Package ‘miscTools’

November 25, 2016

Version 0.6-22
Date 2016-11-25
Title Miscellaneous Tools and Utilities
Author Arne Henningsen, Ott Toomet
Maintainer Arne Henningsen <[email protected]>
Depends R (>= 2.14.0)
Suggests Ecdat (>= 0.1-5)
Description Miscellaneous small tools and utilities.
Many of them facilitate the work with matrices,
e.g. inserting rows or columns, creating symmetric matrices,
or checking for semidefiniteness.
Other tools facilitate the work with regression models,
e.g. extracting the standard errors,
obtaining the number of (estimated) parameters,
or calculating R-squared values.
License GPL (>= 2)

URL http://www.micEcon.org
NeedsCompilation no
Repository CRAN
Date/Publication 2016-11-25 14:14:33

R topics documented:
coefTable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
colMedians . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
compPlot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
ddnorm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
insertCol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
insertRow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
isSemidefinite . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
margEff . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

1
2 coefTable

nObs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
nParam . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
quasiconcavity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
rowMedians . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
rSquared . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
stdEr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
sumKeepAttr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
symMatrix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
triang . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
vecli . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
vecli2m . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
veclipos . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Index 19

coefTable Coefficient Table

Description
Generate Table for Coefficients, Std. Errors, t-values and P-values.

Usage
coefTable( coef, stdErr, df = NULL )

Arguments
coef vector that contains the coefficients.
stdErr vector that contains the standard errors of the coefficients.
df degrees of freedom of the t-test used to calculate P-values.

Value
a matrix with 4 columns: coefficients, standard errors, t-values and P-values. If argument df is not
provided, the last column (P-values) is filled with NAs.

Author(s)
Arne Henningsen

Examples
coefTable( rnorm( 10 ), 0.5 * abs( rnorm( 10 ) ), 20 )
colMedians 3

colMedians Medians of Columns

Description

Compute the sample medians of the columns (non-rows) of a data.frame or array.

Usage

colMedians( x, na.rm = FALSE )

Arguments

x a data.frame or array.
na.rm a logical value indicating whether NA values should be stripped before the com-
putation proceeds.

Value

A vector or array of the medians of each column (non-row) of x with dimension dim( x )[-1].

Author(s)

Arne Henningsen

See Also

rowMedians,median,colMeans.

Examples
data( "Electricity", package = "Ecdat" )
colMedians( Electricity )

a4 <- array( 1:120, dim = c(5,4,3,2),

dimnames = list( c("a","b","c","d","e"), c("A","B","C","D"),
c("x","y","z"), c("Y","Z") ) )
colMedians( a4 )
median( a4[ , "B", "x", "Z" ] ) # equal to
colMedians( a4 )[ "B", "x", "Z" ]
4 ddnorm

compPlot Scatterplot to Compare two Variables

Description
Plot a scatterplot to compare two variables.

Usage
compPlot( x, y, lim = NULL, ... )

Arguments
x values of the first variable (on the X axis).
y values of the second variable (on the Y axis).
lim optional vector of two elements specifying the limits of both axes).
... further arguments are passed to plot.

Author(s)
Arne Henningsen

Examples
set.seed( 123 )
x <- runif( 25 )
y <- 2 + 3 * x + rnorm( 25 )
ols <- lm( y ~ x )

compPlot( y, fitted( ols ) )

compPlot( y, fitted( ols ), lim = c( 0, 10 ) )
compPlot( y, fitted( ols ), pch = 20 )
compPlot( y, fitted( ols ), xlab = "observed", ylab = "fitted" )
compPlot( y, fitted( ols ), log = "xy" )

ddnorm Derivative of the Normal Distribution’s Density Function

Description
This function returns the derivative(s) of the density function of the normal (Gaussian) distribution
with respect to the quantile, evaluated at the quantile(s), mean(s), and standard deviation(s) specified
by arguments x, mean, and sd, respectively.
insertCol 5

Usage
ddnorm( x, mean = 0, sd = 1 )

Arguments
x quantile or vector of quantiles.
mean mean or vector of means.
sd standard deviation or vector of standard deviations.

