Package Cubature': July 6, 2020

Package ‘cubature’
July 6, 2020
Type Package
Title Adaptive Multivariate Integration over Hypercubes
Version 2.0.4.1
VignetteBuilder knitr
SystemRequirements GNU make
URL https://bnaras.github.io/cubature
BugReports https://github.com/bnaras/cubature/issues
Description R wrappers around the cubature C library of Steven
G. Johnson for adaptive multivariate integration over hypercubes
and the Cuba C library of Thomas Hahn for deterministic and
Monte Carlo integration. Scalar and vector interfaces for
cubature and Cuba routines are provided; the vector interfaces
are highly recommended as demonstrated in the package
vignette.
License GPL-3
Encoding UTF-8
LinkingTo Rcpp
Imports Rcpp
NeedsCompilation yes
RoxygenNote 7.0.1
Suggests testthat, knitr, mvtnorm, benchr
Author Balasubramanian Narasimhan [aut, cre],
Manuel Koller [ctb],
Steven G. Johnson [aut],
Thomas Hahn [aut],
Annie Bouvier [aut],
Kiên Kiêu [aut],
Simen Gaure [ctb]
Maintainer Balasubramanian Narasimhan <naras@stat.stanford.edu>
Repository CRAN
Date/Publication 2020-07-06 12:44:44
1
2 cubintegrate
R topics documented:
cubature-package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
cubintegrate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
cuhre . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
default_args . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
divonne . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
hcubature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
suave . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
vegas . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Index 27
cubature-package Cubature is a package for adaptive and monte-carlo multidimensional

integration over hypercubes
Description
Cubature is a package for adaptive and monte-carlo multidimensional integration over hypercubes.
It is a wrapper around the pure C, GPLed implementations by Steven G. Johnson (cubature) and
Thomas Hahn (Cuba) libraries.
Author(s)
C code by Steven G. Johnson and Thomas Hahn, R by Balasubramanian Narasimhan, Manuel

Koller, Simen Gaure, Kiên Kiêu, and Annie Bouvier
Maintainer: Balasubramanian Narasimhannaras@stat.stanford.edu
cubintegrate Unified Cubature Integration Interface
Description
Integrate a function within specified limits using method specified. Further arguments specific to
method as well as other arguments to f may be passed. For defaults used in each method, see help
on the method or default_args’s.
cubintegrate 3
Usage
cubintegrate(
f,
lower,
upper,
fDim = 1,
method = c("hcubature", "pcubature", "cuhre", "divonne", "suave", "vegas"),
relTol = 1e-05,
absTol = 1e-12,
maxEval = 10^6,
nVec = 1L,
...
)
Arguments
f The function (integrand) to be integrated. Can be vectorized version, but the
additional arguments ... must indicate via either vectorInterface = TRUE for
hcubature and pcubature, or a value for nVec. See details on each method.
lower The lower limit of integration, a vector for hypercubes.
upper The upper limit of integration, a vector for hypercubes.
fDim The number of components of f, default 1, bears no relation to the dimension of
the hypercube over which integration is performed.
method the method to use should be one of "hcubature", "pcubature", "cuhre", "di-
vonne", "suave" or "vegas".
relTol The maximum tolerance, default 1e-5.
absTol the absolute tolerance, default 1e-12.
maxEval The maximum number of function evaluations needed, default 10^6. Note that
the actual number of function evaluations performed is only approximately guar-
anteed not to exceed this number.
nVec the number of vectorization points for Cuba C library, default 1, but can be set
to an integer > 1 for vectorization, for example, 1024. The function f above
needs to handle the vector of points appropriately; see vignette examples. Un-
like Cuba, the cubature C library manages the number of points on its own and
can vary between calls. Therefore, any value for nVec greater than one implies
vectorization for a cubature method.
... All other arguments which may include integration method specific parameters
and those for f. Unrecognized parameters for integration method are presumed
to be intended for f and so processed.
Value
The returned value is a list of items: -
integral the value of the integral
-
4 cuhre
error the estimated relative error for cubature; for Cuba it is the estimated absolute
error
neval the number of times the function was evaluated
returnCode the actual integer return code of the C routine; a non-zero value usually indicates
problems; further interpretation depends on method
nregions for Cuba routines, the actual number of subregions needed

