Package ‘MESS’

August 21, 2023

Type Package
Title Miscellaneous Esoteric Statistical Scripts
Version 0.5.12
Date 2023-07-21
Maintainer Claus Thorn Ekstrøm <claus@rprimer.dk>
Depends R (>= 3.5)
Imports MASS, Matrix, Rcpp, clipr, geepack, geeM, ggplot2, ggformula,
glmnet, kinship2, methods, mvtnorm, parallel
LinkingTo Rcpp, RcppArmadillo
Suggests knitr, lme4, magrittr, rmarkdown, testthat
Description A mixed collection of useful and semi-useful diverse
statistical functions, some of which may even be referenced in
The R Primer book.

URL https://github.com/ekstroem/MESS

BugReports https://github.com/ekstroem/MESS/issues
Encoding UTF-8
ByteCompile true
License GPL-2
RoxygenNote 7.2.3
NeedsCompilation yes
Author Claus Thorn Ekstrøm [aut, cre],
Niels Aske Lundtorp Olsen [ctb]
Repository CRAN
Date/Publication 2023-08-20 22:52:48 UTC

1
2 R topics documented:

R topics documented:
adaptive.weights . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
add_torows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
age . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
auc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
bdstat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
bees . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
bin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
categorize . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
clipit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
clotting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
cmd . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
col.alpha . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
col.shade . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
col.tint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
colCumSum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
common.shared . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
conditional_rowMeans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
cumsumbinning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
dCor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
dCov . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
drop1.geeglm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
drop1.geem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
earthquakes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
expand_table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
extended.shared . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
fac2num . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
feature.test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
filldown . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
founder.shared . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
geekin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
gkgamma . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
greenland . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
happiness . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
ht . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
hwe_frequencies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
icecreamads . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
ks_cumtest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
kwdata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
lifeexpect . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
loadRData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
lower.tri.vector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
matched . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
maximum_subarray . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
MESS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
mfastLmCpp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
monte_carlo_chisq_test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
R topics documented: 3

nh4 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
ordered.clusters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
pairwise.cor.test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
pairwise_combination_indices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
pairwise_Schur_product . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
panel.hist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
panel.r2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
picea . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
plr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
power_binom_test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
power_mcnemar_test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
power_prop_test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
power_t_test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
prepost.test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
qdiag . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
QIC.geeglm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
qpcr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
quadform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
rainman . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
repmat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
residualplot.default . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
residual_plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
rmvt.pedigree . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
rmvtnorm.pedigree . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
rnorm_perfect . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
rootonorm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
round_percent . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
rud . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
scorefct . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
screen_variables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
segregate.genes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
sinv . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
smokehealth . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
soccer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
superroot2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
tracemp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
usd . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
wallyplot.default . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
write.xml . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90

Index 92
4 adaptive.weights

adaptive.weights Compute weights for use with adaptive lasso.

Description
Fast computation of weights needed for adaptive lasso based on Gaussian family data.

Usage
adaptive.weights(x, y, nu = 1, weight.method = c("multivariate", "univariate"))

Arguments
x input matrix, of dimension nobs x nvars; each row is an observation vector.
y response variable.
nu non-negative tuning parameter
weight.method Should the weights be computed for multivariate regression model (only possi-
ble when the number of observations is larger than the number of parameters)
or by individual marginal/"univariate" regression coefficients.

Details
The weights returned are 1/abs(beta_hat)^nu where the beta-parameters are estimated from the
corresponding linear model (either multivariate or univariate).

Value
Returns a list with two elements:

weights the computed weights

nu the value of nu used for the computations

Author(s)
Claus Ekstrom <claus@rprimer.dk>

References
Xou, H (2006). The Adaptive Lasso and Its Oracle Properties. JASA, Vol. 101.

See Also
glmnet
add_torows 5

Examples

set.seed(1)
x <- matrix(rnorm(50000), nrow=50)
y <- rnorm(50, mean=x[,1])
weights <- adaptive.weights(x, y)

if (requireNamespace("glmnet", quietly = TRUE)) {

res <- glmnet::glmnet(x, y, penalty.factor=weights$weights)
head(res)
}

add_torows Fast addition of vector to each row of matrix

Description
Fast addition of vector to each row of a matrix. This corresponds to t(t(x) + v)

Usage
add_torows(x, v)

Arguments
x A matrix with dimensions n*k.
v A vector of length k.

Value
A matrix of dimension n*k where v is added to each row of x

Author(s)
Claus Ekstrom <claus@rprimer.dk>

Examples

A <- matrix(1:12, ncol=3)

B <- c(1, 2, 3)

add_torows(A, B)
6 age

age Compute the age of a person from two dates.

Description

Compute the age in years of an individual based on the birth date and another (subsequent) date

Usage

age(from, to)

Arguments

from a vector of dates (birth dates)

to a vector of current dates

Details

Returns the full number of years that a person is old on a given date.

Value

A vector of ages (in years)

Author(s)

Claus Ekstrom <claus@rprimer.dk>

See Also

as.POSIXlt

Examples

born <- c("1971-08-18", "2000-02-28", "2001-12-20")

check <- c("2016-08-28")
age(born, check)
auc 7

auc Compute the area under the curve for two vectors.

Description

Compute the area under the curve using linear or natural spline interpolation for two vectors where
one corresponds to the x values and the other corresponds to the y values.

Usage

auc(
x,
y,
from = min(x, na.rm = TRUE),
to = max(x, na.rm = TRUE),
type = c("linear", "spline"),
absolutearea = FALSE,
subdivisions = 100,
...
)

Arguments

x a numeric vector of x values.

y a numeric vector of y values of the same length as x.
from The value from where to start calculating the area under the curve. Defaults to
the smallest x value.
to The value from where to end the calculation of the area under the curve. Defaults
to the greatest x value.
type The type of interpolation. Defaults to "linear" for area under the curve for linear
interpolation. The value "spline" results in the area under the natural cubic spline
interpolation.
absolutearea A logical value that determines if negative areas should be added to the total area
under the curve. By default the auc function subtracts areas that have negative
y values. Set absolutearea=TRUE to _add_ the absolute value of the negative
areas to the total area.
subdivisions an integer telling how many subdivisions should be used for integrate (for non-
linear approximations)
... additional arguments passed on to approx (for linear approximations). In partic-
ular rule can be set to determine how values outside the range of x is handled.
8 bdstat

Details
For linear interpolation the auc function computes the area under the curve using the composite
trapezoid rule. For area under a spline interpolation, auc uses the splinefun function in combination
with the integrate to calculate a numerical integral. The auc function can handle unsorted time
values, missing observations, ties for the time values, and integrating over part of the area or even
outside the area.

Value
The value of the area under the curve.

Author(s)
Claus Ekstrom <claus@rprimer.dk>

See Also
approx, splinefun, integrate

Examples

x <- 1:4
y <- c(0, 1, 1, 5)
auc(x, y)

# AUC from 0 to max(x) where we allow for extrapolation

auc(x, y, from=0, rule=2)

# Use value 0 to the left

auc(x, y, from=0, rule=2, yleft=0)

# Use 1/2 to the left

auc(x, y, from=0, rule=2, yleft=.5)

# Use 1/2 to the left with spline interpolation

auc(x, y, from=0, rule=2, yleft=.5)

bdstat Danish live births and deaths

Description
Monthly live births and deaths in Denmark from January 1901 to March 2013.
bees 9

Format
A data frame with 1356 observations on the following 4 variables.

year a numeric vector giving the month

month a numeric vector giving the year
births a numeric vector. The number of births for the given month and year
dead a numeric vector. The number of deaths for the given month and year

Source
Data were obtained from the StatBank from Danmarks Statistik, see http://www.statbank.dk.

Examples

data(bdstat)

plot(bdstat$year + bdstat$month/13, bdstat$birth, type="l")

# Create a table of births

# Remove year 2013 as it is incomplete
btable <- xtabs(births ~ year + month, data=bdstat, subset=(year<2013))

# Compute yearly birth frequencies per month

btable.freq <- prop.table(btable, margin=1)

bees Bee data. Number of different types of bees caught.

Description
Number of different types of bees caught in plates of different colours. There are four locations and
within each location there are three replicates consisting of three plates of the three different colours
(yellow, white and blue). Data are collected at 5 different dates over the summer season. Only data
from one date available until data has been published.

Format
A data frame with 72 observations on the following 7 variables.

Locality a factor with levels Havreholm Kragevig Saltrup Svaerdborg. Four different localities
in Denmark.
Replicate a factor with levels A B C
Color a factor with levels Blue White Yellow. Colour of plates
10 bin

Time a factor with levels july1 july14 june17 june3 june6. Data collected at different dates in
summer season. Only one day is present in the current data frame until the full data has been
released.
Type a factor with levels Bumblebees Solitary. Type of bee.
Number a numeric vector. The response variable with number of bees catched.
id a numeric vector. The id of the clusters (each containg three plates).

Source
Data were kindly provided by Casper Ingerslev Henriksen, Department of Agricultural Sciences,
KU-LIFE. Added by Torben Martinussen <tma@life.ku.dk>

Examples

data(bees)
model <- glm(Number ~ Locality + Type*Color,
family=poisson, data=bees)

bin Fast binning of numeric vector into equidistant bins

Description
Fast binning of numeric vector into equidistant bins

Usage
bin(x, width, origin = 0, missinglast = FALSE)

Arguments
x A matrix of regressor variables. Must have the same number of rows as the
length of y.
width The width of the bins
origin The starting point for the bins. Any number smaller than origin will be disre-
garded
missinglast Boolean. Should the missing observations be added as a separate element at the
end of the returned count vector.

Details
Missing values (NA, Inf, NaN) are added at the end of the vector as the last bin returned if missin-
glast is set to TRUE
categorize 11

Value
An list with elements counts (the frequencies), origin (the origin), width (the width), missing (the
number of missings), and last_bin_is_missing (boolean) telling whether the missinglast is true or
not.

Author(s)
Hadley Wickham (from SO: https://stackoverflow.com/questions/13661065/superimpose-histogram-
fits-in-one-plot-ggplot) - adapted here by Claus Ekstrøm <claus@rprimer.dk>

Examples

set.seed(1)
x <- sample(10, 20, replace = TRUE)
bin(x, 15)

categorize A table function to use with magrittr pipes

Description
Accepts a data frame as input and computes a contingency table for direct use in combination with
the magrittr package.

Usage
categorize(.data, ...)

Arguments
.data A data frame
... A formula (as in xtabs) or one or more objects which can be interpreted as factors
(including character strings), or a list (or data frame) whose components can be
so interpreted.

Details
categorize is a wrapper to xtabs or table such that a data frame can be given as the first argument.

Value
A table (possibly as an xtabs class if a model formula was used)

Author(s)
Claus Ekstrom <claus@rprimer.dk>
12 clipit

Examples

if (requireNamespace("magrittr", quietly = TRUE)) {

library(magrittr)

esoph %>% categorize(alcgp, agegp)

esoph %>% categorize(~ alcgp + agegp)
}

clipit Copy an object as R-code to the clipboard

Description
Copies an R object to the clipboard so it can be pasted in elsewhere.

