spam: SPArse Matrix
Version 1.4-0

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.

Browse man pages Browse package API and functions Browse package files

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
URL http://www.math.uzh.ch/furrer/software/spam/
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("spam")

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

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

Files

inst
inst/0LICENSE
inst/CITATION
inst/0ChangeLog
inst/0NEWS
inst/NEWS
inst/demodata
inst/demodata/germany.adjacency
inst/doc
inst/doc/jss15.pdf.asis
inst/doc/jss15.pdf
tests
tests/demo_article-jss.R
tests/diff.R
tests/subsetting.R
tests/xybind.R
tests/jss_areal_counts.R
tests/dim.R
tests/math.R
tests/demo_cholesky.R
tests/foreign.R
tests/kronecker.R
tests/mle.R
tests/demo_timing.R
tests/rowcolstats.R
tests/overall.R
tests/demo_article-jss-example1.R
tests/ops.R
tests/dist.R
tests/helper.R
tests/spamlist.R
tests/crossprod.R
tests/displays.R
tests/permutation.R
tests/demo_spam.R
tests/demo_article-jss-example2.R
tests/covmat.R
tests/demo_jss15-Leroux.R
tests/solve.R
tests/norm.R
tests/constructors.R
tests/demo_jss15-BYM.R
src
src/spamown2.f
src/dist.f
src/xybind.f
src/fromsparsekit.f
src/rowcolstats.f
src/permutation.f
src/bckslvmodified.f
src/cholmodified.f
src/spamown.f
src/kronecker.f
NAMESPACE
demo
demo/article-jss.R
demo/cholesky.R
demo/article-jss-example2.R
demo/article-jss-example1.R
demo/jss10-example1.R
demo/spam.R
demo/00Index
demo/jss15-Leroux.R
demo/timing.R
demo/jss10-example2.R
demo/jss15-BYM.R
data
data/USprecip.rda
data/germany.rda
data/Oral.rda
data/UScounties.ndorder.rda
data/UScounties.storder.rda
R
R/diff.R
R/plotting.R
R/subset.R
R/xybind.R
R/spam_solve.R
R/dim.R
R/math.R
R/foreign.R
R/makeprec.R
R/rmvnorm.R
R/profile.R
R/kronecker.R
R/mle.R
R/toepliz.R
R/rowcolstats.R
R/apply.R
R/image_spam.R
R/tailhead.R
R/precmat.R
R/dist.R
R/s3only.R
R/helper.R
R/spamlist.R
R/permutation.R
R/s4coerce.R
R/covmat.R
R/tcrossprod.R
R/definitions.R
R/norm.R
R/constructors.R
vignettes
vignettes/jss15.pdf.asis
MD5
README
build
build/vignette.rds
DESCRIPTION
ChangeLog
man
man/diag.Rd
man/adjacency.Rd
man/diff.Rd
man/rmvnorm.Rd
man/chol.Rd
man/makeprec.Rd
man/spam.chol.NgPeyton-class.Rd
man/precmat.Rd
man/kronecker.Rd
man/math.Rd
man/cleanup.Rd
man/solve.Rd
man/coerce.Rd
man/det.Rd
man/foreign.Rd
man/cov.Rd
man/mle.Rd
man/spam-class.Rd
man/version.Rd
man/math2.Rd
man/ordering.Rd
man/pad.Rd
man/spam.creation.Rd
man/bandwidth.Rd
man/complexity.Rd
man/import.Rd
man/lu.tri.Rd
man/grid_trace2.Rd
man/options.Rd
man/grid_zoom.Rd
man/nearestdist.Rd
man/operations.Rd
man/circulant.Rd
man/display.Rd
man/history.spam.Rd
man/germanydata.Rd
man/landkreis.Rd
man/powerboost.Rd
man/headtail.Rd
man/s3only.Rd
man/triplet.Rd
man/spam-deprecated.Rd
man/rmvnorm.const.Rd
man/permutation.Rd
man/constructors.Rd
man/Oral.Rd
man/coercion.Rd
man/rowcolstats.Rd
man/todo.Rd
man/toeplitz.Rd
man/image.Rd
man/bdiag.Rd
man/apply.Rd
man/spam-package.Rd
man/methods.Rd
man/rdist.Rd
man/print.Rd
man/isSymmetric.Rd
man/allequal.Rd
man/dim.Rd
man/crossprod.Rd
man/UScounties.Rd
man/summary.Rd
man/germany.Rd
man/USprecip.Rd
man/xybind.Rd
man/spam.internal.Rd
spam documentation built on May 29, 2017, 12:05 p.m.