diff --git a/NEWS.md b/NEWS.md index d4d7664..66bf7b4 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,6 +1,6 @@ # CCAMLRGIS 4.0.1 -Re-built manual as per CRAN instructions (switch to HTML5) +Re-built manual as per CRAN instructions (switch to HTML5): Removed bold emphasis on text. # CCAMLRGIS 4.0.0 diff --git a/R/CCAMLRGIS_DataDescription.R b/R/CCAMLRGIS_DataDescription.R index af6327a..ea48314 100644 --- a/R/CCAMLRGIS_DataDescription.R +++ b/R/CCAMLRGIS_DataDescription.R @@ -152,8 +152,8 @@ NULL #' Bathymetry dataset derived from the GEBCO 2021 (see \url{https://www.gebco.net/}) dataset. #' Subsampled at a 10,000m resolution. Projected using the CCAMLR standard projection (\code{\link{CCAMLRp}}). #' To highlight the Fishable Depth range, use \code{\link{Depth_cols2}} and \code{\link{Depth_cuts2}}. -#' \strong{To be only used for large scale illustrative purposes. Please refer to \code{\link{load_Bathy}} -#' to get higher resolution data.} +#' To be only used for large scale illustrative purposes. Please refer to \code{\link{load_Bathy}} +#' to get higher resolution data. #' #' #' @docType data diff --git a/R/Pies.R b/R/Pies.R index 509d333..2c71f03 100644 --- a/R/Pies.R +++ b/R/Pies.R @@ -13,9 +13,9 @@ #' @param NamesIn character vector of length 4 specifying the column names of Latitude, Longitude, #' Class and value fields in the \code{Input}. #' -#' \strong{Names must be given in that order, e.g.: +#' Names must be given in that order, e.g.: #' -#' \code{NamesIn=c('Latitude','Longitude','Class','Value')}}. +#' \code{NamesIn=c('Latitude','Longitude','Class','Value')}. #' #' @param Classes character, optional vector of classes to be displayed. If this excludes classes that are in the \code{Input}, #' those excluded classes will be pooled in a 'Other' class. diff --git a/R/assign_areas.r b/R/assign_areas.r index dc2d088..22c5797 100644 --- a/R/assign_areas.r +++ b/R/assign_areas.r @@ -6,17 +6,17 @@ #' #' @param Input dataframe containing - at the minimum - Latitudes and Longitudes to be assigned to polygons. #' -#' \strong{If \code{NamesIn} is not provided, the columns in the \code{Input} must be in the following order: -#' Latitude, Longitude, Variable 1, Variable 2, ... Variable x.}. +#' If \code{NamesIn} is not provided, the columns in the \code{Input} must be in the following order: +#' Latitude, Longitude, Variable 1, Variable 2, ... Variable x.. #' #' @param NamesIn character vector of length 2 specifying the column names of Latitude and Longitude fields in -#' the \code{Input}. \strong{Latitudes name must be given first, e.g.: +#' the \code{Input}. Latitudes name must be given first, e.g.: #' -#' \code{NamesIn=c('MyLatitudes','MyLongitudes')}}. +#' \code{NamesIn=c('MyLatitudes','MyLongitudes')}. #' #' @param Polys character vector of polygon names (e.g., \code{Polys=c('ASDs','RBs')}). #' -#' \strong{Must be matching the names of the pre-loaded spatial objects (loaded via e.g., \code{ASDs=load_ASDs()})} +#' Must be matching the names of the pre-loaded spatial objects (loaded via e.g., \code{ASDs=load_ASDs()}). #' #' @param AreaNameFormat dependent on the polygons loaded. For the Secretariat's spatial objects loaded via 'load_' functions, #' we have the following: diff --git a/R/create.R b/R/create.R index 95217a8..4cc544a 100644 --- a/R/create.R +++ b/R/create.R @@ -4,18 +4,18 @@ #' #' @param Input input dataframe. #' -#' \strong{If \code{NamesIn} is not provided, the columns in the \code{Input} must be in the following order: +#' If \code{NamesIn} is not provided, the columns in the \code{Input} must be in the following order: #' #' Polygon name, Latitude, Longitude. #' -#' Latitudes and Longitudes must be given clockwise.