remove some trailing whitespace in code

R/AllClass.R

@@ -727,7 +727,7 @@ setFlagsInternal <- function(object, name=NULL, i=NULL, value=NULL, debug=getOpt
     ## Ensure proper argument setup.
     if (is.null(name))
         stop("must supply a name")
-    if (is.null(i)) 
+    if (is.null(i))
         stop("must supply 'i'")
     if (is.null(value))
         stop("must supply 'value'")

R/adp.R

@@ -486,7 +486,7 @@ setMethod(f="summary",
               ## 20170107: drop the printing of these. In the new scheme, we can subsample
               ## 20170107: files, and therefore do not read to the end, and it seems silly
               ## 20170107: to use time going through the whole file to find this out. If we
-              ## 20170107: decide that this is needed, we could do a seek() to the end of the 
+              ## 20170107: decide that this is needed, we could do a seek() to the end of the
               ## 20170107: and then go back to find the final time.
 
               ## cat(sprintf("* Measurements:       %s %s to %s %s sampled at %.4g Hz\n",
@@ -3146,15 +3146,15 @@ binmapAdp <- function(x, debug=getOption("oceDebug"))
 #' averaging during post-processing, thereby reducing the overall
 #' size of the data set and decreasing the uncertainty of the
 #' velocity estimates (by averaging out Doppler noise).
-#' 
+#'
 #' @param x an \code{adp} object, i.e. one inheriting from \code{\link{adp-class}}.
 #' @param n number of pings to average together.
 #' @param leftover a logical value indicating how to proceed in cases
 #' where \code{n} does not divide evenly into the number of ensembles
 #' in \code{x}. If \code{leftover} is \code{FALSE} (the default) then any extra
 #' ensembles at the end of \code{x} are ignored. Otherwise, they are used
 #' to create a final ensemble in the returned value.
-#' @param na.rm a logical value indicating whether NA values should be stripped 
+#' @param na.rm a logical value indicating whether NA values should be stripped
 #' before the computation proceeds
 #' @param ... extra arguments to be passed to the \code{mean()} function.
 #'
@@ -3166,7 +3166,7 @@ binmapAdp <- function(x, debug=getOption("oceDebug"))
 #' data(adp)
 #' adpAvg <- adpEnsembleAverage(adp, n=2)
 #' plot(adpAvg)
-#' 
+#'
 #' @family things related to \code{adp} data
 adpEnsembleAverage <- function(x, n=5, leftover=FALSE, na.rm=TRUE, ...)
 {

R/air.R

@@ -1,10 +1,10 @@
 #' Wind dataset
-#' 
+#'
 #' Wind data inferred from Figure 5 of Koch et al. (1983), provided to
 #' illustrate the \code{\link{interpBarnes}} function.
 #' Columns \code{wind$x} and \code{wind$y} are location, while \code{wind$z} is
 #' the wind speed, in m/s.
-#' 
+#'
 #' @name wind
 #' @docType data
 #'
@@ -16,13 +16,13 @@ NULL
 
 
 #' Air density
-#' 
+#'
 #' Compute, \eqn{\rho}{rho}, the \emph{in-situ} density of air.
-#' 
+#'
 #' This will eventually be a proper equation of state, but for now it's just
 #' returns something from wikipedia (i.e. not trustworthy), and not using
 #' humidity.
-#' 
+#'
 #' @param temperature \emph{in-situ} temperature [\eqn{^\circ}{deg}C]
 #' @param pressure pressure in Pa (NOT kPa) -- ignored at present
 #' @param humidity ignored at present

