spam: SPArse Matrix

Set of functions for sparse matrix algebra. Differences with SparseM/Matrix are: (1) we only support (essentially) one sparse matrix format, (2) based on transparent and simple structure(s), (3) tailored for MCMC calculations within GMRF. (4) S3 and S4 like-"compatible" ... and it is fast.

AuthorReinhard Furrer [aut, cre], Florian Gerber [ctb]
Date of publication2016-08-30 15:18:05
MaintainerReinhard Furrer <reinhard.furrer@math.uzh.ch>
LicenseLGPL-2
Version1.4-0
http://www.math.uzh.ch/furrer/software/spam/

View on CRAN

Man pages

adjacency: Administrative districts of Germany

allequal: Test if Two 'spam' Objects are (Nearly) Equal

apply: Apply Functions Over Sparse Matrix Margins

bandwidth: Bandwidth of a Sparse Matrix

bdiag: Binds Arrays Corner-to-Corner

chol: Cholesky Factorization for Sparse Matrices

circulant: Create Circulant Matrices

cleanup: Cleaning up sparse matrices

coerce: Force a 'spam' Object to Belong to a Class

coercion: Coercion to a Vector

complexity: Complexity for Sparse Matrices

constructors: Slot modification

cov: Covariance functions

crossprod: Spam Matrix Crossproduct

det: Calculate the determinant of a positive definite Sparse...

diag: Sparse Matrix diagonals

diff: Lagged Differences

dim: Dimensions of an Object

display: Graphially Represent the Nonzero Entries

foreign: Transformation to other sparse formats

germany: Plot administrative districts of Germany

germanydata: Meta-data about administrative districts of Germany

grid_trace2: Two trace plots and a scatter plot.

grid_zoom: grid_zoom

headtail: Return the First or Last Part of an Object

history.spam: Brief Overview of the History

image: Display a spam Object as Color Image

import: Read External Matrix Formats

isSymmetric: Test if a spam matrix is Symmetric

kronecker: Kronecker Products on Sparse Matrices

landkreis: Administrative districts of Germany

lu.tri: Lower and Upper Triangular Part of a Sparse Matrix

makeprec: Create Precision Matrices

math: Mathematical functions

math2: Rounding of Numbers

methods: Methods for sparse matrices

mle: Maximum likelihood estimates

nearestdist: Distance Matrix Computation

operations: Basic Linear Algebra for Sparse Matrices

options: Options Settings

Oral: Oral Cavity Cancer

ordering: Extract the permutation

pad: Padding a (sparse) matrix

permutation: Permute a matrix

powerboost: Specific options Setting

precmat: IGMRF Precision Matrices

print: Printing and summarizing sparse matrices

rdist: Wrapper for Distance Matrix Computation

rmvnorm: Draw Multivariate Normals

rmvnorm.const: Draw Constrainted Multivariate Normals

rowcolstats: Form Row and Column Sums and Means

s3only: Wappers for Sparse Matrices

solve: Linear Equation Solving for Sparse Matrices

spam.chol.NgPeyton-class: Class "spam.chol.NgPeyton"

spam-class: Class "spam"

spam.creation: Sparse Matrix Class

spam-deprecated: Deprecated Objects in Package 'spam'

spam.internal: Spam internal and auxiliary functions

spam-package: SPArse Matrix Package

summary: Rounding of Numbers

todo: Small "ToDo" list

toeplitz: Create Toeplitz Matrices

triplet: Transform a spam format to triplets

UScounties: Adjacency structure of the counties in the contiguous United...

USprecip: Monthly total precipitation (mm) for April 1948 in the...