} +#' Latitudes and Longitudes must be given clockwise. #' #' @param NamesIn character vector of length 3 specifying the column names of polygon identifier, Latitude #' and Longitude fields in the \code{Input}. #' -#' \strong{Names must be given in that order, e.g.: +#' Names must be given in that order, e.g.: #' -#' \code{NamesIn=c('Polygon ID','Poly Latitudes','Poly Longitudes')}}. +#' \code{NamesIn=c('Polygon ID','Poly Latitudes','Poly Longitudes')}. #' #' @param Buffer numeric, distance in nautical miles by which to expand the polygons. Can be specified for #' each polygon (as a numeric vector). @@ -101,14 +101,14 @@ create_Polys=function(Input,NamesIn=NULL,Buffer=0,Densify=TRUE,Clip=FALSE,Separa #' #' @param Input input dataframe. #' -#' \strong{If \code{NamesIn} is not provided, the columns in the \code{Input} must be in the following order: +#' If \code{NamesIn} is not provided, the columns in the \code{Input} must be in the following order: #' -#' Latitude, Longitude, Variable 1, Variable 2 ... Variable x.} +#' Latitude, Longitude, Variable 1, Variable 2 ... Variable x. #' #' @param NamesIn character vector of length 2 specifying the column names of Latitude and Longitude fields in -#' the \code{Input}. \strong{Latitudes name must be given first, e.g.: +#' the \code{Input}. Latitudes name must be given first, e.g.: #' -#' \code{NamesIn=c('MyLatitudes','MyLongitudes')}}. +#' \code{NamesIn=c('MyLatitudes','MyLongitudes')}. #' #' @param dlon numeric, width of the grid cells in decimal degrees of longitude. #' @param dlat numeric, height of the grid cells in decimal degrees of latitude. @@ -198,19 +198,19 @@ create_PolyGrids=function(Input,NamesIn=NULL,dlon=NA,dlat=NA,Area=NA,cuts=100,co #' #' @param Input input dataframe. #' -#' \strong{If \code{NamesIn} is not provided, the columns in the \code{Input} must be in the following order: +#' If \code{NamesIn} is not provided, the columns in the \code{Input} must be in the following order: #' #' Line name, Latitude, Longitude. #' #' If a given line is made of more than two points, the locations of points -#' must be given in order, from one end of the line to the other.} +#' must be given in order, from one end of the line to the other. #' #' @param NamesIn character vector of length 3 specifying the column names of line identifier, Latitude #' and Longitude fields in the \code{Input}. #' -#' \strong{Names must be given in that order, e.g.: +#' Names must be given in that order, e.g.: #' -#' \code{NamesIn=c('Line ID','Line Latitudes','Line Longitudes')}}. +#' \code{NamesIn=c('Line ID','Line Latitudes','Line Longitudes')}. #' #' @param Buffer numeric, distance in nautical miles by which to expand the lines. Can be specified for #' each line (as a numeric vector). @@ -313,14 +313,14 @@ create_Lines=function(Input,NamesIn=NULL,Buffer=0,Densify=FALSE,Clip=FALSE,Separ #' #' @param Input input dataframe. #' -#' \strong{If \code{NamesIn} is not provided, the columns in the \code{Input} must be in the following order: +#' If \code{NamesIn} is not provided, the columns in the \code{Input} must be in the following order: #' -#' Latitude, Longitude, Variable 1, Variable 2, ... Variable x} +#' Latitude, Longitude, Variable 1, Variable 2, ... Variable x. #' #' @param NamesIn character vector of length 2 specifying the column names of Latitude and Longitude