prob the χ2 -probability (not the χ2 -value itself!) that error is not a reliable estimate
of the true integration error.
See Also
default_args, hcubature, pcubature, cuhre, vegas, suave, divonne
Examples
I.1d <- function(x) {
sin(4*x) *
x * ((x * ( x * (x*x-4) + 1) - 1))
}
I.1d_v <- function(x) {
matrix(apply(x, 2, function(z)
sin(4 * z) *
z * ((z * ( z * (z * z - 4) + 1) - 1))),
ncol = ncol(x))
}
cubintegrate(f = I.1d, lower = -2, upper = 2, method = "pcubature")
cubintegrate(f = I.1d, lower = -2, upper = 2, method = "cuhre", flags=list(verbose = 2))
cubintegrate(f = I.1d_v, lower = -2, upper = 2, method = "hcubature", nVec = 2L)
cubintegrate(f = I.1d_v, lower = -2, upper = 2, method = "cuhre", nVec = 128L)
cuhre Integration by a Deterministic Iterative Adaptive Algorithm
Description
Implement a deterministic algorithm for multidimensional numerical integration. Its algorithm uses
one of several cubature rules in a globally adaptive subdivision scheme. The subdivision algorithm
is similar to suave’s.
cuhre 5
Usage
cuhre(
f,
nComp = 1L,
lowerLimit,
upperLimit,
...,
relTol = 1e-05,
absTol = 1e-12,
minEval = 0L,
maxEval = 10^6,
flags = list(verbose = 0L, final = 1L, keep_state = 0L, level = 0L),
key = 0L,
nVec = 1L,
stateFile = NULL
)
Arguments
f The function (integrand) to be integrated. For cuhre, it can be something as
simple as a function of a single argument, say x.
nComp The number of components of f, default 1, bears no relation to the dimension of
lowerLimit The lower limit of integration, a vector for hypercubes.
upperLimit The upper limit of integration, a vector for hypercubes.
... All other arguments passed to the function f.
minEval the minimum number of function evaluations required
flags flags governing the integration. The list here is exhaustive to keep the docu-
mentation and invocation uniform, but not all flags may be used for a particular
method as noted below. List components:
verbose encodes the verbosity level, from 0 (default) to 3. Level 0 does not
print any output, level 1 prints reasonable information on the progress of
the integration, level 2 also echoes the input parameters, and level 3 further
prints the subregion results.
final when 0, all sets of samples collected on a subregion during the various
iterations or phases contribute to the final result. When 1, only the last
(largest) set of samples is used in the final result.
smooth Applies to Suave and Vegas only. When 0, apply additional smoothing
to the importance function, this moderately improves convergence for many
integrands. When 1, use the importance function without smoothing, this
should be chosen if the integrand has sharp edges.
6 cuhre
keep_state when nonzero, retain state file if argument stateFile is non-null,

else delete stateFile if specified.
load_state Applies to Vegas only. Reset the integrator’s state even if a state
file is present, i.e. keep only the grid. Together with keep_state this allows
a grid adapted by one integration to be used for another integrand.
level applies only to Divonne, Suave and Vegas. When 0, Mersenne Twister
random numbers are used. When nonzero Ranlux random numbers are
used, except when rngSeed is zero which forces use of Sobol quasi-random
numbers. Ranlux implements Marsaglia and Zaman’s 24-bit RCARRY al-
gorithm with generation period p, i.e. for every 24 generated numbers used,
another p-24 are skipped. The luxury level for the Ranlux generator may
be encoded in level as follows:
Level 1 (p = 48) gives very long period, passes the gap test but fails spec-
tral test
Level 2 (p = 97) passes all known tests, but theoretically still defective
Level 3 (p = 223) any theoretically possible correlations have very small
chance of being observed
Level 4 (p = 389) highest possible luxury, all 24 bits chaotic
Levels 5-23 default to 3, values above 24 directly specify the period p.
Note that Ranlux’s original level 0, (mis)used for selecting Mersenne Twister
in Cuba, is equivalent to level = 24.
key the quadrature rule key: key = 7,9,11,13 selects the cubature rule of degree
key. Note that the degree-11 rule is available only in 3 dimensions, the degree-
13 rule only in 2 dimensions. For other values, including the default 0, the rule
is the degree-13 rule in 2 dimensions, the degree-11 rule in 3 dimensions, and
the degree-9 rule otherwise.
nVec the number of vectorization points, default 1, but can be set to an integer > 1 for
vectorization, for example, 1024 and the function f above needs to handle the
vector of points appropriately. See vignette examples.
stateFile the name of an external file. Vegas can store its entire internal state (i.e. all the
information to resume an interrupted integration) in an external file. The state
file is updated after every iteration. If, on a subsequent invocation, Vegas finds a
file of the specified name, it loads the internal state and continues from the point
it left off. Needless to say, using an existing state file with a different integrand
generally leads to wrong results. Once the integration finishes successfully, i.e.
the prescribed accuracy is attained, the state file is removed. This feature is
useful mainly to define ‘check-points’ in long-running integrations from which
the calculation can be restarted.
Details
See details in the documentation.
Value
A list with components:
cuhre 7
nregions the actual number of subregions needed

