From 1db40393515c9b8c0286ab2cea8d8b05b831286c Mon Sep 17 00:00:00 2001 From: Yu ISHIKAWA Date: Tue, 25 Aug 2015 15:00:55 +0900 Subject: [PATCH 1/5] Add `@name` to each methods and modify `@aliases` in DataFrame.R --- R/pkg/R/DataFrame.R | 83 +++++++++++++++++++++++++++++++++++++-------- 1 file changed, 68 insertions(+), 15 deletions(-) diff --git a/R/pkg/R/DataFrame.R b/R/pkg/R/DataFrame.R index 895603235011e..19417be0c53b4 100644 --- a/R/pkg/R/DataFrame.R +++ b/R/pkg/R/DataFrame.R @@ -27,6 +27,7 @@ setOldClass("jobj") #' \code{jsonFile}, \code{table} etc. #' @rdname DataFrame #' @seealso jsonFile, table +#' @docType class #' #' @param env An R environment that stores bookkeeping states of the DataFrame #' @param sdf A Java object reference to the backing Scala DataFrame @@ -84,6 +85,7 @@ setMethod("printSchema", #' @param x A SparkSQL DataFrame #' #' @rdname schema +#' @name schema #' @export #' @examples #'\dontrun{ @@ -106,6 +108,7 @@ setMethod("schema", #' @param x A SparkSQL DataFrame #' @param extended Logical. If extended is False, explain() only prints the physical plan. #' @rdname explain +#' @name explain #' @export #' @examples #'\dontrun{ @@ -135,6 +138,7 @@ setMethod("explain", #' @param x A SparkSQL DataFrame #' #' @rdname isLocal +#' @name isLocal #' @export #' @examples #'\dontrun{ @@ -158,6 +162,7 @@ setMethod("isLocal", #' @param numRows The number of rows to print. Defaults to 20. #' #' @rdname showDF +#' @name showDF #' @export #' @examples #'\dontrun{ @@ -206,6 +211,7 @@ setMethod("show", "DataFrame", #' @param x A SparkSQL DataFrame #' #' @rdname dtypes +#' @name dtypes #' @export #' @examples #'\dontrun{ @@ -230,6 +236,8 @@ setMethod("dtypes", #' @param x A SparkSQL DataFrame #' #' @rdname columns +#' @name columns +#' @aliases names #' @export #' @examples #'\dontrun{ @@ -248,7 +256,7 @@ setMethod("columns", }) #' @rdname columns -#' @aliases names,DataFrame,function-method +#' @name names setMethod("names", signature(x = "DataFrame"), function(x) { @@ -256,6 +264,7 @@ setMethod("names", }) #' @rdname columns +#' @name names<- setMethod("names<-", signature(x = "DataFrame"), function(x, value) { @@ -273,6 +282,7 @@ setMethod("names<-", #' @param tableName A character vector containing the name of the table #' #' @rdname registerTempTable +#' @name registerTempTable #' @export #' @examples #'\dontrun{ @@ -299,6 +309,7 @@ setMethod("registerTempTable", #' the existing rows in the table. #' #' @rdname insertInto +#' @name insertInto #' @export #' @examples #'\dontrun{ @@ -347,6 +358,7 @@ setMethod("cache", #' #' @param x The DataFrame to persist #' @rdname persist +#' @name persist #' @export #' @examples #'\dontrun{ @@ -372,6 +384,7 @@ setMethod("persist", #' @param x The DataFrame to unpersist #' @param blocking Whether to block until all blocks are deleted #' @rdname unpersist-methods +#' @name unpersist #' @export #' @examples #'\dontrun{ @@ -397,6 +410,7 @@ setMethod("unpersist", #' @param x A SparkSQL DataFrame #' @param numPartitions The number of partitions to use. #' @rdname repartition +#' @name repartition #' @export #' @examples #'\dontrun{ @@ -446,6 +460,7 @@ setMethod("toJSON", #' @param x A SparkSQL DataFrame #' @param path The directory where the file is saved #' @rdname saveAsParquetFile +#' @name saveAsParquetFile #' @export #' @examples #'\dontrun{ @@ -467,6 +482,7 @@ setMethod("saveAsParquetFile", #' #' @param x A SparkSQL DataFrame #' @rdname distinct +#' @name distinct #' @export #' @examples #'\dontrun{ @@ -488,7 +504,8 @@ setMethod("distinct", #' @description Returns a new DataFrame containing distinct rows in this DataFrame #' #' @rdname unique -#' @aliases unique +#' @name unique +#' @aliases distinct