Value
numeric value(s): derivative(s) of the density function of the normal distribution with respect to the
quantile

Author(s)
Arne Henningsen

See Also
dnorm

Examples
ddnorm( c( -1, 0, 1 ) )

insertCol Insert Column into a Matrix

Description
Insert a new column into a matrix.

Usage
insertCol( m, c, v = NA, cName = "" )

Arguments
m matrix.
c column number where the new column should be inserted.
v optional values of the new column.
cName optional character string: the name of the new column.

Value
a matrix with one more column than the provided matrix m.
6 insertRow

Author(s)
Arne Henningsen

See Also
insertRow.

Examples
m <- matrix( 1:4, 2 )
insertCol( m, 2, 5:6 )

insertRow Insert Row into a Matrix

Description
Insert a new row into a matrix.

Usage
insertRow( m, r, v = NA, rName = "" )

Arguments
m matrix.
r row number where the new row should be inserted.
v optional values for the new row.
rName optional character string: the name of the new row.

Value
a matrix with one more row than the provided matrix m.

Author(s)
Arne Henningsen

See Also
insertCol.

Examples
m <- matrix( 1:4, 2 )
insertRow( m, 2, 5:6 )
isSemidefinite 7

isSemidefinite Positive or Negative Semidefiniteness

Description
Check whether a symmetric matrix is positive or negative semidefinite.

Usage
isSemidefinite( m, ... )

## Default S3 method:
isSemidefinite( m, ... )

## S3 method for class 'matrix'

isSemidefinite( m, positive = TRUE,
tol = 100 * .Machine$double.eps,
method = ifelse( nrow( m ) < 13, "det", "eigen" ), ... )

## S3 method for class 'list'

isSemidefinite( m, ... )

semidefiniteness( m, ... )

Arguments
m a symmetric quadratic matrix or a list containing symmetric quadratic matrices.
positive logical. Check for positive semidefiniteness (if TRUE, default) or for negative
semidefiniteness (if FALSE).
tol tolerance level (values between -tol and tol are considered to be zero).
method method to test for semidefiniteness, either checking the signs of the principal
minors (if "det", default for matrices with up to 12 rows/columns) or checking
the signs of the eigenvalues (if "eigen", default for matrices with 13 or more
rows/columns).
... further arguments of isSemidefinite.list are passed to isSemidefinite.matrix;.
further arguments of semidefiniteness are passed to isSemidefinite; fur-
ther arguments of other functions are currently ignored.

Details
Function semidefiniteness() passes all its arguments to isSemidefinite(). It is only kept for
backward-compatibility and may be removed in the future.
If argument positive is set to FALSE, isSemidefinite() checks for negative semidefiniteness by
checking for positive semidefiniteness of the negative of argument m, i.e. -m.
If method "det" is used (default for matrices with up to 12 rows/columns), isSemidefinite()
checks whether all principal minors (not only the leading principal minors) of the matrix m (or
8 isSemidefinite

of the matrix -m if argument positive is FALSE) are larger than -tol. Due to rounding errors,
which are unavoidable on digital computers, the calculated determinants of singular (sub-)matrices
(which should theoretically be zero) can considerably deviate from zero. In order to reduce the
probability of incorrect results due to rounding errors, isSemidefinite() does not calculate the
determinants of (sub-)matrices with reciprocal condition numbers smaller than argument tol but
sets the corresponding
PN principal minors to (exactly) zero. The number of principal minors of an
N × N matrix is k=1 (N choose k), which gets very large for large matrices. Therefore, it is not
recommended to use method "det" for matrices with, say, more than 12 rows/columns.
If method "eigen" (default for matrices with 13 or more rows/columns) is used, isSemidefinite()
checks whether all eigenvalues of the matrix m (or of the matrix -m if argument positive is
FALSE) are larger than -tol. Due to rounding errors, which are unavoidable on digital comput-
ers, those eigenvalues of a singular matrix that should theoretically be zero can considerably de-
viate from zero. In order to reduce the probability of incorrect results due to rounding errors,
isSemidefinite() does not calculate the eigenvalues of an N × N matrix with reciprocal condi-
tion number smaller than argument tol but checks whether all N (N − 1) × (N − 1) submatrices
with row i and column i, i = 1, ..., N , removed are positive semidefinite. If necessary, this proce-
dure is done recursively.
Please note that a matrix can be neither positive semidefinite nor negative semidefinite.

