# SPArse Matrix

## Documentation for package ‘spam’ version 1.4-0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.
- Package NEWS.

## Help Pages

A B C D E F G H I K L M N O P R S T U V misc

## -- A --

abs-method | Mathematical functions
abs.spam | Mathematical functions
acos-method | Mathematical functions
acos.spam | Mathematical functions
acosh-method | Mathematical functions
acosh.spam | Mathematical functions
adjacency | Administrative districts of Germany
adjacency.landkreis | Administrative districts of Germany
adjacency.spam | Administrative districts of Germany
all-method | Rounding of Numbers
all.equal-method | Test if Two 'spam' Objects are (Nearly) Equal
all.equal.spam | Test if Two 'spam' Objects are (Nearly) Equal
all.spam | Rounding of Numbers
any-method | Rounding of Numbers
any.spam | Rounding of Numbers
apply.spam | Apply Functions Over Sparse Matrix Margins
Arith-method | Class "spam"
as.dgCMatrix.spam | Transformation to other sparse formats
as.dgRMatrix.spam | Transformation to other sparse formats
as.matrix-method | Class "spam"
as.matrix-method | Class "spam.chol.NgPeyton"
as.matrix.spam | Class "spam"
as.spam | Sparse Matrix Class
as.spam-method | Class "spam.chol.NgPeyton"
as.spam-method | Sparse Matrix Class
as.spam.chol.NgPeyton | Sparse Matrix Class
as.spam.dgCMatrix | Transformation to other sparse formats
as.spam.dgRMatrix | Transformation to other sparse formats
as.spam.dist | Sparse Matrix Class
as.spam.list | Sparse Matrix Class
as.spam.matrix | Sparse Matrix Class
as.spam.matrix.csr | Transformation to other sparse formats
as.spam.numeric | Sparse Matrix Class
as.spam.spam | Sparse Matrix Class
as.vector-method | Coercion to a Vector
as.vector.spam | Coercion to a Vector
asin-method | Mathematical functions
asin.spam | Mathematical functions
asinh-method | Mathematical functions
asinh.spam | Mathematical functions
assign.spam | Basic Linear Algebra for Sparse Matrices
atan-method | Mathematical functions
atan.spam | Mathematical functions
atanh-method | Mathematical functions
atanh.spam | Mathematical functions

## -- B --

backsolve | Linear Equation Solving for Sparse Matrices
backsolve-method | Linear Equation Solving for Sparse Matrices
backsolve-method | Class "spam.chol.NgPeyton"
backsolve-methods | Linear Equation Solving for Sparse Matrices
backsolve.spam | Linear Equation Solving for Sparse Matrices
bandwidth | Bandwidth of a Sparse Matrix
bdiag | Binds Arrays Corner-to-Corner
bdiag.spam | Binds Arrays Corner-to-Corner

## -- C --

c-method | Class "spam"
c-method | Class "spam.chol.NgPeyton"
cbind-method | Combine spam Matrices by Rows or Columns
cbind.spam | Combine spam Matrices by Rows or Columns
ceiling-method | Mathematical functions
ceiling.spam | Mathematical functions
chol-method | Cholesky Factorization for Sparse Matrices
chol-method | Class "spam.chol.NgPeyton"
chol.spam | Cholesky Factorization for Sparse Matrices
chol2inv-method | Linear Equation Solving for Sparse Matrices
chol2inv.spam | Linear Equation Solving for Sparse Matrices
circulant.spam | Create Circulant Matrices
cleanup | Cleaning up sparse matrices
coerce-method | Force a 'spam' Object to Belong to a Class
coerce.spam | Force a 'spam' Object to Belong to a Class
colindices | Slot modification
colindices<- | Slot modification
colMeans | Form Row and Column Sums and Means
colMeans-method | Form Row and Column Sums and Means
colMeans.spam | Form Row and Column Sums and Means
colSums | Form Row and Column Sums and Means
colSums-method | Form Row and Column Sums and Means
colSums.spam | Form Row and Column Sums and Means
Compare-method | Class "spam"
complexities | Complexity for Sparse Matrices
complexity | Complexity for Sparse Matrices
constructors | Slot modification
cos-method | Mathematical functions
cos.spam | Mathematical functions
cosh-method | Mathematical functions
cosh.spam | Mathematical functions
cov.exp | Covariance functions
cov.mat | Covariance functions
cov.nug | Covariance functions
cov.sph | Covariance functions
cov.wend1 | Covariance functions
cov.wend2 | Covariance functions
cov.wu1 | Covariance functions
cov.wu2 | Covariance functions
cov.wu3 | Covariance functions
covmat | Covariance functions
crossprod-method | Class "spam"
crossprod.default | Spam Matrix Crossproduct
crossprod.spam | Spam Matrix Crossproduct
cummax-method | Mathematical functions
cummax.spam | Mathematical functions
cummin-method | Mathematical functions
cummin.spam | Mathematical functions
cumprod-method | Mathematical functions
cumprod.spam | Mathematical functions
cumsum-method | Mathematical functions
cumsum.spam | Mathematical functions