version: Spam Version Information

xybind: Combine spam Matrices by Rows or Columns

Functions

abs.spam Man page
abs,spam-method Man page
acosh.spam Man page
acosh,spam-method Man page
acos.spam Man page
acos,spam-method Man page
adjacency Man page
adjacency.landkreis Man page
adjacency.spam Man page
all.equal,matrix,spam-method Man page
all.equal.spam Man page
all.equal,spam,matrix-method Man page
all.equal,spam,spam-method Man page
all.spam Man page
all,spam-method Man page
\%*\%,ANY,ANY-method Man page
any.spam Man page
any,spam-method Man page
^,ANY,spam-method Man page
|,ANY,spam-method Man page
-,ANY,spam-method Man page
/,ANY,spam-method Man page
*,ANY,spam-method Man page
&,ANY,spam-method Man page
+,ANY,spam-method Man page
apply.spam Man page
Arith,ANY,spam-method Man page
Arith,spam,ANY-method Man page
Arith,spam,spam-method Man page
as.dgCMatrix.spam Man page
as.dgRMatrix.spam Man page
asinh.spam Man page
asinh,spam-method Man page
asin.spam Man page
asin,spam-method Man page
as.matrix.csr.spam Man page
as.matrix.spam Man page
as.matrix,spam.chol.NgPeyton-method Man page
as.matrix,spam-method Man page
assign.spam Man page
as.spam Man page
as.spam.chol.NgPeyton Man page
as.spam.dgCMatrix Man page
as.spam.dgRMatrix Man page
as.spam.dist Man page
as.spam,dist-method Man page
as.spam.list Man page
as.spam,list-method Man page
as.spam.matrix Man page
as.spam.matrix.csr Man page
as.spam,matrix-method Man page
as.spam.numeric Man page
as.spam,numeric-method Man page
as.spam.spam Man page
as.spam,spam.chol.NgPeyton-method Man page
as.spam,spam-method Man page
as.vector.spam Man page
as.vector,spam.chol.NgPeyton-method Man page
as.vector,spam-method Man page
atanh.spam Man page
atanh,spam-method Man page
atan.spam Man page
atan,spam-method Man page
backsolve Man page
backsolve,ANY-method Man page
backsolve,matrix-method Man page
backsolve-methods Man page
backsolve.spam Man page
backsolve,spam.chol.NgPeyton-method Man page
backsolve,spam-method Man page
bandwidth Man page
bdiag Man page
bdiag.spam Man page
cbind.spam Man page
cbind,spam-method Man page
ceiling.spam Man page
ceiling,spam-method Man page
chol2inv.spam Man page
chol2inv,spam.chol.NgPeyton-method Man page
chol2inv,spam-method Man page
chol,ANY-method Man page
chol,matrix-method Man page
chol.spam Man page
chol,spam.chol.NgPeyton-method Man page
chol,spam-method Man page
circulant.spam Man page
cleanup Man page
coerce.spam Man page
coerce,spam,integer-method Man page
coerce,spam,list-method Man page
coerce,spam,logical-method Man page
coerce,spam,matrix-method Man page
coerce,spam,vector-method Man page
colindices Man page
colindices<- Man page
colMeans Man page
colMeans.spam Man page
colMeans,spam-method Man page
colSums Man page
colSums.spam Man page
colSums,spam-method Man page
Compare,ANY,spam-method Man page
Compare,spam,ANY-method Man page
Compare,spam,spam-method Man page
complexities Man page
complexity Man page
constructors Man page
cosh.spam Man page
cosh,spam-method Man page
cospi.spam Man page
cospi,spam-method Man page
cos.spam Man page
cos,spam-method Man page
cov.exp Man page
covmat Man page
cov.mat Man page
cov.nug Man page
cov.sph Man page
cov.wend1 Man page
cov.wend2 Man page
cov.wu1 Man page
cov.wu2 Man page
cov.wu3 Man page
crossprod,ANY,spam-method Man page
crossprod.default Man page
crossprod.spam Man page
crossprod,spam,missing-method Man page
c,spam.chol.NgPeyton-method Man page
c,spam-method Man page
cummax.spam Man page
cummax,spam-method Man page
