made with an
 #' upward-pointing ADP manufactured by Teledyne-RDI, as part of the St Lawrence
@@ -1347,7 +1347,7 @@ read.adp <- function(file, from, to, by, tz=getOption("oceTz"),
 }
 
 
-#' Plot ADP Data
+#' Plot an adp Object
 #'
 #' Create a summary plot of data measured by an acoustic doppler profiler.
 #'

R/adp.rdi.R

@@ -559,7 +559,7 @@ decodeHeaderRDI <- function(buf, debug=getOption("oceDebug"), tz=getOption("oceT
 #'
 #' The following two-byte ID codes are recognized by `read.adp.rdi`
 #' at this time (with bytes listed in natural order, LSB byte before
-#' MSB). Items preceeded by an asterisk are recognized, but not handled,
+#' MSB). Items preceded by an asterisk are recognized, but not handled,
 #' and so produce a warning.
 #'\tabular{rrrr}{
 #'   \tab **Byte 1** \tab **Byte 2** \tab **Meaning**\cr

R/adp.sontek.R

@@ -440,7 +440,8 @@ read.adp.sontek.serial <- function(file, from=1, to, by=1, tz=getOption("oceTz")
                                    type=c("adp", "pcadp"),
                                    beamAngle=25, orientation,
                                    monitor=FALSE, processingLog,
-                                   debug=getOption("oceDebug"))
+                                   debug=getOption("oceDebug"),
+                                   ...)
 {
     if (!missing(file) && is.character(file) && 0 == file.info(file)$size)
         stop("empty file")

R/adv.R

@@ -42,7 +42,7 @@
 #' @family things related to adv data
 setClass("adv", contains="oce")
 
-#' ADV (acoustic-doppler velocimeter) dataset
+#' Sample adv (acoustic-doppler velocimeter) dataset
 #'
 #' This [adv-class] object is a sampling of measurements made with a
 #' Nortek Vector acoustic Doppler velocimeter deployed as part of the St Lawrence
@@ -387,7 +387,7 @@ read.adv <- function(file, from=1, to, by=1, tz=getOption("oceTz"),
 
 
 
-#' Plot ADV data
+#' Plot an adv Object
 #'
 #' Plot [adv-class] data.
 #'

R/amsr.R

@@ -46,8 +46,8 @@
 #' 2. A simple interface for viewing and downloading data is at
 #' `http://images.remss.com/amsr/amsr2_data_daily.html`.
 #'
-#' @seealso The documenation for the [landsat-class] class has
-#' more informatoin on the handling data from the Landsat-8 satellite.
+#' @seealso The documentation for the [landsat-class] class has
+#' more information on the handling data from the Landsat-8 satellite.
 #'
 #' @family things related to amsr data
 setClass("amsr", contains="satellite")
@@ -328,7 +328,7 @@ setMethod(f="subset",
 #' @param x an [amsr-class] object.
 #'
 #' @param y String indicating the name of the band to plot; if not provided,
-#' `SST` is used; see the documenation for the [amsr-class] class for a list of bands.
+#' `SST` is used; see the documentation for the [amsr-class] class for a list of bands.
 #'
 #' @param asp Optional aspect ratio for plot.
 #'

R/argo.R

@@ -254,10 +254,12 @@ setMethod(f="initialize",
               return(.Object)
           })
 
+## a local function -- no need to pollute namespace with it
 maybeLC <- function(s, lower)
     if (lower) tolower(s) else s
 
