prepare CRAN submission 5

DESCRIPTION

@@ -1,11 +1,11 @@
 Package: openSTARS
 Type: Package
-Title: An Open Source Implementation of the ArcGIS Toolbox STARS
-Description: An open source implementation of the STARS toolbox
-    (Peterson & Ver Hoef, 2014)) using R and GRASS GIS.
-    It prepares the *.ssn object needed for the SSN package.
+Title: An Open Source Implementation of the 'ArcGIS' Toolbox 'STARS'
+Description: An open source implementation of the 'STARS' toolbox
+    (Peterson & Ver Hoef, 2014, doi:10.18637/jss.v056.i02)) using 'R' and 'GRASS GIS'.
+    It prepares the *.ssn object needed for the 'SSN' package.
     A digital elevation model (DEM) is used to derive stream networks 
-    (in contrast to STARS that can clean an existing stream network).
+    (in contrast to 'STARS' that can clean an existing stream network).
 Version: 1.0.0
 Authors@R: c(person("Mira", "Kattwinkel", role = c("aut","cre"),
               email = "mira.kattwinkel@gmx.net"),

R/calc_edges.R

@@ -16,7 +16,7 @@
 #'
 #'@return Nothing. The function produces the following map: \itemize{
 #'  \item{'edges'} {derived stream segments with computed attributes needed for
-#'  SSN (vector)} }
+#'  'SSN' (vector)} }
 #'
 #'@note \code{\link{setup_grass_environment}}, \code{\link{import_data}} and
 #'  \code{\link{derive_streams}} must be run before.

R/calc_prediction_sites.R

@@ -1,4 +1,4 @@
-#'Calculate prediction sites for SSN object.
+#'Calculate prediction sites for 'SSN' object.
 #'
 #'@description A vector (points) map of prediction sites is created and several
 #'attributes are assigned.
@@ -16,7 +16,7 @@
 #'smaller than \code{nsites}.
 #'
 #'Steps include: \itemize{ \item{Place points on edges with given distance form
-#'each other} \item{Assign unique identifiers (needed by the SSN package) 'pid'
+#'each other} \item{Assign unique identifiers (needed by the 'SSN' package) 'pid'
 #'and 'locID'.} \item{Get 'rid' and 'netID' of the stream segment the site
 #'intersects with (from map 'edges').} \item{Calculate upstream distance for
 #'each point ('upDist').} \item{Calculate distance ratio ('distRatio') between

R/check_ssn.R

@@ -1,6 +1,6 @@
-#' Checking SSN object.
+#' Checking 'SSN' object.
 #'
-#' This function roughly checks the SSN object. It returns FALSE if some 
+#' This function roughly checks the 'SSN' object. It returns FALSE if some 
 #' essential columns are missing or values have illegal values.
 #'
 #' @importFrom rgdal readOGR

R/correct_compl_junctions.R

@@ -10,7 +10,7 @@
 #' vertexmove). So far, this function works only for junctions with three
 #' inflows, not more.
 #'
-#' @param clean logical; should intermediate files be removed from GRASS
+#' @param clean logical; should intermediate files be removed from 'GRASS'
 #'   session?
 #' @param celltoldig integer; number of digits the cell size dimensions are
 #'  rounded to before it is checked whether they are identical

R/derive_streams.R

@@ -18,7 +18,7 @@
 #' @param dem_name character vector, optional; default: 'dem'; useful if
 #'   conditioned and / or burnt in DEM raster from previous runs shall be used.
 #' @param clean logical; should intermediate raster layer of imported streams
-#'   ('streams_or') be removed from GRASS session?
+#'   ('streams_or') be removed from 'GRASS' session?
 #' @param mem logical; should -m flag in GRASS r.watershed be used (as indicated in its help)
 #'   see also \code{\link{watershed_memory}}-function
 #'

R/export_ssn.R

@@ -1,7 +1,7 @@
-#' Export .ssn object
+#' Export 'SSN' object
 #'
 #' This function exports the calculated sites, edges and binary IDs
-#' to a folder which then can be read using the SSN package.
+#' to a folder which then can be read using the 'SSN' package.
 #'
 #' @import rgrass7
 #' @importFrom utils write.table
@@ -14,7 +14,7 @@
 #' @return Nothing. Files are written to the specified folder
 #'
 #' @details First it is checked if one of the column names is longer than 10
-#' characters (which cannot be exported to ESRI shape files as required by SSN).
+#' characters (which cannot be exported to ESRI shape files as required by 'SSN').
 #'
 #' \code{delete_directory = TRUE} is useful if the same directory name has been
 #' used before and the existing data shall be overwritten.

