Package ‘gmatrix’
August 29, 2016
Type Package
Title GPU Computing in R
Version 0.3
Date 2015-11-23
Author Nathan Morris
Maintainer Nathan Morris <njm18@case.edu>
Description A general framework for utilizing R to harness the power of NVIDIA GPU's. The ``gmatrix'' and ``gvector'' classes allow for easy management of the separate device and host memory spaces. Numerous numerical operations are implemented for these objects on the GPU. These operations include matrix multiplication, addition, subtraction, the kronecker product, the outer product, comparison operators, logical operators, trigonometric functions, indexing, sorting, random number generation and many more.
License GPL-3 | file LICENSE
SystemRequirements Nvidia's CUDA toolkit (>= release 5.0) and Nvidia
GPU with compute capibility >=2.0
OS_type unix
URL https://github.com/njm18/gmatrix
Depends methods, stats
NeedsCompilation yes
Repository CRAN
Date/Publication 2015-12-01 08:01:12
R topics documented:
gmatrix-package . . . . . . . . . . . . . . . . . . . . .
as.gmatrix, as.gvector . . . . . . . . . . . . . . . . . . .
as.numeric, as.integer, as.logical, as.vector and as.matrix
checkDevice . . . . . . . . . . . . . . . . . . . . . . . .
chol . . . . . . . . . . . . . . . . . . . . . . . . . . . .
colMeans . . . . . . . . . . . . . . . . . . . . . . . . .
colnames . . . . . . . . . . . . . . . . . . . . . . . . .
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R topics documented:
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convertType . . . . . . . . .
crossprod,tcrossprod . . . .
device . . . . . . . . . . . .
diag . . . . . . . . . . . . .
dim . . . . . . . . . . . . .
dimnames . . . . . . . . . .
elementwise binary operators
elementwise functions . . .
g . . . . . . . . . . . . . . .
g.rep . . . . . . . . . . . . .
gBasicHMC . . . . . . . . .
gdbeta . . . . . . . . . . . .
gdbinom . . . . . . . . . . .
gdgamma . . . . . . . . . .
gdpois . . . . . . . . . . . .
gdup . . . . . . . . . . . . .
ggc . . . . . . . . . . . . . .
gident . . . . . . . . . . . .
gkroneckerProd . . . . . . .
gmatrix . . . . . . . . . . .
gmatrix-class . . . . . . . .
gmatTimesDiagVec . . . . .
gmm . . . . . . . . . . . . .
gnamestrip . . . . . . . . . .
gorder . . . . . . . . . . . .
gouter . . . . . . . . . . . .
gqr-class . . . . . . . . . . .
gRowLogSums . . . . . . .
grunif . . . . . . . . . . . .
gseq . . . . . . . . . . . . .
gset.seed . . . . . . . . . . .
gsumby . . . . . . . . . . .
gsvd-class . . . . . . . . . .
gtest . . . . . . . . . . . . .
gvector . . . . . . . . . . .
gvector-class . . . . . . . .
ifelse . . . . . . . . . . . . .
indexing . . . . . . . . . . .
length . . . . . . . . . . . .
lpgr-class . . . . . . . . . .
matrix multiplication . . . .
max . . . . . . . . . . . . .
mean, sum . . . . . . . . . .
names . . . . . . . . . . . .
ncol . . . . . . . . . . . . .
normal . . . . . . . . . . . .
rsample . . . . . . . . . . .
setDevice . . . . . . . . . .
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gmatrix-package
setTuningPameters
show . . . . . . . .
sort . . . . . . . .
t . . . . . . . . . .
type . . . . . . . .
which . . . . . . .
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Index
gmatrix-package
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Making GPU power available in R
Description
This package implements a general framework for utilizing R to harness the power of NVIDIA
GPU’s. The gmatrix and gvector classes allow for easy management of the separate device and
host memory spaces. Numerous numerical operations are implemented for these objects on the
GPU. These operations include matrix multiplication, addition, subtraction, the kronecker product, the outer product, comparison operators, logical operators, trigonometric functions, indexing,
sorting, random number generation and many more.
Details
Package:
Type:
Version:
Date:
License:
LazyLoad:
Depends:
gmatrix
Package
0.1
2013-5-10
GPL-2
yes
methods
To move an R object to the GPU use the g function. To move the object back the the host use the h
function. Standard operations such as matrix multiplication or addition may be performed on GPU
objects as with any matrix or vector object in R. The gmatrix and gvector classes contain a type
slot which determines if the data is stored as a "double", "single", "integer" or "logical."
The gmatrix and gvector objects store only a pointer to an object on the GPU device. Thus, a line
such as y<-x will duplicate the pointer but not the actual data on the GPU. One should use instead
y<-gdup(x). Numerous random number generators such as grnorm have been implemented in this
package. This package is intended to work with the companion package rcula which implements
matrix factorization and inversions methods.
Author(s)
Nathan Morris
4
as.gmatrix, as.gvector
References
None
See Also
rcula-package, g, h, gmatrix-class, gvector-class
Examples
#Look at available GPU devices (use setDevice to change the device)
listDevices()
#Creating GPU objects
g_x=g(1:10) #transfer a sequence to the GPU
g_y=gseq(1,10) #create a sequence on the GPU
g_A=gmatrix(grnorm(100),10,10,dup=FALSE) #create a random 10x10 matrix
#look at and change the properties of these objects
type(g_x)
type(g_A)
type(g_x)="d" #'d' may be used as short form of"double"
length(g_x)
dim(g_A)
nrow(g_A)
#Perform some simple calculations
g_ans=g_x %*% log(abs(g_A)) %*% sin(-g_y)
g_rowsum= rowSums(g_A)
#Move data back to the host
h_ans=h(g_x)
h_roswum =h(g_A)
as.gmatrix, as.gvector
Methods for coercing an object to a GPU class
Description
The as.gmatrix and as.gvector methods may be used to coerce an object to a given GPU class
(i.e. gmatrix or gvector).
Arguments
x, data
object to be coerced
type
The type to convert the object to. There are three different ways to specify
this. One may use the "double", "single", "integer" or "logical" notation.
Alternatively the short form "d", "s", "i" or "s" notation may be used. Finally
the internal integer representation of 0L, 1L, 2L or 3L may be used.
as.numeric, as.integer, as.logical, as.vector and as.matrix
5
dup
This may be set to ’FALSE’ to avoid duplicating x in the event that it is on the
GPU allready and the original type is the same as the type argument.
nrow,ncol,byrow,dimnames
these attributes should generally only be set by a direct call to gmatrix
Details
The as.gmatrix and as.gvector methods may be used to move an R object to the current GPU
device and returns an object of class gmatrix or gvector respectively. The methods have the
following arguments:
as.gmatrix(data = NA, nrow = 1L, ncol = 1L, byrow = FALSE, dimnames = NULL, type = NULL,
dup = TRUE) as.gvector(x, type=NULL, dup=TRUE)
The dup argument is used only when the input argument (data) is all ready on the GPU. dup=FALSE
will return the original data without duplicating it on the GPU.
Value
An object of type gmatrix or gvector
Author(s)
Nathan Morris
See Also
g, gmatrix and gvector
Examples
A=matrix(1:10,2,5)
B=as.gmatrix(A)
as.numeric, as.integer, as.logical, as.vector and as.matrix
Methods to coerce a GPU object to an R object
Description
The functions as.numeric, as.integer, as.matrix and as.vector are intended to bring a GPU
object to the main host memory and coerce it into the given type.
Methods
signature(x = "gmatrix")
signature(x = "gvector")
6
chol
See Also
h
checkDevice
Check that the specified integer is the current device.
Description
Mostly for internal uses.
Usage
checkDevice(x)
Arguments
x
A vector of integers
Details
Errors out if x is not the current device.
Value
Returns TRUE or errors out.
Author(s)
Nathan Morris
See Also
getDevice, setDevice and device
chol
Method to calculate the Choleski decomposition square symmetric
posative definite matrix
Description
Takes a square symmetric posative definite gmatrix object. Note that no checking for symmetry is
done. An error will be thrown if the the matrix is not posative definite. Returns a gmatrix object
that is upper triangular.
Methods
signature(x = "ANY")
signature(x = "gmatrix")
colMeans
colMeans
7
Methods to Form Row and Column Sums and Means
Description
This documents the colMeans, rowMeans, colSums and rowSums methods for objects of class
gmatrix. These functions form row and column sums and means for an object of class gmatrix.
This is implement very similarly to the base package (see rowSums, but the na.rm and dims arguments are not implemented).
Methods
signature(x = "ANY")
signature(x = "gmatrix")
colnames
Methods to get and set the ’rownames’ and ’colnames’ of a matrix.
Description
This documents the functions rownames and colnames for objects of class gmatrix. These methods
are very similar to those defined in R base (see rownames in R base).
Methods
signature(x = "ANY")
signature(x = "gmatrix")
convertType
Convert the type of a GPU object
Description
This function is used to convert the type (i.e. "double", "single", "integer" or "logical") of a
gmatrix or gvector object.
Usage
convertType(x, to, dup = TRUE)
8
crossprod,tcrossprod
Arguments
x
A GPU object of class gvector or gmatrix
to
The type to convert the object to. There are three different ways to specify
this. One may use the "double", "single", "integer" or "logical" notation.
Alternatively the short form "d", "s", "i" or "s" notation may be used. Finally
the internal integer representation of 0L, 1L, 2L or 3L may be used.
dup
This may be set to ’FALSE’ to avoid duplicating x in the event the original type
and the to type are the same
Value
Returns the x after converting it to a new type.
Author(s)
Nathan Morris
See Also
type
Examples
x=gseq(1,10)
y=convertType(x,'d')
type(y)
crossprod,tcrossprod
Matrix Crossproduct
Description
Given matrices x and y as arguments, return a matrix cross-product. This is formally equivalent to
(but usually slightly faster than) the call t(x) %*% y (crossprod) or x %*% t(y) (tcrossprod).
Methods
signature(x = "ANY", y = "ANY")
signature(x = "gmatrix", y = "gmatrix")
signature(x = "gmatrix", y = "gvector")
signature(x = "gmatrix", y = "logical")
signature(x = "gmatrix", y = "matrix")
signature(x = "gmatrix", y = "missing")
crossprod,tcrossprod
signature(x = "gmatrix", y = "numeric")
signature(x = "gvector", y = "gmatrix")
signature(x = "gvector", y = "gvector")
signature(x = "gvector", y = "logical")
signature(x = "gvector", y = "missing")
signature(x = "gvector", y = "numeric")
signature(x = "logical", y = "gmatrix")
signature(x = "logical", y = "gvector")
signature(x = "matrix", y = "gmatrix")
signature(x = "numeric", y = "gmatrix")
signature(x = "numeric", y = "gvector")
signature(x = "ANY", y = "ANY")
signature(x = "gmatrix", y = "gmatrix")
signature(x = "gmatrix", y = "gvector")
signature(x = "gmatrix", y = "logical")
signature(x = "gmatrix", y = "matrix")
signature(x = "gmatrix", y = "missing")
signature(x = "gmatrix", y = "numeric")
signature(x = "gvector", y = "gmatrix")
signature(x = "gvector", y = "gvector")
signature(x = "gvector", y = "logical")
signature(x = "gvector", y = "missing")
signature(x = "gvector", y = "numeric")
signature(x = "logical", y = "gmatrix")
signature(x = "logical", y = "gvector")
signature(x = "matrix", y = "gmatrix")
signature(x = "numeric", y = "gmatrix")
signature(x = "numeric", y = "gvector")
9
10
dim
device
Get and set methods for the device slot of a gvector or gmatrix object
Description
The device methods can be used to find what GPU device an object is stored on. The device<- can
be used to move the object to a different GPU. Note that this is currently implemented by moving
the object to host memory first.
Methods
signature(x = "gmatrix")
signature(x = "gvector")
See Also
gdup and setDevice
diag
Matrix Diagonals
Description
Extract or replace the diagonal of a matrix, or construct a diagonal matrix. Implemented much the
same as in R base.
Methods
signature(x = "ANY")
signature(x = "gmatrix")
dim
Dimensions of an Object
Description
Retrieve or set the dimension of an object. Implemented much the same as in R base. However, any
redimensioning of a matrix must result in a matrix with the same number of elements.
Methods
signature(x = "gmatrix")
See Also
dim
dimnames
dimnames
11
Dimnames of an Object
Description
Retrieve or set the dimnames of an object. Implemented much the same as R base.
Methods
signature(x = "gmatrix")
See Also
dimnames, colnames
elementwise binary operators
Binary Operators
Description
This page documents the operators "*", "+", "-", "/", "^", "%%", "=", "<", ">", ">=", "<=",
"!=", "&" and "|". These are all element-wise binary operations that can be performed on a
gmatrix or gvector object. Operators work in much that same way as in R base. The command e1 %lgspadd% e2 yields the vector log(exp(e1)+exp(e2)) calculated in a numericaly stable
way. If one object is shorter than the other, items in the shorter object are recycled as in R base. All
operations return a GPU object (i.e. a gmatrix or gvector).
Methods
signature(e1 = "gmatrix", e2 = "gmatrix")
signature(e1 = "gmatrix", e2 = "gvector")
signature(e1 = "gmatrix", e2 = "logical")
signature(e1 = "gmatrix", e2 = "matrix")
signature(e1 = "gmatrix", e2 = "numeric")
signature(e1 = "gvector", e2 = "gmatrix")
signature(e1 = "gvector", e2 = "gvector")
signature(e1 = "gvector", e2 = "logical")
signature(e1 = "gvector", e2 = "matrix")
signature(e1 = "gvector", e2 = "numeric")
signature(e1 = "logical", e2 = "gmatrix")
signature(e1 = "logical", e2 = "gvector")
12
g
signature(e1 = "matrix", e2 = "gmatrix")
signature(e1 = "matrix", e2 = "gvector")
signature(e1 = "numeric", e2 = "gmatrix")
signature(e1 = "numeric", e2 = "gvector")
Warning
The operator %% is known to be numericaly instable compared to the R version.
elementwise functions Elementwise functions/operators
Description
This is the documentation for the functions abs, exp, expm1, log, log2, log10, log1p, sin, cos,
tan, asin, acos, atan, sinh, cosh, tanh, asinh, acosh, atanh, abs, lgamma, gamma, sign, round,
ceiling, is.na, is.nan, is.finite, is.infinite and !. These functions are elementwise functions/operators which are defined much the same as the functions the R base package. When operation on object of class gmatrix or gvector the work will be performed by the GPU and will return
a GPU object of the same dimension as the input.
Methods
signature(x = "gmatrix") Returns an object of type gmatrix with the same dimensions as the
input.
signature(x = "gvector") Returns an object of type gvector with the same dimensions as the
input.
g
Transfer and R object to and from the GPU.
Description
The function g transfers the object to the GPU. The function h transfers it back to the host.
