[R]: update manuals.

Rpkg/R/FlashR.R

@@ -2079,6 +2079,7 @@ setMethod("is.finite", signature(x = "fmV"), function(x) {
 #' @param x a FlashR factor
 #' @return The length of \code{levels(x)}, which is zero if \code{x}
 #' has no levels.
+#' @name nlevels
 setMethod("nlevels", signature(x = "fmFactorV"), function(x) x@num.levels)
 
 #' Levels Attributes
@@ -2090,6 +2091,7 @@ setMethod("nlevels", signature(x = "fmFactorV"), function(x) x@num.levels)
 #'
 #' @param x a FlashR factor.
 #' @return a FlashR vector that contains the value of the levels.
+#' @name levels
 setMethod("levels", signature(x = "fmFactorV"), function(x)
 		  fm.seq.int(1, x@num.levels, 1))
 

Rpkg/man/Arithmetic.Rd

@@ -156,16 +156,16 @@
 \S4method{^}{fmV,ANY}(e1, e2)
 }
 \arguments{
-\item{e1,e2}{One of the operands need to be a FlashMatrix object. If one operand
+\item{e1,e2}{One of the operands need to be a FlashR object. If one operand
 is a matrix and the other is a vector, we perform the arithmetic operation
 on the vector and every column of the matrix. If one operand is a scalar,
 we perform the operation on the scalar with every element in the matrix or
 the vector.
 
 There are a few exceptions. For example, the left operand of "^" has to be
-a FlashMatrix object and the right operand has to be a scalar.}
+a FlashR object and the right operand has to be a scalar.}
 }
 \description{
-Perform unary or binary arithmetic operations on FlashMatrix objects.
+Perform unary or binary arithmetic operations on FlashR objects.
 }
 

Rpkg/man/Comparison.Rd

@@ -186,7 +186,7 @@
 \S4method{<}{ANY,fmV}(e1, e2)
 }
 \arguments{
-\item{e1,e2}{One of the operands need to be a FlashMatrix object. If one operand
+\item{e1,e2}{One of the operands need to be a FlashR object. If one operand
 is a matrix and the other is a vector, we perform the arithmetic operation
 on the vector and every column of the matrix. If one operand is a scalar,
 we perform the operation on the scalar with every element in the matrix or

Rpkg/man/Extract.Rd

@@ -26,7 +26,7 @@ or numeric vectors.}
 \item{drop}{for matrices. If \code{TRUE}, the result is coerced to a vector.}
 }
 \description{
-Operators acting on FlashMatrix vectors and matrices to extract parts of
+Operators acting on FlashR vectors and matrices to extract parts of
 the objects.
 }
 \details{

Rpkg/man/Extremes.Rd

@@ -96,21 +96,21 @@ pmin2(e1, e2)
 \S4method{pmax}{fmV}(..., na.rm = FALSE)
 }
 \arguments{
-\item{e1,e2}{One of the operands need to be a FlashMatrix object. If one
+\item{e1,e2}{One of the operands need to be a FlashR object. If one
 operand is a matrix and the other is a vector, we perform the operation
 on the vector and every column of the matrix. If one operand is a scalar,
 we perform the operation on the scalar with every element in the matrix or
 the vector.}
 
-\item{x}{a FlashMatrix vector or matrix.}
+\item{x}{a FlashR vector or matrix.}
 
-\item{...}{FlashMatrix vectors or matrices.}
+\item{...}{FlashR vectors or matrices.}
 
 \item{na.rm}{a logical indicating whether missing values should be removed.}
 }
 \value{
 \code{pmin2}, \code{pmax2}, \code{pmin} and \code{pmax} return
-        a FlashMatrix object, and \code{min} and \code{max} return an R scalar.
+        a FlashR object, and \code{min} and \code{max} return an R scalar.
 }
 \description{
 Returns the (parallel) maxima and minima of the input values.