Usage
clipit(x)

Arguments
x object to copy

Details
Returns nothing but will place the object in the clipboard

Value
Nothing but will put the R object into the clipboard as a side effect

Author(s)
Jonas LindeLøv posted on twitter. Copied shamelessly by Claus Ekstrom <claus@rprimer.dk>

Examples

## Not run:
clipit(mtcars$mpg)

## End(Not run)
clotting 13

clotting Blood clotting for 158 rats

Description
Blood clotting activity (PCA) is measured for 158 Norway rats from two locations just before
(baseline) and four days after injection of an anticoagulant (bromadiolone). Normally this would
cause reduced blood clotting after 4 days compared to the baseline, but these rats are known to
possess anticoagulent resistence to varying extent. The purpose is to relate anticoagulent resistence
to gender and location and perhaps weight. Dose of injection is, however, admistered according to
weight and gender.

Format
A data frame with 158 observations on the following 6 variables.

rat a numeric vector

locality a factor with levels Loc1 Loc2
sex a factor with levels F M
weight a numeric vector
PCA0 a numeric vector with percent blood clotting activity at baseline
PCA4 a numeric vector with percent blood clotting activity on day 4

Source
Ann-Charlotte Heiberg, project at The Royal Veterinary and Agricultural University, 1999.
Added by Ib M. Skovgaard <ims@life.ku.dk>

Examples

data(clotting)
dim(clotting)
head(clotting)
day0= transform(clotting, day=0, pca=PCA0)
day4= transform(clotting, day=4, pca=PCA4)
day.both= rbind(day0,day4)
m1= lm(pca ~ rat + day*locality + day*sex, data=day.both)
anova(m1)
summary(m1)
m2= lm(pca ~ rat + day, data=day.both)
anova(m2)
## Log transformation suggested.
## Random effect of rat.
## maybe str(clotting) ; plot(clotting) ...
14 cmd

cmd Correlation matrix distance

Description

Computes the correlation matrix distance between two correlation matrices

Usage

cmd(x, y)

Arguments

x First correlation matrix

y Second correlation matrix

Value

Returns the correlation matrix distance, which is a value between 0 and 1. The correlation matrix
distance becomes zero for equal correlation matrices and unity if they differ to a maximum extent.

Author(s)

Claus Ekstrom <claus@rprimer.dk>

References

Herdin, M., and Czink, N., and Ozcelik, H., and Bonek, E. (2005). Correlation matrix distance, a
meaningful measure for evaluation of non-stationary mimo channels. IEEE VTC.

Examples

m1 <- matrix(rep(1, 16), 4)

m2 <- matrix(c(1, 0, .5, .5, 0, 1, .5, .5, .5, .5, 1, .5, .5, .5, .5, 1), 4)
m3 <- matrix(c(1, 1, 0, 0, 1, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1), 4)
cmd(m1, m1)
cmd(m1, m2)
cmd(m2, m3)
col.alpha 15

col.alpha Add and set alpha channel for RGB color

Description
Add and set alpha channel

Usage
col.alpha(col, alpha = 1)

Arguments
col a vector of RGB color(s)
alpha numeric value between 0 and 1. Zero results fully transparent and 1 means full
opacity

Details
This function adds and set an alpha channel to a RGB color

Author(s)
Claus Ekstrom <claus@rprimer.dk>

References
Ekstrom, CT (2011) The R Primer.

Examples

newcol <- col.alpha("blue", .5)

col.shade Shade an RGB color

Description
Shades an RBG color

Usage
col.shade(col, shade = 0.5)
16 col.tint

Arguments
col a vector of RGB color(s)
shade numeric value between 0 and 1. Zero means no change and 1 results in black

Details
This function shades an RGB color and returns the shaded RGB color (with alpha channel added)

Author(s)
Claus Ekstrom <claus@rprimer.dk>

References
Ekstrom, CT (2011) The R Primer.

Examples

newcol <- col.shade("blue")

col.tint Tint an RGB color

Description
Tints an RBG color

Usage
col.tint(col, tint = 0.5)

Arguments
col a vector of RGB color(s)
tint numeric value between 0 and 1. Zero results in white and 1 means no change

Details
This function tints an RGB color and returns the tinted RGB color (with alpha channel added)

Author(s)
Claus Ekstrom <claus@rprimer.dk>
colCumSum 17

References

Ekstrom, CT (2011) The R Primer.

Examples

newcol <- col.tint("blue")

colCumSum Apply cumsum to each column of matrix

Description

Fast computation of apply(m, 2, cumsum)

Usage

colCumSum(m)

Arguments

m A matrix

Value

A matrix the same size as m with the column-wise cumulative sums.

Author(s)

Claus Ekstrom <claus@rprimer.dk>

Examples

# Generate a 100 by 10000 matrix

x <- matrix(rnorm(100*10000), nrow=100)
result <- colCumSum(x)
18 common.shared

common.shared Compute a common shared environment matrix

Description

Compute the common shared environment matrix for a set of related subjects. The function is
generic, and can accept a pedigree, or pedigreeList as the first argument.

Usage

common.shared(id, ...)

## S3 method for class 'pedigreeList'

common.shared(id, ...)

## S3 method for class 'pedigree'

common.shared(id, ...)

Arguments

id either a pedigree object or pedigreeList object

... Any number of optional arguments. Not used at the moment

Details

When called with a pedigreeList, i.e., with multiple families, the routine will create a block-
diagonal-symmetric ‘bdsmatrix’ object. Since the [i,j] value of the result is 0 for any two unrelated
individuals i and j and a ‘bdsmatix’ utilizes sparse representation, the resulting object is often or-
ders of magnitude smaller than an ordinary matrix. When called with a single pedigree and ordinary
matrix is returned.

Value

a matrix of shared environment coefficients

Author(s)

Claus Ekstrom <claus@rprimer.dk>

See Also

pedigree, kinship,
conditional_rowMeans 19

Examples

library(kinship2)
test1 <- data.frame(id =c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14),
mom =c(0, 0, 0, 0, 2, 2, 4, 4, 6, 2, 0, 0, 12, 13),
dad =c(0, 0, 0, 0, 1, 1, 3, 3, 3, 7, 0, 0, 11, 10),
sex =c(1, 2, 1, 2, 1, 2, 1, 2, 1, 1, 1, 2, 2, 2))
tped <- with(test1, pedigree(id, dad, mom, sex))
common.shared(tped)

conditional_rowMeans Form row means conditional on number of non-missing

Description

Form row means for multiple vectors, numeric arrays (or data frames) conditional on the number of
non-missing observations. NA is returned unless a minimum number of observations is observed.

Usage

conditional_rowMeans(..., minobs = 1L)

Arguments

... a series of numeric vectors, arrays, or data frames that have can be combined
with cbind
minobs an integer stating the minimum number of non-NA observations necessary to
compute the row mean. Defaults to 1.

Value

A numeric vector containing the row sums or NA if not enough non-NA observations are present

Examples
conditional_rowMeans(1:5, c(1:4, NA), c(1:3, NA, NA))
conditional_rowMeans(1:5, c(1:4, NA), c(1:3, NA, NA), minobs=0)
conditional_rowMeans(1:5, c(1:4, NA), c(1:3, NA, NA), minobs=2)
20 cumsumbinning

cumsumbinning Binning based on cumulative sum with reset above threshold

Description
Fast binning of cumulative vector sum with new groups when the sum passes a threshold or the
group size becomes too large

Usage
cumsumbinning(x, threshold, cutwhenpassed = FALSE, maxgroupsize = NULL)

Arguments
x A matrix of regressor variables. Must have the same number of rows as the
length of y.
threshold The value of the threshold that the cumulative group sum must not cross OR the
threshold that each group sum must pass (when the argument cuwhatpassed is
set to TRUE).
cutwhenpassed A boolean. Should the threshold be the upper limit of the group sum (the default)
or the value that each group sum needs to pass (when set to TRUE).
maxgroupsize An integer that defines the maximum number of elements in each group. NAs
count as part of each group but do not add to the group sum. NULL (the default)
corresponds to no group size limits.

Details
Missing values (NA, Inf, NaN) are completely disregarded and pairwise complete cases are used f

Value
An integer vector giving the group indices

Author(s)
Claus Ekstrom <claus@rprimer.dk>

Examples

set.seed(1)
x <- sample(10, 20, replace = TRUE)
cumsumbinning(x, 15)
cumsumbinning(x, 15, 3)

x <- c(3, 4, 5, 12, 1, 5, 3)

cumsumbinning(x, 10)
cumsumbinning(x, 10, cutwhenpassed=TRUE)
dCor 21

dCor Fast distance correlation matrix

Description
Fast computation of the distance correation matrix between two matrices with the same number of
rows. Note that this is not the same as the correlation matrix distance that can be computed with the
cmd function.

Usage
dCor(x, y)

Arguments
x A matrix with dimensions n*k.
y A matrix with dimensions n*l.

Value
A number between 0 and 1 representing the distance covariance between x and y

Author(s)
Claus Ekstrom <claus@rprimer.dk>

dCov Fast distance covariance matrix

Description
Fast computation of the distance covariance between two matrices with the same number of rows.

Usage
dCov(x, y)

Arguments
x A matrix with dimensions n*k.
y A matrix with dimensions n*l.

Value
A number representing the distance covariance between x and y
22 drop1.geeglm

Author(s)
Claus Ekstrom <claus@rprimer.dk>

drop1.geeglm Drop All Possible Single Terms to a geeglm Model Using Wald or
Score Test

Description
Compute all the single terms in the scope argument that can dropped from the model, and compute
a table of the corresponding Wald test statistics.

Usage
## S3 method for class 'geeglm'
drop1(
object,
scope,
test = c("Wald", "none", "score", "sasscore"),
method = c("robust", "naive", "sandwich"),
...
)

Arguments
object a fitted object of class geese.
scope a formula giving the terms to be considered for adding or dropping.
test the type of test to include.
method Indicates which method is used for computing the standard error. robust is
the default and corresponds to the modified sandwich estimator. naive is the
classical naive cariance estimate. sandwich is an alias for robust.
... other arguments. Not currently used

Value
An object of class "anova" summarizing the differences in fit between the models.

Author(s)
Claus Ekstrom <claus@ekstroem.dk>

See Also
drop1, geeglm, geese
drop1.geem 23

Examples

library(geepack)
data(ohio)
fit <- geeglm(resp ~ age + smoke + age:smoke, id=id, data=ohio,
family=binomial, corstr="exch", scale.fix=TRUE)
drop1(fit)

drop1.geem Drop All Possible Single Terms to a geem Model Using Wald or Score
Test

Description
Compute all the single terms in the scope argument that can dropped from the model, and compute
a table of the corresponding Wald test statistics.

Usage
## S3 method for class 'geem'
drop1(
object,
scope,
test = c("Wald", "none", "score", "sasscore"),
method = c("robust", "naive", "sandwich"),
...
)

Arguments
object a fitted object of class geese.
scope a formula giving the terms to be considered for adding or dropping.
test the type of test to include.
method Indicates which method is used for computing the standard error. robust is
the default and corresponds to the modified sandwich estimator. naive is the
classical naive cariance estimate. sandwich is an alias for robust.
... other arguments. Not currently used

Value
An object of class "anova" summarizing the differences in fit between the models.