neval the actual number of integrand evaluations needed
returnCode if zero, the desired accuracy was reached, if -1, dimension out of range, if 1, the
accuracy goal was not met within the allowed maximum number of integrand evaluations.
integral vector of length nComp; the integral of integrand over the hypercube
error vector of length nComp; the presumed absolute error of integral
prob vector of length nComp; the χ2 -probability (not the χ2 -value itself!) that error is not a
reliable estimate of the true integration error.
References
J. Berntsen, T. O. Espelid (1991) An adaptive algorithm for the approximate calculation of multiple
integrals. ACM Transactions on Mathematical Software, 17(4), 437-451.
T. Hahn (2005) CUBA-a library for multidimensional numerical integration. Computer Physics
Communications, 168, 78-95.
See http://www.feynarts.de/cuba/
See Also
vegas, suave, divonne
Examples
integrand <- function(arg) {

x <- arg[1]
y <- arg[2]
z <- arg[3]
ff <- sin(x)*cos(y)*exp(z);
return(ff)
} # End integrand
NDIM <- 3
NCOMP <- 1
cuhre(f = integrand,
lowerLimit = rep(0, NDIM),
upperLimit = rep(1, NDIM),
relTol = 1e-3, absTol= 1e-12,
flags = list(verbose = 2, final = 0))
8 divonne
default_args Default arguments for each integration method
Description
Since each method has a different set of parameters, this function returns the default values of all
parameters that can be modified and passed to integration routines.
Usage
default_args()
Value
a named list of parameters for each method.
Examples
default_args()
divonne Integration by Stratified Sampling for Variance Reduction
Description
Divonne works by stratified sampling, where the partioning of the integration region is aided by
methods from numerical optimization.
Usage
divonne(
f,
nComp = 1L,
lowerLimit,
upperLimit,
...,
relTol = 1e-05,
absTol = 1e-12,
minEval = 0L,
maxEval = 10^6,
flags = list(verbose = 0L, final = 1L, keep_state = 0L, level = 0L),
rngSeed = 0L,
nVec = 1L,
key1 = 47L,
key2 = 1L,
key3 = 1L,
divonne 9
maxPass = 5L,
border = 0,
maxChisq = 10,
minDeviation = 0.25,
xGiven = NULL,
nExtra = 0L,
peakFinder = NULL,
stateFile = NULL
)
Arguments
f The function (integrand) to be integrated as in cuhre. Optionally, the function
can take an additional arguments in addition to the variable being integrated:
- cuba_phase. The last argument, phase, indicates the integration phase: 0.
sampling of the points in xgiven, 1. partitioning phase, 2. final integration
phase, 3. refinement phase. This information might be useful if the integrand
takes long to compute and a sufficiently accurate approximation of the integrand
is available. The actual value of the integral is only of minor importance in the
partitioning phase, which is instead much more dependent on the peak structure
of the integrand to find an appropriate tessellation. An approximation which
reproduces the peak structure while leaving out the fine details might hence
be a perfectly viable and much faster substitute when cuba_phase < 2. In all
other instances, phase can be ignored and it is entirely admissible to define the
integrand without it. which is the
10 divonne
tral test
rngSeed seed, default 0, for the random number generator. Note the articulation with
level settings for flag
key1 integer that determines sampling in the partitioning phase: key1 = 7,9,11,13
selects the cubature rule of degree key1. Note that the degree-11 rule is available
only in 3 dimensions, the degree-13 rule only in 2 dimensions. For other values
of key1, a quasi-random sample of n = |key1| points is used, where the sign of
key1 determines the type of sample, key1 = 0, use the default rule. key1 > 0, use
a Korobov quasi-random sample, key1 < 0, use a Sobol quasi-random sample if
flags$seed is zero, otherwise a “standard” sample (Mersenne Twister) pseudo-
random sample
key2 integer that determines sampling in the final integration phase: same as key1,
but here
n = |key2|
determines the number of points, n > 39, sample n points, n < 40, sample
n nneed points, where nneed is the number of points needed to reach the pre-
scribed accuracy, as estimated by Divonne from the results of the partitioning
phase.
divonne 11
key3 integer that sets the strategy for the refinement phase: key3 = 0, do not treat
the subregion any further. key3 = 1, split the subregion up once more. Other-
wise, the subregion is sampled a third time with key3 specifying the sampling
parameters exactly as key2 above.
maxPass integer that controls the thoroughness of the partitioning phase: The partition-
ing phase terminates when the estimated total number of integrand evaluations
(partitioning plus final integration) does not decrease for maxPass successive
iterations. A decrease in points generally indicates that Divonne discovered
new structures of the integrand and was able to find a more effective partition-
ing. maxPass can be understood as the number of “safety” iterations that are
performed before the partition is accepted as final and counting consequently
restarts at zero whenever new structures are found.
border the relative width of the border of the integration region. Points falling into the
border region will not be sampled directly, but will be extrapolated from two
samples from the interior. Use a non-zero border if the integrand subroutine
cannot produce values directly on the integration boundary. The relative width
of the border is identical in all the dimensions. For example, set border=0.1
for a border of width equal to 10\ width of the integration region.
maxChisq the maximum χ2 value a single subregion is allowed to have in the final integra-
tion phase. Regions which fail this χ2 test and whose sample averages differ by
more than min.deviation move on to the refinement phase.
minDeviation a bound, given as the fraction of the requested error of the entire integral, which
determines whether it is worthwhile further examining a region that failed the
χ2 test. Only if the two sampling averages obtained for the region differ by more
than this bound is the region further treated.
xGiven a matrix ( nDim, nGiven). A list of nGiven points where the integrand might
have peaks. Divonne will consider these points when partitioning the integration
region. The idea here is to help the integrator find the extrema of the integrand
in the presence of very narrow peaks. Even if only the approximate location of
such peaks is known, this can considerably speed up convergence.
nExtra the maximum number of extra points the peak-finder subroutine will return. If
nextra is zero, peakfinder is not called and an arbitrary object may be passed
in its place, e.g. just 0.
peakFinder the peak-finder subroutine. This R function is called whenever a region is up for
subdivision and is supposed to point out possible peaks lying in the region, thus
acting as the dynamic counterpart of the static list of points supplied in xgiven.
It is expected to be declared as peakFinder <-function(bounds,nMax) where
bounds is a matrix of dimension (2,nDim) which contains the lower (row 1) and
upper (row 2) bounds of the subregion. The returned value should be a matrix
(nX,nDim) where nX is the actual number of points (should be less or equal to
nMax).
12 divonne
Details
Divonne uses stratified sampling for variance reduction, that is, it partitions the integration region
such that all subregions have an approximately equal value of a quantity called the spread (volume
times half-range).
Value