Rpkg/man/Logic.Rd

@@ -72,7 +72,7 @@
 \method{!}{fmV}(e1)
 }
 \arguments{
-\item{e1,e2}{One of the operands need to be a FlashMatrix object. If one operand
+\item{e1,e2}{One of the operands need to be a FlashR object. If one operand
 is a matrix and the other is a vector, we perform the arithmetic operation
 on the vector and every column of the matrix. If one operand is a scalar,
 we perform the operation on the scalar with every element in the matrix or

Rpkg/man/MathFun.Rd

@@ -7,8 +7,7 @@
 \alias{abs,fmV-method}
 \alias{sqrt,fm-method}
 \alias{sqrt,fmV-method}
-\title{\code{abs(x)} computes the absolute value of x, \code{sqrt(x)} computes the square
-root of x.}
+\title{Miscellaneous Mathematical Functions}
 \usage{
 \S4method{abs}{fm}(x)
 

Rpkg/man/NA.Rd

@@ -12,10 +12,10 @@
 \S4method{is.na}{fmV}(x)
 }
 \arguments{
-\item{x}{an FlashMatrix vector or matrix.}
+\item{x}{an FlashR vector or matrix.}
 }
 \value{
-a logical FlashMatrix vector or matrix.
+a logical FlashR vector or matrix.
 }
 \description{
 This function indicates which elements are missing.

Rpkg/man/all.Rd

@@ -15,7 +15,7 @@ fm.all(x, lazy = FALSE)
 \S4method{all}{fmV}(x, ..., na.rm = FALSE)
 }
 \arguments{
-\item{x}{a logical FlashMatrix vector.}
+\item{x}{a logical FlashR vector.}
 
 \item{lazy}{indicates whether or not to evaluate it lazily.}
 

Rpkg/man/any.Rd

@@ -15,7 +15,7 @@ fm.any(x, lazy = FALSE)
 \S4method{any}{fmV}(x, ..., na.rm = FALSE)
 }
 \arguments{
-\item{x}{a logical FlashMatrix vector.}
+\item{x}{a logical FlashR vector.}
 
 \item{lazy}{indicates whether or not to evaluate it lazily.}
 

Rpkg/man/colSums.Rd

@@ -24,15 +24,15 @@ fm.colSums(x, lazy = FALSE)
 \S4method{colMeans}{fm}(x, na.rm)
 }
 \arguments{
-\item{x}{a FlashMatrix matrix.}
+\item{x}{a FlashR matrix.}
 
 \item{lazy}{logical. indicates whether to evaluate the expression lazily.}
 
 \item{na.rm}{logical. Should missing values (including NaN) be omitted
 from the calculations?}
 }
 \value{
-a FlashMatrix vector.
+a FlashR vector.
 }
 \description{
 Form row and column sums and means for numeric arrays.

Rpkg/man/cov.wt-fm-method.Rd → Rpkg/man/cov.wt.Rd

@@ -1,8 +1,8 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/FlashR_stats.R
 \docType{methods}
-\name{cov.wt,fm-method}
-\alias{cov.wt,fm-method}
+\name{cov.wt}
+\alias{cov.wt}
 \title{Weighted Covariance Matrices}
 \usage{
 \S4method{cov.wt}{fm}(x, wt = rep(1/nrow(x), nrow(x)), cor = FALSE,

Rpkg/man/dim.Rd

@@ -4,14 +4,14 @@
 \name{dim}
 \alias{dim}
 \alias{dim,fm-method}
-\title{Dimensions of an FlashMatrix Object}
+\title{Dimensions of an FlashR Object}
 \usage{
 \S4method{dim}{fm}(x)
 }
 \arguments{
-\item{x}{A FlashMatrix matrix.}
+\item{x}{A FlashR matrix.}
 }
 \description{
-Retrieve the dimension of an FlashMatrix object.
+Retrieve the dimension of an FlashR object.
 }
 

Rpkg/man/dimnames.Rd

@@ -18,7 +18,7 @@
 \S4method{dimnames}{fmV,list}(x) <- value
 }
 \arguments{
-\item{x}{a FlashMatrix matrix.}
+\item{x}{a FlashR matrix.}
 