Usage
g(x, type = NULL, dup = TRUE)
h(x)
g.rep
13
Arguments
x
The object to be transfered.
type
The type to convert the object to. There are three different ways to specify
this. One may use the "double", "single", "integer" or "logical" notation.
Alternatively the short form "d", "s", "i" or "s" notation may be used. Finally
the internal integer representation of 0L, 1L, 2L or 3L may be used.
dup
This may be set to ’FALSE’ to avoid duplicating x in the event that it is on the
GPU allready and the original type is the same as the type argument.
Details
These functions may be more convenient than functions such as ’as.gmatrix’ or ’as.gvector’. In
addition to having a very short name, one does not need to consider whether the object is a vector
or matrix.
Value
The ’h’ function transfers device data back to the host and returns a matrix or vector, while the ’g’
function returns an object of class gmatrix or gvector storing the data on the GPU.
Author(s)
Nathan Morris
See Also
as.gmatrix and as.numeric
Examples
h_x=1:10
g_x=g(h_x) #Transfer to the device
g_ans=crossprod(g_x) #Do a a calculation
h_ans=h(g_ans) #Transfer back to the host
g.rep
Replicate Elements of a vector or gvector,
Description
g.rep replicates the ’vector’ or gvector.
Usage
g.rep(x, times = 1L, each = 1L, type = NULL)
14
gBasicHMC
Arguments
x
a ’vector’ or ’gvector.’
times
a single integer representing the number of times the object should be replicated.
each
a single integer representing the number of times each element should be replicated. If each is specified, the times will be ignored.
type
coerce the output to the given type (i.e "double", "single", "integer" or
"logical").
Details
g.rep is somewhat simplified from the R base rep function. It is called g.rep to avoid conflict
with the grep function. It can replicate in two different ways. If times is specified then the entire
vector is replicated, while when each is specified each element is replicated one at a time.
Value
a gvector object with the replicated information
Author(s)
Nathan Morris
See Also
rep
Examples
x=g.rep(1:2, 2) #returns (1,2,1,2)
x=g.rep(1:2, each=2) #returns (1,1,2,2)
gBasicHMC
Performing Hamiltonian MCMC
Description
This function performs Hamiltonian MCMC for continuous distributions.
Usage
gBasicHMC(lpgrf, initial, nsims, nsteps, step,
burnin = 1, nstepsburnin = nsteps, stepburnin = step,
Tstart = 1, r = 1,
keep=keep, thin = 1, report = 100)
gBasicHMC
15
Arguments
lpgrf
This lpgrf input must be a function which takes as its input a list of parameters and gives as its output the log probability (lp) excluding the normalization
constant and a first derivative of the log probability (gr). Both the lp and gr
information must be returned as slots in an object of class lpgr. See details.
initial
Starting values as a list. Again each element of the starting value must be a
matrix on the CPU or GPU. The number columns of each matrix is the number
of parrallel runs.
nsims
Total number of simulations includeing burnin.
nsteps
Tuning parameter for HMC representing the number of leepfrog steps for each
iteration.
step
Tuning parameter for HMC controls the length of each leepfrog steps for each
iteration.
nstepsburnin
Tuning parameter for HMC representing the number of leepfrog steps for each
iteration. This parameter is used only during burnin.
stepburnin
Tuning parameter for HMC controls the length of each leepfrog steps for each
iteration. This parameter is used only during burnin.
Tstart
During the burnin phase only tempering is used to get the simulation moving.
Tstart is the starting temperature.
r
The temperature during the burning phase is exponentially decreased at a rate r.
The temperature is set to 1 if it drops below 1. Also, the temperature is set to 1
once the burnin phas is done.
burnin
The number of iterations used for burnin. All burnin samples are discarded.
keep
Function to extract samples to keep. If defualt keep function is defined as
keep = function(q) lapply(q, function(x) if(any(class(x) %in% c("gmatrix","gvector")))
thin
Selects the number of samples to keep. thin=1 keeps all the samples. thin=5
keeps only ever fifth sample.
report
Controls how often an update of the progress is printed out.
Details
The most important input of gBasicHMC() is the lpgrf parameter. This lpgrf input must be a
function which takes as its input a list of parameters and gives as its output the log probability (lp)
excluding the normalization constant and a first derivative of the log probability (gr). Both the lp
and gr information must be returned as slots in an object of class lpgrf. The lp slot must be a
numberic CPU vector while gr slot must be a list with elements either on the CPU or GPU.The
function gBasicHMC() is designed to run multiple chains simultaneously. Thus each element in
the input is expected to be a matrix where the number of columns is the number of parallel chains
and the number of rows is the dimension of the random variable being simulated. The input is
assumed to be a list of parameters because in many cases there are different types of parameters
such as hyper-parameters. Tracking the current stated of the chain using a list is therefore often
quite natural. As a result of this convention, the gr slot for lpgr object returned by the lpgrf
function must also be a list.
16
gdbeta
Value
Output is a list:
sims
A list with the simulation results from each iteration as elements.
lp
A matrix with the simulation log probabilities for all simulations.
AcceptanceRate
Acceptence rate for each parallel chain.
BurninAcceptanceRate
Acceptence rate during the burnin phase for each parallel chain.
Author(s)
Nathan Morris (this is actually a significantly modified version of an HMC implementation created
by Radford Neal: http://www.cs.utoronto.ca/~radford/GRIMS.html)
References
Neal, Radford M. "MCMC using Hamiltonian dynamics." Handbook of Markov Chain Monte Carlo
2 (2011).
Beam, Andrew L., Sujit K. Ghosh, and Jon Doyle. "Fast hamiltonian monte carlo using gpu computing." Journal of Computational and Graphical Statistics just-accepted (2015): 00-00.
See Also
lpgr-class
gdbeta
The Beta Distribution
Description
Density and random generation for the Beta distribution with parameters shape1 and shape2.
Usage
gdbeta(x, shape1, shape2, ncp = 0, log = FALSE, type = "d")
grbeta(n, shape1, shape2, ncp = 0, type = "d")
Arguments
x
vector of quantiles
n
number of random values to return
shape1, shape2 positive parameters of the Beta distribution
ncp
must be 0 at this point
log
logical; if TRUE, probabilities p are given as log(p)
type
specify the type; may be "double", "single" (or short form "d" or "s")
gdbinom
17
Details
Very similar to the R stats functionality.
Value
gdbeta gives the density and grbeta generates random deviates.
Author(s)
Nathan Morris
See Also
dbeta
Examples
myRndNums = grbeta(10,c(1,2), c(1,2,3,4,5))
gdbinom
The Binomial Distribution
Description
Density and random generation for the binomial distribution with parameters size and prob.
Usage
gdbinom(x, size, prob, log = FALSE, type = "d")
grbinom(n, size, prob)
Arguments
x
vector of quantiles.
n
number of observations
size
number of trials (zero or more)
prob
probability of success on each trial
log
logical; if TRUE, probabilities p are given as log(p).
type
specify the type; may be "double", "single" (or short form "d" or "s")
Details
Very similar to the R stats functionality.
Value
gdbinom gives the density and grbinom generates random deviates
18
gdgamma
Note
The algorythm for simulating from the poisson distribution was modified from the GSL library
which uses the modified from the GSL library which uses the Knuth method.
Author(s)
Nathan Morris
See Also
dbinom
Examples
myRndNums = grbinom(10,10,.6)
gdgamma
The Gamma Distribution
Description
Density, and random generation for the Gamma distribution with parameters shape and scale.
Usage
gdgamma(x, shape, rate = 1, scale = 1/rate, log = FALSE, type = "d")
grgamma(n, shape, rate = 1, scale = 1/rate, type = "d")
Arguments
x
vector of quantiles
n
number of random values to return
shape,scale
shape and scale parameters. Must be positive, scale strictly
rate
an alternative way to specify the scale
log
logical; if TRUE, probabilities/densities p are returned as log(p)
type
specify the type; may be "double", "single" (or short form "d" or "s")
Details
Works in much the same way as the R base functions.
Value
gdgamma gives the density and grgamma generates random deviates.
gdpois
19
Author(s)
Nathan Morris
References
Random gamma simulation was implemented using the algorithm described in: Marsaglia and
Tsang (2000) A Simple Method for Generating Gamma Variables. ACM Transactions on Mathematical Software. Volume 26 Issue 3, Pages 363-372.
See Also
dgamma
Examples
myRndNums = grgamma(10, c(1,2))
gdpois
The Poisson Distribution
Description
Density and random generation for the Poisson distribution with parameter lambda.
Usage
gdpois(x, lambda, log = FALSE, type = "d")
grpois(n, lambda)
Arguments
x
vector of (non-negative integer) quantiles
n
number of random values to return
lambda
vector of (non-negative) means
log
logical; if TRUE, probabilities p are given as log(p)
type
specify the type; may be "double", "single" (or short form "d" or "s")
Details
Very similar to the R stats functionality.
Value
gdpois gives the (log) density, and grpois generates random deviates.
20
gdup
Note
The algorithm for simulating from the poisson distribution was modified from the GSL library
which uses the Knuth method.
Author(s)
Nathan Morris
See Also
dpois
Examples
myRndNums = grpois(10,4)
gdup
Duplicate a GPU object
Description
This function duplicates a gmatrix or gvector object on the specified device.
Usage
gdup(x, dev=getDevice())
Arguments
x
object to duplicate
dev
device to duplicate the object on
Details
This function is very important because the gmatrix and gvector classes store only a pointer to an
object on the GPU device. Thus, a line such as y<-x will duplicate the pointer but not the actual
data on the GPU. One should use instead y<-gdup(x). The gdup function is also useful for copying
the data to a different GPU device.
Value
a gmatrix or gvector object.
Author(s)
Nathan Morris
ggc
21
See Also
To move data to a different device instead of copying it see device
Examples
#problematic code
x=gseq(1,10)
y=x
x[1]=1000
show(y)#changes to x also change y
#correct
x=gseq(1,10)
y=gdup(x)
x[1]=1000
show(y) #changes to x do not change y
#copy to a different device
#y=gdup(x, dev=2L)
ggc
GPU Garbage Collection
Description
Performs Garbage Collection and reports the available memory.
Usage
ggc(silent=FALSE)
Arguments
silent
If silent is TRUE then nothing will be printed out.
Details
Used for garbage collection, and also used to discover the amount of memory on the graphics card
which is still available.
Value
returns TRUE, but prints the amount of memory left.
Author(s)
Nathan Morris
22
gident
See Also
gc
Examples
ggc()
gident
Create an identity matrix on the GPU.
Description
Create an identity matrix on the GPU size
Usage
gident(n,val=1, type="d")
Arguments
n
Integer specifying the dimensions of the matrix.
val
The constant number to put on the diagonal. 1 leads to an identity matrix
type
The type of matrix to return
Value
Returns and n x n matrix with zeros on the of diagonals.
Author(s)
Nathan Morris
See Also
as.gmatrix and as.numeric
Examples
ga = gident(40)
da = diag(40)
sum(h(ga) == da)
gkroneckerProd
23
gkroneckerProd
Kronecker Product
Description
Calculates the kronecker product of two matrices.
Usage
gkroneckerProd(A, B)
A
Arguments
A
A gmatrix, gvector, matrix or vector
B
A gmatrix, gvector, matrix or vector
Value
A GPU object storing the Kronecker product.
Author(s)
Nathan Morris
gmatrix
Create and object of class gmatrix
Description
This function creates a gmatrix object from an input value.
Usage
gmatrix(data = NA, nrow = 1L, ncol = 1L, byrow = FALSE,
dimnames = NULL, type = NULL, dup = TRUE)
Arguments
data
The input data. Must be a vector or gvector.
nrow
the desired number of rows
ncol
the desired number of rows.
byrow
logical. If FALSE (the default) the matrix is filled by columns, otherwise the
matrix is filled by rows.
24
gmatrix-class
dimnames
A dimnames attribute for the matrix: NULL or a list of length 2 giving the row
and column names respectively. An empty list is treated as NULL.
type
The type (i.e. "double", "single", "integer" or "logical")
dup
dup=FALSE will return the original data without duplicating it on the GPU. The
dup=FALSE should only be used if the data in the input will not be used in it’s
original form again.
Details
This is implemented in a very similar fashion to the matrix function in R base.
Value
returns a gmatrix object.
Author(s)
Nathan Morrris
See Also
matrix
Examples
x=gmatrix(grnorm(100),10,10, type='d') #this makes an unneeded duplication
x=gmatrix(grnorm(100),10,10, dup=FALSE) #this avoids the duplication
#problematic code
x=grnorm(100)
y=as.gmatrix(x,10,10, dup=FALSE) #don't do this
y[1,1]=100 #this changes both y and x because both point to the same spot in GPU memory
x
gmatrix-class
Class "gmatrix"
Description
This object contains a pointer to a matrix on a NVIDIA GPU.