References
J. H. Friedman, M. H. Wright (1981) A nested partitioning procedure for numerical multiple inte-
gration. ACM Trans. Math. Software, 7(1), 76-92.
J. H. Friedman, M. H. Wright (1981) User’s guide for DIVONNE. SLAC Report CGTM-193-REV,
CGTM-193, Stanford University.
See Also
cuhre, suave, vegas
Examples
integrand <- function(arg, phase) {
x <- arg[1]
y <- arg[2]
z <- arg[3]
return(ff)
}
divonne(integrand, relTol=1e-3, absTol=1e-12, lowerLimit = rep(0, 3), upperLimit = rep(1, 3),
hcubature 13
flags=list(verbose = 2), key1= 47)
# Example with a peak-finder function

nDim <- 3L
peakf <- function(bounds, nMax) {
# print(bounds) # matrix (ndim,2)
x <- matrix(0, ncol = nMax, nrow = nDim)
pas <- 1 / (nMax - 1)
# 1ier point
x[, 1] <- rep(0, nDim)
# Les autres points
for (i in 2L:nMax) {
x[, i] <- x[, (i - 1)] + pas
}
x
} #end peakf
divonne(integrand, relTol=1e-3, absTol=1e-12,

lowerLimit = rep(0, 3), upperLimit = rep(1, 3),
flags=list(verbose = 2), peakFinder = peakf, nExtra = 4L)
hcubature Adaptive multivariate integration over hypercubes (hcubature and