Author(s)
Claus Ekstrom <claus@ekstroem.dk>
24 earthquakes

See Also
drop1, geem

Examples

library(geeM)
library(geepack)
data(ohio)
## Not run:
fit <- geem(resp ~ age + smoke + age:smoke, id=id, data=ohio,
family="binomial", corstr="exch", scale.fix=TRUE)
drop1(fit)

## End(Not run)

earthquakes Earthquakes in 2015

Description
Information on earthquakes worldwide in 2015 with a magnitude greater than 3 on the Richter scale.
The variables are just a subset of the variables available at the source

Format
A data frame with 19777 observations on the following 22 variables.
time a factor with time of the earthquake
latitude a numeric vector giving the decimal degrees latitude. Negative values for southern lati-
tudes
longitude a numeric vector giving the decimal degrees longitude. Negative values for western
longitudes
depth Depth of the event in kilometers
mag The magnitude for the event
place a factor giving a textual description of named geographic region near to the event.
type a factor with levels earthquake mining explosion rock burst

Source
https://www.usgs.gov/programs/earthquake-hazards

Examples

data(earthquakes)
with(earthquakes, place[which.max(mag)])
expand_table 25

expand_table Expand table or matrix to data frame

Description
Expands a contingency table to a data frame where each observation in the table becomes a single
observation in the data frame with corresponding information for each for each combination of the
table dimensions.

Usage
expand_table(x)

Arguments
x A table or matrix

Value
A data frame with the table or matrix expanded

Author(s)
Claus Ekstrom <claus@rprimer.dk>

Examples

expand_table(diag(3))
m <- matrix(c(2, 1, 3, 0, 0, 2), 3)
expand_table(m)
result <- expand_table(UCBAdmissions)
head(result)

# Combine into table again

xtabs(~Admit + Gender + Dept, data=result)

extended.shared Compute a common shared environment matrix

Description
Compute the common shared environment matrix for a set of related subjects. The function is
generic, and can accept a pedigree, or pedigreeList as the first argument.
26 extended.shared

Usage
extended.shared(id, rho = 1, theta = 1, ...)

## S3 method for class 'pedigreeList'

extended.shared(id, rho = 1, theta = 1, ...)

## S3 method for class 'pedigree'

extended.shared(id, rho = 1, theta = 1, ...)

Arguments
id either a pedigree object or pedigreeList object
rho The correlation between spouses
theta The partial path coefficient from parents to offspring
... Any number of optional arguments. Not used at the moment

Details
When called with a pedigreeList, i.e., with multiple families, the routine will create a block-
diagonal-symmetric ‘bdsmatrix’ object. Since the [i,j] value of the result is 0 for any two unrelated
individuals i and j and a ‘bdsmatix’ utilizes sparse representation, the resulting object is often or-
ders of magnitude smaller than an ordinary matrix. When called with a single pedigree and ordinary
matrix is returned.

Value
a matrix of shared environment coefficients

Author(s)
Claus Ekstrom <claus@rprimer.dk>

See Also
pedigree, kinship,

Examples

library(kinship2)
test1 <- data.frame(id =c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14),
mom =c(0, 0, 0, 0, 0, 2, 2, 4, 0, 6, 8, 0, 10, 11),
dad =c(0, 0, 0, 0, 0, 1, 1, 3, 0, 5, 7, 0, 9, 12),
sex =c(1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 2, 1, 2, 2))

tped <- with(test1, pedigree(id, dad, mom, sex))

extended.shared(tped)
fac2num 27

fac2num Convert factor to numeric vector

Description

Converts the factor labels to numeric values and returns the factor as a numeric vector

Usage

fac2num(x)

Arguments

x A factor

Details

Returns a vector of numeric values. Elements in the input factor that cannot be converted to numeric
will produce NA.

Value

Returns a numeric vector of the same length as x

Author(s)

Claus Ekstrom <claus@rprimer.dk>

Examples

f <- factor(c(1,2,1,3,2,1,2,3,1))
fac2num(f)

feature.test Inference for features identified by the Lasso

Description

Performs randomization tests of features identified by the Lasso

28 feature.test

Usage
feature.test(
x,
y,
B = 100,
type.measure = "deviance",
s = "lambda.min",
keeplambda = FALSE,
olsestimates = TRUE,
penalty.factor = rep(1, nvars),
alpha = 1,
control = list(trace = FALSE, maxcores = 24),
...
)

Arguments
x input matrix, of dimension nobs x nvars; each row is an observation vector.
y quantitative response variable of length nobs
B The number of randomizations used in the computations
type.measure loss to use for cross-validation. See cv.glmnet for more information
s Value of the penalty parameter ’lambda’ at which predictions are required. De-
fault is the entire sequence used to create the model. See coef.glmnet for more
information
keeplambda If set to TRUE then the estimated lambda from cross validation from the original
dataset is kept and used for evaluation in the subsequent randomization datasets.
This reduces computation time substantially as it is not necessary to perform
cross validation for each randomization. If set to a value then that value is used
for the value of lambda. Defaults to FALSE
olsestimates Logical. Should the test statistic be based on OLS estimates from the model
based on the variables selected by the lasso. Defaults to TRUE. If set to FALSE
then the coefficients from the lasso is used as test statistics.
penalty.factor a vector of weights used for adaptive lasso. See glmnet for more information.
alpha The elasticnet mixing parameter. See glmnet for more information.
control A list of options that control the algorithm. Currently trace is a logical and if set
to TRUE then the function produces more output. maxcores sets the maximum
number of cores to use with the parallel package
... Other arguments passed to glmnet

Value
Returns a list of 7 variables:

p.full The p-value for the test of the full set of variables selected by the lasso (based
on the OLS estimates)
filldown 29

ols.selected A vector of the indices of the non-zero variables selected by glmnet sorted from
(numerically) highest to lowest based on their ols test statistic.
p.maxols The p-value for the maximum of the OLS test statistics
lasso.selected
A vector of the indices of the non-zero variables selected by glmnet sorted from
(numerically) highest to lowest based on their absolute lasso coefficients.
p.maxlasso The p-value for the maximum of the lasso test statistics
lambda.orig The value of lambda used in the computations
B The number of permutations used

Author(s)
Claus Ekstrom <ekstrom@sund.ku.dk> and Kasper Brink-Jensen <kbrink@life.ku.dk>

References
Brink-Jensen, K and Ekstrom, CT 2014. Inference for feature selection using the Lasso with high-
dimensional data. https://arxiv.org/abs/1403.4296

See Also
glmnet

Examples

# Simulate some data

x <- matrix(rnorm(30*100), nrow=30)
y <- rnorm(30, mean=1*x[,1])

# Make inference for features

## Not run:
feature.test(x, y)

## End(Not run)

filldown Fill down NA with the last observed observation

Description
Fill down missing values with the latest non-missing value
30 founder.shared

Usage
filldown(x)

Arguments
x A vector

Value
A vector or list with the NA’s replaced by the last observed value.

Author(s)
Claus Ekstrom <claus@rprimer.dk>

Examples

a <- c(1:5, "Howdy", NA, NA, 2:3, NA)

filldown(a)
filldown(c(NA, NA, NA, 3:5))

founder.shared Compute a common shared environment matrix

Description
Compute the common shared environment matrix for a set of related subjects. The function is
generic, and can accept a pedigree, or pedigreeList as the first argument.

Usage
founder.shared(id, ...)

## S3 method for class 'pedigreeList'

founder.shared(id, ...)

## S3 method for class 'pedigree'

founder.shared(id, ...)

Arguments
id either a pedigree object or pedigreeList object
... Any number of optional arguments. Not used at the moment
geekin 31

Details
When called with a pedigreeList, i.e., with multiple families, the routine will create a block-
diagonal-symmetric ‘bdsmatrix’ object. Since the [i,j] value of the result is 0 for any two unrelated
individuals i and j and a ‘bdsmatix’ utilizes sparse representation, the resulting object is often or-
ders of magnitude smaller than an ordinary matrix. When called with a single pedigree and ordinary
matrix is returned.

Value
a matrix of shared environment coefficients

Author(s)
Claus Ekstrom <claus@rprimer.dk>

See Also
pedigree, kinship,

Examples

library(kinship2)
test1 <- data.frame(id =c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14),
mom =c(0, 0, 0, 0, 2, 2, 4, 4, 6, 2, 0, 0, 12, 13),
dad =c(0, 0, 0, 0, 1, 1, 3, 3, 3, 7, 0, 0, 11, 10),
sex =c(1, 2, 1, 2, 1, 2, 1, 2, 1, 1, 1, 2, 2, 2))
tped <- with(test1, pedigree(id, dad, mom, sex))
founder.shared(tped)

geekin Fit a generalized estimating equation (GEE) model with fixed additive
correlation structure

Description
The geekin function fits generalized estimating equations but where the correlation structure is given
as linear function of (scaled) fixed correlation structures.

Usage
geekin(
formula,
family = gaussian,
data,
weights,
subset,
32 geekin

id,
na.action,
control = geepack::geese.control(...),
varlist,
...
)

Arguments

formula See corresponding documentation to glm.

family See corresponding documentation to glm.
data See corresponding documentation to glm.
weights See corresponding documentation to glm.
subset See corresponding documentation to glm.
id a vector which identifies the clusters. The length of id should be the same as the
number of observations. Data must be sorted so that observations on a cluster
are contiguous rows for all entities in the formula. If not the function will give
an error
na.action See corresponding documentation to glm.
control See corresponding documentation to glm.
varlist a list containing one or more matrix or bdsmatrix objects that represent the cor-
relation structures
... further arguments passed to or from other methods.

Details

The geekin function is essentially a wrapper function to geeglm. Through the varlist argument, it
allows for correlation structures of the form
R = sum_i=1^k alpha_i R_i
where alpha_i are(nuisance) scale parameters that are used to scale the off-diagonal elements of the
individual correlation matrices, R_i.

Value

Returns an object of type geeglm.