R/argo.R

@@ -63,7 +63,7 @@ setClass("argo", contains="oce")
 #' @source This file was downloaded using the unix command
 #'\preformatted{
 #' ftp ftp://ftp.ifremer.fr/ifremer/argo/dac/bodc/6900388/6900388_prof.nc
-#'} issued on 2017 July 7. 
+#'} issued on 2017 July 7.
 #'
 #' @family datasets provided with \code{oce}
 #' @family things related to \code{argo} data
@@ -79,7 +79,7 @@ NULL
 #'
 #' There are several possibilities, depending on the nature of \code{i}.
 #'\itemize{
-#' \item If \code{i} is the string \code{"SA"}, then 
+#' \item If \code{i} is the string \code{"SA"}, then
 #' Absolute Salinity is computed using \code{\link[gsw]{gsw_SA_from_SP}},
 #' with \code{salinityAdjusted} (etc) if available in the \code{data}
 #' slot of \code{x}, otherwise using \code{salinity} (etc).
@@ -195,23 +195,23 @@ getData <- function(file, name) # a local function -- no need to pollute namesap
 #' Convert Argo Data Name to Oce Name
 #'
 #' This function is used internally by \code{\link{read.argo}} to convert Argo-convention
-#' data names to oce-convention names. Users should not call this directly, since 
+#' data names to oce-convention names. Users should not call this directly, since
 #' its return value may be changed at any moment (e.g. to include units as well
 #' as names).
-#' 
+#'
 #'
 #' The inference of names was done
 #' by inspection of some data files, using [1] as a reference. It should be noted,
 #' however, that the data files examined contain some names that are not
-#' undocumented in [1], and others that are listed only in its changelog, 
+#' undocumented in [1], and others that are listed only in its changelog,
 #' with no actual definitions being given. For example, the files had six distinct
 #' variable names that seem to relate to phase in the oxygen sensor, but
 #' these are not translated by the present function because these
 #' variable names are not defined in [1], or not defined uniquely
 #' in [2].
 #'
 #' The names are converted with
-#' \code{\link{gsub}}, using the \code{ignore.case} argument of the present 
+#' \code{\link{gsub}}, using the \code{ignore.case} argument of the present
 #' function.
 #' The procedure
 #' is to first handle the items listed in the following table, with string

R/cm.R

@@ -412,7 +412,7 @@ as.cm <- function(time, u=NULL, v=NULL,
 #' @return An object of \code{\link{cm-class}}.
 #' The \code{data} slot will contain all the data in the file, with names
 #' determined from the tokens in line 3 in that file, passed through
-#' \code{\link{make.names}}, except that 
+#' \code{\link{make.names}}, except that
 #' \code{Vnorth} is renamed \code{v} (after conversion from cm/s to m/s),
 #' \code{Veast} is renamed \code{u} (after conversion from cm/s to m/s),
 #' \code{Cond} is renamed \code{conductivity},

R/coastline.R

@@ -48,7 +48,7 @@ setClass("coastline", contains="oce")
 #' startup file.
 #' @author Dan Kelley
 #' @source Downloaded from \url{http://www.naturalearthdata.com}, in
-#' \code{ne_110m_admin_0_countries.shp} in July 2015, with an 
+#' \code{ne_110m_admin_0_countries.shp} in July 2015, with an
 #' update on December 16, 2017.
 #' @family datasets provided with \code{oce}
 #' @family things related to \code{coastline} data
@@ -651,7 +651,7 @@ setMethod(f="plot",
                           ylabels <- formatPosition(yr.pretty, isLat=TRUE, type='expression',
                                                     showHemi=geographical==3)
                       }
- 
+
                       axis(1, at=xr.pretty, labels=xlabels, pos=usrTrimmed[3], cex.axis=cex.axis)
                       oceDebug(debug, "putting bottom x axis at", usrTrimmed[3], "with labels:", xlabels, "\n")
                       axis(2, at=yr.pretty, labels=ylabels, pos=usrTrimmed[1], cex.axis=cex.axis, cex=cex.axis)

R/ctd.R

@@ -609,7 +609,7 @@ setMethod(f="[[",
                       if (!(j %in% c("", "ratio", "uS/cm", "mS/cm", "S/m")))
                           stop("unknown conductivity unit \"", unit, "\"; must be \"\", \"ratio\", \"uS/cm\", \"mS/cm\" or \"S/m\"")
                       if (j == "")
-                          j <- "ratio" # lets us use switch() 
+                          j <- "ratio" # lets us use switch()
                       unit <- x@metadata$units$conductivity$unit
                       if (is.null(unit) || !length(unit)) {
                           ## FIXME: maybe should look at median value, to make a guess