fields in -#' the \code{Input}. \strong{Latitudes name must be given first, e.g.: +#' the \code{Input}. Latitudes name must be given first, e.g.: #' -#' \code{NamesIn=c('MyLatitudes','MyLongitudes')}}. +#' \code{NamesIn=c('MyLatitudes','MyLongitudes')}. #' #' @param Buffer numeric, radius in nautical miles by which to expand the points. Can be specified for #' each point (as a numeric vector). diff --git a/R/get_depths.R b/R/get_depths.R index 0dbbe9e..f4882b3 100644 --- a/R/get_depths.R +++ b/R/get_depths.R @@ -5,14 +5,14 @@ #' dependent on the resolution of the bathymetry raster (see \code{\link{load_Bathy}} to get high resolution data). #' #' @param Input dataframe with, at least, Latitudes and Longitudes. -#' \strong{If \code{NamesIn} is not provided, the columns in the \code{Input} must be in the following order: +#' If \code{NamesIn} is not provided, the columns in the \code{Input} must be in the following order: #' -#' Latitude, Longitude, Variable 1, Variable 2, ... Variable x} +#' Latitude, Longitude, Variable 1, Variable 2, ... Variable x. #' #' @param NamesIn character vector of length 2 specifying the column names of Latitude and Longitude fields in -#' the \code{Input}. \strong{Latitudes name must be given first, e.g.: +#' the \code{Input}. Latitudes name must be given first, e.g.: #' -#' \code{NamesIn=c('MyLatitudes','MyLongitudes')}}. +#' \code{NamesIn=c('MyLatitudes','MyLongitudes')}. #' #' @param Bathy bathymetry raster with the appropriate \code{\link[CCAMLRGIS:CCAMLRp]{projection}}, #' such as \code{\link[CCAMLRGIS:SmallBathy]{this one}}. It is highly recommended to use a raster of higher diff --git a/R/load.R b/R/load.R index 2bb038c..97c999d 100644 --- a/R/load.R +++ b/R/load.R @@ -314,7 +314,7 @@ load_EEZs=function(){ #' To download the data, you must either have set your working directory using \code{\link[base]{setwd}}, or be working within an Rproject. #' In any case, your file will be downloaded to the folder path given by \code{\link[base]{getwd}}. #' -#' \strong{It is strongly recommended to first download the lowest resolution data (set \code{Res=5000}) to ensure it is working as expected.} +#' It is strongly recommended to first download the lowest resolution data (set \code{Res=5000}) to ensure it is working as expected. #' #' To re-use the downloaded data, you must provide the full path to that file, for example: #' diff --git a/R/project_data.r b/R/project_data.r index 943b22f..e80df08 100644 --- a/R/project_data.r +++ b/R/project_data.r @@ -8,9 +8,9 @@ #' @param Input dataframe containing - at the minimum - Latitudes and Longitudes to be projected (or Y and X to be back-projected). #' #' @param NamesIn character vector of length 2 specifying the column names of Latitude and Longitude fields in -#' the \code{Input}. \strong{Latitudes (or Y) name must be given first, e.g.: +#' the \code{Input}. Latitudes (or Y) name must be given first, e.g.: #' -#' \code{NamesIn=c('MyLatitudes','MyLongitudes')}}. +#' \code{NamesIn=c('MyLatitudes','MyLongitudes')}. #' #' @param NamesOut character vector of length 2, optional. Names of the resulting columns in the output dataframe, #' with order matching that of \code{NamesIn} (e.g., \code{NamesOut=c('Y','X')}). diff --git a/cran-comments.md b/cran-comments.md index 03c7b15..c555f69 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -7,8 +7,9 @@ ## R CMD check results -* There were no ERRORS, WARNINGS, or NOTES on Windows OS. - +* There were no ERRORS, WARNINGS, or NOTES. Except for: +* On