cummin.spam Man page
cummin,spam-method Man page
cumprod.spam Man page
cumprod,spam-method Man page
cumsum.spam Man page
cumsum,spam-method Man page
\%d*\% Man page
\%d+\% Man page
dcheck Man page
determinant Man page
determinant.spam Man page
determinant.spam.chol Man page
determinant.spam.chol.NgPeyton Man page
determinant,spam.chol.NgPeyton-method Man page
determinant,spam.chol.NgPeyton-method Man page
determinant,spam-method Man page
det.spam Man page
det,spam.chol.NgPeyton-method Man page
det,spam-method Man page
diag Man page
diag<- Man page
diag<-,ANY-method Man page
diag,ANY-method Man page
diag.assign,spam-method Man page
diag.of.spam Man page
diag<-.spam Man page
diag.spam Man page
diag.spam<- Man page
diag,spam.chol.NgPeyton-method Man page
diag<-,spam-method Man page
diag,spam-method Man page
diff.spam Man page
diff,spam-method Man page
digamma.spam Man page
digamma,spam-method Man page
dim,ANY-method Man page
dimension<- Man page
dim<-.spam Man page
dim.spam Man page
dim<-,spam.chol.NgPeyton-method Man page
dim,spam.chol.NgPeyton-method Man page
dim<-,spam-method Man page
dim,spam-method Man page
display Man page
display.spam Man page
display,spam.chol.NgPeyton-method Man page
display,spam.chol.NgPeyton-method Man page
display,spam-method Man page
distance Man page
dist.spam Man page
\%d*\%,matrix,ANY-method Man page
\%d+\%,matrix,ANY-method Man page
\%d*\%,matrix,spam-method Man page
\%d+\%,matrix,spam-method Man page
\%d*\%,numeric,matrix-method Man page
\%d+\%,numeric,matrix-method Man page
\%d*\%,numeric,numeric-method Man page
\%d+\%,numeric,numeric-method Man page
\%d*\%,numeric,spam-method Man page
\%d+\%,numeric,spam-method Man page
\%d*\%,spam,ANY-method Man page
\%d+\%,spam,ANY-method Man page
\%d*\%,spam,numeric-method Man page
\%d+\%,spam,numeric-method Man page
\%d*\%,spam,spam-method Man page
\%d+\%,spam,spam-method Man page
eigen.spam Man page
entries Man page
entries<- Man page
exp.spam Man page
exp,spam-method Man page
floor.spam Man page
floor,spam-method Man page
foreign Man page
forwardsolve Man page
forwardsolve,ANY-method Man page
forwardsolve,matrix-method Man page
forwardsolve-methods Man page
forwardsolve.spam Man page
forwardsolve,spam.chol.NgPeyton-method Man page
forwardsolve,spam-method Man page
gamma.spam Man page
gamma,spam-method Man page
germany Man page
germany.data Man page
germany.graph Man page
germany.info Man page
germany.plot Man page
germany.poly Man page
germany.spam Man page
grid_trace2 Man page
grid_zoom Man page
head.spam Man page
head,spam.chol.NgPeyton-method Man page
head,spam-method Man page
history Man page
history.spam Man page
icheck Man page
image.spam Man page
image.spam.chol Man page
image,spam.chol.NgPeyton-method Man page
image,spam.chol.NgPeyton-method Man page
image,spam-method Man page
import Man page
initialize,spam-method Man page
is.spam Man page
isSymmetric.spam Man page
isSymmetric,spam-method Man page
kronecker,ANY,spam-method Man page
kronecker.default Man page
kronecker.spam Man page
kronecker,spam,ANY-method Man page
kronecker,spam,spam-method Man page
length<-,spam.chol.NgPeyton-method Man page
length,spam.chol.NgPeyton-method Man page
length<-,spam-method Man page
length,spam-method Man page
lgamma.spam Man page
lgamma,spam-method Man page
log10.spam Man page
log10,spam-method Man page
log2.spam Man page
log2,spam-method Man page
log.spam Man page
log,spam-method Man page
lower.tri Man page
lower.tri.spam Man page
lower.tri,spam-method Man page