R/ctd.itp.R

@@ -76,7 +76,7 @@ read.ctd.itp <- function(file, columns=NULL, station=NULL, missingValue, monitor
                     unit <- gsub("(.*)\\((.*)\\)", "\\2", tokens[i])
                     if (unit == "umol/kg")
                         units[[names[i]]] <- list(unit=expression(mu*mol/kg), scale="")
-                    else 
+                    else
                         units[[names[i]]] <- list(unit=expression(unit), scale="")
                 } else if (names[i] != "year" && names[i] != "day") {
                     unit <- gsub("(.*)\\((.*)\\)", "\\2", tokens[i])

R/ctd.odf.R

@@ -11,7 +11,7 @@
 #' The ODF format, used by the Canadian Department of Fisheries and Oceans, is
 #' described to some extent in the documentation for \code{\link{read.odf}}.  It
 #' is not clear that ODF format is handled correctly in \code{read.ctd.odf}, or
-#' the more general function \code{\link{read.odf}}, because the format 
+#' the more general function \code{\link{read.odf}}, because the format
 #' varies between some sample files the author has encountered in his research.
 #' @family things related to \code{ctd} data
 #' @family things related to \code{odf} data

R/ctd.sbe.R

@@ -881,7 +881,7 @@ read.ctd.sbe <- function(file, columns=NULL, station=NULL, missingValue,
             if (0 < (r<-regexpr("station:", lline)))
                 station <- sub("[ ]*$", "", sub("(.*)station:([ ])*", "", ignore.case=TRUE, line))
             if (0 < (r<-regexpr("station_name:", lline)))
-                station <- sub("[ ]*$", "", sub("(.*)station_name:([ ])*", "", ignore.case=TRUE, line)) 
+                station <- sub("[ ]*$", "", sub("(.*)station_name:([ ])*", "", ignore.case=TRUE, line))
         }
         if (0 < (r<-regexpr("recovery:", lline)))
             recovery <- sub("(.*)recovery:([ ])*", "", lline)

R/ctd.woce.R

@@ -52,7 +52,7 @@ oceNames2whpNames <- function(names)
 
 #' Translate oce unit to WHP unit
 #'
-#' Translate oce units to WHP-style strings, 
+#' Translate oce units to WHP-style strings,
 #' to match patterns. For example, the pattern \code{"oxygen"}
 #' is taken to mean \code{"CTDOXY"}.
 #'
@@ -198,7 +198,7 @@ woceNames2oceNames <- function(names)
 #' @family things related to \code{ctd} data
 #' @family functions that interpret variable names and units from headers
 woceUnit2oceUnit <- function(woceUnit)
-{   
+{
     ## message("woceUnit2oceUnit(\"", woceUnit, "\")", sep="")
     if (woceUnit == "DB" || woceUnit == "DBAR")
         return(list(unit=expression(dbar), scale=""))
@@ -706,7 +706,7 @@ read.ctd.woce.other <- function(file, columns=NULL, station=NULL, missingValue,
     if (length(names) == length(units)) {
         n <- length(names)
         ## example
-        ##  "DBAR"    "ITS-90"  "PSS-7"   "UMOL/KG" "V"       "V"       "OBS."    "*"      
+        ##  "DBAR"    "ITS-90"  "PSS-7"   "UMOL/KG" "V"       "V"       "OBS."    "*"
         for (i in 1:n) {
             if (units[i] == "DBAR") {
                 res@metadata$units[[names[i]]] <- list(unit=expression(dbar), scale="")

R/echosounder.R

@@ -836,7 +836,7 @@ read.echosounder <- function(file, channel=1, soundSpeed,
     c <- matrix(NA_real_, nrow=1, ncol=1)
     ## FIXME: find out whether samplesPerPing is always defined prior to use in the code1==0x15 blocks.
     ## The Rstudio code-diagnostic complains that this variable is used before being defined,
-    ## but when I run test code there is no problem, because the variable has been defined. What I 
+    ## but when I run test code there is no problem, because the variable has been defined. What I
     ## do *not* know is whether files will always have these byte groupsing in this order, but at
     ## least setting to a zero value is likely to cause an error, if that ever occurs. (I may just
     ## need to reorder some code, if problems arise.)
@@ -1017,7 +1017,7 @@ read.echosounder <- function(file, channel=1, soundSpeed,
     res@metadata$fileType <- fileType
     res@metadata$blankedSamples <- blankedSamples
     if (missing(soundSpeed)) {
-        res@metadata$soundSpeed <- swSoundSpeed(35, 10, 30, eos="unesco") 
+        res@metadata$soundSpeed <- swSoundSpeed(35, 10, 30, eos="unesco")
     } else {
         res@metadata$soundSpeed <- soundSpeed
     }

