fix spelling errors noticed during pre-submission

R/adp.R

@@ -88,7 +88,7 @@
 #' Teledyne-RDI profilers have an additional item \code{g} (for
 #' percent-good).
 #'
-#' VmDas-equiped Teledyne-RDI profilers additional navigation data, with
+#' VmDas-equipped Teledyne-RDI profilers additional navigation data, with
 #' details listed in the table below; note that the RDI documentation [2] and
 #' the RDI gui use inconsistent names for most items.
 #'
@@ -2260,7 +2260,7 @@ toEnuAdp <- function(x, declination=0, debug=getOption("oceDebug"))
 #' multiplying by \code{count2db}.  Then, the signal decrease owing to
 #' spherical spreading is compensated for by adding the term
 #' \eqn{20\log10(r)}{20*log10(r)}, where \eqn{r}{r} is the distance from the
-#' sensor head to the water from which scattering is occuring.  \eqn{r}{r} is
+#' sensor head to the water from which scattering is occurring.  \eqn{r}{r} is
 #' given by \code{x[["distance"]]}.
 #'
 #' @param x An \code{adp} object, i.e. one inheriting from \code{\link{adp-class}}.
@@ -2366,7 +2366,7 @@ beamUnspreadAdp <- function(x, count2db=c(0.45, 0.45, 0.45, 0.45), asMatrix=FALS
 #'
 #' @param x an object of class \code{"adp"}.
 #' @template debugTemplate
-#' @return An object with the first 3 velocitiy indices having been altered to
+#' @return An object with the first 3 velocity indices having been altered to
 #' represent velocity components in xyz (or instrument) coordinates.  (For
 #' \code{rdi} data, the values at the 4th velocity index are changed to
 #' represent the "error" velocity.)

R/adp.nortek.R

@@ -30,7 +30,7 @@
 #' but can be used directly as well.  The code is based on information in the
 #' Nortek System Integrator Guide (2008) and on postings on the Nortek
 #' ``knowledge center'' discussion board.  One might assume that the latter is
-#' less authorative than the former.  For example, the inference of cell size
+#' less authoritative than the former.  For example, the inference of cell size
 #' follows advice found at
 #' \url{http://www.nortekusa.com/en/knowledge-center/forum/hr-profilers/736804717}
 #' (downloaded June 2012)), which contains a typo in an early posting that is

R/adp.rdi.R

@@ -308,7 +308,7 @@ decodeHeaderRDI <- function(buf, debug=getOption("oceDebug"), tz=getOption("oceT
         ## also teledyne2014ostm page 144 says could be Surveyor or Observer
     } else {
         instrumentSubtype <- "unknown"
-        ## FIXME: I think this is a poor way to determine the intrument type. Why do we even try?
+        ## FIXME: I think this is a poor way to determine the instrument type. Why do we even try?
         ##> warning("unexpected length ", FLDLength, " of fixed-leader-data header; expecting 50 for
         ##>         'surveyor/observor' or 59 for 'workhorse'.")
     }
@@ -454,7 +454,7 @@ decodeHeaderRDI <- function(buf, debug=getOption("oceDebug"), tz=getOption("oceT
 #' not a format that R supports. These velocities become 8-byte (numeric) values
 #' in R. Thus, the R object created by \code{read.adp.rdi} will require more memory
 #' than that of the data file. A scale factor can be estimated by ignoring
-#' vector quanties (e.g. time, which has just one value per profile) and concentrating on matrix properties
+#' vector quantities (e.g. time, which has just one value per profile) and concentrating on matrix properties
 #' such as velocity, backscatter, and correlation. These three elements have equal dimensions.
 #' Thus, each 4-byte slide in the data file (2 bytes + 1 byte + 1 byte)
 #' corresponds to 10 bytes in the object (8 bytes + 1 byte + 1 byte).