pcubature)
Description
The function performs adaptive multidimensional integration (cubature) of (possibly) vector-valued
integrands over hypercubes. The function includes a vector interface where the integrand may be
evaluated at several hundred points in a single call.
Usage
hcubature(
f,
lowerLimit,
upperLimit,
...,
tol = 1e-05,
fDim = 1,
maxEval = 0,
absError = 0,
doChecking = FALSE,
vectorInterface = FALSE,
norm = c("INDIVIDUAL", "PAIRED", "L2", "L1", "LINF")
)
pcubature(
f,
14 hcubature
lowerLimit,
upperLimit,
...,
tol = 1e-05,
fDim = 1,
maxEval = 0,
absError = 0,
doChecking = FALSE,
vectorInterface = FALSE,
norm = c("INDIVIDUAL", "PAIRED", "L2", "L1", "LINF")
)
Arguments
f The function (integrand) to be integrated
lowerLimit The lower limit of integration, a vector for hypercubes
upperLimit The upper limit of integration, a vector for hypercubes
... All other arguments passed to the function f
tol The maximum tolerance, default 1e-5.
fDim The dimension of the integrand, default 1, bears no relation to the dimension of
the hypercube
maxEval The maximum number of function evaluations needed, default 0 implying no
limit. Note that the actual number of function evaluations performed is only
approximately guaranteed not to exceed this number.
absError The maximum absolute error tolerated
doChecking As of version 2.0, this flag is ignored and will be dropped in forthcoming ver-
sions
vectorInterface
A flag that indicates whether to use the vector interface and is by default FALSE.
See details below
norm For vector-valued integrands, norm specifies the norm that is used to measure
the error and determine convergence properties. See below.
Details
The function merely calls Johnson’s C code and returns the results.
One can specify a maximum number of function evaluations (default is 0 for no limit). Otherwise,
the integration stops when the estimated error is less than the absolute error requested, or when the
estimated error is less than tol times the integral, in absolute value, or the maximum number of
iterations is reached (see parameter info below), whichever is earlier.
For compatibility with earlier versions, the adaptIntegrate function is an alias for the underlying
hcubature function which uses h-adaptive integration. Otherwise, the calling conventions are the
same.
We highly recommend referring to the vignette to achieve the best results!
hcubature 15
The hcubature function is the h-adaptive version that recursively partitions the integration domain
into smaller subdomains, applying the same integration rule to each, until convergence is achieved.
The p-adaptive version, pcubature, repeatedly doubles the degree of the quadrature rules until
convergence is achieved, and is based on a tensor product of Clenshaw-Curtis quadrature rules.
This algorithm is often superior to h-adaptive integration for smooth integrands in a few (<=3)
dimensions, but is a poor choice in higher dimensions or for non-smooth integrands. Compare with
hcubature which also takes the same arguments.
The vector interface requires the integrand to take a matrix as its argument. The return value should
also be a matrix. The number of points at which the integrand may be evaluated is not under user
control: the integration routine takes care of that and this number may run to several hundreds. We
strongly advise vectorization; see vignette.
The norm argument is irrelevant for scalar integrands and is ignored. Given vectors v and e of
estimated integrals and errors therein, respectively, the norm argument takes on one of the following
values:
INDIVIDUAL Convergence is achieved only when each integrand (each component of v and e) in-
dividually satisfies the requested error tolerances
L1, L2, LINF The absolute error is measured as |e| and the relative error as |e|/|v|, where |...| is the
L1 , L2 , or ∞ norm, respectively
PAIRED Like INDIVIDUAL, except that the integrands are grouped into consecutive pairs, with the
error tolerance applied in an L2 sense to each pair. This option is mainly useful for integrating
vectors of complex numbers, where each consecutive pair of real integrands is the real and
imaginary parts of a single complex integrand, and the concern is only the error in the complex
plane rather than the error in the real and imaginary parts separately
Value
The returned value is a list of four items:
integral the value of the integral

error the estimated relative error
functionEvaluations
the number of times the function was evaluated
returnCode the actual integer return code of the C routine
Author(s)
Balasubramanian Narasimhan
Examples
## Not run:
## Test function 0
## Compare with original cubature result of
## ./cubature_test 2 1e-4 0 0
## 2-dim integral, tolerance = 0.0001
## integrand 0: integral = 0.708073, est err = 1.70943e-05, true err = 7.69005e-09
16 hcubature
## #evals = 17
testFn0 <- function(x) {

prod(cos(x))
}
hcubature(testFn0, rep(0,2), rep(1,2), tol=1e-4)
pcubature(testFn0, rep(0,2), rep(1,2), tol=1e-4)
M_2_SQRTPI <- 2/sqrt(pi)
## Test function 1
## #evals = 5115

val <- sum (((1-x) / x)^2)
scale <- prod(M_2_SQRTPI/x^2)
exp(-val) * scale
}
hcubature(testFn1, rep(0, 3), rep(1, 3), tol=1e-4)

pcubature(testFn1, rep(0, 3), rep(1, 3), tol=1e-4)
##
## Test function 2
## #evals = 166141