R/imagep.R

@@ -1034,7 +1034,7 @@ imagep <- function(x, y, z,
             zlim <- c(-1, 1) * max(abs(z), na.rm=TRUE)
         }
     }
- 
+
     zlimHistogram <- zlimGiven && zlim == "histogram"
     breaksGiven <- !missing(breaks)
     colormapGiven <- !missing(colormap)

R/index.R

@@ -1,28 +1,28 @@
 #' Read a NOAA ocean index file
-#' 
+#'
 #' Read an ocean index file, in the format used by NOAA.
-#' 
+#'
 #' @details
-#' Reads a text-format index file, in either of two formats. If 
+#' Reads a text-format index file, in either of two formats. If
 #' \code{format} is missing, then the first line of the file is examined. If
 #' that line contains 2 (whitespace-separated) tokens, then \code{"noaa"}
 #' format is assumed. If it contains 13 tokens, then \code{"ucar"} format is assumed.
 #' Otherwise, an error is reported.
 #'
-#' In the \code{"noaa"} format, the two tokens on the first line are taken to 
+#' In the \code{"noaa"} format, the two tokens on the first line are taken to
 #' be the start year and the end year, respectively. The second line
 #' must contain a single token, the missing value. All further lines must contain
 #' 12 tokens, for the values in January, February, etc.
 #'
 #' In the \code{"ucar"} format, all data lines must contain the 13 tokens,
 #' the first of which is the year, with the following 12 being the values
 #' for January, February, etc.
-#' 
+#'
 #' @param file a connection or a character string giving the name of the file
 #' to load.  May be a URL.
 #' @param format optional character string indicating the format type. If not
 #' supplied, a guess will be made, based on examination of the first few lines
-#' of the file. If supplied, the possibilities are \code{"noaa"} and 
+#' of the file. If supplied, the possibilities are \code{"noaa"} and
 #' \code{"ucar"}. See \dQuote{Details}.
 #' @param missingValue If supplied, this is a numerical value that indicates
 #' invalid data. In some datasets, this is -99.9, but other values may be used.
@@ -40,7 +40,7 @@
 #' @references See \url{https://www.esrl.noaa.gov/psd/data/climateindices/list/}
 #' for a list of indices.
 #' @examples
-#' 
+#'
 #' \dontrun{
 #' library(oce)
 #' par(mfrow=c(2, 1))

R/lobo.R

@@ -307,7 +307,7 @@ setMethod(f="plot",
                       oce.plot.ts(x[["time"]], x[["salinity"]], ylab=resizableLabel("S"), debug=debug-1, ...)
                   } else if (w == 3) {
                       if (any(!is.na(x[['pressure']]))) {
-                          plotTS(as.ctd(x[["salinity"]], x[["temperature"]], x[["pressure"]]), eos="unesco", debug=debug-1, ...) 
+                          plotTS(as.ctd(x[["salinity"]], x[["temperature"]], x[["pressure"]]), eos="unesco", debug=debug-1, ...)
                       } else {
                           plotTS(as.ctd(x[["salinity"]], x[["temperature"]], 0), eos="unesco", debug=debug-1, ...)
                       }

R/misc.R

@@ -3186,8 +3186,7 @@ coriolis <- function(latitude, degrees=TRUE)
 {
     ## Siderial day 86164.1 s.
     if (degrees) latitude <- latitude * 0.0174532925199433
-    ## http://www.iag-aig.org/attach/e354a3264d1e420ea0a9920fe762f2a0/51-groten.pdf
-    7292115e-11 
+    ## http://www.iag-aig.org/attach/e354a3264d1e420ea0a9920fe762f2a0/51-groten.pdf 7292115e-11
     2 * 7292115e-11 * sin(latitude)
 }
 