Author(s)

Claus Ekstrom <claus@rprimer.dk>

See Also

lmekin, geeglm
gkgamma 33

Examples

# Get dataset
library(kinship2)
library(mvtnorm)
data(minnbreast)

breastpeda <- with(minnbreast[order(minnbreast$famid), ], pedigree(id,

fatherid, motherid, sex,
status=(cancer& !is.na(cancer)), affected=proband,
famid=famid))

set.seed(10)

nfam <- 6
breastped <- breastpeda[1:nfam]

# Simulate a response

# Make dataset for lme4

df <- lapply(1:nfam, function(xx) {
as.data.frame(breastped[xx])
})

mydata <- do.call(rbind, df)

mydata$famid <- rep(1:nfam, times=unlist(lapply(df, nrow)))

y <- lapply(1:nfam, function(xx) {

x <- breastped[xx]
rmvtnorm.pedigree(1, x, h2=0.3, c2=0)
})
yy <- unlist(y)

library(geepack)

geekin(yy ~ 1, id=mydata$famid, varlist=list(2*kinship(breastped)))

# lmekin(yy ~ 1 + (1|id), data=mydata, varlist=list(2*kinship(breastped)),method="REML")

gkgamma Goodman-Kruskal’s gamma statistic for a two-dimensional table

Description
Compute Goodman-Kruskal’s gamma statistic for a two-dimensional table of ordered categories
34 gkgamma

Usage
gkgamma(x, conf.level = 0.95)

Arguments
x A matrix or table representing the two-dimensional ordered contingency table
of observations
conf.level Level of confidence interval

Value
A list with class htest containing the following components:

statistic the value the test statistic for testing no association

p.value the p-value for the test
estimate the value the gamma estimate
conf.int the confidence interval for the gamma estimate
method a character string indicating the type of test performed
data.name a character string indicating the name of the data input
observed the observed counts
s0 the SE used when computing the test statistics
s1 the SE used when computing the confidence interval

Author(s)
Claus Ekstrom <claus@rprimer.dk>

References
Goodman, Leo A. and Kruskal, William H. (1954). "Measures of Association for Cross Classifica-
tions". Journal of the American Statistical Association 49 (268): 732-764.

See Also
chisq.test

Examples

# Data from the Glostrup study comparing smoking to overall health in males
smoke <- matrix(c(16, 15, 13, 10, 1, 73, 75, 59, 81, 29, 6, 6, 7, 17, 3, 1, 0, 1, 3, 1), ncol=4)
colnames(smoke) <- c("VGood", "Good", "Fair", "Bad") # General health status
rownames(smoke) <- c("Never", "No more", "1-14", "15-24", "25+") # Smoke amount
gkgamma(smoke)
chisq.test(smoke)
greenland 35

greenland Average yearly summer air temperature for Tasiilaq, Greenland

Description

Average yearly summer (June, July, August) air temperature for Tasiilaq, Greenland

Format

A data frame with 51 observations on the following 2 variables.

year year
airtemp average air temperature (degrees Celcius)

Source

Data provided by Sebastian Mernild.

Originally obtained from http://www.dmi.dk/dmi/index/gronland/vejrarkiv-gl.htm.
Added by Claus Ekstrom <ekstrom@life.ku.dk>

References

Aktuelt Naturvidenskab september 2010.

http://aktuelnaturvidenskab.dk/fileadmin/an/nr-4/an4_2010gletscher.pdf

Examples

data(greenland)
model <- lm(airtemp ~ year, data=greenland)
plot(greenland$year, greenland$airtemp, xlab="Year", ylab="Air temperature")
abline(model, col="red")

happiness Happiness score and tax rates for 148 countries

Description

Dataset on subjective happiness, tax rates, population sizes, continent, and major religion for 148
countries
36 happiness

Format
A data frame with 148 observations on the following 6 variables.
country a factor with 148 levels that contain the country names
happy a numeric vector with the average subject happiness score (on a scale from 0-10)
tax a numeric vector showing the tax revenue as percentage of GDP
religion a factor with levels Buddhist Christian Hindu Muslim None or Other
continent a factor with levels AF, AS, EU, NA, OC, SA, corresponding to the continents Africa, Asia,
Europe, North America, Ocenaia, South American, respectively
population a numeric vector showing the population (in millions)

Source
Data collected by Ellen Ekstroem.
Population sizes are from Wikipedia per August 2nd, 2012 https://en.wikipedia.org/wiki/
List_of_countries_by_population
Major religions are from Wikipedia per August 2nd, 2012 https://en.wikipedia.org/wiki/
Religions_by_country
Tax rates are from Wikipedia per August 2nd, 2012 https://en.wikipedia.org/wiki/List_of_
countries_by_tax_revenue_as_percentage_of_GDP
Average happiness scores are from "Veenhoven, R. Average happiness in 148 nations 2000-2009,
World Database of Happiness, Erasmus University Rotterdam, The Netherlands". Assessed on Au-
gust 2nd, 2012 at: https://worlddatabaseofhappiness-archive.eur.nl/hap_nat/findingreports/
RankReport_AverageHappiness.php

Examples

data(happiness)
with(happiness, symbols(tax, happy, circles=sqrt(population)/8, inches=FALSE, bg=continent))

#
# Make a prettier image with transparent colors
#

newcols <- rgb(t(col2rgb(palette())),

alpha=100, maxColorValue=255)

with(happiness, symbols(tax, happy, circles=sqrt(population)/8,

inches=FALSE, bg=newcols[continent],
xlab="Tax (% of GDP)", ylab="Happiness"))

#
# Simple analysis
#
res <- lm(happy ~ religion + population + tax:continent, data=happiness)
summary(res)
ht 37

ht Show the head and tail of an object

Description

Show both the head and tail of an R object

Usage

ht(x, n = 6L, m = n, returnList = FALSE, ...)

Arguments

x The object to show

n The number of elements to list for the head
m The number of elements to list for the tail
returnList Logical. Should the result be returned as a list
... additional arguments passed to functions (not used at the moment)

Details

This function does no error checking and it is up to the user to ensure that the input is indeed
symmetric, positive-definite, and a matrix.

Value

NULL unless returnList is set to TRUE in which case a list is returned

Author(s)

Claus Ekstrom, <claus@rprimer.dk>.

Examples
ht(trees)
ht(diag(20))
ht(1:20)
ht(1:20, returnList=TRUE)
38 hwe_frequencies

hwe_frequencies Fast estimation of allele and genotype frequencies under Hardy-

Weinberg equilibrium

Description

Alleles are assumed to be numerated from 1 and up with no missing label. Thus if the largest
value in either allele1 or allele2 is K then we assume that there can be at least K possible alleles.
Genotypes are sorted such the the smallest allele comes first, i.e., 2x1 -> 1x2, and 2x3 -> 2x3

Usage

hwe_frequencies(allele1, allele2, min_alleles = 0L)

Arguments

allele1 An integer vector (starting with values 1 upwards) of first alleles

allele2 An integer vector (starting with values 1 upwards) of second alleles
min_alleles A minimum number of unique alleles available

Value

A list with three variables: allele_freq for estimated allele frequencies, genotype_freq for es-
timated genotype_frequencies (under HWE assumption), obs_genotype is the frequency of the
genotypes, available_genotypes is the number of available genotypes used for the estimation, and
unique_alleles is the number of unique alleles (matches the length of allele_freq)

Author(s)

Claus Ekstrom <claus@rprimer.dk>

Examples

al1 <- sample(1:5, size=1000, replace=TRUE, prob=c(.4, .2, .2, .1, .1))
al2 <- sample(1:5, size=1000, replace=TRUE, prob=c(.4, .2, .2, .1, .1))
hwe_frequencies(al1, al2)
icecreamads 39

icecreamads Ice cream consumption and advertising

Description
The impact of advertizing impact, temperature, and price on ice cream consumption

Format
A data frame with 30 observations on the following 4 variables.

Price a numeric vector character vector giving the standardized price

Temperature temperature in degrees Fahrenheit
Consumption a factor with levels 1_low 2_medium 3_high
Advertise a factor with levels posters radio television

Source
Unknown origin

Examples

data("icecreamads")

ks_cumtest Kolmogorov-Smirnov goodness of fit test for cumulative discrete data

Description
Kolmogorov-Smirnov goodness of fit test for cumulative discrete data.

Usage
ks_cumtest(x, B = 10000L, prob = NULL)

Arguments
x A vector representing the contingency table.
B The number of simulations used to compute the p-value.
prob A positive vector of the same length as x representing the distribution under the
null hypothesis. It will be scaled to sum to 1. If NULL (the default) then a
uniform distribution is assumed.
40 kwdata

Details
The name of the function might change in the future so keep that in mind!
Simulation is done by random sampling from the null hypothesis.

Value
A list of class "htest" giving the simulation results.

Author(s)
Claus Ekstrom <claus@rprimer.dk>

Examples

x <- 1:6
ks_cumtest(x)

kwdata Non-parametric Kruskal Wallis data example

Description
Artificial dataset to show that the p-value obtained for the Kruskal Wallis is only valid _after_ the
distributional form has been checked to be the same for all groups.

Format
An artificial data frame with 18 observations in each of three groups.

x measurements for group 1

y measurements for group 2
z measurements for group 3

Source
Data example found on the internet

Examples

data(kwdata)
newdata <- stack(kwdata)
kruskal.test(values ~ ind, newdata)
lifeexpect 41

lifeexpect Estimated life expectancy for Danish newborns

Description
The estimated life expectancy for newborn Danes split according to gender.

Format
A data frame with 70 observations on the following 3 variables.
year a character vectorgiving the calendar interval on which the estimation was based.
male a numeric vectorLife expectancy for males (in years).
female a numeric vectorLife expectancy for females (in years)
myear a numeric vectorThe midpoint of the year interval

Source
Data collected from Danmarks Statistik. See https://www.dst.dk/en for more information.

Examples

data(lifeexpect)
plot(lifeexpect$myear, lifeexpect$male)

loadRData Load and extract object from RData file

Description
Loads and extracts an object from an RData file

Usage
loadRData(filename)

Arguments
filename The path to the RData file

Details
Returns an R object
42 lower.tri.vector

Value
An R object

Author(s)
ricardo (from GitHub)

See Also
load

Examples

## Not run:
d <- loadRData("~/blah/ricardo.RData")

## End(Not run)

lower.tri.vector Split Matrix by Clusters and Return Lower Triangular Parts as Vector

Description
Split a matrix into block diagonal sub matrices according to clusters and combine the lower trian-
gular parts into a vector

Usage
lower.tri.vector(x, cluster = rep(1, nrow(x)), diag = FALSE)

Arguments
x a square matrix
cluster numeric or factor. Is used to identify the sub-matrices of x from which the lower
triangular parts are extracted. Defaults to the full matrix.
diag logical. Should the diagonal be included?

Value
Returns a numeric vector containing the elements of the lower triangular sub matrices.

Author(s)
Claus Ekstrom <claus@ekstroem.dk>
matched 43

See Also
lower.tri

Examples

m <- matrix(1:64, ncol=8)

cluster <- c(1, 1, 1, 1, 2, 2, 3, 3)
lower.tri.vector(m, cluster)

matched Flu hospitalization

Description
Researchers in a Midwestern county tracked flu cases requiring hospitalization in those residents
aged 65 and older during a two-month period one winter. They matched each case with 2 controls
by sex and age (150 cases, 300 controls). They used medical records to determine whether cases and
controls had received a flu vaccine shot and whether they had underlying lung disease. They wanted
to know whether flu vaccination prevents hospitalization for flu (severe cases of flu). Underlying
lung disease is a potential confounder.

Format
A data frame with 450 observations on the following 4 variables.

id a numeric vector
iscase a factor with levels Control Case
vaccine a factor with levels Not Vaccinated
lung a factor with levels None Disease

Source
Modified from: Stokes, Davis, Koch (2000). "Categorical Data Analysis Using the SAS System,"
Chapter 10.