map.landkreis Man page
Math2.spam Man page
Math2,spam-method Man page
Math2,spam,numeric-method Man page
Math.spam Man page
Math,spam-method Man page
-,matrix,spam-method Man page
\%*\%,matrix,spam-method Man page
+,matrix,spam-method Man page
max.spam Man page
max,spam-method Man page
\%*\%-methods Man page
methods.spam Man page
min.spam Man page
min,spam-method Man page
mle Man page
mle.nomean Man page
mle.nomean.spam Man page
mle.spam Man page
ncol,spam-method Man page
nearest.dist Man page
neg2loglikelihood Man page
neg2loglikelihood.spam Man page
norm Man page
norm,ANY-method Man page
norm,matrix,character-method Man page
norm,matrix,missing-method Man page
norm,numeric,character-method Man page
norm,numeric,missing-method Man page
norm.spam Man page
norm,spam,character-method Man page
norm,spam,missing-method Man page
nrow,spam-method Man page
\%*\%,numeric,spam-method Man page
Ops.spam Man page
options.spam Man page
Oral Man page
oral.spam Man page
Oral.spam Man page
ordering Man page
ordering,matrix-method Man page
ordering-methods Man page
ordering.spam Man page
ordering.spam.chol Man page
ordering.spam.chol.NgPeyton Man page
ordering,spam.chol.NgPeyton-method Man page
ordering,spam.chol.NgPeyton-method Man page
ordering,spam-method Man page
overview Man page
pad Man page
pad<- Man page
pad<-,matrix-method Man page
pad<-.spam Man page
pad.spam Man page
pad<-,spam-method Man page
permutation Man page
permutation,matrix-method Man page
permutation.spam Man page
permutation,spam-method Man page
plot.spam Man page
plot,spam,missing-method Man page
plot,spam,spam-method Man page
powerboost Man page
precmat Man page
precmat.GMRFreglat Man page
precmat.IGMRFirreglat Man page
precmat.IGMRFreglat Man page
precmat.RW1 Man page
precmat.RW2 Man page
precmat.RWn Man page
precmat.season Man page
print.spam Man page
print.spam.chol Man page
print.spam.chol.NgPeyton Man page
print,spam.chol.NgPeyton-method Man page
print,spam.chol.NgPeyton-method Man page
print,spam-method Man page
prod.spam Man page
prod,spam-method Man page
range.spam Man page
range,spam-method Man page
rbind.spam Man page
rbind,spam-method Man page
rdist.dist Man page
read.HB Man page
read.MM Man page
rmvnorm.canonical Man page
rmvnorm.canonical.const Man page
rmvnorm.const Man page
rmvnorm.prec Man page
rmvnorm.prec.const Man page
rmvnorm.spam Man page
round.spam Man page
round,spam-method Man page
rowMeans Man page
rowMeans.spam Man page
rowMeans,spam-method Man page
rowpointers Man page
rowpointers<- Man page
rowSums Man page
rowSums.spam Man page
rowSums,spam-method Man page
show,spam.chol.NgPeyton-method Man page
show,spam-method Man page
signif.spam Man page
signif,spam-method Man page
sin.spam Man page
sin,spam-method Man page
solve,ANY-method Man page
solve.spam Man page
solve,spam-method Man page
spam Man page
[<-.spam Man page
[.spam Man page
Spam Man page
.Spam Man page
SPAM Man page
[<-,spam,ANY,ANY,ANY-method Man page
[,spam,ANY,ANY,ANY-method Man page
[<-,spam,ANY,ANY-method Man page
^,spam,ANY-method Man page
|,spam,ANY-method Man page
-,spam,ANY-method Man page
/,spam,ANY-method Man page
[<-,spam,ANY-method Man page
*,spam,ANY-method Man page
&,spam,ANY-method Man page
+,spam,ANY-method Man page
spam.chol.NgPeyton-class Man page
spam-class Man page
spam.class Man page
spam.creation Man page
spam-deprecated Man page
spam_diag Man page
spam.getOption Man page
spam.history Man page
spam.list Man page
spam,list-method Man page
[<-,spam,matrix,matrix,ANY-method Man page