R/adp.sontek.R

@@ -2,7 +2,7 @@
 
 #' Read a Sontek ADP File
 #'
-#' Read a Sontek acoustic-Dopplerprofiler file [1].
+#' Read a Sontek acoustic-Doppler profiler file [1].
 #"
 #' @param despike if \code{TRUE}, \code{\link{despike}} will be used to clean
 #' anomalous spikes in heading, etc.
@@ -410,12 +410,12 @@ sontek.time <- function(t, tz=getOption("oceTz"))
 
 #' Read a serial Sontek ADP file
 #'
-#' Read a Sontek acoustic-Dopplerprofiler file, in a serial form that
+#' Read a Sontek acoustic-Doppler profiler file, in a serial form that
 #' is possibly unique to Dalhousie University.
 #'
 #' @param beamAngle angle between instrument axis and beams, in degrees.
-#' @param type A character string indicating the type of instrument.
-#' @param orientation Ooptional character string specifying the orientation of the
+#' @param type a character string indicating the type of instrument.
+#' @param orientation optional character string specifying the orientation of the
 #' sensor, provided for those cases in which it cannot be inferred from the
 #' data file.  The valid choices are \code{"upward"}, \code{"downward"}, and
 #' \code{"sideward"}.

R/adv.R

@@ -1,6 +1,6 @@
 #' Class to Hold adv Data
 #'
-#' This class holds data from acoustic-Dopper velocimeters.
+#' This class holds data from acoustic-Doppler velocimeters.
 #'
 #' The \code{metadata} slot
 #'     contains various items relating to the dataset, including source file name,
@@ -146,7 +146,7 @@ setMethod(f="summary",
 #' In addition to the usual extraction of elements by name, some shortcuts
 #' are also provided, e.g. \code{u1} retrieves \code{v[,1]}, and similarly
 #' for the other velocity components. The \code{a} and \code{q}
-#' data can be retrived in \code{\link{raw}} form
+#' data can be retrieved in \code{\link{raw}} form
 #' or numeric form; see \dQuote{Examples}.
 #'
 #' It is also worth noting that heading, pitch, etc. may be stored in
@@ -529,7 +529,7 @@ read.adv <- function(file, from=1, to, by=1, tz=getOption("oceTz"),
 #' which case the rows are used, in order, for the panels of the graph.
 #'
 #' @param brushCorrelation Optional number between 0 and 100, indicating a
-#' per-beam correlation threshhold below which data are to be considered suspect.
+#' per-beam correlation threshold below which data are to be considered suspect.
 #' If the plot type is \code{p}, the suspect points (velocity, backscatter
 #' amplitude, or correlation) will be coloured red; otherwise, this argument is
 #' ignored.
@@ -1246,7 +1246,7 @@ beamToXyzAdv <- function(x, debug=getOption("oceDebug"))
 #' Generally, the transformation must be done on a time-by-time basis, which is
 #' a slow operation.  However, this function checks whether the vectors for
 #' heading, pitch and roll, are all of unit length, and in that case, the
-#' calculation is altered, resulting in shorter executation times.  Note that
+#' calculation is altered, resulting in shorter execution times.  Note that
 #' the angles are held in (\code{data$timeSlow}, \code{data$headingSlow}, ...)
 #' for Nortek instruments and (\code{data$time}, \code{data$heading}, ...) for
 #' Sontek instruments.

R/air.R

@@ -9,7 +9,7 @@
 #' @docType data
 #'
 #' @references S. E.  Koch and M.  DesJardins and P. J. Kocin, 1983.  ``An
-#' interactive Barnes objective map anlaysis scheme for use with satellite and
+#' interactive Barnes objective map analysis scheme for use with satellite and
 #' conventional data,'' \emph{J.  Climate Appl.  Met.}, vol 22, p. 1487-1503.
 #' @family datasets provided with \code{oce}
 NULL

R/amsr.R

@@ -5,7 +5,7 @@
 #' The Advanced Microwave Scanning Radiometer (AMSR-2) is in current operation on
 #' the Japan Aerospace Exploration Agency (JAXA) GCOM-W1 space craft, launched in
 #' May 2012. Data are processed by Remote Sensing Systems. The satellite
-#' completes an ascending and descending pass during local daytime and nightime
+#' completes an ascending and descending pass during local daytime and nighttime
 #' hours respectively. Each daily file contains 7 daytime and 7 nighttime
 #' maps of variables named as follows within the \code{data}
 #' slot of amsr objects: \code{timeDay},
@@ -295,7 +295,7 @@ setMethod(f="subset",
 
 #' Plot an amsr Object
 #'
-#' @param x An object inherting from \code{\link{amsr-class}}.
+#' @param x An object inheriting from \code{\link{amsr-class}}.
 #' @param y String indicating the name of the band to plot; if not provided,
 #' \code{SST} is used; see \code{\link{amsr-class}} for a list of bands.
 #' @param asp Optional aspect ratio for plot.