setMethod("unique", signature(x = "DataFrame"), function(x) { @@ -526,7 +543,7 @@ setMethod("sample", }) #' @rdname sample -#' @aliases sample +#' @name sample_frac setMethod("sample_frac", signature(x = "DataFrame", withReplacement = "logical", fraction = "numeric"), @@ -541,6 +558,7 @@ setMethod("sample_frac", #' @param x A SparkSQL DataFrame #' #' @rdname count +#' @aliases nrow #' @export #' @examples #'\dontrun{ @@ -574,6 +592,7 @@ setMethod("nrow", #' @param x a SparkSQL DataFrame #' #' @rdname ncol +#' @name ncol #' @export #' @examples #'\dontrun{ @@ -593,6 +612,7 @@ setMethod("ncol", #' @param x a SparkSQL DataFrame #' #' @rdname dim +#' @name dim #' @export #' @examples #'\dontrun{ @@ -613,8 +633,8 @@ setMethod("dim", #' @param x A SparkSQL DataFrame #' @param stringsAsFactors (Optional) A logical indicating whether or not string columns #' should be converted to factors. FALSE by default. - -#' @rdname collect-methods +#' @rdname collect +#' @name collect #' @export #' @examples #'\dontrun{ @@ -650,6 +670,7 @@ setMethod("collect", #' @return A new DataFrame containing the number of rows specified. #' #' @rdname limit +#' @name limit #' @export #' @examples #' \dontrun{ @@ -669,6 +690,7 @@ setMethod("limit", #' Take the first NUM rows of a DataFrame and return a the results as a data.frame #' #' @rdname take +#' @name take #' @export #' @examples #'\dontrun{ @@ -696,6 +718,7 @@ setMethod("take", #' @return A data.frame #' #' @rdname head +#' @name head #' @export #' @examples #'\dontrun{ @@ -717,6 +740,7 @@ setMethod("head", #' @param x A SparkSQL DataFrame #' #' @rdname first +#' @name first #' @export #' @examples #'\dontrun{ @@ -769,6 +793,7 @@ setMethod("toRDD", #' @seealso GroupedData #' @aliases group_by #' @rdname groupBy +#' @name groupBy #' @export #' @examples #' \dontrun{ @@ -792,7 +817,7 @@ setMethod("groupBy", }) #' @rdname groupBy -#' @aliases group_by +#' @name group_by setMethod("group_by", signature(x = "DataFrame"), function(x, ...) { @@ -805,6 +830,7 @@ setMethod("group_by", #' #' @param x a DataFrame #' @rdname DataFrame +#' @name agg #' @aliases summarize #' @export setMethod("agg", @@ -814,7 +840,7 @@ setMethod("agg", }) #' @rdname DataFrame -#' @aliases agg +#' @name summarize setMethod("summarize", signature(x = "DataFrame"), function(x, ...) { @@ -890,12 +916,14 @@ getColumn <- function(x, c) { } #' @rdname select +#' @name $ setMethod("$", signature(x = "DataFrame"), function(x, name) { getColumn(x, name) }) #' @rdname select +#' @name $<- setMethod("$<-", signature(x = "DataFrame"), function(x, name, value) { stopifnot(class(value) == "Column" || is.null(value)) @@ -923,6 +951,7 @@ setMethod("$<-", signature(x = "DataFrame"), }) #' @rdname select +#' @name [[ setMethod("[[", signature(x = "DataFrame"), function(x, i) { if (is.numeric(i)) { @@ -933,6 +962,7 @@ setMethod("[[", signature(x = "DataFrame"), }) #' @rdname select +#' @name [ setMethod("[", signature(x = "DataFrame", i = "missing"), function(x, i, j, ...) { if (is.numeric(j)) { @@ -1008,6 +1038,7 @@ setMethod("select", #' @param ... Additional expressions #' @return A DataFrame #' @rdname selectExpr +#' @name selectExpr #' @export #' @examples #'\dontrun{ @@ -1034,6 +1065,8 @@ setMethod("selectExpr", #' @param col A Column expression. #' @return A DataFrame with the new column added. #' @rdname withColumn +#' @name withColumn +#' @aliases mutate #' @export #' @examples #'\dontrun{ @@ -1057,7 +1090,7 @@ setMethod("withColumn", #' @param col a named argument of the form name = col #' @return A new DataFrame with the new columns added. #' @rdname withColumn -#' @aliases withColumn +#' @name mutate #' @export #' @examples #'\dontrun{ @@ -1094,6 +1127,7 @@ setMethod("mutate", #' @param