[,spam,matrix,matrix,ANY-method Man page
[<-,spam,matrix,matrix-method Man page
[<-,spam,matrix,matrix,numeric-method Man page
-,spam,matrix-method Man page
\%*\%,spam,matrix-method Man page
+,spam,matrix-method Man page
[<-,spam,matrix,missing,ANY-method Man page
[,spam,matrix,missing,logical-method Man page
[<-,spam,matrix,missing-method Man page
[,spam,matrix,missing,missing-method Man page
[<-,spam,matrix,missing,numeric-method Man page
^,spam-method Man page
<=,spam-method Man page
<,spam-method Man page
==,spam-method Man page
>=,spam-method Man page
>,spam-method Man page
!=,spam-method Man page
!,spam-method Man page
\%/\%,spam-method Man page
\%\%,spam-method Man page
-,spam,missing-method Man page
+,spam,missing-method Man page
[<-,spam,missing,missing,ANY-method Man page
[,spam,missing,missing,ANY-method Man page
[<-,spam,missing,missing-method Man page
[<-,spam,missing,missing,numeric-method Man page
[<-,spam,missing,vector,ANY-method Man page
[,spam,missing,vector,ANY-method Man page
[<-,spam,missing,vector-method Man page
[<-,spam,missing,vector,numeric-method Man page
[<-,spam,missing,vector,spam-method Man page
spam.numeric Man page
\%*\%,spam,numeric-method Man page
spam,numeric-method Man page
spam.ops Man page
spam.options Man page
spam_rdist Man page
spam_rdist.earth Man page
spam.spam Man page
^,spam,spam-method Man page
|,spam,spam-method Man page
-,spam,spam-method Man page
/,spam,spam-method Man page
*,spam,spam-method Man page
\%*\%,spam,spam-method Man page
&,spam,spam-method Man page
+,spam,spam-method Man page
spam,spam-method Man page
[<-,spam,spam,missing,ANY-method Man page
[,spam,spam,missing,ANY-method Man page
[<-,spam,spam,missing-method Man page
[<-,spam,spam,missing,numeric-method Man page
[<-,spam,vector,missing,ANY-method Man page
[,spam,vector,missing,logical-method Man page
[<-,spam,vector,missing-method Man page
[,spam,vector,missing,missing-method Man page
[<-,spam,vector,missing,numeric-method Man page
[<-,spam,vector,missing,spam-method Man page
[<-,spam,vector,vector,ANY-method Man page
[,spam,vector,vector,ANY-method Man page
[<-,spam,vector,vector-method Man page
[<-,spam,vector,vector,numeric-method Man page
[<-,spam,vector,vector,spam-method Man page
spam.version Man page
spam.Version Man page
sqrt.spam Man page
sqrt,spam-method Man page
subset.rows.spam Man page
subset.spam Man page
summary.spam Man page
Summary.spam Man page
summary.spam.chol Man page
summary.spam.chol.NgPeyton Man page
summary,spam.chol.NgPeyton-method Man page
summary,spam.chol.NgPeyton-method Man page
summary,spam-method Man page
Summary,spam-method Man page
sum.spam Man page
sum,spam-method Man page
tail.spam Man page
tail,spam.chol.NgPeyton-method Man page
tail,spam-method Man page
tan.spam Man page
tan,spam-method Man page
t,ANY-method Man page
tcrossprod,ANY,spam-method Man page
tcrossprod.spam Man page
tcrossprod,spam,missing-method Man page
todo Man page
todo.spam Man page
toeplitz.spam Man page
trigamma.spam Man page
trigamma,spam-method Man page
triplet Man page
trunc.spam Man page
trunc,spam-method Man page
t.spam Man page
t,spam.chol.NgPeyton-method Man page
t,spam-method Man page
update.spam Man page
update.spam.chol.NgPeyton Man page
update,spam.chol.NgPeyton-method Man page
upper.tri Man page
upper.tri.spam Man page
upper.tri,spam-method Man page
UScounties Man page
UScounties.ndorder Man page
UScounties.storder Man page
USprecip Man page
validspamobject Man page
var.spam Man page
version Man page