R/argo.R

@@ -1137,7 +1137,7 @@ as.argo <- function(time, longitude, latitude,
 #' default, in order to use more space for the data and less for the axes.
 #'
 #' @param projection indication of the projection to be used
-#' in trajetory maps. If this is \code{NULL}, no projection is used, although
+#' in trajectory maps. If this is \code{NULL}, no projection is used, although
 #' the plot aspect ratio will be set to yield zero shape distortion at the
 #' mean float latitude.  If \code{projection="automatic"}, then one
 #' of two projections is used: stereopolar (i.e. \code{"+proj=stere +lon_0=X"}

R/bremen.R

@@ -59,12 +59,12 @@ setMethod(f="[[<-",
 #' Plot a \code{bremen} object, i.e. one inheriting from \code{\link{bremen-class}}.
 #' If \code{x} seems to be a CTD dataset, uses \code{\link{plot,ctd-method}};
 #' otherwise, \code{x} is assumed to be a lowered-adp object, and a two-panel
-#' plot is created with \code{\link{plot,ladp-method}} to show velocity varation with
+#' plot is created with \code{\link{plot,ladp-method}} to show velocity variation with
 #' pressure.
 #'
 #' @param x A \code{bremen} object, e.g. as read by \code{\link{read.bremen}}.
 #' @param type Optional string indicating the type to which \code{x} should be
-#' coerced before ploting. The choices are \code{ctd} and \code{ladp}.
+#' coerced before plotting. The choices are \code{ctd} and \code{ladp}.
 #' @param ... Other arguments, passed to plotting functions.
 #' @author Dan Kelley
 #' @family functions that plot \code{oce} data
@@ -157,7 +157,7 @@ findInHeaderBremen <- function(key, lines)
 #' @return An object of \code{\link{bremen-class}}.
 #' @section Issues: This function may be renamed (or removed) without notice.
 #' It was created to read some data being used in a particular research
-#' project, and will be rendered uselss if Bremen changes this data format.
+#' project, and will be rendered useless if Bremen changes this data format.
 #' @author Dan Kelley
 #' @family things related to \code{bremen} data
 read.bremen <- function(file)

R/cm.R

@@ -200,7 +200,7 @@ setMethod(f="subset",
 #' @param conductivity Optional vector of conductivity.
 #' Ignored if the first argument contains an \code{oce} object holding pressure.
 #' @param salinity Optional vector of salinity, assumed to be Practical Salinity.
-#' Ignored if the first argument contains an \code{oce} object holding saliity
+#' Ignored if the first argument contains an \code{oce} object holding salinity
 #' @param temperature Optional vector of temperature.
 #' Ignored if the first argument contains an \code{oce} object holding temperature
 #' @param longitude Optional longitude in degrees East.

R/coastline.R

@@ -242,7 +242,7 @@ as.coastline <- function(longitude, latitude, fillable=FALSE)
 #' plot edges (a problem that plagues map projections).  If \code{projection}
 #' is not set, a Mercator projection is used for latitudes below about 70
 #' degrees, as if \code{projection="+proj=merc"} had been supplied, or a
-#' Stereopoloar one is used as if \code{projection="+proj=stere"}.  Otherwise,
+#' Stereopolar one is used as if \code{projection="+proj=stere"}.  Otherwise,
 #' \code{projection} must be a character string identifying a projection
 #' accepted by \code{\link{mapPlot}}.
 #'
@@ -694,7 +694,7 @@ setMethod(f="plot",
 #'
 #' @template downloadDestTemplate
 #'
-#' @param server A character value specifying the server that is to suppply
+#' @param server A character value specifying the server that is to supply
 #' the data. At the moment, the only permitted value is \code{"naturalearth"},
 #' which is the default if \code{server} is not supplied.
 #'