Windows Server 2022, R-devel, 64 bit: +NOTE: Found the following files/directories: 'lastMiKTeXException' ## Notes about CRAN edits diff --git a/man/SmallBathy.Rd b/man/SmallBathy.Rd index 8db5f73..7ec5ac6 100644 --- a/man/SmallBathy.Rd +++ b/man/SmallBathy.Rd @@ -14,8 +14,8 @@ data(SmallBathy) Bathymetry dataset derived from the GEBCO 2021 (see \url{https://www.gebco.net/}) dataset. Subsampled at a 10,000m resolution. Projected using the CCAMLR standard projection (\code{\link{CCAMLRp}}). To highlight the Fishable Depth range, use \code{\link{Depth_cols2}} and \code{\link{Depth_cuts2}}. -\strong{To be only used for large scale illustrative purposes. Please refer to \code{\link{load_Bathy}} -to get higher resolution data.} +To be only used for large scale illustrative purposes. Please refer to \code{\link{load_Bathy}} +to get higher resolution data. } \examples{ plot(SmallBathy,breaks=Depth_cuts,col=Depth_cols,axes=FALSE,box=FALSE) diff --git a/man/assign_areas.Rd b/man/assign_areas.Rd index 8d17b4d..7649516 100644 --- a/man/assign_areas.Rd +++ b/man/assign_areas.Rd @@ -16,12 +16,12 @@ assign_areas( \arguments{ \item{Input}{dataframe containing - at the minimum - Latitudes and Longitudes to be assigned to polygons. -\strong{If \code{NamesIn} is not provided, the columns in the \code{Input} must be in the following order: -Latitude, Longitude, Variable 1, Variable 2, ... Variable x.}.} +If \code{NamesIn} is not provided, the columns in the \code{Input} must be in the following order: +Latitude, Longitude, Variable 1, Variable 2, ... Variable x..} \item{Polys}{character vector of polygon names (e.g., \code{Polys=c('ASDs','RBs')}). -\strong{Must be matching the names of the pre-loaded spatial objects (loaded via e.g., \code{ASDs=load_ASDs()})}} +Must be matching the names of the pre-loaded spatial objects (loaded via e.g., \code{ASDs=load_ASDs()}).} \item{AreaNameFormat}{dependent on the polygons loaded. For the Secretariat's spatial objects loaded via 'load_' functions, we have the following: @@ -41,9 +41,9 @@ Can be specified for each of the \code{Polys} (e.g., \code{Buffer=c(2,5)}). Usef \code{Buffer} nautical miles of a polygon.} \item{NamesIn}{character vector of length 2 specifying the column names of Latitude and Longitude fields in -the \code{Input}. \strong{Latitudes name must be given first, e.g.: +the \code{Input}. Latitudes name must be given first, e.g.: -\code{NamesIn=c('MyLatitudes','MyLongitudes')}}.} +\code{NamesIn=c('MyLatitudes','MyLongitudes')}.} \item{NamesOut}{character, names of the resulting column names in the output dataframe, with order matching that of \code{Polys} (e.g., \code{NamesOut=c('Recapture_ASD','Recapture_RB')}). diff --git a/man/create_Lines.Rd b/man/create_Lines.Rd index bcac617..4248b17 100644 --- a/man/create_Lines.Rd +++ b/man/create_Lines.Rd @@ -16,19 +16,19 @@ create_Lines( \arguments{ \item{Input}{input dataframe. -\strong{If \code{NamesIn} is not provided, the columns in the \code{Input} must be in the following order: +If \code{NamesIn} is not provided, the columns in the \code{Input} must be in the following order: Line name, Latitude, Longitude. If a given line is made of more than two points, the locations of points -must be given in order, from one end of the line to the other.}} +must be given in order, from one end of the line to the other.} \item{NamesIn}{character vector of length 3 specifying the column names of line identifier, Latitude and Longitude fields in the \code{Input}. -\strong{Names must be given in that order, e.g.: +Names must be given in that order, e.g.: -\code{NamesIn=c('Line ID','Line Latitudes','Line Longitudes')}}.