Objects from the Class
Objects should NOT be created by calls of the form new("gmatrix", ...). Instead use the
gmatrix, ’as.gmatrix’ or ’g’ functions.
gmatrix-class
25
Slots
ptr: Represents an external pointer to the data on the GPU
nrow: Object of class "integer" representing the number of rows for the matrix
ncol: Object of class "integer" representing the number of cols for the matrix
rownames: Should be a character vector with length equal nrow
colnames: Should be a character vector with length equal nrow
type: Must be 0L, 1L, 2L or 3L. These integers represent the types "double", "single", "integer"
or "logical" respectively.
device: Object of class "integer" representing the device
Methods
- signature(e1 = "gmatrix", e2 = "gmatrix"): subtraction operator
- signature(e1 = "gmatrix", e2 = "gvector"): subtraction operator
- signature(e1 = "gmatrix", e2 = "logical"): subtraction operator
- signature(e1 = "gmatrix", e2 = "matrix"): subtraction operator
- signature(e1 = "gmatrix", e2 = "missing"): subtraction operator
- signature(e1 = "gmatrix", e2 = "numeric"): subtraction operator
- signature(e1 = "gvector", e2 = "gmatrix"): subtraction operator
- signature(e1 = "logical", e2 = "gmatrix"): subtraction operator
- signature(e1 = "matrix", e2 = "gmatrix"): subtraction operator
- signature(e1 = "numeric", e2 = "gmatrix"): subtraction operator
! signature(x = "gmatrix"): not operator
!= signature(e1 = "gmatrix", e2 = "gmatrix"): not equal operator
!= signature(e1 = "gmatrix", e2 = "gvector"): not equal operator
!= signature(e1 = "gmatrix", e2 = "logical"): not equal operator
!= signature(e1 = "gmatrix", e2 = "matrix"): not equal operator
!= signature(e1 = "gmatrix", e2 = "numeric"): not equal operator
!= signature(e1 = "gvector", e2 = "gmatrix"): not equal operator
!= signature(e1 = "logical", e2 = "gmatrix"): not equal operator
!= signature(e1 = "matrix", e2 = "gmatrix"): not equal operator
!= signature(e1 = "numeric", e2 = "gmatrix"): not equal operator
%% signature(e1 = "gmatrix", e2 = "gmatrix"): mod operator
%% signature(e1 = "gmatrix", e2 = "gvector"): mod operator
%% signature(e1 = "gmatrix", e2 = "logical"): mod operator
%% signature(e1 = "gmatrix", e2 = "matrix"): mod operator
%% signature(e1 = "gmatrix", e2 = "numeric"): mod operator
%% signature(e1 = "gvector", e2 = "gmatrix"): mod operator
26
gmatrix-class
%% signature(e1 = "logical", e2 = "gmatrix"): mod operator
%% signature(e1 = "matrix", e2 = "gmatrix"): mod operator
%% signature(e1 = "numeric", e2 = "gmatrix"): mod operator
%*% signature(x = "gmatrix", y = "gmatrix"): matrix multiplication operator
%*% signature(x = "gmatrix", y = "gvector"): matrix multiplication operator
%*% signature(x = "gmatrix", y = "logical"): matrix multiplication operator
%*% signature(x = "gmatrix", y = "matrix"): matrix multiplication operator
%*% signature(x = "gmatrix", y = "numeric"): matrix multiplication operator
%*% signature(x = "gvector", y = "gmatrix"): matrix multiplication operator
%*% signature(x = "logical", y = "gmatrix"): matrix multiplication operator
%*% signature(x = "matrix", y = "gmatrix"): matrix multiplication operator
%*% signature(x = "numeric", y = "gmatrix"): matrix multiplication operator
%x% signature(X = "gmatrix", Y = "gmatrix"): kronecker product
%x% signature(X = "gmatrix", Y = "gvector"): kronecker product
%x% signature(X = "gmatrix", Y = "numeric"): kronecker product
%x% signature(X = "gvector", Y = "gmatrix"): kronecker product
%x% signature(X = "numeric", Y = "gmatrix"): kronecker product
& signature(e1 = "gmatrix", e2 = "gmatrix"): and operator
& signature(e1 = "gmatrix", e2 = "gvector"): and operator
& signature(e1 = "gmatrix", e2 = "logical"): and operator
& signature(e1 = "gmatrix", e2 = "matrix"): and operator
& signature(e1 = "gmatrix", e2 = "numeric"): and operator
& signature(e1 = "gvector", e2 = "gmatrix"): and operator
& signature(e1 = "logical", e2 = "gmatrix"): and operator
& signature(e1 = "matrix", e2 = "gmatrix"): and operator.
& signature(e1 = "numeric", e2 = "gmatrix"): and operator.
* signature(e1 = "gmatrix", e2 = "gmatrix"): elementwise multiplication
* signature(e1 = "gmatrix", e2 = "gvector"): elementwise multiplication
* signature(e1 = "gmatrix", e2 = "logical"): elementwise multiplication
* signature(e1 = "gmatrix", e2 = "matrix"): elementwise multiplication
* signature(e1 = "gmatrix", e2 = "numeric"): elementwise multiplication
* signature(e1 = "gvector", e2 = "gmatrix"): elementwise multiplication
* signature(e1 = "logical", e2 = "gmatrix"): elementwise multiplication
* signature(e1 = "matrix", e2 = "gmatrix"): elementwise multiplication
* signature(e1 = "numeric", e2 = "gmatrix"): elementwise multiplication
/ signature(e1 = "gmatrix", e2 = "gmatrix"): division operator
/ signature(e1 = "gmatrix", e2 = "gvector"): division operator
gmatrix-class
27
/ signature(e1 = "gmatrix", e2 = "logical"): division operator
/ signature(e1 = "gmatrix", e2 = "matrix"): division operator
/ signature(e1 = "gmatrix", e2 = "numeric"): division operator
/ signature(e1 = "gvector", e2 = "gmatrix"): division operator
/ signature(e1 = "logical", e2 = "gmatrix"): division operator
/ signature(e1 = "matrix", e2 = "gmatrix"): division operator
/ signature(e1 = "numeric", e2 = "gmatrix"): division operator
[ signature(x = "gmatrix", i = "gvector", j = "gvector"): indexing
[ signature(x = "gmatrix", i = "gvector", j = "missing"): indexing
[ signature(x = "gmatrix", i = "gvector", j = "numeric"): indexing
[ signature(x = "gmatrix", i = "numeric", j = "gvector"): indexing
[ signature(x = "gmatrix", i = "numeric", j = "missing"): indexing
[ signature(x = "gmatrix", i = "numeric", j = "numeric"): indexing
[ signature(x = "gmatrix", i = "missing", j = "missing", k = "missing"): indexing
[<- signature(x = "gmatrix", i = "gvector", j = "gvector"): indexing
[<- signature(x = "gmatrix", i = "gvector", j = "missing"): indexing
[<- signature(x = "gmatrix", i = "gvector", j = "numeric"): indexing .
[<- signature(x = "gmatrix", i = "numeric", j = "gvector"): indexing
[<- signature(x = "gmatrix", i = "numeric", j = "missing"): indexing
[<- signature(x = "gmatrix", i = "numeric", j = "numeric"): indexing
[<- signature(x = "gmatrix", i = "missing", j = "missing", k = "missing"): indexing
^ signature(e1 = "gmatrix", e2 = "gmatrix"): power operator
^ signature(e1 = "gmatrix", e2 = "gvector"): power operator
^ signature(e1 = "gmatrix", e2 = "logical"): power operator
^ signature(e1 = "gmatrix", e2 = "matrix"): power operator
^ signature(e1 = "gmatrix", e2 = "numeric"): power operator
^ signature(e1 = "gvector", e2 = "gmatrix"): power operator
^ signature(e1 = "logical", e2 = "gmatrix"): power operator
^ signature(e1 = "matrix", e2 = "gmatrix"): power operator
^ signature(e1 = "numeric", e2 = "gmatrix"): power operator
| signature(e1 = "gmatrix", e2 = "gmatrix"): or operator
| signature(e1 = "gmatrix", e2 = "gvector"): or operator
| signature(e1 = "gmatrix", e2 = "logical"): or operator
| signature(e1 = "gmatrix", e2 = "matrix"): or operator
| signature(e1 = "gmatrix", e2 = "numeric"): or operator
| signature(e1 = "gvector", e2 = "gmatrix"): or operator
| signature(e1 = "logical", e2 = "gmatrix"): or operator
28
gmatrix-class
| signature(e1 = "matrix", e2 = "gmatrix"): or operator
| signature(e1 = "numeric", e2 = "gmatrix"): or operator
+ signature(e1 = "gmatrix", e2 = "gmatrix"): plus operator
+ signature(e1 = "gmatrix", e2 = "gvector"): plus operator
+ signature(e1 = "gmatrix", e2 = "logical"): plus operator
+ signature(e1 = "gmatrix", e2 = "matrix"): plus operator
+ signature(e1 = "gmatrix", e2 = "missing"): plus operator
+ signature(e1 = "gmatrix", e2 = "numeric"): plus operator
+ signature(e1 = "gvector", e2 = "gmatrix"): plus operator
+ signature(e1 = "logical", e2 = "gmatrix"): plus operator
+ signature(e1 = "matrix", e2 = "gmatrix"): plus operator
+ signature(e1 = "numeric", e2 = "gmatrix"): plus operator
< signature(e1 = "gmatrix", e2 = "gmatrix"): less than operator
< signature(e1 = "gmatrix", e2 = "gvector"): less than operator
< signature(e1 = "gmatrix", e2 = "logical"): less than operator
< signature(e1 = "gmatrix", e2 = "matrix"): less than operator
< signature(e1 = "gmatrix", e2 = "numeric"): less than operator
< signature(e1 = "gvector", e2 = "gmatrix"): less than operator
< signature(e1 = "logical", e2 = "gmatrix"): less than operator
< signature(e1 = "matrix", e2 = "gmatrix"): less than operator
< signature(e1 = "numeric", e2 = "gmatrix"): less than operator
<= signature(e1 = "gmatrix", e2 = "gmatrix"): less than or equal operator
<= signature(e1 = "gmatrix", e2 = "gvector"): less than or equal operator
<= signature(e1 = "gmatrix", e2 = "logical"): less than or equal operator
<= signature(e1 = "gmatrix", e2 = "matrix"): less than or equal operator
<= signature(e1 = "gmatrix", e2 = "numeric"): less than or equal operator
<= signature(e1 = "gvector", e2 = "gmatrix"): less than or equal operator
<= signature(e1 = "logical", e2 = "gmatrix"): less than or equal operator
<= signature(e1 = "matrix", e2 = "gmatrix"): less than or equal operator
<= signature(e1 = "numeric", e2 = "gmatrix"): less than or equal operator
== signature(e1 = "gmatrix", e2 = "gmatrix"): equal operator
== signature(e1 = "gmatrix", e2 = "gvector"): equal operator
== signature(e1 = "gmatrix", e2 = "logical"): equal operator
== signature(e1 = "gmatrix", e2 = "matrix"): equal operator
== signature(e1 = "gmatrix", e2 = "numeric"): equal operator
== signature(e1 = "gvector", e2 = "gmatrix"): equal operator
== signature(e1 = "logical", e2 = "gmatrix"): equal operator
gmatrix-class
== signature(e1 = "matrix", e2 = "gmatrix"): equal operator
== signature(e1 = "numeric", e2 = "gmatrix"): equal operator
> signature(e1 = "gmatrix", e2 = "gmatrix"): greater than operator
> signature(e1 = "gmatrix", e2 = "gvector"): greater than operator
> signature(e1 = "gmatrix", e2 = "logical"): greater than operator
> signature(e1 = "gmatrix", e2 = "matrix"): greater than operator
> signature(e1 = "gmatrix", e2 = "numeric"): greater than operator
> signature(e1 = "gvector", e2 = "gmatrix"): greater than operator
> signature(e1 = "logical", e2 = "gmatrix"): greater than operator
> signature(e1 = "matrix", e2 = "gmatrix"): greater than operator
> signature(e1 = "numeric", e2 = "gmatrix"): greater than operator
>= signature(e1 = "gmatrix", e2 = "gmatrix"): greater than or equal operator
>= signature(e1 = "gmatrix", e2 = "gvector"): greater than or equal operator
>= signature(e1 = "gmatrix", e2 = "logical"): greater than or equal operator
>= signature(e1 = "gmatrix", e2 = "matrix"): greater than or equal operator
>= signature(e1 = "gmatrix", e2 = "numeric"): greater than or equal operator
>= signature(e1 = "gvector", e2 = "gmatrix"): greater than or equal operator
>= signature(e1 = "logical", e2 = "gmatrix"): greater than or equal operator
>= signature(e1 = "matrix", e2 = "gmatrix"): greater than or equal operator
>= signature(e1 = "numeric", e2 = "gmatrix"): greater than or equal operator
as.gmatrix signature(data = "gmatrix"): coersion function
as.gvector signature(x = "gmatrix"): coersion function
as.integer signature(x = "gmatrix"): coersion function
as.logical signature(x = "gmatrix"): coersion function
as.matrix signature(x = "gmatrix"): coersion function
as.numeric signature(x = "gmatrix"): coersion function
as.vector signature(x = "gmatrix"): coersion function
abs signature(x = "gmatrix"): absolute value
acos signature(x = "gmatrix"): inverse cosine
acosh signature(x = "gmatrix"): inverse hyperbolic cosine
asin signature(x = "gmatrix"): inverse sin
asinh signature(x = "gmatrix"): inverse hyperbolic sin
atan signature(x = "gmatrix"): inverse tangent
atanh signature(x = "gmatrix"): inverse hyperbolic tangent
ceiling signature(x = "gmatrix"): ceiling function
colMeans signature(x = "gmatrix"): mean of each column
colnames signature(x = "gmatrix"): column names
29
30
gmatrix-class
colnames<- signature(x = "gmatrix"): set column names
colSums signature(x = "gmatrix"): sum of each column
cos signature(x = "gmatrix"): cos function
cosh signature(x = "gmatrix"): hyperbolic cos
crossprod signature(x = "gmatrix", y = "gmatrix"): calculates: t(x) %*% y
crossprod signature(x = "gmatrix", y = "gvector"): calculates: t(x) %*% y
crossprod signature(x = "gmatrix", y = "logical"): calculates: t(x) %*% y
crossprod signature(x = "gmatrix", y = "matrix"): calculates: t(x) %*% y
crossprod signature(x = "gmatrix", y = "missing"): calculates: t(x) %*% y
crossprod signature(x = "gmatrix", y = "numeric"): calculates: t(x) %*% y
crossprod signature(x = "gvector", y = "gmatrix"): calculates: t(x) %*% y
crossprod signature(x = "logical", y = "gmatrix"): calculates: t(x) %*% y
crossprod signature(x = "matrix", y = "gmatrix"): calculates: t(x) %*% y
crossprod signature(x = "numeric", y = "gmatrix"): calculates: t(x) %*% y
tcrossprod signature(x = "gmatrix", y = "gmatrix"): calculates: x %*% t(y)
tcrossprod signature(x = "gmatrix", y = "gvector"): calculates: x %*% t(y)
tcrossprod signature(x = "gmatrix", y = "logical"): calculates: x %*% t(y)
tcrossprod signature(x = "gmatrix", y = "matrix"): calculates: x %*% t(y)
tcrossprod signature(x = "gmatrix", y = "missing"): calculates: x %*% t(y)
tcrossprod signature(x = "gmatrix", y = "numeric"): calculates: x %*% t(y)
tcrossprod signature(x = "gvector", y = "gmatrix"): calculates: x %*% t(y)
tcrossprod signature(x = "logical", y = "gmatrix"): calculates: x %*% t(y)
tcrossprod signature(x = "matrix", y = "gmatrix"): calculates: x %*% t(y)
tcrossprod signature(x = "numeric", y = "gmatrix"): calculates: x %*% t(y)
device signature(x = "gmatrix"): get device property
device<- signature(x = "gmatrix"): set device property
diag signature(x = "gmatrix"): diagonal
diag<- signature(x = "gmatrix"): set the diagonal of a matrix
dim signature(x = "gmatrix"): dimension
dim<- signature(x = "gmatrix"): set dimension
dimnames signature(x = "gmatrix"): get dimnames
dimnames<- signature(x = "gmatrix"): set dimnames
exp signature(x = "gmatrix"): exponentiate function
expm1 signature(x = "gmatrix"): computes exp(x) - 1
floor signature(x = "gmatrix"): floor function
gamma signature(x = "gmatrix"): gamma function
ifelse signature(test = "gmatrix"): conditional selection
gmatrix-class
is.finite signature(x = "gmatrix"): finite status
is.infinite signature(x = "gmatrix"): infinite status
is.na signature(x = "gmatrix"): missing status
is.nan signature(x = "gmatrix"): not a number status
length signature(x = "gmatrix"): total number of elements in object
lgamma signature(x = "gmatrix"): log gamma function
log signature(x = "gmatrix"): logarithm function
log10 signature(x = "gmatrix"): base 10 log
log1p signature(x = "gmatrix"): log(1+x)
log2 signature(x = "gmatrix"): base 2 log
max signature(x = "gmatrix"): maximum of all elements
mean signature(x = "gmatrix"): mean of all elements
min signature(x = "gmatrix"): min of all elements
ncol signature(x = "gmatrix"): number of columns
nrow signature(x = "gmatrix"): number of rows
round signature(x = "gmatrix"): round function (only to nearest whole number)
rowMeans signature(x = "gmatrix"): mean of each row
rownames signature(x = "gmatrix"): names of rows
rownames<- signature(x = "gmatrix"): set row names
rowSums signature(x = "gmatrix"): sum of each row
show signature(object = "gmatrix"): show the data
sign signature(x = "gmatrix"): return the sign
sin signature(x = "gmatrix"): sin function
sinh signature(x = "gmatrix"): hyperbolic sin
sqrt signature(x = "gmatrix"): square root
sum signature(x = "gmatrix"): sum
t signature(x = "gmatrix"): transpose
tan signature(x = "gmatrix"): tangent
tanh signature(x = "gmatrix"): hyperbolic tangent
type signature(x = "gmatrix"): get type (e.g "double")
type<- signature(x = "gmatrix"): set type
solve signature(a = "gmatrix", b="ANY"): set type
Author(s)
Nathan Morris
See Also
gvector
Examples
showClass("gmatrix")
31
32
gmatTimesDiagVec
gmatTimesDiagVec
Multiply a matrix times the ’diag’ of a vector quickly.