R/import_data.R

@@ -1,6 +1,6 @@
-#' Import data into GRASS.
+#' Import data into 'GRASS.'
 #'
-#' This function loads dem and sites data (both required) into the GRASS session.
+#' This function loads dem and sites data (both required) into the 'GRASS' session.
 #' Optionally, prediction sites and streams data can be loaded and the streams 
 #' may be corrected by snapping to prevent lose ends.
 #'
@@ -13,19 +13,19 @@
 #'  If available it can be burnt into DEM.
 #' @param snap_streams boolean (optional); snap line ends.
 #'  If TRUE line ends of the streams are snapped to the next feature if they are
-#'   unconnected with threshold of 10 m using GRASS function v.clean.
+#'   unconnected with threshold of 10 m using 'GRASS' function v.clean.
 #' @param pred_sites character vector (optional); paths to prediction sites 
 #' vector files
 #' @param predictor_maps character vector (optional); paths to raster data to 
 #' import as predictors.
 #' @param predictor_names character vector (optional); names for potential predictor
 #' variables.
 #'
-#' @return Nothing, the data is loaded into the GRASS session (mapset PERMANENT).
+#' @return Nothing, the data is loaded into the 'GRASS' session (mapset PERMANENT).
 #' The DEM is stored as raster 'dem', sites as vector 'sites_o', prediction sites
 #' vector(s) using the original file names with an appended '_o' (without extension),
-#' streams as vector 'streams_o' in the GRASS location. Additionally, predictor 
-#' map raster(s) can be read in and are stored in GRASS using either the 
+#' streams as vector 'streams_o' in the 'GRASS' location. Additionally, predictor 
+#' map raster(s) can be read in and are stored in 'GRASS' using either the 
 #' original file names (without extension) or using the names provides in 
 #' predictor_names. The latter option may be useful if ArcGIS grid data 
 #' (typically stored as 'grid_name/w001001.adf') are used.

R/openSTARS.R

@@ -1,8 +1,8 @@
-#' openSTARS: An Open Source Implementation of the ArcGIS Toolbox STARS.
+#' openSTARS: An Open Source Implementation of the 'ArcGIS' Toolbox 'STARS'.
 #'
 #' openSTARS provides functions to prepare data so that it can be imported by
 #' the \code{\link[SSN]{SSN}} package for spatial modelling on stream networks.
-#' GRASS GIS 7.0 (or greater) with installed addons r.stream.basins,
+#' 'GRASS GIS 7.0' (or greater) with installed addons r.stream.basins,
 #' r.stream.distance, r.stream.order, and r.hydrodem is needed.
 #'
 #' @import rgrass7

R/setup_grass_environment.R

@@ -1,6 +1,6 @@
-#' Setup GRASS environment.
+#' Setup 'GRASS' environment.
 #'
-#' This function sets the GRASS mapset to PERMANENT and sets its projection and extension.
+#' This function sets the 'GRASS' mapset to PERMANENT and sets its projection and extension.
 #'
 #' @param dem character; path to DEM.
 #' @param sites character string or object; path to sites vector file (shape) 
@@ -9,14 +9,14 @@
 #' @param proj4 (optional) proj4 string; character string of projection arguments
 #'  
 #'
-#' @return Nothing, the GRASS mapset is set to PERMANENT,
+#' @return Nothing, the 'GRASS' mapset is set to PERMANENT,
 #' projection is set to the one of the sites shape, to the proj4 string or to 
 #' the epsg code provided, the extent of the region is set to the one of bounding
 #' box of the dem.
 #'
 #' @note Either \code{sites}, \code{epsg} or \code{proj4} must be provided. Make
 #' sure that all raster and vector files are in the same projection; it will be
-#' overwritten without warning. A GRASS session must be initiated before, see
+#' overwritten without warning. A 'GRASS' session must be initiated before, see
 #' \code{\link[rgrass7]{initGRASS}}.
 #' 
 #' @author Mira Kattwinkel, \email{mira.kattwinkel@@gmx.net}

cran-comments.md

@@ -1,7 +1,7 @@
 ---
 title: "cran-comments.md"
 author: "Mira Kattwinkel"
-date: "August 8, 2017"
+date: "August 9, 2017"
 output: html_document
 ---
 
@@ -27,4 +27,12 @@ Some examples take quite a while to run (> 5s) because they all contain the full
 workflow of loading and processing GIS files to be stand-alone examples.
 
 ## Downstream dependencies
-There are no downstream dependencies as this is the first release of the package.
+There are no downstream dependencies as this is the first release of the package.
+
+## Submission review comments
+All comments were taken into account except one:
+"Please explain the acronym DEM in your description."
+
+This is already done in the description right before giving the acronym:
+"A digital elevation model (DEM) is used to derive stream networks"
+