## discontinuous objective: volume of hypersphere
radius <- as.double(0.50124145262344534123412)
ifelse(sum(x*x) < radius*radius, 1, 0)
}
hcubature(testFn2, rep(0, 2), rep(1, 2), tol=1e-4)

pcubature(testFn2, rep(0, 2), rep(1, 2), tol=1e-4)
##
## Test function 3
## integrand 3: integral = 1, est err = 0, true err = 2.22045e-16
## #evals = 33
hcubature 17

prod(2*x)
}

##
## Test function 4 (Gaussian centered at 1/2)
## integrand 4: integral = 1, est err = 9.84399e-05, true err = 2.78894e-06
## #evals = 1853

a <- 0.1
s <- sum((x - 0.5)^2)
(M_2_SQRTPI / (2. * a))^length(x) * exp (-s / (a * a))
}

##
## Test function 5 (double Gaussian)
## #evals = 59631

a <- 0.1
s1 <- sum((x - 1/3)^2)
s2 <- sum((x - 2/3)^2)
0.5 * (M_2_SQRTPI / (2. * a))^length(x) * (exp(-s1 / (a * a)) + exp(-s2 / (a * a)))
}

##
## Test function 6 (Tsuda's example)
## #evals = 18753

a <- (1 + sqrt(10.0)) / 9.0
prod(a / (a + 1) * ((a + 1) / (a + x))^2)
18 hcubature

##
## Test function 7
## test integrand from W. J. Morokoff and R. E. Caflisch, "Quasi=
## Monte Carlo integration," J. Comput. Phys 122, 218-230 (1995).
## Designed for integration on [0,1]^dim, integral = 1. */
## #evals = 7887

n <- length(x)
p <- 1/n
(1 + p)^n * prod(x^p)
}

## Example from web page

## http://ab-initio.mit.edu/wiki/index.php/Cubature
##
## f(x) = exp(-0.5(euclidean_norm(x)^2)) over the three-dimensional
## hyperbcube [-2, 2]^3
## Compare with original cubature result
testFnWeb <- function(x) {
exp(-0.5 * sum(x^2))
}
hcubature(testFnWeb, rep(-2,3), rep(2,3), tol=1e-4)

pcubature(testFnWeb, rep(-2,3), rep(2,3), tol=1e-4)
## Test function I.1d from

## Numerical integration using Wang-Landau sampling
## Y. W. Li, T. Wust, D. P. Landau, H. Q. Lin
## Computer Physics Communications, 2007, 524-529
## Compare with exact answer: 1.63564436296
##
sin(4*x) *
x * ((x * ( x * (x*x-4) + 1) - 1))
}
hcubature(I.1d, -2, 2, tol=1e-7)

pcubature(I.1d, -2, 2, tol=1e-7)
hcubature 19
## Test function I.2d from

## Numerical integration using Wang-Landau sampling
## Y. W. Li, T. Wust, D. P. Landau, H. Q. Lin
## Computer Physics Communications, 2007, 524-529
## Compare with exact answer: -0.01797992646
##
##
x1 = x[1]
x2 = x[2]
sin(4*x1+1) * cos(4*x2) * x1 * (x1*(x1*x1)^2 - x2*(x2*x2 - x1) +2)
}
hcubature(I.2d, rep(-1, 2), rep(1, 2), maxEval=10000)

pcubature(I.2d, rep(-1, 2), rep(1, 2), maxEval=10000)
##
## Example of multivariate normal integration borrowed from
## package mvtnorm (on CRAN) to check ... argument
## Compare with output of
## pmvnorm(lower=rep(-0.5, m), upper=c(1,4,2), mean=rep(0, m), corr=sigma, alg=Miwa())
## 0.3341125. Blazing quick as well! Ours is, not unexpectedly, much slower.
##
dmvnorm <- function (x, mean, sigma, log = FALSE) {
if (is.vector(x)) {
x <- matrix(x, ncol = length(x))
}
if (missing(mean)) {
mean <- rep(0, length = ncol(x))
}
if (missing(sigma)) {
sigma <- diag(ncol(x))
}
if (NCOL(x) != NCOL(sigma)) {
stop("x and sigma have non-conforming size")
}
if (!isSymmetric(sigma, tol = sqrt(.Machine$double.eps),
check.attributes = FALSE)) {
stop("sigma must be a symmetric matrix")
}
if (length(mean) != NROW(sigma)) {
stop("mean and sigma have non-conforming size")
}
distval <- mahalanobis(x, center = mean, cov = sigma)
logdet <- sum(log(eigen(sigma, symmetric = TRUE, only.values = TRUE)$values))
logretval <- -(ncol(x) * log(2 * pi) + logdet + distval)/2
if (log)
return(logretval)
exp(logretval)
}
m <- 3
20 suave
sigma <- diag(3)