## -- D --

det-method | Calculate the determinant of a positive definite Sparse Matrix
det.spam | Calculate the determinant of a positive definite Sparse Matrix
determinant | Calculate the determinant of a positive definite Sparse Matrix
determinant-method | Calculate the determinant of a positive definite Sparse Matrix
determinant-method | Class "spam.chol.NgPeyton"
determinant.spam | Calculate the determinant of a positive definite Sparse Matrix
determinant.spam.chol | Calculate the determinant of a positive definite Sparse Matrix
determinant.spam.chol.NgPeyton | Calculate the determinant of a positive definite Sparse Matrix
diag | Sparse Matrix diagonals
diag-method | Sparse Matrix diagonals
diag-method | Class "spam.chol.NgPeyton"
diag.assign-method | Sparse Matrix diagonals
diag.of.spam | Sparse Matrix diagonals
diag.spam | Sparse Matrix diagonals
diag.spam<- | Sparse Matrix diagonals
diag<- | Sparse Matrix diagonals
diag<--method | Sparse Matrix diagonals
diag<-.spam | Sparse Matrix diagonals
diff-method | Lagged Differences
diff.spam | Lagged Differences
digamma-method | Mathematical functions
digamma.spam | Mathematical functions
dim-method | Basic Linear Algebra for Sparse Matrices
dim-method | Class "spam.chol.NgPeyton"
dim.spam | Dimensions of an Object
dim<--method | Dimensions of an Object
dim<--method | Class "spam.chol.NgPeyton"
dim<-.spam | Dimensions of an Object
dimension<- | Slot modification
display | Graphially Represent the Nonzero Entries
display-method | Graphially Represent the Nonzero Entries
display-method | Class "spam.chol.NgPeyton"
display.spam | Graphially Represent the Nonzero Entries
dist.spam | Distance Matrix Computation
distance | Distance Matrix Computation

## -- E --

eigen.spam | Wappers for Sparse Matrices
entries | Slot modification
entries<- | Slot modification
exp-method | Mathematical functions
exp.spam | Mathematical functions

## -- F --

floor-method | Mathematical functions
floor.spam | Mathematical functions
foreign | Transformation to other sparse formats
forwardsolve | Linear Equation Solving for Sparse Matrices
forwardsolve-method | Linear Equation Solving for Sparse Matrices
forwardsolve-method | Class "spam.chol.NgPeyton"
forwardsolve-methods | Linear Equation Solving for Sparse Matrices
forwardsolve.spam | Linear Equation Solving for Sparse Matrices

## -- G --

gamma-method | Mathematical functions
gamma.spam | Mathematical functions
germany | Meta-data about administrative districts of Germany
germany.data | Meta-data about administrative districts of Germany
germany.graph | Administrative districts of Germany
germany.info | Meta-data about administrative districts of Germany
germany.plot | Plot administrative districts of Germany
germany.poly | Meta-data about administrative districts of Germany
germany.spam | Meta-data about administrative districts of Germany
grid_trace2 | Two trace plots and a scatter plot.
grid_zoom | grid_zoom

## -- H --

head-method | Return the First or Last Part of an Object
head.spam | Return the First or Last Part of an Object

## -- I --

image-method | Display a spam Object as Color Image
image-method | Class "spam.chol.NgPeyton"
image.spam | Display a spam Object as Color Image
image.spam.chol | Display a spam Object as Color Image
import | Read External Matrix Formats
initialize-method | Sparse Matrix Class
is.spam | Sparse Matrix Class
isSymmetric-method | Test if a spam matrix is Symmetric
isSymmetric.spam | Test if a spam matrix is Symmetric

## -- K --

kronecker-method | Class "spam"
kronecker.default | Kronecker Products on Sparse Matrices
kronecker.spam | Kronecker Products on Sparse Matrices

## -- L --

length-method | Class "spam"
length-method | Class "spam.chol.NgPeyton"
length<--method | Class "spam"
length<--method | Class "spam.chol.NgPeyton"
lgamma-method | Mathematical functions
lgamma.spam | Mathematical functions
log-method | Mathematical functions
log.spam | Mathematical functions
log10-method | Mathematical functions
log10.spam | Mathematical functions
log2-method | Mathematical functions
log2.spam | Mathematical functions
lower.tri | Lower and Upper Triangular Part of a Sparse Matrix
lower.tri-method | Class "spam"
lower.tri.spam | Lower and Upper Triangular Part of a Sparse Matrix