Description
This function calculates A %*% diag(v). It is much faster than the direct calculation as it avoids
the huge matrix multiplication problem.
Usage
gmatTimesDiagVec(A, v)
Arguments
A
An object of class gmatrix or ’matrix’.
v
An object of class ’gvecotr’ or a ’vector’.
Value
Returns a gmatrix
Note
Note that to calculate the diag(v) %*% A one may use the efficient formula v*A.
Author(s)
Nathan Morris
See Also
diag
Examples
v=grnorm(10)
A=gmatrix(grnorm(100),10,10,dup=FALSE)
gmatTimesDiagVec(A, v)
gmm
33
gmm
Multiply two matrices with the output matrix allready allocated.
Description
In effect this function sets C <- A %*% B. This makes it possible to avoid repeated allocation and
deallocation steps which are very computationaly costly.
Usage
gmm(A, B, C, trA=FALSE, trB=FALSE,
accum=FALSE)
Arguments
A, B
Matrices to multiply together.
C
Matrices where output will be saved.
trA, trB
Should A or B be transposed.
accum
if accum is set to TRUE, the multiplied matrix will be added to C (i.e. C<-C+A
%*% B).
Details
This function takes advantage of the fact that gmatrix objects are stored as pointers making it posible
modify the input to a function. Thus the area of memory on the GPU pointed to by the C object is
modified to contain A %*% B.
Value
Returns C invisibly.
Author(s)
Nathan Morris
Examples
A=gmatrix(rnorm(10), 2, 5)
B=gmatrix(rnorm(10), 5, 2)
C=gmatrix(0,2,2)
gmm(A,B,C)
gmm(B,A,C,TRUE,TRUE)
34
gorder
gnamestrip
Strip a GPU object of it names, or row/colnames.
Description
Returns a GPU object without any names or row/colnames. This may speed up certian operations.
Usage
gnamestrip(x, dup = TRUE)
Arguments
x
input object to be stripped of names
dup
if FALSE then don’t duplicate x on the GPU. Return object will point to the
same GPU memory as the original object.
Value
Returns the original object with no names.
Author(s)
Nathan Morris
See Also
names, colnames and dimnames
Examples
x=gseq(1,2)
names(x)=c("bill","joe")
gnamestrip(x)
gorder
Ordering Permutation
Description
gorder returns a permutation which rearranges its first argument into ascending or descending
order.
Usage
gorder(x, decreasing = FALSE, stable = TRUE, sortx=FALSE)
gouter
35
Arguments
x
decreasing
stable
sortx
object to be ordered
logical to specify sort order
make sure that ties are in the original order
if sortx=TRUE, then x will be modified by sorting it. This avoids an extra duplication of the x. By leaving sortx=FALSE, an extra duplication of x is performed
to avoid changing the input value.
Details
Unlike the base R function, only one input column may be given. The thrust library is used for this
operation.
Value
a gvector of type "integer" which will permute the input vector to the proper sort order.
Author(s)
Nathan Morris
See Also
order
Examples
x=grnorm(10)
i=gorder(x)
x[i] #sort x
gouter
GPU generalized outer product.
Description
This function calculates the outer product of two gvectors.
Usage
gouter(x, y, FUN = "*", normalOrder = TRUE)
Arguments
x
y
FUN
normalOrder
a ’vector’ or gvector object
a ’vector’ or gvector object
one of the following characters ’*’, ’+’, ’-’, ’/’ or ’^’
logical input determining which order the operation should be performed in.
36
gqr-class
Details
This function is similar to the outer function in R base. It performs the specified operation on
all posible combinations of elements from the first vector with the second. This function does not
behave the same as R base when operating on matrices. Also, the operator %o% may be used as in
the R base package.
Value
returns a gmatrix with the specified operation performed
Author(s)
Nathan Morris
See Also
outer, %o%
Examples
gouter(grnorm(10), grnorm(10), FUN="-")
gqr-class
Class "gqr"
Description
Contains the results of a QR decomposition from using the qr() method on a gmatrix object. Note
that the gmatrix solve function uses QR decompostion. Also, qr.coef can act on the gqr object.
The qr method does not use pivoting or check the matrix rank. The QR and related methods are
only available for cuda v7.0 or greater.
Objects from the Class
Objects can be created by calls of the qr() method.
Slots
qr: Information about the Q and R matrices stored as and bject of class "gmatrix".
qraux: Information about the Q matrix stored as an object of class "gvector".
Methods
qr.coef Simular to the qr.coef function.
solve Simular to the solve.qr function.
gRowLogSums
37
Author(s)
Nathan Morris
See Also
qr, qr.coef, solve.qr, solve
Examples
M=gmatrix(grnorm(25), 5,5,dup=FALSE)
y=grnorm(5)
solve(M)
solve(M,y)
myqr =qr(M)
solve(myqr,y)
gRowLogSums
Sum the up the rows in log space.
Description
Sum up the rows in log space.
Usage
gRowLogSums(x, startCol=1, endCol=ncol(x))
Arguments
x
A matrix
startCol
May be used to perform the log sum on only selected columns
endCol
May be used to perform the log sum on only selected columns
Details
Calculates for each row vector v the value log(sum(exp(v))) in a way that avoids overflow. This
function may be useful for mixture models. This function is only efficient for a large number of
rows and a smaller number of columns.
Value
Returns a vector with a value for each row.
Author(s)
Nathan Morris
38
grunif
See Also
%lgspadd%-methods
grunif
The Uniform Distribution
Description
These functions provide information about the uniform distribution on the interval from min to max.
dunif gives the density and runif generates random deviates.
Usage
gdunif(x, min = 0, max = 1, log = FALSE, type = "d")
grunif(n, min = 0, max = 1, type = "d")
Arguments
x
vector of quantiles.
n
number of observations
min, max
lower and upper limits of the distribution
log
logical; if TRUE, probabilities/densities p are returned as log(p)
type
specify the type; may be "double", "single" (or short form "d" or "s")
Details
If min or max are not specified they assume the default values of 0 and 1 respectively. Works very
similarly to the R stats functions.
Note
Random number generation implemented with the cuRAND library.
Author(s)
Nathan Morris
See Also
runif
Examples
myRndNums = grunif(10)
gseq
gseq
39
Sequence
Description
Create a sequence on the GPU.
Usage
gseq(from = 1, to = 1, by = ((to - from)/(length.out - 1)),
length.out = NULL, along.with = NULL, type = NULL)
Arguments
from, to
the starting and (maximal) end value of the sequence.
by
number: increment of the sequence.
length.out
desired length of the sequence. A non-negative number, which for seq and
seq.int will be rounded up if fractional.
along.with
take the length from the length of this argument
type
output type (i.e. "double", "single", "integer" or "logical")
Value
returns a gvector with the specified sequence. In addition the operator %to% mimics the R base
oporator :.
Author(s)
Nathan Morris
See Also
seq
Examples
gseq(1,100)
1%to%10
40
gsumby
gset.seed
Set the seed values, and number of states for the GPU.
Description
This function enables the user to set a seed value for reproducible random number generation. It
also allows the user to set the number of states to tune the efficiency of random number generator
for the GPU.
Usage
gset.seed(seed=unclass(Sys.time()), total_states=as.integer(32*14*16), silent=TRUE)
Arguments
seed
Must be a positive integer.
total_states
Random numbers are generated from separate streams in parallel with each
stream having a current state. This variable must be a positive integer. It is
recommended that the integer be a multiple of 32. If the number of states are
two small or two large the GPU efficiency may be poor.
silent
Don’t print any messages besides errors.
Author(s)
Nathan Morris
gsumby
Sumby
Description
Find sub-sums of a gvector
Usage
gsumby(v, startPos, stopPos)
Arguments
v
a gvector
startPos
a vector of start positions
stopPos
a vector of stop positions
gsvd-class
41
Details
startPos and stopPos must be of the same length.
Value
returns a gvector object of the same length as startPos and stopPos. Each element is the sum of
elements in v.
Author(s)
Nathan Morris
Examples
gsumby(g(1:10), c(1,6), c(5,10)) # g(c(15,40))
gsvd-class
Class "gsvd"
Description
Contains the results of an SVD decomposition as returned by the svd method. The SVD method is
only available for cuda v7.0 or greater.
Objects from the Class
Objects should be created by a call to the svd() method on a gmatrix object. The slots of this
object are essentually the same as those created by the base svd function. However the VT is the
transpose of the v slot in R base. The gmatrix svd function does not allow the user to select the
number of singular values.
Slots
U: Object of class "gmatrix" whose columns contain the left singular vectors.
S: Object of class "gvector" containing the singular values.
VT: Object of class "gmatrix" whose columns contain the TRANSPOSE of the left singular vectors.
Author(s)
Nathan Morris
See Also
svd
42
gvector
Examples
M=gmatrix(grnorm(25), 5,5,dup=FALSE)
mysvd=svd(M)
mysvd@U
gtest
Testing
Description
This function performs a large number of tests to determine if the package is working properly. Any
problems are printed to the screen. It is recomended to be run at least once after installation.
Usage
gtest()
Value
TRUE
Author(s)
Nathan Morris
gvector
Create a gvector object
Description
Creates a gvector object of given length and initializes all elements to 0.
Usage
gvector(length, type = "d")
Arguments
length
length of the object
type
The type (i.e. "double", "single", "integer" or "logical")
Value
Returns a gvector object.
gvector-class
43
Author(s)
Nathan Morris
See Also
vector
gvector-class
Class "gvector"
Description
This object contains a pointer to a vector on a NVIDIA GPU.
Objects from the Class
Objects should NOT be created by calls of the form new("gmatrix", ...). Instead use the
gvector, as.gvector or g functions.
Slots
ptr: Represents an external pointer to the data on the GPU
length: Object of class "integer" representing the number of elements in the vector
names: Should be a character vector with length equal nrow
type: Must be 0L, 1L, 2L or 3L. These integers represent the types "double", "single", "integer"
or "logical" respectively.
device: Object of class "integer" representing the device
Methods
- signature(e1 = "gmatrix", e2 = "gvector"): subtraction operator
- signature(e1 = "gvector", e2 = "gmatrix"): subtraction operator
- signature(e1 = "gvector", e2 = "gvector"): subtraction operator
- signature(e1 = "gvector", e2 = "logical"): subtraction operator
- signature(e1 = "gvector", e2 = "matrix"): subtraction operator
- signature(e1 = "gvector", e2 = "missing"): subtraction operator
- signature(e1 = "gvector", e2 = "numeric"): subtraction operator
- signature(e1 = "logical", e2 = "gvector"): subtraction operator
- signature(e1 = "matrix", e2 = "gvector"): subtraction operator.
- signature(e1 = "numeric", e2 = "gvector"):subtraction operator
! signature(x = "gvector"): not operator
!= signature(e1 = "gmatrix", e2 = "gvector"): not equal operator
44
gvector-class
!= signature(e1 = "gvector", e2 = "gmatrix"): not equal operator
!= signature(e1 = "gvector", e2 = "gvector"): not equal operator
!= signature(e1 = "gvector", e2 = "logical"): not equal operator
!= signature(e1 = "gvector", e2 = "matrix"): not equal operator
!= signature(e1 = "gvector", e2 = "numeric"): not equal operator
!= signature(e1 = "logical", e2 = "gvector"): not equal operator
!= signature(e1 = "matrix", e2 = "gvector"): not equal operator
!= signature(e1 = "numeric", e2 = "gvector"): not equal operator
%% signature(e1 = "gmatrix", e2 = "gvector"): mod operator
%% signature(e1 = "gvector", e2 = "gmatrix"): mod operator
%% signature(e1 = "gvector", e2 = "gvector"): mod operator
%% signature(e1 = "gvector", e2 = "logical"): mod operator
%% signature(e1 = "gvector", e2 = "matrix"): mod operator
%% signature(e1 = "gvector", e2 = "numeric"): mod operator
%% signature(e1 = "logical", e2 = "gvector"): mod operator
%% signature(e1 = "matrix", e2 = "gvector"): mod operator
%% signature(e1 = "numeric", e2 = "gvector"): mod operator
%*% signature(x = "gmatrix", y = "gvector"): matrix multiplication operator
%*% signature(x = "gvector", y = "gmatrix"): matrix multiplication operator
%*% signature(x = "gvector", y = "gvector"): matrix multiplication operator
%*% signature(x = "gvector", y = "logical"): matrix multiplication operator
%*% signature(x = "gvector", y = "matrix"): matrix multiplication operator
%*% signature(x = "gvector", y = "numeric"): matrix multiplication operator
%*% signature(x = "logical", y = "gvector"): matrix multiplication operator
%*% signature(x = "matrix", y = "gvector"): matrix multiplication operator
%*% signature(x = "numeric", y = "gvector"): matrix multiplication operator
%o% signature(X = "gvector", Y = "gvector"): outer product
%o% signature(X = "gvector", Y = "logical"): outer product
%o% signature(X = "gvector", Y = "numeric"): outer product
%o% signature(X = "logical", Y = "gvector"): outer product
%o% signature(X = "numeric", Y = "gvector"): outer product
%x% signature(X = "gmatrix", Y = "gvector"): kronecker product
%x% signature(X = "gvector", Y = "gmatrix"): kronecker product.