sigma[2,1] <- sigma[1, 2] <- 3/5 ; sigma[3,1] <- sigma[1, 3] <- 1/3
sigma[3,2] <- sigma[2, 3] <- 11/15
hcubature(dmvnorm, lower=rep(-0.5, m), upper=c(1,4,2),
mean=rep(0, m), sigma=sigma, log=FALSE,
maxEval=10000)
pcubature(dmvnorm, lower=rep(-0.5, m), upper=c(1,4,2),
mean=rep(0, m), sigma=sigma, log=FALSE,
maxEval=10000)
## End(Not run)
suave Integration with SUbregion-Adaptive Vegas Algorithm
Description
Suave uses vegas-like importance sampling combined with a globally adaptive subdivision strategy:
Until the requested accuracy is reached, the region with the largest error at the time is bisected in the
dimension in which the fluctuations of the integrand are reduced most. The number of new samples
in each half is prorated for the fluctuation in that half.
Usage
suave(
f,
nComp = 1L,
lowerLimit,
upperLimit,
...,
relTol = 1e-05,
absTol = 1e-12,
minEval = 0L,
maxEval = 10^6,
flags = list(verbose = 0L, final = 1L, smooth = 0L, keep_state = 0L, level = 0L),
rngSeed = 0L,
nVec = 1L,
nNew = 1000L,
nMin = 50L,
flatness = 50,
stateFile = NULL
)
Arguments
can take two additional arguments in addition to the variable being integrated: -
suave 21
cuba_weight which is the weight of the point being sampled, - cuba_iter the
current iteration number. The function author may choose to use these in any
appropriate way or ignore them altogether.
tral test
22 suave

nNew the number of new integrand evaluations in each subdivision.
nMin the minimum number of samples a former pass must contribute to a subregion
to be considered in that region’s compound integral value. Increasing nmin may
reduce jumps in the χ2 value.
flatness the parameter p, or the type of norm used to compute the fluctuation of a sample.
This determines how prominently "outliers," i.e. individual samples with a large
fluctuation, figure in the total fluctuation, which in turn determines how a region
is split up. As suggested by its name, flatness should be chosen large for "flat"
integrands and small for "volatile" integrands with high peaks. Note that since
flatness appears in the exponent, one should not use too large values (say, no
more than a few hundred) lest terms be truncated internally to prevent overflow.
Details
Value
vegas 23
References
See Also
cuhre, divonne, vegas
Examples
integrand <- function(arg) {

x <- arg[1]
y <- arg[2]
z <- arg[3]
return(ff)
} # end integrand
suave(integrand, lowerLimit = rep(0, 3), upperLimit = rep(1, 3),
relTol=1e-3, absTol=1e-12,
flags=list(verbose=2, final=0))
vegas Integration by a Monte Carlo Algorithm
Description
Implement a Monte Carlo algorithm for multidimensional numerical integration. This algorithm
uses importance sampling as a variance-reduction technique. Vegas iteratively builds up a piecewise
constant weight function, represented on a rectangular grid. Each iteration consists of a sampling
step followed by a refinement of the grid.
Usage
vegas(
f,
nComp = 1L,
lowerLimit,
upperLimit,
...,
relTol = 1e-05,
absTol = 1e-12,
minEval = 0L,
maxEval = 10^6,
flags = list(verbose = 0L, final = 1L, smooth = 0L, keep_state = 0L, load_state = 0L,
level = 0L),
rngSeed = 12345L,
24 vegas
nVec = 1L,
nStart = 1000L,
nIncrease = 500L,
nBatch = 1000L,
gridNo = 0L,
stateFile = NULL
)
Arguments
can take two additional arguments in addition to the variable being integrated: -
cuba_weight which is the weight of the point being sampled, - cuba_iter the
current iteration number. The function author may choose to use these in any
appropriate way or ignore them altogether.
vegas 25
tral test
nStart the number of integrand evaluations per iteration to start with.
nIncrease the increase in the number of integrand evaluations per iteration. The j-th itera-
tion evaluates the integrand at nStart+(j-1)*nincrease points.
nBatch Vegas samples points not all at once, but in batches of a predetermined size, to
avoid excessive memory consumption. nbatch is the number of points sampled
in each batch. Tuning this number should usually not be necessary as perfor-
mance is affected significantly only as far as the batch of samples fits into the
CPU cache.
gridNo an integer. Vegas may accelerate convergence to keep the grid accumulated
during one integration for the next one, if the integrands are reasonably similar
to each other. Vegas maintains an internal table with space for ten grids for this
purpose. If gridno is a number between 1 and 10, the grid is not discarded
at the end of the integration, but stored in the respective slot of the table for a
future invocation. The grid is only re-used if the dimension of the subsequent
integration is the same as the one it originates from. In repeated invocations it
may become necessary to flush a slot in memory. In this case the negative of the
grid number should be set. Vegas will then start with a new grid and also restore
the grid number to its positive value, such that at the end of the integration the
grid is again stored in the indicated slot.
26 vegas
Details
Value
References
G. P. Lepage (1978) A new algorithm for adaptive multidimensional integration. J. Comput. Phys.,
27, 192-210.
G. P. Lepage (1980) VEGAS - An adaptive multi-dimensional integration program. Research Re-
port CLNS-80/447. Cornell University, Ithaca, N.-Y.
See Also
cuhre, suave, divonne
Examples
integrand <- function(arg, weight) {