 \item{value}{a list that provides values for dimension names.}
 }

Rpkg/man/drop-fm-method.Rd → Rpkg/man/drop.Rd

@@ -1,20 +1,20 @@
 % Generated by roxygen2 (4.1.1): do not edit by hand
 % Please edit documentation in R/FlashR_base.R
 \docType{methods}
-\name{drop,fm-method}
-\alias{drop,fm-method}
+\name{drop}
+\alias{drop}
 \title{Drop Redundant Extent Information}
 \usage{
 \S4method{drop}{fm}(x)
 }
 \arguments{
-\item{x}{a FlashMatrix matrix.}
+\item{x}{a FlashR matrix.}
 }
 \value{
-a FlashMatrix matrix or vector.
+a FlashR matrix or vector.
 }
 \description{
-Delete the dimensions of a FlashMatrix matrix which have only one level.
+Delete the dimensions of a FlashR matrix which have only one level.
 }
 \details{
 If the input matrix has only one row or one column, it works the same as

Rpkg/man/fm-class.Rd

@@ -3,9 +3,9 @@
 \docType{class}
 \name{fm-class}
 \alias{fm-class}
-\title{An S4 class to represent a FlashMatrix matrix.}
+\title{An S4 class to represent a FlashR matrix.}
 \description{
-An S4 class to represent a FlashMatrix matrix.
+An S4 class to represent a FlashR matrix.
 }
 \section{Slots}{
 

Rpkg/man/fm.agg.Rd

@@ -5,7 +5,7 @@
 \alias{fm.agg.lazy}
 \alias{fm.agg.mat}
 \alias{fm.agg.mat.lazy}
-\title{Aggregation on a FlashMatrix object.}
+\title{Aggregation on a FlashR object.}
 \usage{
 fm.agg(fm, op)
 
@@ -16,7 +16,7 @@ fm.agg.mat(fm, margin, op)
 fm.agg.mat.lazy(fm, margin, op)
 }
 \arguments{
-\item{fm}{a FlashMatrix object}
+\item{fm}{a FlashR object}
 
 \item{op}{the reference or the name of a predefined basic operator or
 the reference to an aggregation operator returned by
@@ -26,12 +26,12 @@ the reference to an aggregation operator returned by
 }
 \value{
 \code{fm.agg} returns a scalar, \code{fm.agg.mat} returns
-        a FlashMatrix vector, \code{fm.agg.lazy} and \code{fm.agg.mat.lazy}
-        return a FlashMatrix sink matrix.
+        a FlashR vector, \code{fm.agg.lazy} and \code{fm.agg.mat.lazy}
+        return a FlashR sink matrix.
 }
 \description{
 This function accepts a basic operator and perform aggregation on
-the FlashMatrix object with the basic operator.
+the FlashR object with the basic operator.
 }
 \details{
 \code{fm.agg} aggregates over the entire object.

Rpkg/man/fm.agg.op-class.Rd

@@ -4,10 +4,10 @@
 \name{fm.agg.op-class}
 \alias{fm.agg.op-class}
 \title{An S4 class to represent an aggregation operator used in aggregation
-operations in FlashMatrix.}
+operations in FlashR.}
 \description{
 An S4 class to represent an aggregation operator used in aggregation
-operations in FlashMatrix.
+operations in FlashR.
 }
 \section{Slots}{
 

Rpkg/man/fm.apply.Rd

@@ -7,17 +7,17 @@
 fm.apply(x, margin, FUN)
 }
 \arguments{
-\item{x}{a FlashMatrix matrix.}
+\item{x}{a FlashR matrix.}
 
 \item{margin}{an integer. \code{1} indicates rows and \code{2} indicates columns.}
 
 \item{FUN}{a string that indicates the name of the predefined function.}
 }
 \value{
-a FlashMatrix matrix.
+a FlashR matrix.
 }
 \description{
-Apply a predefined function on rows/columns of a FlashMatrix matrix.
+Apply a predefined function on rows/columns of a FlashR matrix.
 The predefined function always output a vector of the same length. Thus,
 the output of \code{fm.apply} is a matrix.
 }