## -- M --

map.landkreis | Administrative districts of Germany
Math-method | Mathematical functions
Math.spam | Mathematical functions
Math2-method | Rounding of Numbers
Math2.spam | Rounding of Numbers
max-method | Rounding of Numbers
max.spam | Rounding of Numbers
min-method | Rounding of Numbers
min.spam | Rounding of Numbers
mle | Maximum likelihood estimates
mle.nomean | Maximum likelihood estimates
mle.nomean.spam | Maximum likelihood estimates
mle.spam | Maximum likelihood estimates

## -- N --

ncol-method | Basic Linear Algebra for Sparse Matrices
nearest.dist | Distance Matrix Computation
neg2loglikelihood | Maximum likelihood estimates
neg2loglikelihood.spam | Maximum likelihood estimates
norm | Basic Linear Algebra for Sparse Matrices
norm-method | Basic Linear Algebra for Sparse Matrices
norm.spam | Basic Linear Algebra for Sparse Matrices
nrow-method | Basic Linear Algebra for Sparse Matrices

## -- O --

Ops.spam | Basic Linear Algebra for Sparse Matrices
options.spam | Options Settings
Oral | Oral Cavity Cancer
Oral.spam | Oral Cavity Cancer
oral.spam | Oral Cavity Cancer
ordering | Extract the permutation
ordering-method | Extract the permutation
ordering-method | Class "spam.chol.NgPeyton"
ordering-methods | Extract the permutation
ordering.spam | Extract the permutation
ordering.spam.chol | Extract the permutation
ordering.spam.chol.NgPeyton | Extract the permutation
overview | SPArse Matrix Package

## -- P --

pad | Padding a (sparse) matrix
pad.spam | Padding a (sparse) matrix
pad<- | Padding a (sparse) matrix
pad<--method | Padding a (sparse) matrix
pad<-.spam | Padding a (sparse) matrix
permutation | Permute a matrix
permutation-method | Permute a matrix
permutation.spam | Permute a matrix
plot-method | Class "spam"
plot.spam | Basic Linear Algebra for Sparse Matrices
powerboost | Specific options Setting
precmat | IGMRF Precision Matrices
precmat.GMRFreglat | Create Precision Matrices
precmat.IGMRFirreglat | IGMRF Precision Matrices
precmat.IGMRFreglat | IGMRF Precision Matrices
precmat.RW1 | IGMRF Precision Matrices
precmat.RW2 | IGMRF Precision Matrices
precmat.RWn | IGMRF Precision Matrices
precmat.season | IGMRF Precision Matrices
print-method | Printing and summarizing sparse matrices
print-method | Class "spam.chol.NgPeyton"
print.spam | Printing and summarizing sparse matrices
print.spam.chol | Printing and summarizing sparse matrices
print.spam.chol.NgPeyton | Printing and summarizing sparse matrices
prod-method | Rounding of Numbers
prod.spam | Rounding of Numbers

## -- R --

range-method | Rounding of Numbers
range.spam | Rounding of Numbers
rbind-method | Combine spam Matrices by Rows or Columns
rbind.spam | Combine spam Matrices by Rows or Columns
rdist.dist | Wrapper for Distance Matrix Computation
read.HB | Read External Matrix Formats
read.MM | Read External Matrix Formats
rmvnorm.canonical | Draw Multivariate Normals
rmvnorm.canonical.const | Draw Constrainted Multivariate Normals
rmvnorm.const | Draw Constrainted Multivariate Normals
rmvnorm.prec | Draw Multivariate Normals
rmvnorm.prec.const | Draw Constrainted Multivariate Normals
rmvnorm.spam | Draw Multivariate Normals
round-method | Rounding of Numbers
round.spam | Rounding of Numbers
rowMeans | Form Row and Column Sums and Means
rowMeans-method | Form Row and Column Sums and Means
rowMeans.spam | Form Row and Column Sums and Means
rowpointers | Slot modification
rowpointers<- | Slot modification
rowSums | Form Row and Column Sums and Means
rowSums-method | Form Row and Column Sums and Means
rowSums.spam | Form Row and Column Sums and Means