Value
isSemidefinite() and semidefiniteness() return a locigal value (if argument m is a matrix) or
a logical vector (if argument m is a list) indicating whether the matrix (or each of the matrices) is
positive/negative (depending on argument positive) semidefinite.

Author(s)
Arne Henningsen

References
Chiang, A.C. (1984): Fundamental Methods of Mathematical Economics, 3rd ed., McGraw-Hill.
Gantmacher, F.R. (1959): The Theory of Matrices, Chelsea Publishing.

Examples
# a positive semidefinite matrix
isSemidefinite( matrix( 1, 3, 3 ))

# a negative semidefinite matrix

isSemidefinite( matrix(-1, 3, 3 ), positive = FALSE )

# a matrix that is positive and negative semidefinite

isSemidefinite( matrix( 0, 3, 3 ))
isSemidefinite( matrix( 0, 3, 3 ), positive = FALSE )

# a matrix that is neither positive nor negative semidefinite

isSemidefinite( symMatrix( 1:6 ) )
isSemidefinite( symMatrix( 1:6 ), positive = FALSE )
margEff 9

# checking a list of matrices

ml <- list( matrix( 1, 3, 3 ), matrix(-1, 3, 3 ), matrix( 0, 3, 3 ) )
isSemidefinite( ml )
isSemidefinite( ml, positive = FALSE )

margEff Method for Returning Marginal Effects

Description
Currently, this package just defines the generic function margEff so that it can be used to define
margEff methods for objects of specific classes in other packages.

Usage
margEff( object, ... )

Arguments
object an object of which marginal effects should be calculated.
... further arguments for methods

Author(s)
Arne Henningsen

nObs Return number of observations for statistical models

Description
Returns number of observations for statistical models. The default method assumes presence of a
component param$nObs in x.

Usage
nObs(x, ...)
## Default S3 method:
nObs(x, ...)
## S3 method for class 'lm'
nObs(x, ...)

Arguments
x a statistical model, such as created by lm
... further arguments for methods
10 nParam

Details
This is a generic function. The default method returns the component x$param$nObs. The lm-
method is based on qr-decomposition, in the same way as the does summary.lm.

Value
numeric, number of observations

Author(s)
Ott Toomet, <[email protected]>

See Also
nParam

Examples
# Construct a simple OLS regression:
x1 <- runif(100)
x2 <- runif(100)
y <- 3 + 4*x1 + 5*x2 + rnorm(100)
m <- lm(y~x1+x2) # estimate it
nObs(m)

nParam Number of model parameters

Description
This function returns the number of model parameters. The default method returns the component
x$param$nParam.

Usage
nParam(x, free=FALSE, ...)
## Default S3 method:
nParam(x, ...)
## S3 method for class 'lm'
nParam(x, ...)

Arguments
x a statistical model
free logical, whether to report only the free parameters or the total number of param-
eters (default)
... other arguments for methods
quasiconcavity 11

Details
Free parameters are the parameters with no equality restrictions. Some parameters may be restricted
(e.g. sum of two probabilities may be restricted to equal unity). In this case the total number of
parameters may depend on the normalisation.