%x% signature(X = "gvector", Y = "gvector"): kronecker product
%x% signature(X = "gvector", Y = "numeric"): kronecker product
%x% signature(X = "numeric", Y = "gvector"): kronecker product
& signature(e1 = "gmatrix", e2 = "gvector"): and operator
gvector-class
& signature(e1 = "gvector", e2 = "gmatrix"): and operator
& signature(e1 = "gvector", e2 = "gvector"): and operator
& signature(e1 = "gvector", e2 = "logical"): and operator
& signature(e1 = "gvector", e2 = "matrix"): and operator
& signature(e1 = "gvector", e2 = "numeric"): and operator
& signature(e1 = "logical", e2 = "gvector"): and operator
& signature(e1 = "matrix", e2 = "gvector"): and operator
& signature(e1 = "numeric", e2 = "gvector"): and operator
* signature(e1 = "gmatrix", e2 = "gvector"): elementwise multiplication
* signature(e1 = "gvector", e2 = "gmatrix"): elementwise multiplication
* signature(e1 = "gvector", e2 = "gvector"): elementwise multiplication
* signature(e1 = "gvector", e2 = "logical"): elementwise multiplication
* signature(e1 = "gvector", e2 = "matrix"): elementwise multiplication
* signature(e1 = "gvector", e2 = "numeric"): elementwise multiplication
* signature(e1 = "logical", e2 = "gvector"): elementwise multiplication
* signature(e1 = "matrix", e2 = "gvector"): elementwise multiplication
* signature(e1 = "numeric", e2 = "gvector"): elementwise multiplication
/ signature(e1 = "gmatrix", e2 = "gvector"): division operator
/ signature(e1 = "gvector", e2 = "gmatrix"): division operator
/ signature(e1 = "gvector", e2 = "gvector"): division operator
/ signature(e1 = "gvector", e2 = "logical"): division operator
/ signature(e1 = "gvector", e2 = "matrix"): division operator
/ signature(e1 = "gvector", e2 = "numeric"): division operator
/ signature(e1 = "logical", e2 = "gvector"): division operator
/ signature(e1 = "matrix", e2 = "gvector"): division operator
/ signature(e1 = "numeric", e2 = "gvector"): division operator
[ signature(x = "gmatrix", i = "gvector", j = "gvector"): indexing
[ signature(x = "gmatrix", i = "gvector", j = "missing"): indexing
[ signature(x = "gmatrix", i = "gvector", j = "numeric"): indexing
[ signature(x = "gmatrix", i = "numeric", j = "gvector"): indexing
[ signature(x = "gvector", i = "ANY", j = "ANY"): indexing
[<- signature(x = "gmatrix", i = "gvector", j = "gvector"): indexing
[<- signature(x = "gmatrix", i = "gvector", j = "missing"): indexing
[<- signature(x = "gmatrix", i = "gvector", j = "numeric"): indexing
[<- signature(x = "gmatrix", i = "numeric", j = "gvector"): indexing
[<- signature(x = "gvector", i = "ANY", j = "ANY"): indexing
^ signature(e1 = "gmatrix", e2 = "gvector"): power operator
45
46
gvector-class
^ signature(e1 = "gvector", e2 = "gmatrix"): power operator
^ signature(e1 = "gvector", e2 = "gvector"): power operator
^ signature(e1 = "gvector", e2 = "logical"): power operator
^ signature(e1 = "gvector", e2 = "matrix"): power operator
^ signature(e1 = "gvector", e2 = "numeric"): power operator
^ signature(e1 = "logical", e2 = "gvector"): power operator
^ signature(e1 = "matrix", e2 = "gvector"): power operator
^ signature(e1 = "numeric", e2 = "gvector"): power operator
| signature(e1 = "gmatrix", e2 = "gvector"): or operator
| signature(e1 = "gvector", e2 = "gmatrix"): or operator
| signature(e1 = "gvector", e2 = "gvector"): or operator
| signature(e1 = "gvector", e2 = "logical"): or operator
| signature(e1 = "gvector", e2 = "matrix"): or operator
| signature(e1 = "gvector", e2 = "numeric"): or operator
| signature(e1 = "logical", e2 = "gvector"): or operator
| signature(e1 = "matrix", e2 = "gvector"): or operator
| signature(e1 = "numeric", e2 = "gvector"): or operator
+ signature(e1 = "gmatrix", e2 = "gvector"): plus operator
+ signature(e1 = "gvector", e2 = "gmatrix"): plus operator
+ signature(e1 = "gvector", e2 = "gvector"): plus operator
+ signature(e1 = "gvector", e2 = "logical"): plus operator
+ signature(e1 = "gvector", e2 = "matrix"): plus operator
+ signature(e1 = "gvector", e2 = "missing"): plus operator
+ signature(e1 = "gvector", e2 = "numeric"): plus operator
+ signature(e1 = "logical", e2 = "gvector"): plus operator
+ signature(e1 = "matrix", e2 = "gvector"): plus operator
+ signature(e1 = "numeric", e2 = "gvector"): plus operator
< signature(e1 = "gmatrix", e2 = "gvector"): less than operator
< signature(e1 = "gvector", e2 = "gmatrix"): less than operator
< signature(e1 = "gvector", e2 = "gvector"): less than operator
< signature(e1 = "gvector", e2 = "logical"): less than operator
< signature(e1 = "gvector", e2 = "matrix"): less than operator
< signature(e1 = "gvector", e2 = "numeric"): less than operator
< signature(e1 = "logical", e2 = "gvector"): less than operator
< signature(e1 = "matrix", e2 = "gvector"): less than operator
< signature(e1 = "numeric", e2 = "gvector"): less than operator
<= signature(e1 = "gmatrix", e2 = "gvector"): less than or equal operator
gvector-class
<= signature(e1 = "gvector", e2 = "gmatrix"): less than or equal operator
<= signature(e1 = "gvector", e2 = "gvector"): less than or equal operator
<= signature(e1 = "gvector", e2 = "logical"): less than or equal operator
<= signature(e1 = "gvector", e2 = "matrix"): less than or equal operator
<= signature(e1 = "gvector", e2 = "numeric"): less than or equal operator
<= signature(e1 = "logical", e2 = "gvector"): less than or equal operator
<= signature(e1 = "matrix", e2 = "gvector"): less than or equal operator
<= signature(e1 = "numeric", e2 = "gvector"): less than or equal operator
== signature(e1 = "gmatrix", e2 = "gvector"): equal operator
== signature(e1 = "gvector", e2 = "gmatrix"): equal operator
== signature(e1 = "gvector", e2 = "gvector"): equal operator
== signature(e1 = "gvector", e2 = "logical"): equal operator
== signature(e1 = "gvector", e2 = "matrix"): equal operator
== signature(e1 = "gvector", e2 = "numeric"): equal operator
== signature(e1 = "logical", e2 = "gvector"): equal operator
== signature(e1 = "matrix", e2 = "gvector"): equal operator
== signature(e1 = "numeric", e2 = "gvector"): equal operator
> signature(e1 = "gmatrix", e2 = "gvector"): greater than operator
> signature(e1 = "gvector", e2 = "gmatrix"): greater than operator
> signature(e1 = "gvector", e2 = "gvector"): greater than operator
> signature(e1 = "gvector", e2 = "logical"): greater than operator
> signature(e1 = "gvector", e2 = "matrix"): greater than operator
> signature(e1 = "gvector", e2 = "numeric"): greater than operator
> signature(e1 = "logical", e2 = "gvector"): greater than operator
> signature(e1 = "matrix", e2 = "gvector"): greater than operator
> signature(e1 = "numeric", e2 = "gvector"): greater than operator
>= signature(e1 = "gmatrix", e2 = "gvector"): greater than or equal operator
>= signature(e1 = "gvector", e2 = "gmatrix"): greater than or equal operator
>= signature(e1 = "gvector", e2 = "gvector"): greater than or equal operator
>= signature(e1 = "gvector", e2 = "logical"): greater than or equal operator
>= signature(e1 = "gvector", e2 = "matrix"): greater than or equal operator
>= signature(e1 = "gvector", e2 = "numeric"): greater than or equal operator
>= signature(e1 = "logical", e2 = "gvector"): greater than or equal operator
>= signature(e1 = "matrix", e2 = "gvector"): greater than or equal operator
>= signature(e1 = "numeric", e2 = "gvector"): greater than or equal operator
abs signature(x = "gvector"): absolute value
acos signature(x = "gvector"): inverse cosine
47
48
gvector-class
acosh signature(x = "gvector"): inverse hyperbolic cosine
as.gmatrix signature(data = "gvector"):coersion function
as.gvector signature(x = "gvector"): coersion function
as.integer signature(x = "gvector"): coersion function
as.logical signature(x = "gvector"): coersion function
as.matrix signature(x = "gvector"): coersion function
as.numeric signature(x = "gvector"): coersion function
as.vector signature(x = "gvector"): coersion function
asin signature(x = "gvector"): inverse sine function
asinh signature(x = "gvector"): inverse hyperbolic sine function
atan signature(x = "gvector"): inverse tangent function
atanh signature(x = "gvector"): inverse hyperbolic tangent function
ceiling signature(x = "gvector"): ceiling function
cos signature(x = "gvector"): cosine function
cosh signature(x = "gvector"): hyperbolic cosine
crossprod signature(x = "gmatrix", y = "gvector"): calculates: t(x) %*% y
crossprod signature(x = "gvector", y = "gmatrix"): calculates: t(x) %*% y
crossprod signature(x = "gvector", y = "gvector"): calculates: t(x) %*% y
crossprod signature(x = "gvector", y = "logical"): calculates: t(x) %*% y
crossprod signature(x = "gvector", y = "missing"): calculates: t(x) %*% y
crossprod signature(x = "gvector", y = "numeric"): calculates: t(x) %*% y
crossprod signature(x = "logical", y = "gvector"): calculates: t(x) %*% y
crossprod signature(x = "numeric", y = "gvector"): calculates: t(x) %*% y
device signature(x = "gvector"): get device
device<- signature(x = "gvector"): set device
exp signature(x = "gvector"): exponential function
expm1 signature(x = "gvector"): computes exp(x) - 1
floor signature(x = "gvector"): floor function
gamma signature(x = "gvector"): gamma function
ifelse signature(test = "gvector"): conditional selection
is.finite signature(x = "gvector"): finite status
is.infinite signature(x = "gvector"): infinite status
is.na signature(x = "gvector"): missing status
is.nan signature(x = "gvector"): not a number status
length signature(x = "gvector"): total number of elements in object
lgamma signature(x = "gvector"): log gamma function
log signature(x = "gvector"): logarithm function
gvector-class
log10 signature(x = "gvector"): base 10 log
log1p signature(x = "gvector"): log(1+x)
log2 signature(x = "gvector"): base 2 log
max signature(x = "gvector"): maximum of all elements
mean signature(x = "gvector"): mean of all elements
min signature(x = "gvector"): minimum of all elements
names signature(x = "gvector"): get element names
names<- signature(x = "gvector"): set element names
round signature(x = "gvector"): round to neares integer
show signature(object = "gvector"): display object
sign signature(x = "gvector"): sign
sin signature(x = "gvector"): sine function
sinh signature(x = "gvector"): hyperbolic sine function
sort signature(x = "gvector"): sort
sqrt signature(x = "gvector"): square root
sum signature(x = "gvector"): sum of all elements
t signature(x = "gvector"): transpose
tan signature(x = "gvector"): tangent function
tanh signature(x = "gvector"): hyperbolic tangent function
tcrossprod signature(x = "gmatrix", y = "gvector"): calculates:
tcrossprod signature(x = "gvector", y = "gmatrix"): calculates:
tcrossprod signature(x = "gvector", y = "gvector"): calculates:
tcrossprod signature(x = "gvector", y = "logical"): calculates:
tcrossprod signature(x = "gvector", y = "missing"): calculates:
tcrossprod signature(x = "gvector", y = "numeric"): calculates:
tcrossprod signature(x = "logical", y = "gvector"): calculates:
tcrossprod signature(x = "numeric", y = "gvector"): calculates:
type signature(x = "gvector"): get type
type<- signature(x = "gvector"): set type
which signature(x = "gvector"): index list of TRUE positions
Author(s)
Nathan Morris
See Also
gmatrix
Examples
showClass("gvector")
49
x
x
x
x
x
x
x
x
%*%
%*%
%*%
%*%
%*%
%*%
%*%
%*%
t(y)
t(y)
t(y)
t(y)
t(y)
t(y)
t(y)
t(y)
50
indexing
ifelse
Conditional Element Selection
Description
ifelse returns a value with the same shape as test which is filled with elements selected from either
yes or no depending on whether the element of test is TRUE or FALSE.
Methods
signature(test = "ANY")
signature(test = "gmatrix")
signature(test = "gvector")
indexing
Indexing Methods
Description
These methods are used to perform indexing operations. They work in much the same way as the
base R functions. However, if the indexes involve very random numbers, it maybe very difficult for
the GPU to coalesce the memory operations. Therefore it may be faster to move the object back to
the host befor the indexing operations are performed.
Methods
signature(x = "gvector", i = "ANY", j = "ANY")
signature(x = "ANY", i = "ANY", j = "ANY")
signature(x = "gmatrix", i = "index", j = "index")
signature(x = "gmatrix", i = "index", j = "missing")
signature(x = "gmatrix", i = "missing", j = "index")
signature(x = "gmatrix", i = "missing", j = "missing")
signature(x = "gvector", i = "ANY", j = "ANY")
signature(x = "nonStructure", i = "ANY", j = "ANY")
length
length
51
Length of an Object
Description
Get the length of a gvector or gmatrix.
Methods
signature(x = "gmatrix") returns total number of elements in the matrix.
signature(x = "gvector") returns the length of the gvector
lpgr-class
Class "lpgr"
Description
Objects of this class must be returned by any " lprf" function which is used by the gBasicHMC()
function.
Objects from the Class
Objects can be created by calls of the form new("lpgr", ...).
Slots
gr: Object of class "list". Must contain a list of matrices representing the first derivative of
the log probility of a distribution with respect to the random variables. Each column of the
matrices is for a different parrallel run. All matrices may be either on the gpu or cpu
lp: Object of class "numeric". Represent the log probability (without the normalizing constan) of
a distribution. MUST be on the CPU.
Methods
No methods defined with class "lpgr" in the signature.
Author(s)
Nathan Morris
See Also
gBasicHMC
52
max
matrix multiplication Matrix Multiplication
Description
Multiply two matrices together.