} +\code{NamesIn=c('Line ID','Line Latitudes','Line Longitudes')}.} \item{Buffer}{numeric, distance in nautical miles by which to expand the lines. Can be specified for each line (as a numeric vector).} diff --git a/man/create_Pies.Rd b/man/create_Pies.Rd index 7d6f7ba..c76ca03 100644 --- a/man/create_Pies.Rd +++ b/man/create_Pies.Rd @@ -22,9 +22,9 @@ create_Pies( \item{NamesIn}{character vector of length 4 specifying the column names of Latitude, Longitude, Class and value fields in the \code{Input}. -\strong{Names must be given in that order, e.g.: +Names must be given in that order, e.g.: -\code{NamesIn=c('Latitude','Longitude','Class','Value')}}.} +\code{NamesIn=c('Latitude','Longitude','Class','Value')}.} \item{Classes}{character, optional vector of classes to be displayed. If this excludes classes that are in the \code{Input}, those excluded classes will be pooled in a 'Other' class.} diff --git a/man/create_Points.Rd b/man/create_Points.Rd index 08b9586..2efcc5e 100644 --- a/man/create_Points.Rd +++ b/man/create_Points.Rd @@ -15,14 +15,14 @@ create_Points( \arguments{ \item{Input}{input dataframe. -\strong{If \code{NamesIn} is not provided, the columns in the \code{Input} must be in the following order: +If \code{NamesIn} is not provided, the columns in the \code{Input} must be in the following order: -Latitude, Longitude, Variable 1, Variable 2, ... Variable x}} +Latitude, Longitude, Variable 1, Variable 2, ... Variable x.} \item{NamesIn}{character vector of length 2 specifying the column names of Latitude and Longitude fields in -the \code{Input}. \strong{Latitudes name must be given first, e.g.: +the \code{Input}. Latitudes name must be given first, e.g.: -\code{NamesIn=c('MyLatitudes','MyLongitudes')}}.} +\code{NamesIn=c('MyLatitudes','MyLongitudes')}.} \item{Buffer}{numeric, radius in nautical miles by which to expand the points. Can be specified for each point (as a numeric vector).} diff --git a/man/create_PolyGrids.Rd b/man/create_PolyGrids.Rd index 000fb05..c5ade5e 100644 --- a/man/create_PolyGrids.Rd +++ b/man/create_PolyGrids.Rd @@ -17,14 +17,14 @@ create_PolyGrids( \arguments{ \item{Input}{input dataframe. -\strong{If \code{NamesIn} is not provided, the columns in the \code{Input} must be in the following order: +If \code{NamesIn} is not provided, the columns in the \code{Input} must be in the following order: -Latitude, Longitude, Variable 1, Variable 2 ... Variable x.}} +Latitude, Longitude, Variable 1, Variable 2 ... Variable x.} \item{NamesIn}{character vector of length 2 specifying the column names of Latitude and Longitude fields in -the \code{Input}. \strong{Latitudes name must be given first, e.g.: +the \code{Input}. Latitudes name must be given first, e.g.: -\code{NamesIn=c('MyLatitudes','MyLongitudes')}}.} +\code{NamesIn=c('MyLatitudes','MyLongitudes')}.} \item{dlon}{numeric, width of the grid cells in decimal degrees of longitude.} diff --git a/man/create_Polys.Rd b/man/create_Polys.Rd index aafda75..5271cc4 100644 --- a/man/create_Polys.Rd +++ b/man/create_Polys.Rd @@ -16,18 +16,18 @@ create_Polys( \arguments{ \item{Input}{input dataframe. -\strong{If \code{NamesIn} is not provided, the columns in the \code{Input} must be in the following order: +If \code{NamesIn} is not provided, the columns in the \code{Input} must be in the following order: Polygon name, Latitude, Longitude. -Latitudes and Longitudes must be given clockwise.