newCol The new column name. #' @return A DataFrame with the column name changed. #' @rdname withColumnRenamed +#' @name withColumnRenamed #' @export #' @examples #'\dontrun{ @@ -1124,6 +1158,7 @@ setMethod("withColumnRenamed", #' @param newCol A named pair of the form new_column_name = existing_column #' @return A DataFrame with the column name changed. #' @rdname withColumnRenamed +#' @name rename #' @aliases withColumnRenamed #' @export #' @examples @@ -1165,6 +1200,8 @@ setClassUnion("characterOrColumn", c("character", "Column")) #' @param ... Additional sorting fields #' @return A DataFrame where all elements are sorted. #' @rdname arrange +#' @name arrange +#' @aliases orderby #' @export #' @examples #'\dontrun{ @@ -1191,7 +1228,7 @@ setMethod("arrange", }) #' @rdname arrange -#' @aliases orderBy,DataFrame,function-method +#' @name orderby setMethod("orderBy", signature(x = "DataFrame", col = "characterOrColumn"), function(x, col) { @@ -1207,6 +1244,7 @@ setMethod("orderBy", #' or a string containing a SQL statement #' @return A DataFrame containing only the rows that meet the condition. #' @rdname filter +#' @name filter #' @export #' @examples #'\dontrun{ @@ -1228,7 +1266,7 @@ setMethod("filter", }) #' @rdname filter -#' @aliases where,DataFrame,function-method +#' @name where setMethod("where", signature(x = "DataFrame", condition = "characterOrColumn"), function(x, condition) { @@ -1247,6 +1285,7 @@ setMethod("where", #' 'inner', 'outer', 'left_outer', 'right_outer', 'semijoin'. The default joinType is "inner". #' @return A DataFrame containing the result of the join operation. #' @rdname join +#' @name join #' @export #' @examples #'\dontrun{ @@ -1279,8 +1318,9 @@ setMethod("join", dataFrame(sdf) }) -#' rdname merge -#' aliases join +#' @rdname merge +#' @name merge +#' @aliases join setMethod("merge", signature(x = "DataFrame", y = "DataFrame"), function(x, y, joinExpr = NULL, joinType = NULL, ...) { @@ -1298,6 +1338,7 @@ setMethod("merge", #' @param y A Spark DataFrame #' @return A DataFrame containing the result of the union. #' @rdname unionAll +#' @name unionAll #' @export #' @examples #'\dontrun{ @@ -1319,6 +1360,7 @@ setMethod("unionAll", #' @description Returns a new DataFrame containing rows of all parameters. # #' @rdname rbind +#' @name rbind #' @aliases unionAll setMethod("rbind", signature(... = "DataFrame"), @@ -1339,6 +1381,7 @@ setMethod("rbind", #' @param y A Spark DataFrame #' @return A DataFrame containing the result of the intersect. #' @rdname intersect +#' @name intersect #' @export #' @examples #'\dontrun{ @@ -1364,6 +1407,7 @@ setMethod("intersect", #' @param y A Spark DataFrame #' @return A DataFrame containing the result of the except operation. #' @rdname except +#' @name except #' @export #' @examples #'\dontrun{ @@ -1403,6 +1447,8 @@ setMethod("except", #' @param mode One of 'append', 'overwrite', 'error', 'ignore' #' #' @rdname write.df +#' @name write.df +#' @aliases saveDF #' @export #' @examples #'\dontrun{ @@ -1435,7 +1481,7 @@ setMethod("write.df", }) #' @rdname write.df -#' @aliases saveDF +#' @name saveDF #' @export setMethod("saveDF", signature(df = "DataFrame", path = "character"), @@ -1466,6 +1512,7 @@ setMethod("saveDF", #' @param mode One of 'append', 'overwrite', 'error', 'ignore' #' #' @rdname saveAsTable +#' @name saveAsTable #' @export #' @examples #'\dontrun{ @@ -1505,6 +1552,7 @@ setMethod("saveAsTable", #' @param ... Additional expressions #' @return A DataFrame #' @rdname describe +#' @aliases summary #' @export #' @examples #'\dontrun{ @@ -1538,7 +1586,7 @@ setMethod("describe", #' @description Computes statistics for numeric columns of the DataFrame #' #' @rdname summary -#' @aliases describe +#' @name