## -- S --

show-method | Class "spam"
show-method | Class "spam.chol.NgPeyton"
signif-method | Rounding of Numbers
signif.spam | Rounding of Numbers
sin-method | Mathematical functions
sin.spam | Mathematical functions
solve-method | Linear Equation Solving for Sparse Matrices
solve.spam | Linear Equation Solving for Sparse Matrices
SPAM | SPArse Matrix Package
Spam | SPArse Matrix Package
spam | Sparse Matrix Class
spam-class | Class "spam"
spam-deprecated | Deprecated Objects in Package 'spam'
spam-method | Sparse Matrix Class
spam.chol.NgPeyton-class | Class "spam.chol.NgPeyton"
spam.class | Class "spam"
spam.creation | Sparse Matrix Class
spam.getOption | Options Settings
spam.list | Sparse Matrix Class
spam.numeric | Sparse Matrix Class
spam.ops | Basic Linear Algebra for Sparse Matrices
spam.options | Options Settings
spam.Version | Spam Version Information
spam.version | Spam Version Information
spam_diag | Sparse Matrix diagonals
spam_rdist | Wrapper for Distance Matrix Computation
spam_rdist.earth | Wrapper for Distance Matrix Computation
sqrt-method | Mathematical functions
sqrt.spam | Mathematical functions
subset.rows.spam | Deprecated Objects in Package 'spam'
subset.spam | Basic Linear Algebra for Sparse Matrices
sum-method | Rounding of Numbers
sum.spam | Rounding of Numbers
Summary-method | Rounding of Numbers
summary-method | Printing and summarizing sparse matrices
summary-method | Class "spam.chol.NgPeyton"
Summary.spam | Rounding of Numbers
summary.spam | Printing and summarizing sparse matrices
summary.spam.chol | Printing and summarizing sparse matrices
summary.spam.chol.NgPeyton | Printing and summarizing sparse matrices

## -- T --

t-method | Class "spam"
t-method | Class "spam.chol.NgPeyton"
t.spam | Basic Linear Algebra for Sparse Matrices
tail-method | Return the First or Last Part of an Object
tail.spam | Return the First or Last Part of an Object
tan-method | Mathematical functions
tan.spam | Mathematical functions
tcrossprod-method | Class "spam"
tcrossprod.spam | Spam Matrix Crossproduct
toeplitz.spam | Create Toeplitz Matrices
trigamma-method | Mathematical functions
trigamma.spam | Mathematical functions
triplet | Transform a spam format to triplets
trunc-method | Mathematical functions
trunc.spam | Mathematical functions

## -- U --

update-method | Cholesky Factorization for Sparse Matrices
update.spam | Cholesky Factorization for Sparse Matrices
update.spam.chol.NgPeyton | Cholesky Factorization for Sparse Matrices
upper.tri | Lower and Upper Triangular Part of a Sparse Matrix
upper.tri-method | Class "spam"
upper.tri.spam | Lower and Upper Triangular Part of a Sparse Matrix
UScounties | Adjacency structure of the counties in the contiguous United States
UScounties.ndorder | Adjacency structure of the counties in the contiguous United States
UScounties.storder | Adjacency structure of the counties in the contiguous United States
USprecip | Monthly total precipitation (mm) for April 1948 in the contiguous United States

## -- V --

validspamobject | Sparse Matrix Class
var.spam | Wappers for Sparse Matrices
version | Spam Version Information

## -- misc --

!-method | Class "spam"
!=-method | Basic Linear Algebra for Sparse Matrices
%%-method | Basic Linear Algebra for Sparse Matrices
%*%-method | Basic Linear Algebra for Sparse Matrices
%*%-methods | Basic Linear Algebra for Sparse Matrices
%/%-method | Basic Linear Algebra for Sparse Matrices
%d*% | Basic Linear Algebra for Sparse Matrices
%d*%-method | Basic Linear Algebra for Sparse Matrices
%d+% | Basic Linear Algebra for Sparse Matrices
%d+%-method | Basic Linear Algebra for Sparse Matrices
&-method | Basic Linear Algebra for Sparse Matrices
*-method | Basic Linear Algebra for Sparse Matrices
+-method | Basic Linear Algebra for Sparse Matrices
+-method | Class "spam"
--method | Basic Linear Algebra for Sparse Matrices
--method | Class "spam"
.Spam | Options Settings
/-method | Basic Linear Algebra for Sparse Matrices
<-method | Basic Linear Algebra for Sparse Matrices
<=-method | Basic Linear Algebra for Sparse Matrices
==-method | Basic Linear Algebra for Sparse Matrices
>-method | Basic Linear Algebra for Sparse Matrices
>=-method | Basic Linear Algebra for Sparse Matrices
[-method | Class "spam"
[.spam | Basic Linear Algebra for Sparse Matrices
[<--method | Basic Linear Algebra for Sparse Matrices
[<--method | Class "spam"
[<-.spam | Basic Linear Algebra for Sparse Matrices
^-method | Basic Linear Algebra for Sparse Matrices
|-method | Basic Linear Algebra for Sparse Matrices