Examples

data(matched)
44 MESS

maximum_subarray Fast computation of maximum sum subarray

Description
Fast computation of the maximum subarray sum of a vector using Kadane’s algorithm. The imple-
mentation handles purely negative numbers.

Usage
maximum_subarray(x)

Arguments
x A vector

Value
A list with three elements: sum (the maximum subarray sum), start (the starting index of the subar-
ray) and end (the ending index of the subarray)

Author(s)
Claus Ekstrom <claus@rprimer.dk>

Examples

maximum_subarray(1:4)

maximum_subarray(c(-2, 1, -3, 4, -1, 2, 1, -5, 4))

maximum_subarray(rnorm(100000))

MESS Collection of miscellaneous useful and semi-useful functions

Description
Collection of miscellaneous useful and semi-useful functions and add-on functions that enhances a
number of existing packages and provides In particular in relation to statistical genetics
mfastLmCpp 45

Details

Package: MESS
Type: Package
Version: 1.0
Date: 2012-03-29
License: GPL-2

how to use the package, including the most important ~~

Author(s)
Claus Thorn Ekstrøm <claus@rprimer.dk>
Maintainer: Claus Thorn Ekstrøm <claus@rprimer.dk>

References
Ekstrøm, C. (2011). The R Primer. Chapman & Hall.

mfastLmCpp Fast marginal simple regresion analyses

Description
Fast computation of simple regression slopes for each predictor represented by a column in a matrix

Usage
mfastLmCpp(y, x, addintercept = TRUE)

Arguments
y A vector of outcomes.
x A matrix of regressor variables. Must have the same number of rows as the
length of y.
addintercept A logical that determines if the intercept should be included in all analyses
(TRUE) or not (FALSE)

Details
No error checking is done

Value
A data frame with three variables: coefficients, stderr, and tstat that gives the slope estimate, the
corresponding standard error, and their ratio for each column in x.
46 monte_carlo_chisq_test

Author(s)
Claus Ekstrom <claus@rprimer.dk>

Examples
## Not run:
// Generate 100000 predictors and 100 observations
x <- matrix(rnorm(100*100000), nrow=100)
y <- rnorm(100, mean=x[,1])
mfastLmCpp(y, x)

## End(Not run)

monte_carlo_chisq_test
Two-sided table test with fixed margins

Description
Monte Carlo test in a two-way contingency table with the total number of observations fixed, row
margin fixed, or both margins fixed.

Usage
monte_carlo_chisq_test(x, margin = c("N", "rows", "both"), B = 100000L)

Arguments
x A matrix representing the contingency table.
margin A string that determines which margin is fixed: Either "N" for the total number
of observations (the default), "rows" for fixed row sums, and "both" for simulta-
neously fixed row and column sums.
B The number of simulations used to compute the p-value.

Details
Simulation is done by random sampling from the set of all tables with given marginal(s), and works
only if the relevant marginal(s) are strictly positive. Continuity correction is never used, and the
statistic is quoted without it.

Value
A list of class "htest" giving the simulation results.

Author(s)
Claus Ekstrom <claus@rprimer.dk>
nh4 47

Examples

m <- matrix(c(12, 4, 8, 6), 2)

chisq.test(m)
chisq.test(m, correct=FALSE)
monte_carlo_chisq_test(m)

fisher.test(m)
monte_carlo_chisq_test(m, margin="both")

m2 <- matrix(c(9, 3, 3, 7), 2)

monte_carlo_chisq_test(m, margin="N")
monte_carlo_chisq_test(m, margin="both")

nh4 Ammonia nitrogen found in river

Description

Monthly levels of ammonia nitrogen in a river over two years

Format

A data frame with 120 observations on the following 3 variables.

nh4 The ammonia nitrogen levels (mg/l). A value of zero corresponds to a censoring, but it really
is censored at <0.01
cens A logical vector indicating if the value was censored
year The year

Source

Found on the internet and partly simulated

Examples

data(nh4)
48 ordered.clusters

ordered.clusters Check if unique elements of a vector appear in contiguous clusters

Description

ordered.clusters determines if identical elements of a vector appear in contiguous clusters, and

returns TRUE if the do and FALSE otherwise.

Usage

ordered.clusters(id)

Arguments

id a vector

Value

The function returns TRUE if the elements appear in contiguous clusters and FALSE otherwise

Author(s)

Claus Ekstrom <claus@ekstroem.dk> with suggestions from Peter Dalgaard.

See Also

duplicated

Examples

x <- c(1, 1, 1, 2, 2, 3, 4, 1, 5, 5, 5)
ordered.clusters(x)
ordered.clusters(sort(x))
ordered.clusters(x[order(x)])
pairwise.cor.test 49

pairwise.cor.test Pairwise Tests for Association/Correlation Between Paired Samples

Description
Calculate pairwise correlations between group levels with corrections for multiple testing.

Usage
pairwise.cor.test(
x,
g,
p.adjust.method = p.adjust.methods,
method = c("pearson", "kendall", "spearman"),
...
)

Arguments
x response vector.
g grouping vector or factor.
p.adjust.method
method for adjusting p values (see p.adjust). Can be abbreviated.
method string argument to set the method to compute the correlation. Possibilities are
"pearson" (the default), "kendall", and "spearman"
... additional arguments passed to cor.test.

Details
Note that correlation tests require that the two vectors examined are of the same length. Thus, if the
grouping defines groups of varying lengths then the specific correlation is not computed and a NA is
returned instead. The adjusted p values are only based on the actual correlation that are computed.
Extra arguments that are passed on to cor.test may or may not be sensible in this context.

Value
Object of class pairwise.htest

Examples

attach(airquality)
Month <- factor(Month, labels = month.abb[5:9])
pairwise.cor.test(Ozone, Month)
pairwise.cor.test(Ozone, Month, p.adj = "bonf")
detach()
50 pairwise_combination_indices

pairwise_combination_indices
Compute all pairwise combinations of indices

Description

Fast computation of indices of all pairwise element of a vector of length n.

Usage

pairwise_combination_indices(n, self = FALSE)

Arguments

n A number giving the number of elements to create all pairwise indices from
self A logical that determines whether a column should also be multiplied by itself.

Details

Note that the output order of columns corresponds to the order of the columns in x. First column 1
is multiplied with each of the other columns, then column 2 with the remaining columns etc.

Value

A matrix with n*(n+1)/2 rows (if self=TRUE) or n*(n-1)/2 rows (if self=FALSE, the default) and
two columns gicing all possible combinations of indices.

Author(s)

Claus Ekstrom <claus@rprimer.dk>

Examples

pairwise_combination_indices(3)
pairwise_combination_indices(4, self=TRUE)
pairwise_Schur_product 51

pairwise_Schur_product
Compute Schur products (element-wise) of all pairwise combinations
of columns in matrix

Description

Fast computation of all pairwise element-wise column products of a matrix.

Usage

pairwise_Schur_product(x, self = FALSE)

Arguments

x A matrix with dimensions r*c.

self A logical that determines whether a column should also be multiplied by itself.

Details

Note that the output order of columns corresponds to the order of the columns in x. First column 1
is multiplied with each of the other columns, then column 2 with the remaining columns etc.

Value

A matrix with the same number of rows as x and a number of columns corresponding to c choose 2
(+ c if self is TRUE), where c is the number of columns of x.

Author(s)

Claus Ekstrom <claus@rprimer.dk>

Examples

X <- cbind(rep(1, 4), 1:4, 4:1)

pairwise_Schur_product(X)
pairwise_Schur_product(X, self=TRUE)
52 panel.hist

panel.hist Panel plot of histogram and density curve

Description

Prints the histogram and corresponding density curve

Usage

panel.hist(x, col.bar = "gray", ...)

Arguments

x a numeric vector of x values

col.bar the color of the bars
... options passed to hist

Details

This function prints a combined histogram and density curve for use with the pairs function

Author(s)

Claus Ekstrom <claus@rprimer.dk>

References

Ekstrom, CT (2011) The R Primer.

Examples

pairs(~ Ozone + Temp + Wind + Solar.R, data=airquality,

lower.panel=panel.smooth, diag.panel=panel.hist,
upper.panel=panel.r2)
panel.r2 53

panel.r2 Panel plot of R2 values for pairs

Description

Prints the R2 with text size depending on the size of R2

Usage

panel.r2(x, y, digits = 2, cex.cor, ...)

Arguments

x a numeric vector of x values

y a numeric vector of y values
digits a numeric value giving the number of digits to present
cex.cor scaling fator for the size of text
... extra options (not used at the moment)

Details

This function is a slight modification of the panel.cor function defined on the pairs help page. It
calculated and prints the squared correlation, R2, with text size depending on the proportion of
explained variation.

Author(s)

Claus Ekstrom <claus@rprimer.dk>

References

Ekstrom, CT (2011) The R Primer.

Examples

pairs(~ Ozone + Temp + Wind + Solar.R, data=airquality,

lower.panel=panel.smooth, upper.panel=panel.r2)
54 plr

picea Ozone concentration damage to picea spruce

Description
Damage scores (ordinal scale) for Picea Sitchesis shoots at two dates, at four temperatures, and 4
ozone Levels

Format
An artificial data frame with 18 observations in each of three groups.
date a character vector giving the date
temp temperature in degrees Celcius
conc Ozone concentration at 4 different levels
damage the damage score from 0-4, higher is more damage
count The number of occurrences of this group

Source
P.W. Lucas, D.A. Cottam, L.J. Sheppard, B.J. Francis (1988). "Growth Responses and Delayed
Winter Hardening in Sitka Spruce Following Summer Exposure to Ozone," New Phytologist, Vol.
108, pp. 495-504.

Examples

data(picea)

plr Fast computation of several simple linear regressions

Description
Fast computation of several simple linear regression, where the outcome is analyzed with several
marginal analyses, or where several outcome are analyzed separately, or a combination of both.

Usage
plr(y, x, addintercept = TRUE)

## S3 method for class 'numeric'

plr(y, x, addintercept = TRUE)

## S3 method for class 'matrix'

plr(y, x, addintercept = TRUE)
power_binom_test 55

Arguments
y either a vector (of length N) or a matrix (with N rows)
x a matrix with N rows
addintercept boolean. Should the intercept be included in the model by default (TRUE)

Value
a data frame (if Y is a vector) or list of data frames (if Y is a matrix)

Author(s)
Claus Ekstrom <ekstrom@sund.ku.dk>

See Also
mfastLmCpp

Examples

N <- 1000 # Number of observations

Nx <- 20 # Number of independent variables
Ny <- 80 # Number of dependent variables

# Simulate outcomes that are all standard Gaussians

Y <- matrix(rnorm(N*Ny), ncol=Ny)
X <- matrix(rnorm(N*Nx), ncol=Nx)

plr(Y, X)

power_binom_test Power Calculations for Exact Test of a simple null hypothesis in a

Bernoulli experiment

Description
Compute power of test, or determine parameters to obtain target power.