Methods
signature(x = "gmatrix", y = "gmatrix")
signature(x = "gmatrix", y = "gvector")
signature(x = "gmatrix", y = "logical")
signature(x = "gmatrix", y = "matrix")
signature(x = "gmatrix", y = "numeric")
signature(x = "gvector", y = "gmatrix")
signature(x = "gvector", y = "gvector")
signature(x = "gvector", y = "logical")
signature(x = "gvector", y = "matrix")
signature(x = "gvector", y = "numeric")
signature(x = "logical", y = "gmatrix")
signature(x = "logical", y = "gvector")
signature(x = "matrix", y = "gmatrix")
signature(x = "matrix", y = "gvector")
signature(x = "numeric", y = "gmatrix")
signature(x = "numeric", y = "gvector")
max
Maxima and Minima
Description
Returns the maxima and minima of the input values. The na.rm=TRUE option has NOT been implemented.
Methods
signature(x = "gmatrix")
signature(x = "gvector")
mean, sum
mean, sum
53
mean and sum methods
Description
These methods are implement very similarly to the corresponding R base methods.
Methods
signature(x = "ANY")
signature(x = "gmatrix")
signature(x = "gvector")
names
Get and set names
Description
Gets and sets the names slot of a gvector object.
Methods
signature(x = "gvector")
ncol
Mumber of rows/columns
Description
Get the number of rows/columns of a ’gmatrix.’
Methods
signature(x = "ANY")
signature(x = "gmatrix")
54
normal
normal
GPU Normal Distribution
Description
Density, distribution function, quantile function and random generation for the normal distribution
with mean equal to mean and standard deviation equal to sd. All functions performed on the GPU.
Usage
gdnorm(x, mean = 0,
grnorm(n, mean = 0,
gqnorm(q, mean = 0,
warn = TRUE,
gpnorm(p, mean = 0,
warn = TRUE,
sd =
sd =
sd =
type
sd =
type
1, log = FALSE, type = "d")
1, type = "d")
1, lower.tail = TRUE, log.p = FALSE,
= "d")
1, lower.tail = TRUE, log.p = FALSE,
= "d")
Arguments
x,q
vector of quantiles
p
vector of probabilities
n
number of observations
mean
vector of means
sd
vector of standard deviations
log, log.p
logical; if TRUE, probabilities p are given as log(p)
lower.tail
logical; if TRUE (default), probabilities are P[X < x] otherwise, P[X > x].
warn
logical; if FALSE then additional warnings are disabled.
type
specify the type; may be "double", "single" (or short form "d" or "s")
Details
Very similar to the R stats functionality. However, gqnorm and gpnorm are implement currently in
a way that is NOT numerically precise in the deep tails. Future releases may fix this problem.
Value
gdnorm gives the density, gpnorm gives the distribution function, gqnorm gives the quantile function,
and grnorm generates random deviates.
Author(s)
Nathan Morris
See Also
dnorm
rsample
55
Examples
myRndNums1 = grnorm(100) #standard normals
myRndNums2 = grnorm(100, mean=c(1,2), sd=c(1,2,4,6))
rsample
Sample and integer for each row of a gmatrix object.
Description
Sample an integer with the unormalized (log) probabilities specified for each row.
Usage
rsample(P, log=TRUE)
Arguments
P
A matrix conaining unormalizes (log) probabilities in each row.
log
Specifies if the input is on a log scale.
Details
Conceptually, each row is first normalized to sum to one, and then an integer is sampled for each
row under the specified probablility.
Value
Returns a gvector with an integer value for each row.
Author(s)
Nathan Morris
See Also
gRowLogSums
56
setDevice
setDevice
Get and set the current device.
Description
On systems with multiple GPUs the current device may be set or investigated with these functions.
Usage
setDevice(device,force=FALSE,silent=FALSE,...)
getDevice()
listDevices()
Arguments
device
Device number to set the device to
force
Force reset of the tuning parameters even if they have already been set
silent
Prints a message if TRUE
...
Arguments to set the tuning parameters. It’s not a good idea to mess with these
at this point.
Details
All operations are performed on the current GPU device only. An error will be returned if the user
attempts to perform an operation on a device that is not the current device. Details of the available
devices can be obtained with the ’listDevices’ function.
Value
setDevice returns TRUE. getDevice returns the current device number. listDevices returns a
data.frame with information about the available devices.
Author(s)
Nathan Morris
See Also
device, gdup
Examples
listDevices()
getDevice()
#setDevice(1)
setTuningPameters
setTuningPameters
57
Set tuning parameters
Description
This function tunes the kernal calls to a specific GPU if the user is working with CUDA versions
older than 6.5. At this point, these parameters are not well documented and should only be changed
by users who can read the source code.
Usage
setTuningPameters(force = TRUE, threads_per_block = as.integer(2^8),
total_states = as.integer(32 * 14 * 16), state =
unclass(Sys.time()))
Arguments
force
logical - force the change even if the parameters have been previously set.
threads_per_block
number of threads per block
total_states
total states for random number generations
state
starting state for random number generation
Author(s)
Nathan Morris
show
Methods for displaying GPU objects
Description
These methods may be used to display objects of class gmatrix and ’gvector.’
Methods
signature(object = "gmatrix")
signature(object = "gvector")
58
type
sort
Sorting
Description
Sorts a vector
Methods
signature(x = "ANY")
signature(x = "gvector")
t
Transpose
Description
Methods to traspose a gmatrix or gvector.
Methods
signature(x = "ANY")
signature(x = "gmatrix")
signature(x = "gvector")
type
Get or set the type of a GPU object
Description
These functions may be used to get or set the type of a GPU object. May be used as type(x)
type(x)<-value
Arguments
x
A GPU object of class gvector or gmatrix
value
The type to convert the object to. There are three different ways to specify
this. One may use the "double", "single", "integer" or "logical" notation.
Alternatively the short form "d", "s", "i" or "s" notation may be used. Finally
the internal integer representation of 0L, 1L, 2L or 3L may be used.
which
59
Value
type(x) returns the type of x type(x)<-value change the type of x
Author(s)
Nathan Morris
See Also
convertType
Examples
x=g(1:4)
type(x)="d" #change the type from "integer" to "double"
which
Which indices are TRUE?
Description
Give the TRUE indices of a logical gvector.
Methods
signature(x = "ANY")
signature(x = "gvector")
Index
!,gmatrix-method (elementwise
functions), 12
!,gvector-method (elementwise
functions), 12
!-methods (elementwise functions), 12
!=,gmatrix,gmatrix-method (elementwise
binary operators), 11
!=,gmatrix,gvector-method (elementwise
binary operators), 11
!=,gmatrix,logical-method (elementwise
binary operators), 11
!=,gmatrix,matrix-method (elementwise
binary operators), 11
!=,gmatrix,numeric-method (elementwise
binary operators), 11
!=,gvector,gmatrix-method (elementwise
binary operators), 11
!=,gvector,gvector-method (elementwise
binary operators), 11
!=,gvector,logical-method (elementwise
binary operators), 11
!=,gvector,matrix-method (elementwise
binary operators), 11
!=,gvector,numeric-method (elementwise
binary operators), 11
!=,logical,gmatrix-method (elementwise
binary operators), 11
!=,logical,gvector-method (elementwise
binary operators), 11
!=,matrix,gmatrix-method (elementwise
binary operators), 11
!=,matrix,gvector-method (elementwise
binary operators), 11
!=,numeric,gmatrix-method (elementwise
binary operators), 11
!=,numeric,gvector-method (elementwise
binary operators), 11
!=-methods (elementwise binary
operators), 11
∗Topic GPU
gmatrix-package, 3
∗Topic Garbage
ggc, 21
∗Topic HMC
gBasicHMC, 14
∗Topic MCMC
gBasicHMC, 14
∗Topic NVIDIA
gmatrix-package, 3
∗Topic Normal
normal, 54
∗Topic Trig
elementwise functions, 12
∗Topic beta
gdbeta, 16
∗Topic binomial
gdbinom, 17
∗Topic classes
gmatrix-class, 24
gqr-class, 36
gsvd-class, 41
gvector-class, 43
∗Topic copy
gdup, 20
∗Topic device
checkDevice, 6
setDevice, 56
∗Topic gamma
gdgamma, 18
∗Topic gmatrix
gmatrix, 23
∗Topic methods
as.numeric, as.integer,
as.logical, as.vector and
as.matrix, 5
chol, 6
colMeans, 7
colnames, 7
60
INDEX
crossprod,tcrossprod, 8
device, 10
diag, 10
dim, 10
dimnames, 11
elementwise binary operators, 11
elementwise functions, 12
ifelse, 50
indexing, 50
length, 51
matrix multiplication, 52
max, 52
mean, sum, 53
names, 53
ncol, 53
show, 57
sort, 58
t, 58
which, 59
∗Topic multiplication
gmatTimesDiagVec, 32
gmm, 33
∗Topic names
gnamestrip, 34
∗Topic outer
gouter, 35
∗Topic poisson
gdpois, 19
∗Topic replicate
g.rep, 13
∗Topic transfer
g, 12
gident, 22
∗Topic type
convertType, 7
type, 58
∗Topic uniform
grunif, 38
*,gmatrix,gmatrix-method (elementwise
binary operators), 11
*,gmatrix,gvector-method (elementwise
binary operators), 11
*,gmatrix,logical-method (elementwise
binary operators), 11
*,gmatrix,matrix-method (elementwise
binary operators), 11
*,gmatrix,numeric-method (elementwise
binary operators), 11
61
*,gvector,gmatrix-method (elementwise
binary operators), 11
*,gvector,gvector-method (elementwise
binary operators), 11
*,gvector,logical-method (elementwise
binary operators), 11
*,gvector,matrix-method (elementwise
binary operators), 11
*,gvector,numeric-method (elementwise
binary operators), 11
*,logical,gmatrix-method (elementwise
binary operators), 11
*,logical,gvector-method (elementwise
binary operators), 11
*,matrix,gmatrix-method (elementwise
binary operators), 11
*,matrix,gvector-method (elementwise
binary operators), 11
*,numeric,gmatrix-method (elementwise
binary operators), 11
*,numeric,gvector-method (elementwise
binary operators), 11
*-methods (elementwise binary
operators), 11
+,gmatrix,gmatrix-method (elementwise
binary operators), 11
+,gmatrix,gvector-method (elementwise
binary operators), 11
+,gmatrix,logical-method (elementwise
binary operators), 11
+,gmatrix,matrix-method (elementwise
binary operators), 11
+,gmatrix,missing-method (elementwise
binary operators), 11
+,gmatrix,numeric-method (elementwise
binary operators), 11
+,gvector,gmatrix-method (elementwise
binary operators), 11
+,gvector,gvector-method (elementwise
binary operators), 11
+,gvector,logical-method (elementwise
binary operators), 11
+,gvector,matrix-method (elementwise
binary operators), 11
+,gvector,missing-method (elementwise
binary operators), 11
+,gvector,numeric-method (elementwise
binary operators), 11
62
+,logical,gmatrix-method (elementwise
binary operators), 11
+,logical,gvector-method (elementwise
binary operators), 11
+,matrix,gmatrix-method (elementwise
binary operators), 11
+,matrix,gvector-method (elementwise
binary operators), 11
+,numeric,gmatrix-method (elementwise
binary operators), 11
+,numeric,gvector-method (elementwise
binary operators), 11
+-methods (elementwise binary
operators), 11
-,gmatrix,gmatrix-method (elementwise
binary operators), 11
-,gmatrix,gvector-method (elementwise
binary operators), 11
-,gmatrix,logical-method (elementwise
binary operators), 11
-,gmatrix,matrix-method (elementwise
binary operators), 11
-,gmatrix,missing-method (elementwise
binary operators), 11
-,gmatrix,numeric-method (elementwise
binary operators), 11
-,gvector,gmatrix-method (elementwise
binary operators), 11
-,gvector,gvector-method (elementwise
binary operators), 11
-,gvector,logical-method (elementwise
binary operators), 11
-,gvector,matrix-method (elementwise
binary operators), 11
-,gvector,missing-method (elementwise
binary operators), 11
-,gvector,numeric-method (elementwise
binary operators), 11
-,logical,gmatrix-method (elementwise
binary operators), 11
-,logical,gvector-method (elementwise
binary operators), 11
-,matrix,gmatrix-method (elementwise
binary operators), 11
-,matrix,gvector-method (elementwise
binary operators), 11
-,numeric,gmatrix-method (elementwise
binary operators), 11
INDEX
-,numeric,gvector-method (elementwise
binary operators), 11
--methods (elementwise binary
operators), 11
/,gmatrix,gmatrix-method (elementwise
binary operators), 11
/,gmatrix,gvector-method (elementwise
binary operators), 11
/,gmatrix,logical-method (elementwise
binary operators), 11
/,gmatrix,matrix-method (elementwise
binary operators), 11
/,gmatrix,numeric-method (elementwise
binary operators), 11
/,gvector,gmatrix-method (elementwise
binary operators), 11
/,gvector,gvector-method (elementwise
binary operators), 11
/,gvector,logical-method (elementwise
binary operators), 11
/,gvector,matrix-method (elementwise
binary operators), 11
/,gvector,numeric-method (elementwise
binary operators), 11
/,logical,gmatrix-method (elementwise
binary operators), 11
/,logical,gvector-method (elementwise
binary operators), 11
/,matrix,gmatrix-method (elementwise
binary operators), 11
/,matrix,gvector-method (elementwise
binary operators), 11
/,numeric,gmatrix-method (elementwise
binary operators), 11
/,numeric,gvector-method (elementwise
binary operators), 11
/-methods (elementwise binary
operators), 11
<,gmatrix,gmatrix-method (elementwise