x <- arg[1]
y <- arg[2]
z <- arg[3]
return(ff)
} # end integrand
vegas(integrand, lowerLimit = rep(0, 3), upperLimit = rep(1, 3),
relTol=1e-3, absTol=1e-12,
flags=list(verbose=2, final=0))
Index
∗ math
cuhre, 4
divonne, 8
hcubature, 13
suave, 20
vegas, 23
∗ package
cubature-package, 2
adaptIntegrate (hcubature), 13
cubature (cubature-package), 2
cubature-package, 2
cubintegrate, 2
cuhre, 4, 4, 9, 12, 20, 23, 24, 26
default_args, 2, 4, 8
divonne, 4, 7, 8, 23, 26
hcubature, 4, 13
pcubature, 4
pcubature (hcubature), 13
suave, 4, 7, 12, 20, 26
vegas, 4, 7, 12, 20, 23, 23
27

Package Cubature': July 6, 2020

Uploaded by

Copyright:

Available Formats

Package Cubature': July 6, 2020

Uploaded by

Document Information

Original Title

Copyright

Available Formats

Share this document

Share or Embed Document

Sharing Options

Did you find this document useful?

Is this content inappropriate?

Copyright:

Available Formats

Package Cubature': July 6, 2020

Uploaded by

Copyright:

Available Formats

Package ‘cubature’

cubature-package Cubature is a package for adaptive and monte-carlo multidimensional

C code by Steven G. Johnson and Thomas Hahn, R by Balasubramanian Narasimhan, Manuel

cubintegrate Unified Cubature Integration Interface

nregions for Cuba routines, the actual number of subregions needed

default_args, hcubature, pcubature, cuhre, vegas, suave, divonne

cuhre Integration by a Deterministic Iterative Adaptive Algorithm

keep_state when nonzero, retain state file if argument stateFile is non-null,

nregions the actual number of subregions needed

vegas, suave, divonne

integrand <- function(arg) {

default_args Default arguments for each integration method

divonne Integration by Stratified Sampling for Variance Reduction

nregions the actual number of subregions needed

flags=list(verbose = 2), key1= 47)

# Example with a peak-finder function

divonne(integrand, relTol=1e-3, absTol=1e-12,

hcubature Adaptive multivariate integration over hypercubes (hcubature and

integral the value of the integral

testFn0 <- function(x) {

hcubature(testFn0, rep(0,2), rep(1,2), tol=1e-4)

pcubature(testFn0, rep(0,2), rep(1,2), tol=1e-4)

M_2_SQRTPI <- 2/sqrt(pi)

testFn1 <- function(x) {

hcubature(testFn1, rep(0, 3), rep(1, 3), tol=1e-4)

testFn2 <- function(x) {

hcubature(testFn2, rep(0, 2), rep(1, 2), tol=1e-4)

testFn3 <- function(x) {

hcubature(testFn3, rep(0,3), rep(1,3), tol=1e-4)

testFn4 <- function(x) {

hcubature(testFn4, rep(0,2), rep(1,2), tol=1e-4)

testFn5 <- function(x) {

hcubature(testFn5, rep(0,3), rep(1,3), tol=1e-4)

testFn6 <- function(x) {

hcubature(testFn6, rep(0,4), rep(1,4), tol=1e-4)

testFn7 <- function(x) {

hcubature(testFn7, rep(0,3), rep(1,3), tol=1e-4)

## Example from web page

hcubature(testFnWeb, rep(-2,3), rep(2,3), tol=1e-4)

## Test function I.1d from

hcubature(I.1d, -2, 2, tol=1e-7)

## Test function I.2d from

hcubature(I.2d, rep(-1, 2), rep(1, 2), maxEval=10000)

sigma <- diag(3)

suave Integration with SUbregion-Adaptive Vegas Algorithm

Level 4 (p = 389) highest possible luxury, all 24 bits chaotic

integrand <- function(arg) {

vegas Integration by a Monte Carlo Algorithm

integrand <- function(arg, weight) {

suave, 4, 7, 12, 20, 26

vegas, 4, 7, 12, 20, 23, 23

You might also like