Usage
power_binom_test(
n = NULL,
p0 = NULL,
pa = NULL,
sig.level = 0.05,
power = NULL,
alternative = c("two.sided", "less", "greater")
)
56 power_mcnemar_test

Arguments
n Number of observations
p0 Probability under the null
pa Probability under the alternative
sig.level Significance level (Type I error probability)
power Power of test (1 minus Type II error probability)
alternative One- or two-sided test

Details
The procedure uses uniroot to find the root of a discontinuous function so some errors may pop up
due to the given setup that causes the root-finding procedure to fail. Also, since exact binomial tests
are used we have discontinuities in the function that we use to find the root of but despite this the
function is usually quite stable.

Value
Object of class power.htest, a list of the arguments (including the computed one) augmented with
method and note elements.

Author(s)
Claus Ekstrom <claus@rprimer.dk>

See Also
binom.test

Examples

power_binom_test(n = 50, p0 = .50, pa = .75) ## => power = 0.971

power_binom_test(p0 = .50, pa = .75, power = .90) ## => n = 41
power_binom_test(n = 50, p0 = .25, power = .90, alternative="less") ## => pa = 0.0954

power_mcnemar_test Power Calculations for Exact and Asymptotic McNemar Test in a 2 by

2 table

Description
Compute power of test, or determine parameters to obtain target power for matched case-control
studies.
power_mcnemar_test 57

Usage
power_mcnemar_test(
n = NULL,
paid = NULL,
psi = NULL,
sig.level = 0.05,
power = NULL,
alternative = c("two.sided", "one.sided"),
method = c("normal", "exact", "cond.exact")
)

Arguments
n Number of observations (number of pairs)
paid The probability that a case patient is not exposed and that the corresponding
control patient was exposed (specifying p_12 in the 2 x 2 table). It is assumed
that this is the _smaller_ of the two discordant probabilities.
psi The relative probability that a control patient is not exposed and that the cor-
responding case patient was exposed compared to the probability that a case
patient is not exposed and that the corresponding control patient was exposed
(i.e., p_21 / p_12 in the 2x2 table). Also called the discordant proportion ra-
tio. psi must be larger than or equal to 1 since paid was the smaller of the two
discordant probabilities.
sig.level Significance level (Type I error probability)
power Power of test (1 minus Type II error probability)
alternative One- or two-sided test
method Power calculations based on exact or asymptotic test. The default (normal) cor-
responds to an approximative test, "exact" is the unconditional exact test, while
"cond.exact" is a conditional exact test (given fixed n). The "exact" method is
very slow for large values of n so it is most useful for fixed (and moderately-
sized) n.

Value
Object of class power.htest, a list of the arguments (including the computed one) augmented with
method and note elements.

Note
uniroot is used to solve power equation for unknowns, so you may see errors from it, notably
about inability to bracket the root when invalid arguments are given.

Author(s)
Claus Ekstrom <claus@rprimer.dk>
58 power_prop_test

References

Duffy, S (1984). Asymptotic and Exact Power for the McNemar Test and its Analogue with R
Controls per Case
Fagerland MW, Lydersen S, Laake P. (2013) The McNemar test for binary matched-pairs data:
mid-p and asymptotic are better than exact conditional. BMC Medical Research Methodology.

See Also

mcnemar.test

Examples

# Assume that pi_12 is 0.125 and we wish to detect an OR of 2.

# This implies that pi_12=0.25, and with alpha=0.05, and a power of 90% you get
power_mcnemar_test(n=NULL, paid=.125, psi=2, power=.9)

power_mcnemar_test(n=NULL, paid=.1, psi=2, power=.8, method="normal")

power_mcnemar_test(n=NULL, paid=.1, psi=2, power=.8)

power_prop_test Power Calculations for Two-Sample Test for Proportions with unequal
sample size

Description

Compute power of test, or determine parameters to obtain target power for equal and unequal sample
sizes.

Usage

power_prop_test(
n = NULL,
p1 = NULL,
p2 = NULL,
sig.level = 0.05,
power = NULL,
ratio = 1,
alternative = c("two.sided", "one.sided"),
tol = .Machine$double.eps^0.25
)
power_prop_test 59

Arguments

n Number of observations (in group 1)

p1 Probability in one group
p2 Probability in other group
sig.level Significance level (Type I error probability)
power Power of test (1 minus Type II error probability)
ratio The ratio n2/n1 between the larger group and the smaller group. Should be a
value equal to or greater than 1 since n2 is the larger group. Defaults to 1 (equal
group sizes)
alternative String. Can be one- or two-sided test. Can be abbreviated.
tol Numerical tolerance used in root finding, the default providing (at least) four
significant digits

Details

Exactly one of the parameters n, delta, power, sd, sig.level, ratio sd.ratio must be passed as
NULL, and that parameter is determined from the others. Notice that the last two have non-NULL
defaults so NULL must be explicitly passed if you want to compute them.

Value

Object of class power.htest, a list of the arguments (including the computed one) augmented with
method and note elements.

Note

uniroot is used to solve power equation for unknowns, so you may see errors from it, notably
about inability to bracket the root when invalid arguments are given.

Author(s)

Claus Ekstrom <claus@rprimer.dk>

See Also

power.prop.test, power_t_test, power.t.test

Examples
power_prop_test(n=NULL, p1=.65, p2=.85, power=.8, ratio=2)
60 power_t_test

power_t_test Power calculations for one and two sample t tests with unequal sample
size

Description
Compute power of test, or determine parameters to obtain target power for equal and unequal sample
sizes.

Usage
power_t_test(
n = NULL,
delta = NULL,
sd = 1,
sig.level = 0.05,
power = NULL,
ratio = 1,
sd.ratio = 1,
type = c("two.sample", "one.sample", "paired"),
alternative = c("two.sided", "one.sided"),
df.method = c("welch", "classical"),
strict = TRUE
)

Arguments
n Number of observations (in the smallest group if two groups)
delta True difference in means
sd Standard deviation
sig.level Significance level (Type I error probability)
power Power of test (1 minus Type II error probability)
ratio The ratio n2/n1 between the larger group and the smaller group. Should be a
value equal to or greater than 1 since n2 is the larger group. Defaults to 1 (equal
group sizes). If ratio is set to NULL (i.e., find the ratio) then the ratio might be
smaller than 1 depending on the desired power and ratio of the sd’s.
sd.ratio The ratio sd2/sd1 between the standard deviations in the larger group and the
smaller group. Defaults to 1 (equal standard deviations in the two groups)
type Type of t test
alternative One- or two-sided test
df.method Method for calculating the degrees of default. Possibilities are welch (the de-
fault) or classical.
strict Use strict interpretation in two-sided case. Defaults to TRUE unlike the standard
power.t.test function.
prepost.test 61

Details

Exactly one of the parameters n, delta, power, sd, sig.level, ratio sd.ratio must be passed as
NULL, and that parameter is determined from the others. Notice that the last two have non-NULL
defaults so NULL must be explicitly passed if you want to compute them.
The default strict = TRUE ensures that the power will include the probability of rejection in the
opposite direction of the true effect, in the two-sided case. Without this the power will be half the
significance level if the true difference is zero.

Value

Object of class power.htest, a list of the arguments (including the computed one) augmented with
method and note elements.

Note

uniroot is used to solve power equation for unknowns, so you may see errors from it, notably
about inability to bracket the root when invalid arguments are given.

Author(s)

Claus Ekstrom <claus@rprimer.dk>

See Also

power.t.test, power_prop_test, power.prop.test

Examples
# Sampling with a ratio of 1:4
power_t_test(delta=300, sd=450, power=.8, ratio=4)

# Equal group sizes but different sd's

# The sd in the second group is twice the sd in the second group
power_t_test(delta=300, sd=450, power=.8, sd.ratio=2)

# Fixed group one size to 50 individuals, but looking for the number of individuals in the
# second group. Different sd's with twice the sd in the larger group
power_t_test(n=50, delta=300, sd=450, power=.8, ratio=NULL, sd.ratio=2)

prepost.test Pretest-posttest RCT for quantitative observations with possible miss-

ing values
62 prepost.test

Description
In a typical pretest-posttest RCT, subjects are randomized to two treatments, and response is mea-
sured at baseline, prior to intervention with the randomized treatment (pretest), and at prespecified
follow-up time (posttest). Interest focuses on the effect of treatments on the change between mean
baseline and follow-up response. Missing posttest response for some subjects is routine, and disre-
garding missing cases can lead to invalid inference.

Usage
prepost.test(baseline, post, treatment, conf.level = 0.95, delta = "estimate")

Arguments
baseline A vector of quantitative baseline measurements
post A vector of quantitative post-test measurements with same length as baseline.
May contain missing values
treatment A vector of 0s and 1s corresponding to treatment indicator. 1 = treated, Same
length as baseline
conf.level confidence level of the interval
delta A numeric between 0 and 1 OR the string "estimate" (the default). The propor-
tion of observation treated.

Author(s)
Claus Ekstrom <ekstrom@sund.ku.dk>

References
Marie Davidian, Anastasios A. Tsiatis and Selene Leon (2005). "Semiparametric Estimation of
Treatment Effect in a Pretest-Posttest Study with Missing Data". Statistical Science 20, 261-301.

See Also
chisq.test

Examples
# From Altman
expo = c(rep(1,9),rep(0,7))
bp1w = c(137,120,141,137,140,144,134,123,142,139,134,136,151,147,137,149)
bp_base = c(147,129,158,164,134,155,151,141,153,133,129,152,161,154,141,156)
diff = bp1w-bp_base
prepost.test(bp_base, bp1w, expo)
qdiag 63

qdiag Fast extraction of matrix diagonal

Description
Fast extraction of matrix diagonal

Usage
qdiag(x)

Arguments
x The matrix to extract the diagonal from

Details
Note this function can only be used for extraction

Value
A vector with the diagonal elements

Author(s)
Claus Ekstrom <claus@rprimer.dk>

QIC.geeglm Quasi Information Criterion

Description
Function for calculating the quasi-likelihood under the independence model information criterion
(QIC), quasi-likelihood, correlation information criterion (CIC), and corrected QIC for one or sev-
eral fitted geeglm model object from the geepack package.

Usage
## S3 method for class 'geeglm'
QIC(object, tol = .Machine$double.eps, ...)

## S3 method for class 'ordgee'

QIC(object, tol = .Machine$double.eps, ...)

## S3 method for class 'geekin'

QIC(object, tol = .Machine$double.eps, ...)

QIC(object, tol = .Machine$double.eps, ...)

64 QIC.geeglm

Arguments
object a fitted GEE model from the geepack package. Currently only works on geeglm
objects
tol the tolerance used for matrix inversion
... optionally more fitted geeglm model objects

Details
QIC is used to select a correlation structure. The QICu is used to compare models that have the same
working correlation matrix and the same quasi-likelihood form but different mean specifications.
CIC has been suggested as a more robust alternative to QIC when the model for the mean may not
fit the data very well and when models with different correlation structures are compared.
Models with smaller values of QIC, CIC, QICu, or QICC are preferred.
If the MASS package is loaded then the ginv function is used for matrix inversion. Otherwise the
standard solve function is used.