}} +Latitudes and Longitudes must be given clockwise.} \item{NamesIn}{character vector of length 3 specifying the column names of polygon identifier, Latitude and Longitude fields in the \code{Input}. -\strong{Names must be given in that order, e.g.: +Names must be given in that order, e.g.: -\code{NamesIn=c('Polygon ID','Poly Latitudes','Poly Longitudes')}}.} +\code{NamesIn=c('Polygon ID','Poly Latitudes','Poly Longitudes')}.} \item{Buffer}{numeric, distance in nautical miles by which to expand the polygons. Can be specified for each polygon (as a numeric vector).} diff --git a/man/get_depths.Rd b/man/get_depths.Rd index 45a45c0..4e45080 100644 --- a/man/get_depths.Rd +++ b/man/get_depths.Rd @@ -8,18 +8,18 @@ get_depths(Input, Bathy, NamesIn = NULL) } \arguments{ \item{Input}{dataframe with, at least, Latitudes and Longitudes. -\strong{If \code{NamesIn} is not provided, the columns in the \code{Input} must be in the following order: +If \code{NamesIn} is not provided, the columns in the \code{Input} must be in the following order: -Latitude, Longitude, Variable 1, Variable 2, ... Variable x}} +Latitude, Longitude, Variable 1, Variable 2, ... Variable x.} \item{Bathy}{bathymetry raster with the appropriate \code{\link[CCAMLRGIS:CCAMLRp]{projection}}, such as \code{\link[CCAMLRGIS:SmallBathy]{this one}}. It is highly recommended to use a raster of higher resolution than \code{\link{SmallBathy}} (see \code{\link{load_Bathy}}).} \item{NamesIn}{character vector of length 2 specifying the column names of Latitude and Longitude fields in -the \code{Input}. \strong{Latitudes name must be given first, e.g.: +the \code{Input}. Latitudes name must be given first, e.g.: -\code{NamesIn=c('MyLatitudes','MyLongitudes')}}.} +\code{NamesIn=c('MyLatitudes','MyLongitudes')}.} } \value{ dataframe with the same structure as the \code{Input} with an additional depth column \code{'d'}. diff --git a/man/load_Bathy.Rd b/man/load_Bathy.Rd index 58ba386..0f1d361 100644 --- a/man/load_Bathy.Rd +++ b/man/load_Bathy.Rd @@ -24,7 +24,7 @@ re-use it in all your scripts. To download the data, you must either have set your working directory using \code{\link[base]{setwd}}, or be working within an Rproject. In any case, your file will be downloaded to the folder path given by \code{\link[base]{getwd}}. -\strong{It is strongly recommended to first download the lowest resolution data (set \code{Res=5000}) to ensure it is working as expected.} +It is strongly recommended to first download the lowest resolution data (set \code{Res=5000}) to ensure it is working as expected. To re-use the downloaded data, you must provide the full path to that file, for example: diff --git a/man/project_data.Rd b/man/project_data.Rd index 3427122..6063c52 100644 --- a/man/project_data.Rd +++ b/man/project_data.Rd @@ -16,9 +16,9 @@ project_data( \item{Input}{dataframe containing - at the minimum - Latitudes and Longitudes to be projected (or Y and X to be back-projected).} \item{NamesIn}{character vector of length 2 specifying the column names of Latitude and Longitude fields in -the \code{Input}. \strong{Latitudes (or Y) name must be given first, e.g.: +the \code{Input}. Latitudes (or Y) name must be given first, e.g.: -\code{NamesIn=c('MyLatitudes','MyLongitudes')}}.} +\code{NamesIn=c('MyLatitudes','MyLongitudes')}.} \item{NamesOut}{character vector of length 2, optional. Names of the resulting columns in the output dataframe, with order matching that of \code{NamesIn} (e.g., \code{NamesOut=c('Y','X')}).}