R/ctd.R

@@ -481,7 +481,7 @@ setMethod(f="summary",
 #' will detect the setup, and subtract nitrite from the sum to yield
 #' nitrate.
 #'
-#' Below is a list of computed quantities, or at least quantites that are
+#' Below is a list of computed quantities, or at least quantities that are
 #' typically not stored in data files.  (This is a vague statement because
 #' Seabird software permits calculation of many of these and hence storage
 #' within \code{.cnv} files.)
@@ -510,7 +510,7 @@ setMethod(f="summary",
 #' \item \code{SA} or \code{Absolute Salinity}: Absolute Salinity,
 #' computed with \code{\link[gsw]{gsw_SA_from_SP}} in the \code{gsw} package.
 #' The calculation involves location as well as measured water properties.
-#' If the object \code{x} does not containin information on the location,
+#' If the object \code{x} does not containing information on the location,
 #' then 30N and 60W is used for the calculation, and a warning is generated.
 #'
 #' \item \code{sigmaTheta}: A form of potential density anomaly, computed with
@@ -747,7 +747,7 @@ setMethod(f="[[<-",
 #' unless the \code{profile} argument is specified and then that specific
 #' profile is extracted. (3) It can be an object of \code{\link{rsk-class}},
 #' (see \dQuote{Converting rsk objects} for details). (4)
-#' It can be unspecified, in whch case \code{conductivity} becomes a mandatory
+#' It can be unspecified, in which case \code{conductivity} becomes a mandatory
 #' argument, because it will be needed for computing actual salinity,
 #' using \code{\link{swSCTp}}.
 #'
@@ -892,7 +892,7 @@ setMethod(f="[[<-",
 #' contain their information. If required, any data or metadata
 #' element can be added to the value returned by \code{as.ctd}
 #' using \code{\link{oceSetData}} or \code{\link{oceSetMetadata}},
-#' erspectively.
+#' respectively.
 #'
 #' The returned \code{\link{rsk-class}} object contains pressure in a form that
 #' may need to be adjusted, because \code{rsk} objects may contain
@@ -908,7 +908,7 @@ setMethod(f="[[<-",
 #' sum of sea pressure and atmospheric pressure), depending on how the object was
 #' created with \code{\link{as.rsk}} or \code{\link{read.rsk}}.  However,
 #' \code{\link{ctd-class}} objects store sea pressure, which is needed for
-#' plotting, calculating density, etc. This poses no difficulities, however,
+#' plotting, calculating density, etc. This poses no difficulties, however,
 #' because \code{as.ctd} automatically converts absolute pressure to sea pressure,
 #' if the metadata in the \code{\link{rsk-class}} object indicates that this is
 #' appropriate. Further alteration of the pressure can be accomplished with the
@@ -1357,7 +1357,7 @@ as.ctd <- function(salinity, temperature=NULL, pressure=NULL, conductivity=NULL,
 #' @param x A \code{ctd} object, i.e. one inheriting from \code{\link{ctd-class}}.
 #' @param column A column of data to be inserted, in the form of a
 #'     numeric vector, whose length matches that of columns in the
-#'     objecct.
+#'     object.
 #' @param name Character string indicating the name this column is to
 #'     have in the \code{data} slot of \code{x}.
 #' @param label Optional character string or expression indicating the
@@ -1474,7 +1474,7 @@ ctdAddColumn <- function (x, column, name, label, unit=NULL, log=TRUE, originalN
 #' interpolation between neighboring points, using \code{\link{approx}}
 #' with the \code{rule} argument specified here), \code{"lm"} (based on local
 #' regression, with \code{e} setting the size of the local region), \code{"rr"}
-#' (for the Reineger and Ross method, carried out with \code{\link{oce.approx}})
+#' (for the Reiniger and Ross method, carried out with \code{\link{oce.approx}})
 #' and \code{"unesco"} (for the UNESCO method, carried out with.
 #' \code{\link{oce.approx}}.  If \code{method} is a function, then it must take
 #' three arguments, the first being pressure, the second being an arbitrary
@@ -4199,7 +4199,7 @@ drawIsopycnals <- function(nlevels=6, levels, rotate=TRUE, rho1000=FALSE, digits
 #' pressure, using the oceanographic convention of putting lower pressures
 #' nearer the top of the plot. This works for any \code{oce} object that has a
 #' pressure column in its \code{data} slot.
-#' The colours (\code{col.salinity}, etc.) are ony used if two profiles appear
+#' The colours (\code{col.salinity}, etc.) are only used if two profiles appear
 #' on a plot.
 #'
 #' @param x A \code{ctd} object, i.e. one inheriting from \code{\link{ctd-class}}.