Value
A vector or matrix with the QIC, QICu, quasi likelihood, CIC, the number of mean effect parame-
ters, and the corrected QIC for each GEE object

Author(s)
Claus Ekstrom <claus@rprimer.dk>, Brian McLoone <bmcloone@pdx.edu>, and Steven Orzack
<orzack@freshpond.org>

References
Pan, W. (2001). Akaike’s information criterion in generalized estimating equations. Biometrics,
57, 120-125.
Hardin, J.W. and Hilbe, J.M. (2012). Generalized Estimating Equations, 2nd Edition, Chapman
and Hall/CRC: New York.
Hin, L.-Y. and Wang, Y-G. (2009). Working-correlation-structure identification in generalized esti-
mating equations, Statistics in Medicine 28: 642-658.
Thall, P.F. and Vail, S.C. (1990). Some Covariance Models for Longitudinal Count Data with
Overdispersion. Biometrics, 46, 657-671.

See Also
geeglm

Examples

library(geepack)
data(ohio)
fit <- geeglm(resp ~ age + smoke + age:smoke, id=id, data=ohio,
family=binomial, corstr="exch", scale.fix=TRUE)
qpcr 65

QIC(fit)

qpcr Gene expression from real-time quantitative PCR

Description
Gene expression levels from real-time quantitative polymerase chain reaction (qPCR) experiments
on two different plant lines. Each line was used for 7 experiments each with 45 cycles.

Format
A data frame with 630 observations on the following 4 variables.

flour numeric Fluorescence level

line factor Plant lines rnt (mutant) and wt (wildtype)
cycle numeric Cycle number for the experiment
transcript factor Transcript used for the different runs

Source
Data provided by Kirsten Jorgensen <kij@life.ku.dk>.
Added by Claus Ekstrom <ekstrom@life.ku.dk>

References
Morant, M. et al. (2010). Metabolomic, Transcriptional, Hormonal and Signaling Cross-Talk in
Superroot2. Molecular Plant. 3, p.192–211.

Examples

data(qpcr)

#
# Analyze a single run for the wt line, transcript 1
#
run1 <- subset(qpcr, transcript==1 & line=="wt")

model <- nls(flour ~ fmax/(1+exp(-(cycle-c)/b))+fb,

start=list(c=25, b=1, fmax=100, fb=0), data=run1)

print(model)

plot(run1$cycle, run1$flour, xlab="Cycle", ylab="Fluorescence")

lines(run1$cycle, predict(model))
66 rainman

quadform Fast quadratic form computation

Description
Fast computation of a quadratic form t(x) ∗ M ∗ x.

Usage
quadform(x, M, invertM = FALSE, transposex = FALSE)

Arguments
x A matrix with dimensions n*k.
M A matrix with dimenions n*n. If it is to be inverted then the matrix should be
symmetric and positive difinite (no check is done for this)
invertM A logical. If set to TRUE then M will be inverted before computations (defaults
to FALSE)
transposex A logical. Should the matrix be transposed before computations (defaults to
FALSE).

Value
A matrix with dimensions k * k giving the quadratic form

Author(s)
Claus Ekstrom <claus@rprimer.dk>

rainman Perception of points in a swarm

Description
Five raters were asked to guess the number of points in a swarm for 10 different figures (which -
unknown to the raters - were each repeated three times).

Format
A data frame with 30 observations on the following 6 variables.
SAND The true number of points in the swarm. Each picture is replicated thrice
ME Ratings from judge 1
TM Ratings from judge 2
AJ Ratings from judge 3
BM Ratings from judge 4
LO Ratings from judge 5
rainman 67

Details
The raters har approximately 10 seconds to judge each picture, and the thought it was 30 different
pictures. Before starting the experiment they were shown 6 (unrelated) pictures and were told the
number of points in each of those pictures. The SAND column contains the picture id and the true
number of points in the swarm.

Source
Collected by Claus Ekstrom.

Examples

data(rainman)
long <- data.frame(stack(rainman[,2:6]), figure=factor(rep(rainman$SAND,5)))
figind <- interaction(long$figure,long$ind)
# Use a linear random effect model from the
# lme4 package if available
if(require(lme4)) {
model <- lmer(values ~ (1|ind) + (1|figure) + (1|figind), data=long)
}

#
# Point swarms were generated by the following program
#
## Not run:
set.seed(2) # Original
npoints <- sample(4:30)*4
nplots <- 10
pdf(file="swarms.pdf", onefile=TRUE)

s1 <- sample(npoints[1:nplots])
print(s1)
for (i in 1:nplots) {
n <- s1[i]
set.seed(n)
x <- runif(n)
y <- runif(n)
plot(x,y, xlim=c(-.15, 1.15), ylim=c(-.15, 1.15), pch=20, axes=FALSE,
xlab="", ylab="")
}
s1 <- sample(npoints[1:nplots])
print(s1)
for (i in 1:nplots) {
n <- s1[i]
set.seed(n)
x <- runif(n)
y <- runif(n)
plot(y,x, xlim=c(-.15, 1.15), ylim=c(-.15, 1.15), pch=20, axes=FALSE,
xlab="", ylab="")
}
s1 <- sample(npoints[1:nplots])
68 repmat

print(s1)
for (i in 1:nplots) {
n <- s1[i]
set.seed(n)
x <- runif(n)
y <- runif(n)
plot(-x,y, xlim=c(-1.15, .15), ylim=c(-.15, 1.15), pch=20, axes=FALSE,
xlab="", ylab="")
}
dev.off()

## End(Not run)

repmat Fast replication of a matrix

Description
Fast generation of a matrix by replicating a matrix row- and column-wise in a block-like fashion

Usage
repmat(x, nrow = 1L, ncol = 1L)

Arguments
x A matrix with dimensions r*c.
nrow An integer giving the number of times the matrix is replicated row-wise
ncol An integer giving the number of times the matrix is replicated column-wise

Value
A matrix with dimensions (r*nrow) x (c*ncol)

Author(s)
Claus Ekstrom <claus@rprimer.dk>

Examples

m <- matrix(1:6, ncol=3)

repmat(m, 2) # Stack two copies of m on top of each other
repmat(m, 2, 3) # Replicate m with two copies on top and three copies side-by-side
residualplot.default 69

residualplot.default Plots a standardized residual

Description
Plots a standardized residual plot from an lm or glm object and provides additional graphics to help
evaluate the variance homogeneity and mean.

Usage
## Default S3 method:
residualplot(
x,
y = NULL,
candy = TRUE,
bandwidth = 0.3,
xlab = "Fitted values",
ylab = "Std.res.",
col.sd = "blue",
col.alpha = 0.3,
ylim = NA,
...
)

## S3 method for class 'lm'

residualplot(
x,
y,
candy = TRUE,
bandwidth = 0.3,
xlab = "Fitted values",
ylab = "Stud.res.",
col.sd = "blue",
col.alpha = 0.3,
...
)

## S3 method for class 'glm'

residualplot(
x,
y,
candy = TRUE,
bandwidth = 0.4,
xlab = "Fitted values",
ylab = "Std. dev. res.",
col.sd = "blue",
col.alpha = 0.3,
70 residualplot.default

...
)

residualplot(
x,
y = NULL,
candy = TRUE,
bandwidth = 0.3,
xlab = "Fitted values",
ylab = "Std.res.",
col.sd = "blue",
col.alpha = 0.3,
ylim = NA,
...
)

Arguments
x lm object or a numeric vector
y numeric vector for the y axis values
candy logical. Should a lowess curve and local standard deviation of the residual be
added to the plot. Defaults to TRUE
bandwidth The width of the window used to calculate the local smoothed version of the
mean and the variance. Value should be between 0 and 1 and determines the
percentage of the window width used
xlab x axis label
ylab y axis label
col.sd color for the background residual deviation
col.alpha number between 0 and 1 determining the transprency of the standard deviation
plotting color
ylim pair of observations that set the minimum and maximum of the y axis. If set to
NA (the default) then the limits are computed from the data.
... Other arguments passed to the plot function

Details
The y axis shows the studentized residuals (for lm objects) or standardized deviance residuals (for
glm objects). The x axis shows the linear predictor, i.e., the predicted values for lm objects.
The blue area is a smoothed estimate of 1.96*SD of the standardized residuals in a window around
the predicted value. The blue area should largely be rectangular if the standardized residuals have
more or less the same variance.
The dashed line shows the smoothed mean of the standardized residuals and should generally follow
the horizontal line through (0,0).
Solid circles correspond to standardized residuals outside the range from [-1.96; 1.96] while open
circles are inside that interval. Roughly 5
residual_plot 71

Value
Produces a standardized residual plot

Author(s)
Claus Ekstrom <claus@rprimer.dk>

See Also
rstandard, predict

Examples

# Linear regression example

data(trees)
model <- lm(Volume ~ Girth + Height, data=trees)
residualplot(model)
model2 <- lm(Volume ~ Girth + I(Girth^2) + Height, data=trees)
residualplot(model2)

residual_plot Plots a standardized residual

Description
Plots a standardized residual plot from an lm or glm object and provides additional graphics to help
evaluate the variance homogeneity and mean.

Usage
residual_plot(
x,
y = NULL,
candy = TRUE,
bandwidth = 0.3,
xlab = "Fitted values",
ylab = "Std.res.",
col.sd = "blue",
alpha = 0.1,
ylim = NA,
...
)

## Default S3 method:
residual_plot(
x,
72 residual_plot

y = NULL,
candy = TRUE,
bandwidth = 0.3,
xlab = "Fitted values",
ylab = "Std.res.",
col.sd = "blue",
alpha = 0.1,
ylim = NA,
...
)

## S3 method for class 'lm'

residual_plot(
x,
y,
candy = TRUE,
bandwidth = 0.3,
xlab = "Fitted values",
ylab = "Stud.res.",
col.sd = "blue",
alpha = 0.1,
...
)

## S3 method for class 'glm'

residual_plot(
x,
y,
candy = TRUE,
bandwidth = 0.4,
xlab = "Fitted values",
ylab = "Std. dev. res.",
col.sd = "blue",
alpha = 0.1,
...
)

Arguments
x lm object or a numeric vector
y numeric vector for the y axis values
candy logical. Should a lowess curve and local standard deviation of the residual be
added to the plot. Defaults to TRUE
bandwidth The width of the window used to calculate the local smoothed version of the
mean and the variance. Value should be between 0 and 1 and determines the
percentage of the window width used
xlab x axis label
residual_plot 73

ylab y axis label

col.sd color for the background residual deviation
alpha number between 0 and 1 determining the transprency of the standard deviation
plotting color
ylim pair of observations that set the minimum and maximum of the y axis. If set to
NA (the default) then the limits are computed from the data.
... Other arguments passed to the plot function

Details
The y axis shows the studentized residuals (for lm objects) or standardized deviance residuals (for
glm objects). The x axis shows the linear predictor, i.e., the predicted values for lm objects.
The blue area is a smoothed estimate of 1.96*SD of the standardized residuals in a window around
the predicted value. The blue area should largely be rectangular if the standardized residuals have
more or less the same variance.
The dashed line shows the smoothed mean of the standardized residuals and should generally follow
the horizontal line through (0,0).
Solid circles correspond to standardized residuals outside the range from [-1.96; 1.96] while open
circles are inside that interval. Roughly 5

Value
Produces a standardized residual plot

Author(s)
Claus Ekstrom <claus@rprimer.dk>

See Also
rstandard, predict

Examples

# Linear regression example

data(trees)
model <- lm(Volume ~ Girth + Height, data=trees)
residual_plot(model)
model2 <- lm(Volume ~ Girth + I(Girth^2) + Height, data=trees)
residual_plot(model2)

# Add extra information about points by adding geom_text to the object produced

m <- lm(mpg ~ hp + factor(vs), data=mtcars)

residual_plot(m) + ggplot2::geom_point(ggplot2::aes(color=factor(cyl)), data=mtcars)
74 rmvt.pedigree

rmvt.pedigree Simulate residual multivariate t-distributed data from a polygenic

model

Description

Simulates residual multivariate t-distributed response data from a pedigree where the additive ge-
netic, dominance genetic, and shared environmental effects are taken into account.