-getData <- function(file, name) # a local function -- no need to pollute namesapce with it
+## a local function -- no need to pollute namespace with it
+getData <- function(file, name, quiet=FALSE)
 {
     res <- NA
     ## wrap in capture.output to silence what seems like direct printing to stdout()
@@ -267,7 +269,8 @@ getData <- function(file, name) # a local function -- no need to pollute namesap
                        res <- try(ncdf4::ncvar_get(file, name), silent=TRUE)
                    })
     if (inherits(res, "try-error")) {
-        warning(file$filename, " has no variable named '", name, "'\n", sep='')
+        if (!quiet)
+            warning(file$filename, " has no variable named '", name, "'\n", sep='')
         res <- NULL
     }
     if (is.array(res) && 1 == length(dim(res))) res <- matrix(res) else res
@@ -1295,8 +1298,8 @@ read.argo <- function(file, debug=getOption("oceDebug"), processingLog, ...)
         n <- item
         d <- getData(file, maybeLC(n, lc))
         varNames <- varNamesOmit(varNames, n)
-        oceDebug(debug-1, n, "\n")
-        oceDebug(debug-1, "A varNames=", paste(varNames, collapse=","), "\n")
+        oceDebug(debug, n, "\n")
+        oceDebug(debug, "varNames=", paste(varNames, collapse=","), "\n")
         if (!is.null(d)) {
             res@data[[argoNames2oceNames(n)]] <- d
             res@metadata$dataNamesOriginal[[argoNames2oceNames(n)]] <- n
@@ -1305,7 +1308,10 @@ read.argo <- function(file, debug=getOption("oceDebug"), processingLog, ...)
         }
 
         n <- paste(item, maybeLC("_QC", lc), sep="")
-        d <- getData(file, maybeLC(n, lc))
+        oceDebug(debug, "about to try to get '", n, "' from netcdf file\n", sep="")
+        ##if (n == "PRES_QC") browser()
+        d <- getData(file, maybeLC(n, lc), quiet=TRUE)
+        oceDebug(debug, "... got it\n", sep="")
         varNames <- varNamesOmit(varNames, n)
         oceDebug(debug-1, n, "\n")
         oceDebug(debug-1, "B varNames=", paste(varNames, collapse=","), "\n")
@@ -1477,7 +1483,7 @@ as.argo <- function(time, longitude, latitude,
 }
 
 
-#' Plot Argo Data
+#' Plot an argo Object
 #'
 #' Plot a summary diagram for argo data.
 #'
@@ -1544,7 +1550,7 @@ as.argo <- function(time, longitude, latitude,
 #' in the \CRANpkg{rgdal} package; this will be familiar to many readers as
 #' the PROJ.4 notation; see [mapPlot()].
 #'
-#' @param mar value to be used with [par()]("mar").
+#' @param mar value to be used with `par('mar')`.
 #'
 #' @param tformat optional argument passed to [oce.plot.ts()], for plot
 #' types that call that function.  (See [strptime()] for the format

R/bremen.R

@@ -66,7 +66,7 @@ setMethod(f="[[<-",
               callNextMethod(x=x, i=i, j=j, ...=..., value=value) # [[<-
           })
 
-#' Plot a Bremen Object
+#' Plot a bremen Object
 #'
 #' Plot a [bremen-class] object.
 #' If the first argument seems to be a CTD dataset, this uses [plot,ctd-method()];

R/cm.R

@@ -638,7 +638,7 @@ read.cm.s4 <- function(file, from=1, to, by=1, tz=getOption("oceTz"),
 }
 
 
-#' Plot CM data
+#' Plot a cm Object
 #'
 #' Creates a multi-panel summary plot of data measured by a current meter.
 #'

R/coastline.R

@@ -126,7 +126,7 @@ setMethod(f="[[<-",
 #' @param subset An expression indicating how to subset `x`. See \dQuote{Details}.
 #'
 #' @param ... optional additional arguments, the only one of which is considered
-#' is one named `debug`, an integer that controlls the level of debugging. If
+#' is one named `debug`, an integer that controls the level of debugging. If
 #' this is not supplied, `debug` is assumed to be 0, meaning no debugging. If
 #' it is 1, the steps of determining the bounding box are shown. If it is 2 or larger,
 #' then additional processing steps are shown, including the extraction of every
@@ -213,12 +213,9 @@ setMethod(f="subset",
               options(warn=-1)
               na <- which(is.na(cllon))
               nseg <- length(na)
-              oceDebug(debug, "nseg=", nseg, "\n")
-              nnew <- 0
-              outlon <- NULL           # FIXME: remove after transition to sf::
-              outlat <- NULL           # FIXME: remove after transition to sf::
-              outlonSF <- NULL         # FIXME: remove after transition to sf::
-              outlatSF <- NULL         # FIXME: remove after transition to sf:"
+              ##OLD nnew <- 0
+              outlon <- NULL
+              outlat <- NULL
               for (iseg in 2:nseg) {
                   oceDebug(debug, "iseg=", iseg, "\n")
                   look <- seq.int(na[iseg-1]+1, na[iseg]-1)
@@ -311,7 +308,7 @@ as.coastline <- function(longitude, latitude, fillable=FALSE)
 }
 