binary operators), 11
<,gmatrix,gvector-method (elementwise
binary operators), 11
<,gmatrix,logical-method (elementwise
binary operators), 11
<,gmatrix,matrix-method (elementwise
binary operators), 11
<,gmatrix,numeric-method (elementwise
binary operators), 11
INDEX
<,gvector,gmatrix-method (elementwise
binary operators), 11
<,gvector,gvector-method (elementwise
binary operators), 11
<,gvector,logical-method (elementwise
binary operators), 11
<,gvector,matrix-method (elementwise
binary operators), 11
<,gvector,numeric-method (elementwise
binary operators), 11
<,logical,gmatrix-method (elementwise
binary operators), 11
<,logical,gvector-method (elementwise
binary operators), 11
<,matrix,gmatrix-method (elementwise
binary operators), 11
<,matrix,gvector-method (elementwise
binary operators), 11
<,numeric,gmatrix-method (elementwise
binary operators), 11
<,numeric,gvector-method (elementwise
binary operators), 11
<=,gmatrix,gmatrix-method (elementwise
binary operators), 11
<=,gmatrix,gvector-method (elementwise
binary operators), 11
<=,gmatrix,logical-method (elementwise
binary operators), 11
<=,gmatrix,matrix-method (elementwise
binary operators), 11
<=,gmatrix,numeric-method (elementwise
binary operators), 11
<=,gvector,gmatrix-method (elementwise
binary operators), 11
<=,gvector,gvector-method (elementwise
binary operators), 11
<=,gvector,logical-method (elementwise
binary operators), 11
<=,gvector,matrix-method (elementwise
binary operators), 11
<=,gvector,numeric-method (elementwise
binary operators), 11
<=,logical,gmatrix-method (elementwise
binary operators), 11
<=,logical,gvector-method (elementwise
binary operators), 11
<=,matrix,gmatrix-method (elementwise
binary operators), 11
63
<=,matrix,gvector-method (elementwise
binary operators), 11
<=,numeric,gmatrix-method (elementwise
binary operators), 11
<=,numeric,gvector-method (elementwise
binary operators), 11
<=-methods (elementwise binary
operators), 11
==,gmatrix,gmatrix-method (elementwise
binary operators), 11
==,gmatrix,gvector-method (elementwise
binary operators), 11
==,gmatrix,logical-method (elementwise
binary operators), 11
==,gmatrix,matrix-method (elementwise
binary operators), 11
==,gmatrix,numeric-method (elementwise
binary operators), 11
==,gvector,gmatrix-method (elementwise
binary operators), 11
==,gvector,gvector-method (elementwise
binary operators), 11
==,gvector,logical-method (elementwise
binary operators), 11
==,gvector,matrix-method (elementwise
binary operators), 11
==,gvector,numeric-method (elementwise
binary operators), 11
==,logical,gmatrix-method (elementwise
binary operators), 11
==,logical,gvector-method (elementwise
binary operators), 11
==,matrix,gmatrix-method (elementwise
binary operators), 11
==,matrix,gvector-method (elementwise
binary operators), 11
==,numeric,gmatrix-method (elementwise
binary operators), 11
==,numeric,gvector-method (elementwise
binary operators), 11
==-methods (elementwise binary
operators), 11
>,gmatrix,gmatrix-method (elementwise
binary operators), 11
>,gmatrix,gvector-method (elementwise
binary operators), 11
>,gmatrix,logical-method (elementwise
binary operators), 11
64
>,gmatrix,matrix-method (elementwise
binary operators), 11
>,gmatrix,numeric-method (elementwise
binary operators), 11
>,gvector,gmatrix-method (elementwise
binary operators), 11
>,gvector,gvector-method (elementwise
binary operators), 11
>,gvector,logical-method (elementwise
binary operators), 11
>,gvector,matrix-method (elementwise
binary operators), 11
>,gvector,numeric-method (elementwise
binary operators), 11
>,logical,gmatrix-method (elementwise
binary operators), 11
>,logical,gvector-method (elementwise
binary operators), 11
>,matrix,gmatrix-method (elementwise
binary operators), 11
>,matrix,gvector-method (elementwise
binary operators), 11
>,numeric,gmatrix-method (elementwise
binary operators), 11
>,numeric,gvector-method (elementwise
binary operators), 11
>-methods (elementwise binary
operators), 11
>=,gmatrix,gmatrix-method (elementwise
binary operators), 11
>=,gmatrix,gvector-method (elementwise
binary operators), 11
>=,gmatrix,logical-method (elementwise
binary operators), 11
>=,gmatrix,matrix-method (elementwise
binary operators), 11
>=,gmatrix,numeric-method (elementwise
binary operators), 11
>=,gvector,gmatrix-method (elementwise
binary operators), 11
>=,gvector,gvector-method (elementwise
binary operators), 11
>=,gvector,logical-method (elementwise
binary operators), 11
>=,gvector,matrix-method (elementwise
binary operators), 11
>=,gvector,numeric-method (elementwise
binary operators), 11
INDEX
>=,logical,gmatrix-method (elementwise
binary operators), 11
>=,logical,gvector-method (elementwise
binary operators), 11
>=,matrix,gmatrix-method (elementwise
binary operators), 11
>=,matrix,gvector-method (elementwise
binary operators), 11
>=,numeric,gmatrix-method (elementwise
binary operators), 11
>=,numeric,gvector-method (elementwise
binary operators), 11
>=-methods (elementwise binary
operators), 11
[,ANY,ANY,ANY-method (indexing), 50
[,gmatrix,index,index-method
(indexing), 50
[,gmatrix,index,missing-method
(indexing), 50
[,gmatrix,missing,index-method
(indexing), 50
[,gmatrix,missing,missing-method
(indexing), 50
[,gvector,ANY,ANY-method (indexing), 50
[,nonStructure,ANY,ANY-method
(indexing), 50
[-methods (indexing), 50
[<-,ANY,ANY,ANY-method (indexing), 50
[<-,gmatrix,index,index-method
(indexing), 50
[<-,gmatrix,index,missing-method
(indexing), 50
[<-,gmatrix,missing,index-method
(indexing), 50
[<-,gmatrix,missing,missing-method
(indexing), 50
[<-,gvector,ANY,ANY-method (indexing),
50
[<--methods (indexing), 50
%*%,gmatrix,gmatrix-method (matrix
multiplication), 52
%*%,gmatrix,gvector-method (matrix
multiplication), 52
%*%,gmatrix,logical-method (matrix
multiplication), 52
%*%,gmatrix,matrix-method (matrix
multiplication), 52
%*%,gmatrix,numeric-method (matrix
INDEX
multiplication), 52
%*%,gvector,gmatrix-method (matrix
multiplication), 52
%*%,gvector,gvector-method (matrix
multiplication), 52
%*%,gvector,logical-method (matrix
multiplication), 52
%*%,gvector,matrix-method (matrix
multiplication), 52
%*%,gvector,numeric-method (matrix
multiplication), 52
%*%,logical,gmatrix-method (matrix
multiplication), 52
%*%,logical,gvector-method (matrix
multiplication), 52
%*%,matrix,gmatrix-method (matrix
multiplication), 52
%*%,matrix,gvector-method (matrix
multiplication), 52
%*%,numeric,gmatrix-method (matrix
multiplication), 52
%*%,numeric,gvector-method (matrix
multiplication), 52
%*%-methods (matrix multiplication), 52
%%,gmatrix,gmatrix-method (elementwise
binary operators), 11
%%,gmatrix,gvector-method (elementwise
binary operators), 11
%%,gmatrix,logical-method (elementwise
binary operators), 11
%%,gmatrix,matrix-method (elementwise
binary operators), 11
%%,gmatrix,numeric-method (elementwise
binary operators), 11
%%,gvector,gmatrix-method (elementwise
binary operators), 11
%%,gvector,gvector-method (elementwise
binary operators), 11
%%,gvector,logical-method (elementwise
binary operators), 11
%%,gvector,matrix-method (elementwise
binary operators), 11
%%,gvector,numeric-method (elementwise
binary operators), 11
%%,logical,gmatrix-method (elementwise
binary operators), 11
%%,logical,gvector-method (elementwise
binary operators), 11
65
%%,matrix,gmatrix-method (elementwise
binary operators), 11
%%,matrix,gvector-method (elementwise
binary operators), 11
%%,numeric,gmatrix-method (elementwise
binary operators), 11
%%,numeric,gvector-method (elementwise
binary operators), 11
%%-methods (elementwise binary
operators), 11
%lgspadd% (elementwise binary
operators), 11
%lgspadd%,gmatrix,gmatrix-method
(elementwise binary operators),
11
%lgspadd%,gmatrix,gvector-method
(elementwise binary operators),
11
%lgspadd%,gmatrix,logical-method
(elementwise binary operators),
11
%lgspadd%,gmatrix,matrix-method
(elementwise binary operators),
11
%lgspadd%,gmatrix,numeric-method
(elementwise binary operators),
11
%lgspadd%,gvector,gmatrix-method
(elementwise binary operators),
11
%lgspadd%,gvector,gvector-method
(elementwise binary operators),
11
%lgspadd%,gvector,logical-method
(elementwise binary operators),
11
%lgspadd%,gvector,matrix-method
(elementwise binary operators),
11
%lgspadd%,gvector,numeric-method
(elementwise binary operators),
11
%lgspadd%,logical,gmatrix-method
(elementwise binary operators),
11
%lgspadd%,logical,gvector-method
(elementwise binary operators),
11
66
%lgspadd%,matrix,gmatrix-method
(elementwise binary operators),
11
%lgspadd%,matrix,gvector-method
(elementwise binary operators),
11
%lgspadd%,numeric,gmatrix-method
(elementwise binary operators),
11
%lgspadd%,numeric,gvector-method
(elementwise binary operators),
11
%lgspadd%-methods (elementwise binary
operators), 11
%o% (gouter), 35
%o%,ANY,ANY-method (gouter), 35
%o%,gvector,gvector-method (gouter), 35
%o%,gvector,logical-method (gouter), 35
%o%,gvector,numeric-method (gouter), 35
%o%,logical,gvector-method (gouter), 35
%o%,numeric,gvector-method (gouter), 35
%o%-methods (gouter), 35
%to% (gseq), 39
%to%,numeric,numeric-method (gseq), 39
%x%,ANY,ANY-method (gkroneckerProd), 23
%x%,gmatrix,gmatrix-method
(gkroneckerProd), 23
%x%,gmatrix,gvector-method
(gkroneckerProd), 23
%x%,gmatrix,matrix-method
(gkroneckerProd), 23
%x%,gmatrix,numeric-method
(gkroneckerProd), 23
%x%,gvector,gmatrix-method
(gkroneckerProd), 23
%x%,gvector,gvector-method
(gkroneckerProd), 23
%x%,gvector,matrix-method
(gkroneckerProd), 23
%x%,gvector,numeric-method
(gkroneckerProd), 23
%x%,matrix,gmatrix-method
(gkroneckerProd), 23
%x%,matrix,gvector-method
(gkroneckerProd), 23
%x%,numeric,gmatrix-method
(gkroneckerProd), 23
%x%,numeric,gvector-method
INDEX
(gkroneckerProd), 23
%x%-methods (gkroneckerProd), 23
&,gmatrix,gmatrix-method (elementwise
binary operators), 11
&,gmatrix,gvector-method (elementwise
binary operators), 11
&,gmatrix,logical-method (elementwise
binary operators), 11
&,gmatrix,matrix-method (elementwise
binary operators), 11
&,gmatrix,numeric-method (elementwise
binary operators), 11
&,gvector,gmatrix-method (elementwise
binary operators), 11
&,gvector,gvector-method (elementwise
binary operators), 11
&,gvector,logical-method (elementwise
binary operators), 11
&,gvector,matrix-method (elementwise
binary operators), 11
&,gvector,numeric-method (elementwise
binary operators), 11
&,logical,gmatrix-method (elementwise
binary operators), 11
&,logical,gvector-method (elementwise
binary operators), 11
&,matrix,gmatrix-method (elementwise
binary operators), 11
&,matrix,gvector-method (elementwise
binary operators), 11
&,numeric,gmatrix-method (elementwise
binary operators), 11
&,numeric,gvector-method (elementwise
binary operators), 11
&-methods (elementwise binary
operators), 11
%o%, 36
^,gmatrix,gmatrix-method (elementwise
binary operators), 11
^,gmatrix,gvector-method (elementwise
binary operators), 11
^,gmatrix,logical-method (elementwise
binary operators), 11
^,gmatrix,matrix-method (elementwise
binary operators), 11
^,gmatrix,numeric-method (elementwise
binary operators), 11
^,gvector,gmatrix-method (elementwise
INDEX
binary operators), 11
^,gvector,gvector-method (elementwise
binary operators), 11
^,gvector,logical-method (elementwise
binary operators), 11
^,gvector,matrix-method (elementwise
binary operators), 11
^,gvector,numeric-method (elementwise
binary operators), 11
^,logical,gmatrix-method (elementwise
binary operators), 11
^,logical,gvector-method (elementwise
binary operators), 11
^,matrix,gmatrix-method (elementwise
binary operators), 11
^,matrix,gvector-method (elementwise
binary operators), 11
^,numeric,gmatrix-method (elementwise
binary operators), 11
^,numeric,gvector-method (elementwise
binary operators), 11
^-methods (elementwise binary
operators), 11
abs,gmatrix-method (elementwise
functions), 12
abs,gvector-method (elementwise
functions), 12
abs-methods (elementwise functions), 12
acos,gmatrix-method (elementwise
functions), 12
acos,gvector-method (elementwise
functions), 12
acos-methods (elementwise functions), 12
acosh,gmatrix-method (elementwise
functions), 12
acosh,gvector-method (elementwise
functions), 12
acosh-methods (elementwise functions),
12
as.gmatrix, 13, 22
as.gmatrix (as.gmatrix, as.gvector), 4
as.gmatrix, as.gvector, 4
as.gmatrix,ANY-method (as.gmatrix,
as.gvector), 4
as.gmatrix,gmatrix-method (as.gmatrix,
as.gvector), 4
as.gmatrix,gvector-method (as.gmatrix,
as.gvector), 4
67
as.gmatrix,matrix-method (as.gmatrix,
as.gvector), 4
as.gmatrix-methods (as.gmatrix,
as.gvector), 4
as.gvector (as.gmatrix, as.gvector), 4
as.gvector,ANY-method (as.gmatrix,
as.gvector), 4
as.gvector,gmatrix-method (as.gmatrix,
as.gvector), 4
as.gvector,gvector-method (as.gmatrix,
as.gvector), 4
as.gvector-methods (as.gmatrix,
as.gvector), 4
as.integer,gmatrix-method (as.numeric,
as.integer, as.logical,
as.vector and as.matrix), 5
as.integer,gvector-method (as.numeric,
as.integer, as.logical,