Value
Number of parameters in the model

Author(s)
Ott Toomet, <[email protected]>

See Also
nObs for number of observations

Examples
# Construct a simple OLS regression:
x1 <- runif(100)
x2 <- runif(100)
y <- 3 + 4*x1 + 5*x2 + rnorm(100)
m <- lm(y~x1+x2) # estimate it
summary(m)
nParam(m) # you get 3

quasiconcavity Test for quasiconcavity / quasiconvexity

Description
Test wether a function is quasiconcave or quasiconvex. The bordered Hessian of this function is
checked by quasiconcavity() or quasiconvexity().

Usage
quasiconcavity( m, tol = .Machine$double.eps )
quasiconvexity( m, tol = .Machine$double.eps )

Arguments
m a bordered Hessian matrix or a list containing bordered Hessian matrices
tol tolerance level (values between -tol and tol are considered to be zero).

Value
locigal or a logical vector (if m is a list).
12 rowMedians

Author(s)
Arne Henningsen

References
Chiang, A.C. (1984) Fundamental Methods of Mathematical Economics, 3rd ed., McGraw-Hill.

Examples
quasiconcavity( matrix( 0, 3, 3 ) )

quasiconvexity( matrix( 0, 3, 3 ) )

m <- list()
m[[1]] <- matrix( c( 0,-1,-1, -1,-2,3, -1,3,5 ), 3, 3 )
m[[2]] <- matrix( c( 0,1,-1, 1,-2,3, -1,3,5 ), 3, 3 )

quasiconcavity( m )

quasiconvexity( m )

rowMedians Medians of Rows

Description
Compute the sample medians of the rows of a data.frame or matrix.

Usage
rowMedians( x, na.rm = FALSE )

Arguments
x a data.frame or matrix.
na.rm a logical value indicating whether NA values should be stripped before the com-
putation proceeds.

Value
A vector of the medians of each row of x.

Author(s)
Arne Henningsen

See Also
colMedians,median,colMeans.
rSquared 13

Examples
m <- matrix( 1:12, nrow = 4 )
rowMedians( m )

rSquared Calculate R squared value

Description
Calculate R squared value.

Usage
rSquared( y, resid )

Arguments
y vector of endogenous variables
resid vector of residuals

Author(s)
Arne Henningsen

Examples
data( "Electricity", package = "Ecdat" )
reg <- lm( cost ~ q + pl + pk + pf, Electricity )
rSquared( Electricity$cost, reg$residuals )
summary( reg )$r.squared # returns the same value

stdEr Standard deviations

Description
Extract standard deviations from estimated models.

Usage
stdEr(x, ...)
## Default S3 method:
stdEr(x, ...)
## S3 method for class 'lm'
stdEr(x, ...)
14 sumKeepAttr

Arguments
x a statistical model, such as created by lm
... further arguments for methods

Details
stdEr is a generic function with methods for objects of "lm" class. The default method returns the
square root of the diagonal of the variance-covariance matrix.

Value
numeric, the estimated standard errors of the coefficients.

Author(s)
Ott Toomet <[email protected]>

See Also
vcov, summary.

Examples
data(cars)
lmRes <- lm(dist ~ speed, data=cars)
stdEr( lmRes )

sumKeepAttr Sum of an Array While Keeping its Attributes

Description
This function returns the sum of an numeric array (e.g. vector or matrix) while keeping its attributes.

Usage
sumKeepAttr( x, keepNames = FALSE, na.rm = FALSE )

Arguments
x an numeric array (e.g. vector or matrix).
keepNames logical. Should the name(s) of the element(s) ofx be assigned to the returned
sum? (only relevant if codex has only one element).
na.rm logical. Passed to sum. Should missing values be removed?

Value
the sum (see sum).
symMatrix 15

Author(s)
Arne Henningsen

See Also
sum

Examples
a <- 1:10
attr( a, "min" ) <- 1
attr( a, "max" ) <- 10
sum(a)
sumKeepAttr(a)

symMatrix Symmetric Matrix

Description
Create a Symmetric Matrix.