R/ctd.sbe.R

@@ -25,7 +25,7 @@
 #' It is important to note that this table is by no means complete, since there
 #' are a great many SBE names listed in their document [1], plus names
 #' not listed there but present in data files
-#' supplied by prominent archiving agencies. If an SBE name is not recogized,
+#' supplied by prominent archiving agencies. If an SBE name is not recognized,
 #' then the oce name is set to that SBE name. This can cause problems in
 #' some other processing steps (e.g. if \code{\link{swRho}} or a similar
 #' function is called with an \code{oce} object as first argument), and so
@@ -659,7 +659,7 @@ cnvName2oceName <- function(h, columns=NULL, debug=getOption("oceDebug"))
 #' @references
 #' 1. The Sea-Bird SBE 19plus profiler is described at
 #' \code{http://www.seabird.com/products/spec_sheets/19plusdata.htm}.  Some more
-#' information is given in the Sea-Bird data-processing manaual
+#' information is given in the Sea-Bird data-processing manual
 #' \url{http://www.seabird.com/document/sbe-data-processing-manual}.
 #'
 #' 2. A SBE data processing manual is at \url{http://www.seabird.com/document/sbe-data-processing-manual}.

R/echosounder.R

@@ -53,7 +53,7 @@
 #'
 #' \emph{Accessing values.} Data may be accessed as e.g.
 #' \code{echosounder[["time"]]}, \code{echosounder[["depth"]]},
-#' \code{echosounder[["a"]]}, etc.  Items in \code{metadata} must be specifield
+#' \code{echosounder[["a"]]}, etc.  Items in \code{metadata} must be specified
 #' by full name, but those in \code{data} may be abbreviated, so long as the
 #' abbreviation is unique. In addition to the actual data, some derived fields
 #' are also available: \code{echosounder[["distance"]]} calls
@@ -88,7 +88,7 @@ setClass("echosounder", contains="oce")
 #'
 #' @description
 #' This is degraded subsample of measurements that were made with a Biosonics
-#' scientific echousounder, as part of the St Lawrence Internal Wave Experiment
+#' scientific echosounder, as part of the St Lawrence Internal Wave Experiment
 #' (SLEIWEX).
 #'
 #' @name echosounder
@@ -331,7 +331,7 @@ setMethod(f="subset",
 #' 0.1dB(counts/uPa)
 #' @param transmitPower transmit power reduction factor, in dB, denoted
 #' \code{tpow} in [1 p10], where it is in units 0.1 dB.
-#' @param pulseDuration duration of transmited pulse in us
+#' @param pulseDuration duration of transmitted pulse in us
 #' @param beamwidthX x-axis -3dB one-way beamwidth in deg, denoted \code{bwx}
 #' in [1 p16], where the unit is 0.2 deg
 #' @param beamwidthY y-axis -3dB one-way beamwidth in deg, denoted \code{bwx}
@@ -417,7 +417,7 @@ findBottom <- function(x, ignore=5, clean=despike)
 #'
 #' @description
 #' Plot echosounder data.
-#' Simple linear approximation is used when a \code{newx} value is specifie
+#' Simple linear approximation is used when a \code{newx} value is specified
 #' with the \code{which=2} method, but arguably a gridding method should be
 #' used, and this may be added in the future.
 #'
@@ -738,7 +738,7 @@ setMethod(f="plot",
 #' are described in the documentation for the object
 #' \code{\link{echosounder-class}}.
 #' @section Bugs: Only the amplitude information (in counts) is determined.  A
-#' future version of this funciton may provide conversion to dB, etc.  The
+#' future version of this function may provide conversion to dB, etc.  The
 #' handling of dual-beam and split-beam files is limited.  In the dual-beam
 #' cse, only the wide beam signal is processed (I think ... it could be the
 #' narrow beam, actually, given the confusing endian tricks being played).  In
@@ -748,7 +748,7 @@ setMethod(f="plot",
 #' @seealso The documentation for \code{\link{echosounder-class}} explains the
 #' structure of \code{ctd} objects, and also outlines the other functions
 #' dealing with them.
-#' @references Various echousounder instruments provided by BioSonics are
+#' @references Various echosounder instruments provided by BioSonics are
 #' described at the company website, \url{http://www.biosonicsinc.com/}.  The
 #' document listed as [1] below was provided to the author of this function in
 #' November 2011, which suggests that the data format was not changed since