as.vector and as.matrix), 5
as.integer-methods (as.numeric,
as.integer, as.logical,
as.vector and as.matrix), 5
as.logical,gmatrix-method (as.numeric,
as.integer, as.logical,
as.vector and as.matrix), 5
as.logical,gvector-method (as.numeric,
as.integer, as.logical,
as.vector and as.matrix), 5
as.logical-methods (as.numeric,
as.integer, as.logical,
as.vector and as.matrix), 5
as.matrix,ANY-method (as.numeric,
as.integer, as.logical,
as.vector and as.matrix), 5
as.matrix,gmatrix-method (as.numeric,
as.integer, as.logical,
as.vector and as.matrix), 5
as.matrix,gvector-method (as.numeric,
as.integer, as.logical,
as.vector and as.matrix), 5
as.matrix-methods (as.numeric,
as.integer, as.logical,
as.vector and as.matrix), 5
as.matrix.gmatrix (as.numeric,
as.integer, as.logical,
as.vector and as.matrix), 5
as.matrix.gvector (as.numeric,
as.integer, as.logical,
68
as.vector and as.matrix), 5
as.numeric, 13, 22
as.numeric, as.integer, as.logical,
as.vector and as.matrix, 5
as.numeric,gmatrix-method (as.numeric,
as.integer, as.logical,
as.vector and as.matrix), 5
as.numeric,gvector-method (as.numeric,
as.integer, as.logical,
as.vector and as.matrix), 5
as.numeric-methods (as.numeric,
as.integer, as.logical,
as.vector and as.matrix), 5
as.vector,ANY-method (as.numeric,
as.integer, as.logical,
as.vector and as.matrix), 5
as.vector,gmatrix-method (as.numeric,
as.integer, as.logical,
as.vector and as.matrix), 5
as.vector,gvector-method (as.numeric,
as.integer, as.logical,
as.vector and as.matrix), 5
as.vector-methods (as.numeric,
as.integer, as.logical,
as.vector and as.matrix), 5
as.vector.gmatrix (as.numeric,
as.integer, as.logical,
as.vector and as.matrix), 5
as.vector.gvector (as.numeric,
as.integer, as.logical,
as.vector and as.matrix), 5
asin,gmatrix-method (elementwise
functions), 12
asin,gvector-method (elementwise
functions), 12
asin-methods (elementwise functions), 12
asinh,gmatrix-method (elementwise
functions), 12
asinh,gvector-method (elementwise
functions), 12
asinh-methods (elementwise functions),
12
atan,gmatrix-method (elementwise
functions), 12
atan,gvector-method (elementwise
functions), 12
atan-methods (elementwise functions), 12
atanh,gmatrix-method (elementwise
INDEX
functions), 12
atanh,gvector-method (elementwise
functions), 12
atanh-methods (elementwise functions),
12
ceiling,gmatrix-method (elementwise
functions), 12
ceiling,gvector-method (elementwise
functions), 12
ceiling-methods (elementwise
functions), 12
checkDevice, 6
chol, 6
chol,ANY-method (chol), 6
chol,gmatrix-method (chol), 6
chol-methods (chol), 6
colMeans, 7
colMeans,ANY-method (colMeans), 7
colMeans,gmatrix-method (colMeans), 7
colMeans-methods (colMeans), 7
colnames, 7, 11, 34
colnames,ANY-method (colnames), 7
colnames,gmatrix-method (colnames), 7
colnames-methods (colnames), 7
colnames<-,ANY-method (colnames), 7
colnames<-,gmatrix-method (colnames), 7
colnames<--methods (colnames), 7
colSums,ANY-method (colMeans), 7
colSums,gmatrix-method (colMeans), 7
colSums-methods (colMeans), 7
convertType, 7, 59
cos,gmatrix-method (elementwise
functions), 12
cos,gvector-method (elementwise
functions), 12
cos-methods (elementwise functions), 12
cosh,gmatrix-method (elementwise
functions), 12
cosh,gvector-method (elementwise
functions), 12
cosh-methods (elementwise functions), 12
crossprod,ANY,ANY-method
(crossprod,tcrossprod), 8
crossprod,gmatrix,gmatrix-method
(crossprod,tcrossprod), 8
crossprod,gmatrix,gvector-method
(crossprod,tcrossprod), 8
INDEX
crossprod,gmatrix,logical-method
(crossprod,tcrossprod), 8
crossprod,gmatrix,matrix-method
(crossprod,tcrossprod), 8
crossprod,gmatrix,missing-method
(crossprod,tcrossprod), 8
crossprod,gmatrix,numeric-method
(crossprod,tcrossprod), 8
crossprod,gvector,gmatrix-method
(crossprod,tcrossprod), 8
crossprod,gvector,gvector-method
(crossprod,tcrossprod), 8
crossprod,gvector,logical-method
(crossprod,tcrossprod), 8
crossprod,gvector,matrix-method
(crossprod,tcrossprod), 8
crossprod,gvector,missing-method
(crossprod,tcrossprod), 8
crossprod,gvector,numeric-method
(crossprod,tcrossprod), 8
crossprod,logical,gmatrix-method
(crossprod,tcrossprod), 8
crossprod,logical,gvector-method
(crossprod,tcrossprod), 8
crossprod,matrix,gmatrix-method
(crossprod,tcrossprod), 8
crossprod,matrix,gvector-method
(crossprod,tcrossprod), 8
crossprod,numeric,gmatrix-method
(crossprod,tcrossprod), 8
crossprod,numeric,gvector-method
(crossprod,tcrossprod), 8
crossprod,tcrossprod, 8
crossprod-methods
(crossprod,tcrossprod), 8
dbeta, 17
dbinom, 18
device, 6, 10, 21, 56
device,gmatrix-method (device), 10
device,gvector-method (device), 10
device-methods (device), 10
device<- (device), 10
device<-,gmatrix-method (device), 10
device<-,gvector-method (device), 10
device<--methods (device), 10
dgamma, 19
diag, 10, 32
diag,ANY-method (diag), 10
69
diag,gmatrix-method (diag), 10
diag,gvector-method (diag), 10
diag-methods (diag), 10
diag<-,ANY-method (diag), 10
diag<-,gmatrix-method (diag), 10
diag<--methods (diag), 10
dim, 10, 10
dim,gmatrix-method (dim), 10
dim-methods (dim), 10
dim<-,gmatrix-method (dim), 10
dim<--methods (dim), 10
dimnames, 11, 11, 34
dimnames,gmatrix-method (dimnames), 11
dimnames-methods (dimnames), 11
dimnames<-,gmatrix-method (dimnames), 11
dimnames<--methods (dimnames), 11
dnorm, 54
dpois, 20
elementwise binary operators, 11
elementwise functions, 12
exp,gmatrix-method (elementwise
functions), 12
exp,gvector-method (elementwise
functions), 12
exp-methods (elementwise functions), 12
expm1,gmatrix-method (elementwise
functions), 12
expm1,gvector-method (elementwise
functions), 12
expm1-methods (elementwise functions),
12
floor,gmatrix-method (elementwise
functions), 12
floor,gvector-method (elementwise
functions), 12
floor-methods (elementwise functions),
12
g, 4, 5, 12
g.rep, 13
gamma,gmatrix-method (elementwise
functions), 12
gamma,gvector-method (elementwise
functions), 12
gamma-methods (elementwise functions),
12
gBasicHMC, 14, 51
70
gc, 22
gdbeta, 16
gdbinom, 17
gdgamma, 18
gdnorm (normal), 54
gdpois, 19
gdunif (grunif), 38
gdup, 10, 20, 56
getDevice, 6
getDevice (setDevice), 56
ggc, 21
gident, 22
gkroneckerProd, 23
gmatrix, 5, 23, 49
gmatrix-class, 24
gmatrix-package, 3
gmatTimesDiagVec, 32
gmm, 33
gnamestrip, 34
gorder, 34
gouter, 35
gpnorm (normal), 54
gqnorm (normal), 54
gqr-class, 36
gqr.coef (gqr-class), 36
gqr.coef,ANY-method (gqr-class), 36
gqr.coef,gqr-method (gqr-class), 36
gqr.coef-methods (gqr-class), 36
grbeta (gdbeta), 16
grbinom (gdbinom), 17
grgamma (gdgamma), 18
grnorm (normal), 54
gRowLogSums, 37, 55
grpois (gdpois), 19
grunif, 38
gseq, 39
gset.seed, 40
gsumby, 40
gsvd-class, 41
gtest, 42
gvector, 5, 31, 42
gvector-class, 43
h, 4, 6
h (g), 12
ifelse, 50
ifelse,ANY-method (ifelse), 50
ifelse,gmatrix-method (ifelse), 50
INDEX
ifelse,gvector-method (ifelse), 50
ifelse-methods (ifelse), 50
indexing, 50
is.finite,gmatrix-method (elementwise
functions), 12
is.finite,gvector-method (elementwise
functions), 12
is.finite-methods (elementwise
functions), 12
is.infinite,gmatrix-method
(elementwise functions), 12
is.infinite,gvector-method
(elementwise functions), 12
is.infinite-methods (elementwise
functions), 12
is.na,gmatrix-method (elementwise
functions), 12
is.na,gvector-method (elementwise
functions), 12
is.na-methods (elementwise functions),
12
is.nan,gmatrix-method (elementwise
functions), 12
is.nan,gvector-method (elementwise
functions), 12
is.nan-methods (elementwise functions),
12
keep (gBasicHMC), 14
length, 51
length,gmatrix-method (length), 51
length,gvector-method (length), 51
length-methods (length), 51
lgamma,gmatrix-method (elementwise
functions), 12
lgamma,gvector-method (elementwise
functions), 12
lgamma-methods (elementwise functions),
12
listDevices (setDevice), 56
log,gmatrix-method (elementwise
functions), 12
log,gvector-method (elementwise
functions), 12
log-methods (elementwise functions), 12
log10,gmatrix-method (elementwise
functions), 12
INDEX
log10,gvector-method (elementwise
functions), 12
log10-methods (elementwise functions),
12
log1p,gmatrix-method (elementwise
functions), 12
log1p,gvector-method (elementwise
functions), 12
log1p-methods (elementwise functions),
12
log2,gmatrix-method (elementwise
functions), 12
log2,gvector-method (elementwise
functions), 12
log2-methods (elementwise functions), 12
lpgr-class, 16, 51
matrix, 24
matrix multiplication, 52
max, 52
max,gmatrix-method (max), 52
max,gvector-method (max), 52
max-methods (max), 52
mean, sum, 53
mean,ANY-method (mean, sum), 53
mean,gmatrix-method (mean, sum), 53
mean,gvector-method (mean, sum), 53
mean-methods (mean, sum), 53
min,gmatrix-method (max), 52
min,gvector-method (max), 52
min-methods (max), 52
names, 34, 53
names,gvector-method (names), 53
names-methods (names), 53
names<-,gvector-method (names), 53
names<--methods (names), 53
ncol, 53
ncol,ANY-method (ncol), 53
ncol,gmatrix-method (ncol), 53
ncol-methods (ncol), 53
normal, 54
nrow,ANY-method (ncol), 53
nrow,gmatrix-method (ncol), 53
nrow-methods (ncol), 53
order, 35
outer, 36
qr, 37
71
qr,ANY-method (gqr-class), 36
qr,gmatrix-method (gqr-class), 36
qr-methods (gqr-class), 36
qr.coef, 36, 37
rep, 14
round,gmatrix-method (elementwise
functions), 12
round,gvector-method (elementwise
functions), 12
round-methods (elementwise functions),
12
rowMeans,ANY-method (colMeans), 7
rowMeans,gmatrix-method (colMeans), 7
rowMeans-methods (colMeans), 7
rownames, 7
rownames,ANY-method (colnames), 7
rownames,gmatrix-method (colnames), 7
rownames-methods (colnames), 7
rownames<-,ANY-method (colnames), 7
rownames<-,gmatrix-method (colnames), 7
rownames<--methods (colnames), 7
rowSums, 7
rowSums,ANY-method (colMeans), 7
rowSums,gmatrix-method (colMeans), 7
rowSums-methods (colMeans), 7
rsample, 55
runif, 38
seq, 39
setDevice, 6, 10, 56
setTuningPameters, 57
show, 57
show,gmatrix-method (show), 57
show,gvector-method (show), 57
show-methods (show), 57
sign,gmatrix-method (elementwise
functions), 12
sign,gvector-method (elementwise
functions), 12
sign-methods (elementwise functions), 12
sin,gmatrix-method (elementwise
functions), 12
sin,gvector-method (elementwise
functions), 12
sin-methods (elementwise functions), 12
sinh,gmatrix-method (elementwise
functions), 12
72
sinh,gvector-method (elementwise
functions), 12
sinh-methods (elementwise functions), 12
solve, 37
solve (gqr-class), 36
solve,ANY-method (gqr-class), 36
solve,gmatrix-method (gqr-class), 36
solve,gqr-method (gqr-class), 36
solve-methods (gqr-class), 36
solve.qr, 36, 37
sort, 58
sort,ANY-method (sort), 58
sort,gvector-method (sort), 58
sort,jarrayRef-method (sort), 58
sort,jrectRef-method (sort), 58
sort-methods (sort), 58
sqrt,gmatrix-method (elementwise
functions), 12
sqrt,gvector-method (elementwise
functions), 12
sqrt-methods (elementwise functions), 12
sum,gmatrix-method (mean, sum), 53
sum,gvector-method (mean, sum), 53
sum-methods (mean, sum), 53
svd, 41
svd (gsvd-class), 41
svd,ANY-method (gsvd-class), 41
svd,gmatrix-method (gsvd-class), 41
svd-methods (gsvd-class), 41
t, 58
t,ANY-method (t), 58
t,gmatrix-method (t), 58
t,gvector-method (t), 58
t-methods (t), 58
t.gmatrix (t), 58
t.gvector (t), 58
tan,gmatrix-method (elementwise
functions), 12
tan,gvector-method (elementwise
functions), 12
tan-methods (elementwise functions), 12
tanh,gmatrix-method (elementwise
functions), 12
tanh,gvector-method (elementwise
functions), 12
tanh-methods (elementwise functions), 12
tcrossprod,ANY,ANY-method
(crossprod,tcrossprod), 8
INDEX
tcrossprod,gmatrix,gmatrix-method
(crossprod,tcrossprod), 8
tcrossprod,gmatrix,gvector-method
(crossprod,tcrossprod), 8
tcrossprod,gmatrix,logical-method
(crossprod,tcrossprod), 8
tcrossprod,gmatrix,matrix-method
(crossprod,tcrossprod), 8
tcrossprod,gmatrix,missing-method
(crossprod,tcrossprod), 8
tcrossprod,gmatrix,numeric-method
(crossprod,tcrossprod), 8
tcrossprod,gvector,gmatrix-method
(crossprod,tcrossprod), 8
tcrossprod,gvector,gvector-method
(crossprod,tcrossprod), 8
tcrossprod,gvector,logical-method
(crossprod,tcrossprod), 8
tcrossprod,gvector,matrix-method
(crossprod,tcrossprod), 8
tcrossprod,gvector,missing-method
(crossprod,tcrossprod), 8
tcrossprod,gvector,numeric-method
(crossprod,tcrossprod), 8
tcrossprod,logical,gmatrix-method
(crossprod,tcrossprod), 8
tcrossprod,logical,gvector-method
(crossprod,tcrossprod), 8
tcrossprod,matrix,gmatrix-method
(crossprod,tcrossprod), 8
tcrossprod,matrix,gvector-method
(crossprod,tcrossprod), 8
tcrossprod,numeric,gmatrix-method
(crossprod,tcrossprod), 8
tcrossprod,numeric,gvector-method
(crossprod,tcrossprod), 8
tcrossprod-methods
(crossprod,tcrossprod), 8
type, 8, 58
type,gmatrix-method (type), 58
type,gvector-method (type), 58
type-methods (type), 58
type<- (type), 58
type<-,gmatrix-method (type), 58
type<-,gvector-method (type), 58
type<--methods (type), 58
vector, 43
INDEX
which, 59
which,ANY-method (which), 59
which,gvector-method (which), 59
which-methods (which), 59
73