Usage
symMatrix( data = NA, nrow = NULL, byrow = FALSE,
upper = FALSE )

Arguments
data an optional data vector.
nrow the desired number of rows and columns.
byrow logical. If ’FALSE’ (the default) the matrix is filled by columns, otherwise the
matrix is filled by rows.
upper logical. If ’FALSE’ (the default) the lower triangular part of the matrix (includ-
ing the diagonal) is filled, otherwise the upper triangular part of the matrix is
filled.

Value
a symmetric matrix.

Author(s)
Arne Henningsen

See Also
matrix, lower.tri.
16 triang

Examples
# fill the lower triangular part by columns
symMatrix( 1:10, 4 )
# fill the upper triangular part by columns
symMatrix( 1:10, 4, upper = TRUE )
# fill the lower triangular part by rows
symMatrix( 1:10, 4, byrow = FALSE )

triang Upper triangular matrix from a vector

Description

Creates an upper triangular square matrix from a vector.

Usage

triang( v, n )

Arguments

v vector
n desired dimension of the returned square matrix

Note

If the vector has less elements than the upper triangular matrix, the last elements are set to zero.

Author(s)

Arne Henningsen

See Also

veclipos.

Examples
v <- c( 1:5 )
triang( v, 3 )
vecli 17

vecli Vector of linear independent values

Description
Returns a vector containing the linear independent elements of a symmetric matrix (of full rank).

Usage
vecli( m )

Arguments
m symmetric matrix

Author(s)
Arne Henningsen

See Also
veclipos.

Examples
# a symmetric n x n matrix
m <- cbind(c(11,12,13),c(12,22,23),c(13,23,33))
vecli(m) # returns: 11 12 13 22 23 33

vecli2m Convert vector of linear independent values into a Matrix

Description
Converts a vector into a symmetric matrix that the original vector contains the linear independent
values of the returned symmetric matrix.

Usage
vecli2m( v )

Arguments
v a vector.
18 veclipos

Author(s)
Arne Henningsen

See Also
vecli, veclipos.

Examples
v <- c( 11, 12, 13, 22, 23, 33 )
vecli2m( v )

veclipos Position in a vector of linear independent values

Description
Returns the position of the [i,j]th element of a symmetric n × n matrix that this element has in a
vector of the linear independent values of the matrix.

Usage
veclipos( i, j, n )

Arguments
i row of the element in the matrix.
j column of the element in the matrix.
n dimension of the matrix.

Note
A symmetric n × n matrix has n*(n+1)/2 independent values.
The function is: n*(n-1)/2-((n-min(i,j))*(n-min(i,j)+1)/2)+max(i,j)

Author(s)
Arne Henningsen

See Also
vecli, vecli2m.

Examples
veclipos( 1, 2, 3 ) # returns: 2
Index

∗Topic array lower.tri, 15

colMedians, 3
insertCol, 5 margEff, 9
insertRow, 6 matrix, 15
isSemidefinite, 7 median, 3, 12
quasiconcavity, 11
rowMedians, 12 nObs, 9, 11
rSquared, 13 nParam, 10, 10
symMatrix, 15
plot, 4
triang, 16
vecli, 17 quasiconcavity, 11
vecli2m, 17 quasiconvexity (quasiconcavity), 11
veclipos, 18
∗Topic methods rowMedians, 3, 12
ddnorm, 4 rSquared, 13
margEff, 9
nObs, 9 semidefiniteness (isSemidefinite), 7
nParam, 10 stdEr, 13
stdEr, 13 sum, 14, 15
sumKeepAttr, 14 sumKeepAttr, 14
∗Topic models summary, 14
coefTable, 2 summary.lm, 10
compPlot, 4 symMatrix, 15
∗Topic multivariate
rSquared, 13 triang, 16
∗Topic univar
rSquared, 13 vcov, 14
vecli, 17, 18
coefTable, 2 vecli2m, 17, 18
colMeans, 3, 12 veclipos, 16–18, 18
colMedians, 3, 12
compPlot, 4

ddnorm, 4
dnorm, 5

insertCol, 5, 6
insertRow, 6, 6
isSemidefinite, 7

lm, 9, 14

19