Merge pull request #43 from ccamlr/V4

4.0.1 updates

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
 

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

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.

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:

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).

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

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:
 #' 

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')}).

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