Release

feat: release

DESCRIPTION

@@ -15,9 +15,10 @@ URL: https://drieslab.github.io/dbMatrix/
 BugReports: https://github.com/drieslab/dbMatrix/issues
 RoxygenNote: 7.3.2
 Depends:
-    R (>= 4.1.0),
-    MatrixGenerics (>= 1.12.3)
+    R (>= 4.1.0)
 Imports:
+    MatrixGenerics (>= 1.12.3),
+    methods,
     Matrix,
     DBI,
     dplyr,
@@ -26,7 +27,10 @@ Imports:
     data.table (>= 1.12.2),
     glue,
     bit64,
-    crayon
+    crayon,
+    cli,
+    R.utils,
+    checkmate
 Suggests: 
     knitr,
     rmarkdown,

NAMESPACE

@@ -1,23 +1,16 @@
 # Generated by roxygen2: do not edit by hand
 
-export(dbDataFrame)
 export(dbDenseMatrix)
 export(dbMatrix)
 export(dbSparseMatrix)
-export(precompute)
-export(readMM)
-export(read_matrix)
-export(sim_dbDataFrame)
 export(sim_dbDenseMatrix)
 export(sim_dbSparseMatrix)
-exportClasses(dbDataFrame)
 exportClasses(dbDenseMatrix)
 exportClasses(dbSparseMatrix)
 exportMethods("[")
 exportMethods("[<-")
 exportMethods("colnames<-")
 exportMethods("dimnames<-")
-exportMethods("names<-")
 exportMethods("rownames<-")
 exportMethods(Arith)
 exportMethods(Ops)
@@ -27,14 +20,11 @@ exportMethods(colSds)
 exportMethods(colSums)
 exportMethods(colTypes)
 exportMethods(colnames)
-exportMethods(dbDisconnect)
-exportMethods(dbListTables)
 exportMethods(dim)
 exportMethods(dimnames)
 exportMethods(head)
 exportMethods(log)
 exportMethods(mean)
-exportMethods(names)
 exportMethods(ncol)
 exportMethods(nrow)
 exportMethods(rowMeans)
@@ -43,4 +33,10 @@ exportMethods(rowSums)
 exportMethods(rownames)
 exportMethods(t)
 exportMethods(tail)
+importFrom(MatrixGenerics,colMeans)
+importFrom(MatrixGenerics,colSds)
+importFrom(MatrixGenerics,colSums)
+importFrom(MatrixGenerics,rowMeans)
+importFrom(MatrixGenerics,rowSds)
+importFrom(MatrixGenerics,rowSums)
 importFrom(data.table,":=")

R/accessors.R

@@ -1,7 +1,7 @@
 # internal functions ####
 #' get_tblName
 #'
-#' @param dbData
+#' @param dbMatrix
 #'
 #' @keywords internal
 get_tblName <- function(dbMatrix){

R/classes.R

@@ -1,6 +1,5 @@
 # dbData ####
 
-#' @name dbData
 #' @title dbData
 #' @description Base class for all db objects
 #' @slot value dplyr tbl that represents the database data
@@ -24,12 +23,14 @@ setClass(
 
 ### dbMatrix ####
 
-#' @title S4 dbMatrix class
+#' @title S4 virtual class for `dbMatrix`
 #' @description
-#' Representation of sparse matrices using an on-disk database. Each object
+#' Representation of sparse and dense matrices in a database. Each object
 #' is used as a connection to a single table that exists within the database.
+#' Inherits from `dbData`.
 #' @slot dim_names row [1] and col [2] names
 #' @slot dims dimensions of the matrix
+#' @noRd
 #' @export
 dbMatrix = setClass(
   Class = 'dbMatrix',
@@ -45,12 +46,12 @@ dbMatrix = setClass(
 )
 
 #### dbDenseMatrix ####
-#' @title S4 Class for dbDenseMatrix
+#' @title S4 Class for `dbDenseMatrix`
 #'
 #' @description Representation of dense matrices using an on-disk database.
-#' Inherits from dbMatrix.
+#' Inherits from \link{dbMatrix}.
 #'
-#' @slot data A dense ijx dataframe/tibble
+#' @noRd
 #' @export
 dbDenseMatrix = setClass(
   Class = "dbDenseMatrix",
@@ -61,40 +62,16 @@ dbDenseMatrix = setClass(
 #' @title S4 Class for dbSparseMatrix
 #'
 #' @description Representation of sparse matrices using an on-disk database.
-#' Inherits from dbMatrix.
-#'
+#' Inherits from \link{dbMatrix.}
+#' @noRd
 #' @export
 dbSparseMatrix = setClass(
   Class = "dbSparseMatrix",
   contains = "dbMatrix"
 )
 
-### dbDataFrame ####
-
-
-#' @title S4 dbDataFrame class
-#' @description
-#' Representation of dataframes using an on-disk database. Each object
-#' is used as a connection to a single table that exists within the database.
-#' @slot data dplyr tbl that represents the database data
-#' @slot hash unique hash ID for backend
-#' @slot remote_name name of table within database that contains the data
-#' @slot key column to set as key for ordering and subsetting on i
-#' @export
-dbDataFrame = setClass(
-  Class = 'dbDataFrame',
-  contains = 'dbData',
-  slots = list(
-    key = 'character'
-  ),
-  prototype = list(
-    key = NA_character_
-  )
-)
-
 ## dbIndex ####
-#' @title Virtual Class "dbIndex" - Simple Class for dbData indices
-#' @name dbIndex
+#' @title S4 virtual class - Simple Class for dbData indices
 #' @description
 #' This is a virtual class used for indices (in signatures) for indexing
 #' and sub-assignment of 'dbData' objects. Simple class union of 'logical',
@@ -104,27 +81,3 @@ dbDataFrame = setClass(
 #' @noRd
 setClassUnion(name = 'dbIndex',
               members = c('logical', 'numeric', 'integer', 'character'))
-
-#' @title Virtual Class "dbIndexNonChar" - Simple Class for dbData indices
-#' @name dbIndex
-#' @description
-#' This is a virtual class used for indices (in signatures) for indexing
-#' and sub-assignment of 'dbData' objects. Simple class union of 'logical' and
-#' 'numeric'.
-#' Based on the 'index' class implemented in \pkg{Matrix}
-#' @keywords internal
-#' @noRd
-setClassUnion(name = 'dbIndexNonChar',
-              members = c('logical', 'numeric'))
-
-## dbMF ####
-#' @title Virtual Class "dbMFData" - Simple class for dbMatrix and dbDF
-#' @name dbMFData
-#' @description
-#' This is a virtual class used to refer to dbMatrix and dbDataFrame objects as
-#' a single signature.
-#' @keywords internal
-#' @noRd
-setClassUnion(name = 'dbMFData',
-              members = c('dbMatrix', 'dbDataFrame'))
-