 
-#' Plot a Coastline
+#' Plot a coastline Object
 #'
 #' This function plots a coastline.  An attempt is made to fill the space of
 #' the plot, and this is done by limiting either the longitude range or the

R/ctd.R

@@ -630,7 +630,7 @@ setMethod(f="summary",
 #' slot. If it is impossible to determine the sampling time, then
 #' `NULL` is returned. These time variants occur, in the
 #' present version of oce, only for data read by [read.ctd.sbe()],
-#' the documention of which explains how times are computed.
+#' the documentation of which explains how times are computed.
 #'
 #' * `z`: Vertical coordinate in metres above the surface, computed with
 #' [swZ]`(x)`.
@@ -2750,7 +2750,7 @@ write.ctd <- function(object, file, metadata=TRUE, flags=TRUE, format="csv")
 }
 
 
-#' Plot CTD Data
+#' Plot a ctd Object
 #'
 #' Plot CTD data, by default in a four-panel display showing (a) profiles of
 #' salinity and temperature, (b) profiles of density and the square of buoyancy
@@ -3781,10 +3781,10 @@ setMethod(f="plot",
 
 #' Subset a CTD Object
 #'
-#' Return a subset of a section object.
+#' Return a subset of a [ctd-class] object.
 #'
-#' This function is used to subset data within the
-#' levels of a ctd object. There are two ways of working. If
+#' This function is used to subset data within
+#' a ctd object. There are two ways of working. If
 #' `subset` is supplied, then it is a logical expression
 #' that is evaluated within the environment of the `data`
 #' slot of the object (see Example 1). Alternatively, if the

R/ctd.sbe.R

@@ -84,10 +84,10 @@
 #'   `n2satumol/kg`\tab `nitrogenSaturation`           \tab umol/kg              \tab   \cr
 #'   `nbin`        \tab `nbin`                         \tab                      \tab   \cr
 #'   `obsscufa~`   \tab `backscatter`                  \tab NTU; Turner SCUFA    \tab   \cr
-#'   `opoxMg/L`    \tab `oxygen`                       \tab mg/l; Optode, Anderaa\tab   \cr
-#'   `opoxML/L`    \tab `oxygen`                       \tab ml/l; Optode, Anderaa\tab   \cr
-#'   `opoxMm/L`    \tab `oxygen`                       \tab umol/l; Optode, Anderaa\tab \cr
-#'   `opoxPS`      \tab `oxygen`                       \tab percent; Optode, Anderaa\tab   \cr
+#'   `opoxMg/L`    \tab `oxygen`                       \tab mg/l; Optode, Aanderaa\tab   \cr
+#'   `opoxML/L`    \tab `oxygen`                       \tab ml/l; Optode, Aanderaa\tab   \cr
+#'   `opoxMm/L`    \tab `oxygen`                       \tab umol/l; Optode, Aanderaa\tab \cr
+#'   `opoxPS`      \tab `oxygen`                       \tab percent; Optode, Aanderaa\tab   \cr
 #'   `oxsatML/L`   \tab `oxygen`                       \tab ml/l; Weiss          \tab   \cr
 #'   `oxsatMg/L`   \tab `oxygen`                       \tab mg/l; Weiss          \tab   \cr
 #'   `oxsatMm/Kg`  \tab `oxygen`                       \tab umol/kg; Weiss       \tab   \cr
@@ -358,16 +358,16 @@ cnvName2oceName <- function(h, columns=NULL, debug=getOption("oceDebug"))
         unit <- list(unit=expression(NTU), scale="Turner SCUFA")
     } else if (1 == length(grep("^opoxMg/L$", name, useBytes=TRUE))) {
         name <- "oxygen"
-        unit <- list(unit=expression(mg/l), scale="Optode, Anderaa")
+        unit <- list(unit=expression(mg/l), scale="Optode, Aanderaa")
     } else if (1 == length(grep("^opoxML/L$", name, useBytes=TRUE))) {
         name <- "oxygen"
-        unit <- list(unit=expression(ml/l), scale="Optode, Anderaa")
+        unit <- list(unit=expression(ml/l), scale="Optode, Aanderaa")
     } else if (1 == length(grep("^opoxMm/L$", name, useBytes=TRUE))) {
         name <- "oxygen"
-        unit <- list(unit=expression(mu*mol/l), scale="Optode, Anderaa")
+        unit <- list(unit=expression(mu*mol/l), scale="Optode, Aanderaa")
     } else if (1 == length(grep("^opoxPS$", name, useBytes=TRUE))) {
         name <- "oxygenSaturation"
-        unit <- list(unit=expression(percent), scale="Optode, Anderaa")
+        unit <- list(unit=expression(percent), scale="Optode, Aanderaa")
     } else if (1 == length(grep("^oxsatML/L$", name, useBytes=TRUE))) {
         name <- "oxygen"
         unit <- list(unit=expression(ml/l), scale="Weiss")