R/oce.R

@@ -310,7 +310,7 @@ as.oce <- function(x, ...)
 ##DELETE     for (i in seq_len(ndots))
 ##DELETE         if (!inherits(dots[[i]], "oce"))
 ##DELETE             stop("concatenate() argument ", i, " does not inherit from \"oce\"")
-##DELETE 
+##DELETE
 ##DELETE     ## Concatenate the data (and flags, if there are such).
 ##DELETE     res <- dots[[1]]
 ##DELETE     n1 <- sort(names(dots[[1]]@data))

R/odf.R

@@ -154,7 +154,7 @@ setMethod(f="plot",
               data <- x@data
               dataNames <- names(data)
               ## At the start, n is the number of non-time variables, but
-              ## later on we might switch it to equal nok, which is the 
+              ## later on we might switch it to equal nok, which is the
               ## number of non-time variables that contain finite data.
               if (!("time" %in% dataNames)) {
                   finite <- unlist(lapply(data, function(col) any(is.finite(col))))
@@ -181,7 +181,7 @@ setMethod(f="plot",
                           N <- as.integer(0.5 + sqrt(n - 1))
                           M <- as.integer(n / N)
                           ## may need to add 1, but use a loop in case my logic is mixed up
-                          ## if that would 
+                          ## if that would
                           while (N * M < n)
                               M <- M + 1
                           par(mfrow=c(N, M))

R/run.R

@@ -1,5 +1,5 @@
 #' Calculate running linear models
-#' 
+#'
 #' The linear model is calculated from the slope of a localized least-squares
 #' regression model y=y(x).  The localization is defined by the x difference
 #' from the point in question, with data at distance exceeding L/2 being
@@ -8,7 +8,7 @@
 #' weighting function is used; the latter produces smoother derivatives, which
 #' can be useful for noisy data.  The function is based on internal
 #' calculation, not on \code{\link{lm}}.
-#' 
+#'
 #' @param x a vector holding x values.
 #' @param y a vector holding y values.
 #' @param xout optional vector of x values at which the derivative is to be
@@ -25,9 +25,9 @@
 #' returned, and if \code{deriv=1}, a vector of derivatives is returned.
 #' @author Dan Kelley
 #' @examples
-#' 
+#'
 #' library(oce)
-#' 
+#'
 #' # Case 1: smooth a noisy signal
 #' x <- 1:100
 #' y <- 1 + x/100 + sin(x/5)
@@ -37,7 +37,7 @@
 #' plot(x, y, type='l', lwd=7, col='gray')
 #' points(x, yn, pch=20, col='blue')
 #' lines(x, calc$y, lwd=2, col='red')
-#' 
+#'
 #' # Case 2: square of buoyancy frequency
 #' data(ctd)
 #' par(mfrow=c(1,1))

R/section.R

@@ -102,7 +102,7 @@ setMethod(f="initialize",
 #' @title Handle flags in Section Objects
 #'
 #' @details
-#' The default for \code{flags} is based on 
+#' The default for \code{flags} is based on
 #' calling \code{\link{defaultFlags}} based on the
 #' \code{metadata} in the first station in the section. If the
 #' other stations have different flag schemes (which seems highly
@@ -2365,7 +2365,7 @@ read.section <- function(file, directory, sectionId="", flags,
 #' @param method The method to use to decimate data within the stations; see
 #' \code{\link{ctdDecimate}}, which is used for the decimation.
 #'
-#' @template debugTemplate                                        
+#' @template debugTemplate
 #'
 #' @param ... Optional arguments to be supplied to \code{\link{ctdDecimate}},
 #' e.g. \code{rule} controls extrapolation beyond the observed pressure range,
@@ -2426,7 +2426,7 @@ sectionGrid <- function(section, p, method="approx", debug=getOption("oceDebug")
                          "Removed flags from gridded section object. Use handleFlags() first to remove bad data.")
     for (i in 1:n) {
         ##message("i: ", i, ", p before decimation: ", paste(section@data$station[[i]]@data$pressure, " "))
-        suppressWarnings(res@data$station[[i]] <- ctdDecimate(section@data$station[[i]], p=pt, method=method, 
+        suppressWarnings(res@data$station[[i]] <- ctdDecimate(section@data$station[[i]], p=pt, method=method,
                                                               debug=debug-1, ...))
         res@data$station[[i]]@metadata$flags <- NULL
         ##message("i: ", i, ", p after decimation: ", paste(res@data$station[[i]]@data$pressure, " "))