Rpkg/man/fm.as.factor.Rd

@@ -2,19 +2,19 @@
 % Please edit documentation in R/FlashR.R
 \name{fm.as.factor}
 \alias{fm.as.factor}
-\title{Convert a FlashMatrix vector to a FlashMatrix factor vector.}
+\title{Convert a FlashR vector to a FlashR factor vector.}
 \usage{
 fm.as.factor(fm, num.levels = -1)
 }
 \arguments{
-\item{fm}{a FlashMatrix vector.}
+\item{fm}{a FlashR vector.}
 
 \item{num.levels}{The number of levels in the factor vector.}
 }
 \value{
-a FlashMatrix factor vector.
+a FlashR factor vector.
 }
 \description{
-Convert a FlashMatrix vector to a FlashMatrix factor vector.
+Convert a FlashR vector to a FlashR factor vector.
 }
 

Rpkg/man/fm.ase.Rd

@@ -9,7 +9,7 @@ fm.spectral.embedding(fm, nev, which = c("A, Aug, L, nL"), c = 1/nrow(fm),
   ncv = 2 * nev, tol = 1e-12)
 }
 \arguments{
-\item{fm}{The FlashMatrixR object}
+\item{fm}{The FlashR object}
 
 \item{nev}{The number of eigenvalues/vectors required.}
 

Rpkg/man/fm.basic.op.Rd

@@ -37,7 +37,7 @@
 \alias{fm.get.basic.op}
 \alias{fm.get.basic.uop}
 \alias{fm.init.basic.op}
-\title{The basic operators supported by FlashMatrix.}
+\title{The basic operators supported by FlashR.}
 \format{\preformatted{ NULL
 }}
 \usage{
@@ -116,7 +116,7 @@ fm.init.basic.op()
 a reference to the specified basic operator.
 }
 \description{
-The basic operators are mainly used by the FlashMatrix functions that
+The basic operators are mainly used by the FlashR functions that
 accept operators as arguments. Such a function includes \code{fm.mapply},
 \code{fm.inner.prod}, etc.
 }

Rpkg/man/fm.conv.FM2R.Rd

@@ -2,18 +2,18 @@
 % Please edit documentation in R/FlashR.R
 \name{fm.conv.FM2R}
 \alias{fm.conv.FM2R}
-\title{Convert a FlashMatrix object to a regular R object}
+\title{Convert a FlashR object to a regular R object}
 \usage{
 fm.conv.FM2R(obj)
 }
 \arguments{
-\item{obj}{a FlashMatrix object}
+\item{obj}{a FlashR object}
 }
 \value{
 a regular R object.
 }
 \description{
-Convert a FlashMatrix object to a regular R object
+Convert a FlashR object to a regular R object
 }
 \author{
 Da Zheng <dzheng5@jhu.edu>

Rpkg/man/fm.conv.R2FM.Rd

@@ -2,23 +2,22 @@
 % Please edit documentation in R/FlashR.R
 \name{fm.conv.R2FM}
 \alias{fm.conv.R2FM}
-\title{Convert a regular R object to a FlashMatrix object.}
+\title{Convert a regular R object to a FlashR object.}
 \usage{
 fm.conv.R2FM(obj, byrow = FALSE)
 }
 \arguments{
 \item{obj}{a regular R object}
 
-\item{byrow}{a logical value to determine the data layout of a FlashMatrix
-matrix.}
+\item{byrow}{a logical value to determine the data layout of a FlashR matrix.}
 }
 \value{
-a FlashMatrix object. If the input R object has 0 element,
+a FlashR object. If the input R object has 0 element,
         \code{fm.conv.R2FM} returns \code{NULL}.
 }
 \description{
 If the R object is a matrix, \code{byrow} determines how data in the generated
-FlashMatrix object is organized in memory.
+FlashR object is organized in memory.
 }
 \author{
 Da Zheng <dzheng5@jhu.edu>