R/ctd.woce.R

@@ -233,7 +233,7 @@ woceUnit2oceUnit <- function(woceUnit)
 #' This reads WOCE exchange files that start with the string `"CTD"`.
 #' There are two variants: one in which the first 4 characters are
 #' `"CTD,"` and the other in which the first 3 characters are
-#' again `"CTD"` but no other non-whitespace characers occur on
+#' again `"CTD"` but no other non-whitespace characters occur on
 #' the line.
 #'
 #' @template readCtdTemplate

R/echosounder.R

@@ -28,7 +28,7 @@
 #'
 #' @details
 #'
-#' * An infrequently updated record of the intrument position, in
+#' * An infrequently updated record of the instrument position, in
 #' `timeSlow`, `longitudeSlow` and `latitudeSlow`.  These are
 #' used in plotting maps with [plot,echosounder-method()].
 #'
@@ -332,7 +332,7 @@ setMethod(f="subset",
 #' @param sourceLevel source level, in dB (uPa at 1m), denoted `sl` in
 #' reference 1 p15, where it is in units 0.1dB (uPa at 1m)
 #'
-#' @param receiverSensitivity receiver sensivitity of the main element, in
+#' @param receiverSensitivity receiver sensitivity of the main element, in
 #' dB(counts/uPa), denoted `rs` in reference 1 p15, where it is in units of
 #' 0.1dB(counts/uPa)
 #'
@@ -432,7 +432,7 @@ findBottom <- function(x, ignore=5, clean=despike)
 }
 
 
-#' Plot Echosounder Data
+#' Plot an echosounder Object
 #'
 #' Plot echosounder data.
 #' Simple linear approximation is used when a `newx` value is specified
@@ -1092,7 +1092,7 @@ read.echosounder <- function(file, channel=1, soundSpeed,
             if (debug > 1) cat(" comment tuple [1 sec 4.14 p28]\n")
             ## FIXME: other info could be gleaned from the comment, if needed
             numbytes <- .C("uint16_le", buf[offset+34:35], 1L, res=integer(1), NAOK=TRUE, PACKAGE="oce")$res
-            if (debug > 1) cat('numbytes:', numbytes, ' ... NOTHING ELSE DECODED in this verion of oce.\n')
+            if (debug > 1) cat('numbytes:', numbytes, ' ... NOTHING ELSE DECODED in this version of oce.\n')
         } else {
             if (debug > 3) cat(" unknown code IGNORED\n")
         }

R/extdata.R

@@ -20,7 +20,7 @@
 NULL
 
 
-#' Sample RDI Teledyne adp dataset in format
+#' Sample adp (acoustic-doppler profiler) file in RDI format
 #'
 #' @name adp_rdi.000
 #'

R/gps.R

@@ -84,7 +84,7 @@ setMethod(f="[[<-",
           })
 
 
-#' Plot a GPS Object
+#' Plot a gps Object
 #'
 #' This function plots a gps object.  An attempt is made to use the whole space
 #' of the plot, and this is done by limiting either the longitude range or the