summary setMethod("summary", signature(x = "DataFrame"), function(x) { @@ -1562,6 +1610,8 @@ setMethod("summary", #' @return A DataFrame #' #' @rdname nafunctions +#' @name dropna +#' @aliases na.omit #' @export #' @examples #'\dontrun{ @@ -1588,7 +1638,8 @@ setMethod("dropna", dataFrame(sdf) }) -#' @aliases dropna +#' @rdname nafunctions +#' @name na.omit #' @export setMethod("na.omit", signature(x = "DataFrame"), @@ -1615,6 +1666,7 @@ setMethod("na.omit", #' @return A DataFrame #' #' @rdname nafunctions +#' @name fillna #' @export #' @examples #'\dontrun{ @@ -1685,6 +1737,7 @@ setMethod("fillna", #' occurrences will have zero as their counts. #' #' @rdname statfunctions +#' @name crosstab #' @export #' @examples #' \dontrun{ From ea771dff8af0cc4e21a21c14096531de96c20b13 Mon Sep 17 00:00:00 2001 From: Yu ISHIKAWA Date: Tue, 25 Aug 2015 15:02:57 +0900 Subject: [PATCH 2/5] Change `@param` to `@slot` at DataFrame class --- R/pkg/R/DataFrame.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/R/pkg/R/DataFrame.R b/R/pkg/R/DataFrame.R index 19417be0c53b4..749b9d864555d 100644 --- a/R/pkg/R/DataFrame.R +++ b/R/pkg/R/DataFrame.R @@ -29,8 +29,8 @@ setOldClass("jobj") #' @seealso jsonFile, table #' @docType class #' -#' @param env An R environment that stores bookkeeping states of the DataFrame -#' @param sdf A Java object reference to the backing Scala DataFrame +#' @slot env An R environment that stores bookkeeping states of the DataFrame +#' @slot sdf A Java object reference to the backing Scala DataFrame #' @export setClass("DataFrame", slots = list(env = "environment", From b7542c14bc81a4801ab50aed37f95b5a0b530fbb Mon Sep 17 00:00:00 2001 From: Yu ISHIKAWA Date: Tue, 25 Aug 2015 15:11:53 +0900 Subject: [PATCH 3/5] Modify @rdname tags and Add @name in column.R --- R/pkg/R/column.R | 39 +++++++++++++++++++++++++++------------ 1 file changed, 27 insertions(+), 12 deletions(-) diff --git a/R/pkg/R/column.R b/R/pkg/R/column.R index a1f50c383367c..d5dfd4525db0e 100644 --- a/R/pkg/R/column.R +++ b/R/pkg/R/column.R @@ -24,10 +24,9 @@ setOldClass("jobj") #' @title S4 class that represents a DataFrame column #' @description The column class supports unary, binary operations on DataFrame columns - #' @rdname column #' -#' @param jc reference to JVM DataFrame column +#' @slot jc reference to JVM DataFrame column #' @export setClass("Column", slots = list(jc = "jobj")) @@ -122,8 +121,11 @@ createMethods() #' alias #' #' Set a new name for a column - -#' @rdname column +#' +#' @rdname alias +#' @name alias +#' @family colum_func +#' @export setMethod("alias", signature(object = "Column"), function(object, data) { @@ -138,7 +140,9 @@ setMethod("alias", #' #' An expression that returns a substring. #' -#' @rdname column +#' @rdname substr +#' @name substr +#' @family colum_func #' #' @param start starting position #' @param stop ending position @@ -152,7 +156,9 @@ setMethod("substr", signature(x = "Column"), #' #' Test if the column is between the lower bound and upper bound, inclusive. #' -#' @rdname column +#' @rdname between +#' @name between +#' @family colum_func #' #' @param bounds lower and upper bounds setMethod("between", signature(x = "Column"), @@ -167,7 +173,9 @@ setMethod("between", signature(x = "Column"), #' Casts the column to a different data type. #' -#' @rdname column +#' @rdname cast +#' @name cast +#' @family colum_func #' #' @examples \dontrun{ #' cast(df$age, "string") @@ -189,11 +197,15 @@ setMethod("cast", #' Match a column with given values. #' -#' @rdname column +#' @rdname match +#' @name %in% +#' @aliases %in% #' @return a matched values as a result of comparing with given values. -#' @examples \dontrun{ -#' filter(df, "age in (10, 30)") -#' where(df, df$age %in% c(10, 30)) +#' @export +#' @examples +#' \dontrun{ +#' filter(df, "age in (10, 30)") +#' where(df, df$age %in% c(10, 30)) #' } setMethod("%in%", signature(x = "Column"), @@ -208,7 +220,10 @@ setMethod("%in%", #' If values in the specified column are null, returns the value. #' Can be used in conjunction with `when` to specify a default value for expressions. #' -#' @rdname column +#' @rdname otherwise +#' @name otherwise +#' @family colum_func +#' @export setMethod("otherwise", signature(x = "Column", value = "ANY"), function(x, value) { From 949c79d67f2bbacd84316491e8cef43ce6f8c2d3 Mon Sep 17 00:00:00 2001 From: Yu ISHIKAWA Date: Tue, 25 Aug 2015 15:44:27 +0900 Subject: [PATCH 4/5] Add @name tags to cache, count, describe, printSchema and show --- R/pkg/R/DataFrame.R | 8 +++++++- R/pkg/R/column.R | 1 + 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/R/pkg/R/DataFrame.R b/R/pkg/R/DataFrame.R index 749b9d864555d..7918268262ecb 100644 --- a/R/pkg/R/DataFrame.R +++ b/R/pkg/R/DataFrame.R @@ -62,6 +62,7 @@ dataFrame <- function(sdf, isCached = FALSE) { #' @param x A SparkSQL DataFrame #' #' @rdname printSchema +#' @name printSchema #' @export #' @examples #'\dontrun{ @@ -186,6 +187,7 @@ setMethod("showDF", #' @param x A SparkSQL DataFrame #' #' @rdname show +#' @name show #' @export #' @examples #'\dontrun{ @@ -332,7 +334,8 @@ setMethod("insertInto", #' #' @param x A SparkSQL DataFrame #' -#' @rdname cache-methods +#' @rdname cache +#' @name cache #' @export #' @examples #'\dontrun{ @@ -558,6 +561,7 @@ setMethod("sample_frac", #' @param x A SparkSQL DataFrame #' #' @rdname count +#' @name count #' @aliases nrow #' @export #' @examples @@ -1552,6 +1556,7 @@ setMethod("saveAsTable", #' @param ... Additional expressions #' @return A DataFrame #' @rdname describe +#' @name describe #' @aliases summary #' @export #' @examples @@ -1573,6 +1578,7 @@ setMethod("describe", }) #' @rdname describe +#' @name describe setMethod("describe", signature(x = "DataFrame"), function(x) { diff --git a/R/pkg/R/column.R b/R/pkg/R/column.R index d5dfd4525db0e..4805096f3f9c5 100644 --- a/R/pkg/R/column.R +++ b/R/pkg/R/column.R @@ -45,6 +45,7 @@ col <- function(x) { } #' @rdname show +#' @name show setMethod("show", "Column", function(object) { cat("Column", callJMethod(object@jc, "toString"), "\n") From 0a3f176ce2719a86e1430ffffed8c72b76e5fdb6 Mon Sep 17 00:00:00 2001 From: Yu ISHIKAWA Date: Tue, 25 Aug 2015 15:53:25 +0900 Subject: [PATCH 5/5] Move agg and groupBy to each Rd file --- R/pkg/R/DataFrame.R | 6 +++--- R/pkg/R/generics.R | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/R/pkg/R/DataFrame.R b/R/pkg/R/DataFrame.R index 7918268262ecb..10f3c4ea59864 100644 --- a/R/pkg/R/DataFrame.R +++ b/R/pkg/R/DataFrame.R @@ -760,7 +760,7 @@ setMethod("first", take(x, 1) }) -# toRDD() +# toRDD # # Converts a Spark DataFrame to an RDD while preserving column names. # @@ -833,7 +833,7 @@ setMethod("group_by", #' Compute aggregates by specifying a list of columns #' #' @param x a DataFrame -#' @rdname DataFrame +#' @rdname agg #' @name agg #' @aliases summarize #' @export @@ -843,7 +843,7 @@ setMethod("agg", agg(groupBy(x), ...) }) -#' @rdname DataFrame +#' @rdname agg #' @name summarize setMethod("summarize", signature(x = "DataFrame"), diff --git a/R/pkg/R/generics.R b/R/pkg/R/generics.R index 610a8c31223cd..a829d46c1894c 100644 --- a/R/pkg/R/generics.R +++ b/R/pkg/R/generics.R @@ -441,7 +441,7 @@ setGeneric("filter", function(x, condition) { standardGeneric("filter") }) #' @export setGeneric("group_by", function(x, ...) { standardGeneric("group_by") }) -#' @rdname DataFrame +#' @rdname groupBy #' @export setGeneric("groupBy", function(x, ...) { standardGeneric("groupBy") })