[Genabel-commits] r1796 - pkg/DatABEL/R

[noreply at r-forge.r-project.org]

Author: lckarssen
Date: 2014-08-12 11:50:49 +0200 (Tue, 12 Aug 2014)
New Revision: 1796

Modified:
   pkg/DatABEL/R/databel_class.R
Log:
Fixed Roxygen2 documentation in DatABEL-class. Not perfect, but at least R CMD check stopped giving warnings and errors.


Modified: pkg/DatABEL/R/databel_class.R
===================================================================
--- pkg/DatABEL/R/databel_class.R	2014-08-10 15:48:01 UTC (rev 1795)
+++ pkg/DatABEL/R/databel_class.R	2014-08-12 09:50:49 UTC (rev 1796)
@@ -1,17 +1,16 @@
 #' DatABEL class
 #'
-#' @section Slots:
-#'  \describe{
-#'    \item{\code{usedRowIndex}:}{\code{"integer"}}
-#'    \item{\code{usedColIndex}:}{\code{"integer"}}
-#'    \item{\code{uninames}:}{\code{"list"}}
-#'    \item{\code{backingfilename}:}{\code{"character"}}
-#'    \item{\code{cachesizeMb}:}{\code{"integer"}}
-#'    \item{\code{data}:}{\code{"externalptr"}}
-#'  }
+#' DatABEL stores matrix-shape data in such a way that it can be
+#' retrieved fast.
 #'
+#' @slot usedRowIndex (\code{"integer"})
+#' @slot usedColIndex (\code{"integer"})
+#' @slot uninames (\code{"list"})
+#' @slot backingfilename Name of the (stem of the) file that contains
+#' the data stored in DatABEL format ()\code{"character"})
+#' @slot cachesizeMb (\code{"integer"})
+#' @slot data (\code{"externalptr"})
 #' @note Will extend description here
-#' @docType class
 #' @name databel-class
 #' @rdname databel-class
 #' @aliases databel-class
@@ -148,6 +147,7 @@
 
 # replace standard methods
 
+#' @rdname  databel-class
 #' @export
 setMethod(
     f = "show",
@@ -190,7 +190,6 @@
 
 #' @aliases dim,databel-method
 #' @rdname databel-class
-#' @docType methods
 setMethod(
     f = "dim",
     signature = "databel",
@@ -205,7 +204,6 @@
 
 #' @aliases length,databel-method
 #' @rdname databel-class
-#' @docType methods
 setMethod(
     f = "length",
     signature = "databel",
@@ -219,7 +217,7 @@
     );
 
 
-
+#' @rdname databel-class
 setMethod(
     f = "dimnames",
     signature = "databel",
@@ -240,6 +238,7 @@
     );
 
 
+#' @rdname databel-class
 setMethod(
     f = "dimnames<-",
     signature = "databel",
@@ -256,6 +255,8 @@
     );
 
 
+#' @rdname databel-class
+#' @param j Column index
 setMethod(
     f = "[",
     signature = "databel",
@@ -281,7 +282,7 @@
     );
 
 
-
+#' @rdname databel-class
 setMethod(
     f = "[<-",
     signature = "databel",
@@ -375,6 +376,8 @@
 
 ### new generics
 
+#' @aliases get_dimnames,databel-method
+#' @rdname databel-class
 #' @export
 setGeneric(
     name = "get_dimnames",
@@ -395,6 +398,9 @@
     }
     );
 
+
+#' @aliases set_dimnames<-,databel-method
+#' @rdname databel-class
 #' @export
 setGeneric(
     name = "set_dimnames<-",
@@ -460,6 +466,9 @@
     }
     );
 
+
+#' @aliases backingfilename,databel-method
+#' @rdname databel-class
 #' @export
 setGeneric(
     name = "backingfilename",
@@ -475,6 +484,9 @@
     }
     );
 
+
+#' @aliases cachesizeMb,databel-method
+#' @rdname databel-class
 #' @export
 setGeneric(
     name = "cachesizeMb",
@@ -491,6 +503,8 @@
     );
 
 
+#' @aliases cachesizeMb<-,databel-method
+#' @rdname databel-class
 #' @export
 setGeneric(
     name = "cachesizeMb<-",
@@ -515,7 +529,16 @@
     );
 
 
+#' @aliases save_as,databel-method
+#' @rdname databel-class
 #' @export
+#' @param file Filename to save to
+#' @param rows Index for the rows
+#' @param cols Index for the columns
+#' @param cachesizeMb Amount (in MB) of RAM to use for caching DatABEL
+#' data.
+#' @param readonly Boolean that specifies whether the file is to be
+#' used in read-only mode or not
 setGeneric(
     name = "save_as",
     def = function(x, rows, cols, file, cachesizeMb=64, readonly=TRUE)
@@ -558,7 +581,9 @@
     }
     );
 
-#' @docType methods
+
+#' @aliases connect,databel-method
+#' @rdname databel-class
 #' @export
 setGeneric(
     name = "connect",
@@ -595,7 +620,9 @@
     }
     );
 
-#' @docType methods
+
+#' @rdname databel-class
+#' @aliases disconnect,databel-method
 #' @export
 setGeneric(
     name = "disconnect",
@@ -618,10 +645,8 @@
     }
     );
 
-#' setReadOnly method
-#'
-#' @docType methods
-#' @rdname setReadOnly-method
+#' @aliases setReadOnly<-,databel-method
+#' @rdname databel-class
 #' @export
 setGeneric(
     name = "setReadOnly<-",