Files

spam
spam/inst
spam/inst/0LICENSE
spam/inst/CITATION
spam/inst/0ChangeLog
spam/inst/0NEWS
spam/inst/NEWS
spam/inst/demodata
spam/inst/demodata/germany.adjacency
spam/inst/doc
spam/inst/doc/jss15.pdf.asis
spam/inst/doc/jss15.pdf
spam/tests
spam/tests/demo_article-jss.R
spam/tests/diff.R
spam/tests/subsetting.R
spam/tests/xybind.R
spam/tests/jss_areal_counts.R
spam/tests/dim.R
spam/tests/math.R
spam/tests/demo_cholesky.R
spam/tests/foreign.R
spam/tests/kronecker.R
spam/tests/mle.R
spam/tests/demo_timing.R
spam/tests/rowcolstats.R
spam/tests/overall.R
spam/tests/demo_article-jss-example1.R
spam/tests/ops.R
spam/tests/dist.R
spam/tests/helper.R
spam/tests/spamlist.R
spam/tests/crossprod.R
spam/tests/displays.R
spam/tests/permutation.R
spam/tests/demo_spam.R
spam/tests/demo_article-jss-example2.R
spam/tests/covmat.R
spam/tests/demo_jss15-Leroux.R
spam/tests/solve.R
spam/tests/norm.R
spam/tests/constructors.R
spam/tests/demo_jss15-BYM.R
spam/src
spam/src/spamown2.f
spam/src/dist.f
spam/src/xybind.f
spam/src/fromsparsekit.f
spam/src/rowcolstats.f
spam/src/permutation.f
spam/src/bckslvmodified.f
spam/src/cholmodified.f
spam/src/spamown.f
spam/src/kronecker.f
spam/NAMESPACE
spam/demo
spam/demo/article-jss.R
spam/demo/cholesky.R
spam/demo/article-jss-example2.R
spam/demo/article-jss-example1.R
spam/demo/jss10-example1.R
spam/demo/spam.R
spam/demo/00Index
spam/demo/jss15-Leroux.R
spam/demo/timing.R
spam/demo/jss10-example2.R
spam/demo/jss15-BYM.R
spam/data
spam/data/USprecip.rda
spam/data/germany.rda
spam/data/Oral.rda
spam/data/UScounties.ndorder.rda
spam/data/UScounties.storder.rda
spam/R
spam/R/diff.R spam/R/plotting.R spam/R/subset.R spam/R/xybind.R spam/R/spam_solve.R spam/R/dim.R spam/R/math.R spam/R/foreign.R spam/R/makeprec.R spam/R/rmvnorm.R spam/R/profile.R spam/R/kronecker.R spam/R/mle.R spam/R/toepliz.R spam/R/rowcolstats.R spam/R/apply.R spam/R/image_spam.R spam/R/tailhead.R spam/R/precmat.R spam/R/dist.R spam/R/s3only.R spam/R/helper.R spam/R/spamlist.R spam/R/permutation.R spam/R/s4coerce.R spam/R/covmat.R spam/R/tcrossprod.R spam/R/definitions.R spam/R/norm.R spam/R/constructors.R
spam/vignettes
spam/vignettes/jss15.pdf.asis
spam/MD5
spam/README
spam/build
spam/build/vignette.rds
spam/DESCRIPTION
spam/ChangeLog
spam/man
spam/man/diag.Rd spam/man/adjacency.Rd spam/man/diff.Rd spam/man/rmvnorm.Rd spam/man/chol.Rd spam/man/makeprec.Rd spam/man/spam.chol.NgPeyton-class.Rd spam/man/precmat.Rd spam/man/kronecker.Rd spam/man/math.Rd spam/man/cleanup.Rd spam/man/solve.Rd spam/man/coerce.Rd spam/man/det.Rd spam/man/foreign.Rd spam/man/cov.Rd spam/man/mle.Rd spam/man/spam-class.Rd spam/man/version.Rd spam/man/math2.Rd spam/man/ordering.Rd spam/man/pad.Rd spam/man/spam.creation.Rd spam/man/bandwidth.Rd spam/man/complexity.Rd spam/man/import.Rd spam/man/lu.tri.Rd spam/man/grid_trace2.Rd spam/man/options.Rd spam/man/grid_zoom.Rd spam/man/nearestdist.Rd spam/man/operations.Rd spam/man/circulant.Rd spam/man/display.Rd spam/man/history.spam.Rd spam/man/germanydata.Rd spam/man/landkreis.Rd spam/man/powerboost.Rd spam/man/headtail.Rd spam/man/s3only.Rd spam/man/triplet.Rd spam/man/spam-deprecated.Rd spam/man/rmvnorm.const.Rd spam/man/permutation.Rd spam/man/constructors.Rd spam/man/Oral.Rd spam/man/coercion.Rd spam/man/rowcolstats.Rd spam/man/todo.Rd spam/man/toeplitz.Rd spam/man/image.Rd spam/man/bdiag.Rd spam/man/apply.Rd spam/man/spam-package.Rd spam/man/methods.Rd spam/man/rdist.Rd spam/man/print.Rd spam/man/isSymmetric.Rd spam/man/allequal.Rd spam/man/dim.Rd spam/man/crossprod.Rd spam/man/UScounties.Rd spam/man/summary.Rd spam/man/germany.Rd spam/man/USprecip.Rd spam/man/xybind.Rd spam/man/spam.internal.Rd

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