Usage

rmvt.pedigree(n = 1, pedigree, h2 = 0, c2 = 0, d2 = 0, df = 1)

Arguments

n numeric. The number of simulations to generate

pedigree a pedigree object
h2 numeric. The heritability
c2 numeric. The environmentability
d2 numeric. The dominance deviance effect
df numeric. The degrees of freedom for the t distribution

Details

The three parameters should have a sum: h2+c2+d2 that is less than 1. The total variance is set to
1, and the mean is zero.

Value

Returns a matrix with the simulated values with n columns (one for each simulation) and each row
matches the corresponding individual from the pedigree

Author(s)

Claus Ekstrom <claus@rprimer.dk>

See Also

pedigree, kinship,
rmvtnorm.pedigree 75

Examples

library(kinship2)
library(mvtnorm)
mydata <- data.frame(id=1:5,
dadid=c(NA, NA, 1, 1, 1),
momid=c(NA, NA, 2, 2, 2),
sex=c("male", "female", "male", "male", "male"),
famid=c(1,1,1,1,1))
relation <- data.frame(id1=c(3), id2=c(4), famid=c(1), code=c(1))
ped <- pedigree(id=mydata$id, dadid=mydata$dadid, momid=mydata$momid,
sex=mydata$sex, relation=relation)
rmvt.pedigree(2, ped, h2=.25, df=4)

rmvtnorm.pedigree Simulate residual multivariate Gaussian data from a polygenic model

Description
Simulates residual multivariate Gaussian response data from a pedigree where the additive genetic,
dominance genetic, and shared environmental effects are taken into account.

Usage
rmvtnorm.pedigree(n = 1, pedigree, h2 = 0, c2 = 0, d2 = 0)

Arguments
n numeric. The number of simulations to generate
pedigree a pedigree object
h2 numeric. The heritability
c2 numeric. The environmentability
d2 numeric. The dominance deviance effect

Details
The three parameters should have a sum: h2+c2+d2 that is less than 1. The total variance is set to
1, and the mean is zero.

Value
Returns a matrix with the simulated values with n columns (one for each simulation) and each row
matches the corresponding individual from the pedigree

Author(s)
Claus Ekstrom <claus@rprimer.dk>
76 rnorm_perfect

See Also
pedigree, kinship,

Examples

library(kinship2)
library(mvtnorm)
mydata <- data.frame(id=1:5,
dadid=c(NA, NA, 1, 1, 1),
momid=c(NA, NA, 2, 2, 2),
sex=c("male", "female", "male", "male", "male"),
famid=c(1,1,1,1,1))
relation <- data.frame(id1=c(3), id2=c(4), famid=c(1), code=c(1))
ped <- pedigree(id=mydata$id, dadid=mydata$dadid, momid=mydata$momid,
sex=mydata$sex, relation=relation)
rmvtnorm.pedigree(2, ped, h2=.25)

rnorm_perfect Simulate values from a perfect normal distribution

Description
Random generation for a perfect normal distribution with mean equal to mean and standard devia-
tion equal to sd.

Usage
rnorm_perfect(n, mean = 0, sd = 1)

Arguments
n number of observations. If length(n) > 1, the length is taken to be the number
required.
mean number of mean.
sd number of standard deviation.

Details
The function will return the same set of quantiles for fixed n. In that sense there is not much
randomness going on, and the function is mostly useful for illustrative purposes.

Value
Returns a vector of values from a perfect normal distribution
rootonorm 77

Author(s)
Claus Ekstrom <claus@rprimer.dk>

Examples

rnorm_perfect(30, mean=10, sd=2)

rootonorm Hanging rootogram for normal distribution

Description
Create a hanging rootogram for a quantitative numeric vector and compare it to a Gaussian distri-
bution.

Usage
rootonorm(
x,
breaks = "Sturges",
type = c("hanging", "deviation"),
scale = c("sqrt", "raw"),
zeroline = TRUE,
linecol = "red",
rectcol = "lightgrey",
xlab = xname,
ylab = "Sqrt(frequency)",
yaxt = "n",
ylim = NULL,
mu = mean(x),
s = sd(x),
gap = 0.1,
...
)

Arguments
x a numeric vector of values for which the rootogram is desired
breaks Either the character string ‘Sturges’ to use Sturges’ algorithm to decide the num-
ber of breaks or a positive integer that sets the number of breaks.
type if "hanging" then a hanging rootogram is plotted, and if "deviation" then
deviations from zero are plotted.
scale The type of transformation. Defaults to "sqrt" which takes square roots of the
frequencies. "raw" yields untransformed frequencies.
78 rootonorm

zeroline logical; if TRUE a horizontal line is added at zero.

linecol The color of the density line for the normal distribution. The default is to make
a red density line.
rectcol a colour to be used to fill the bars. The default of lightgray yields lightgray
bars.
xlab, ylab plot labels. The xlab and ylab refer to the x and y axes respectively
yaxt Should y axis text be printed. Defaults to n.
ylim the range of y values with sensible defaults.
mu the mean of the Gaussian distribution. Defaults to the sample mean of x.
s the standard deivation of the Gaussian distribution. Defaults to the sample
std.dev. of x.
gap The distance between the rectangles in the histogram.
... further arguments and graphical parameters passed to plot.

Details
The mean and standard deviation of the Gaussian distribution are calculated from the observed data
unless the mu and s arguments are given.

Value
Returns a vector of counts of each bar. This may be changed in the future. The plot is the primary
output of the function.

Author(s)
Claus Ekstrom <claus@rprimer.dk>

References
Tukey, J. W. 1972. Some Graphic and Semigraphic Displays. In Statistical Papers in Honor of
George W. Snedecor, p. 293-316.

Examples

oldpar <- par()

par(mfrow=c(2,2))
rootonorm(rnorm(200))
rootonorm(rnorm(200), type="deviation", scale="raw")
rootonorm(rnorm(200), mu=1)
rootonorm(rexp(200), mu=1)
par(oldpar)
round_percent 79

round_percent Round vector of number to percentages

Description

Rounds a vector of numeric values to percentages ensuring that they add up to 100

Usage

round_percent(x, decimals = 0L, ties = c("random", "last"))

Arguments

x A numeric vector with non-negative values.

decimals An integer giving the number of decimals that are used
ties A string that is either ’random’ (the default) or ’last’. Determines how to break
ties. Random is random, last prefers to break ties at the last position

Details

Returns a vector of numeric values.

Value

Returns a numeric vector of the same length as x

Author(s)

Claus Ekstrom <claus@rprimer.dk>

Examples

f <- c(1,2,1,3,2,1,2,3,1)
round_percent(f)
80 rud

rud Simulate randomized urn design

Description
Simulates a randomized treatment based on an urn model.

Usage
rud(
n,
alpha = c(1, 1),
beta = 1,
labels = seq(1, length(alpha)),
data.frame = FALSE,
startid = 1
)

Arguments
n the number of individuals to randomize
alpha a non-negative integer vector of weights for each treatment group. The length
of the vector corresponds to the number of treatment groups.
beta a non-negative integer of weights added to the groups that were not given treat-
ment
labels a vector of treatment labels. Must be the same length as the length of alpha.
data.frame A logical that determines if the function should return a vector of group indices
(the default, if FALSE) or a data frame (if TRUE).
startid margin paramaters; vector of length 4 (see par)

Details
The urn model can be described as follows: For k different treatments, the urn design is initiated
with a number of balls in an urn corresponding to the start weight (the alpha argument), where each
treatment has a specific colour. Whenever a patient arrives, a random ball is drawn from the urn
and the colour decides the treatment for the patient. For each of the treatments that weren’t chosen
we add beta balls of the corresponding colour(s) to the urn to update the probabilities for the next
patient.

Value
A vector with group indices. If the argument data.frame=TRUE is used then a data frame with three
variables is returned: id, group, and treatment (the group label).
scorefct 81

Examples
rud(5)
rud(5, alpha=c(1,1,10), beta=5)

scorefct Internal functions for the MESS package

Description
Internal functions for the MESS package

Usage
scorefct(o, beta = NULL, testidx = NULL, sas = FALSE)

Arguments
o input geepack object from a geeglm fit.
beta The estimated parameters. If set to NULL then the parameter estimates are ex-
tracted from the model fit object o.
testidx Indices of the beta parameters that should be tested equal to zero
sas Logical. Should the SAS version of the score test be computed. Defaults to
FALSE.

Author(s)
Claus Ekstrom <claus@rprimer.dk>

screen_variables Screen variable before penalized regression

Description
Expands a contingency table to a data frame where each observation in the table becomes a single
observation in the data frame with corresponding information for each for each combination of the
table dimensions.

Usage
screen_variables(x, y, lambda = 0.1, method = c("global-strong", "global-DPP"))
82 segregate.genes

Arguments
x A table or matrix
y A vector of outcomes
lambda a vector of positive values used for the penalization parameter.
method a string giving the method used for screening. Two possibilities are "global-
strong" and "global-DPP"

Details
Note that no standardization is done (not necessary?)

Value
A list with three elements: lambda which contains the lambda values, selected which contains the
indices of the selected variables, and method a string listing the method used.

Author(s)
Claus Ekstrom <claus@rprimer.dk>

References
Hastie, Tibshirani and Wainwright (2015). "Statistical Learning with Sparsity". CRC Press.

Examples

x <- matrix(rnorm(50*100), nrow=50)

y <- rnorm(50, mean=x[,1])
screen_variables(x, y, lambda=c(.1, 1, 2))

segregate.genes Segregate genes through a pedigree

Description
Segregate di-allelic genes down through the generations of a pedigree. It is assumed that the
founders are independent and that the genes are in Hardy Weinberg equilibrium in the population.

Usage
segregate.genes(pedigree, maf)
sinv 83

Arguments
pedigree a pedigree object
maf a vector of minor allele frequencies for each diallelic gene to segregate through
the pedigree

Value
Returns a data frame. Each row matches the order of the individuals in the pedigree and each
column corresponds to each of the segregated genes. The data frame contains values 0, 1, or 2
corresponding to the number of copies of the minor allele frequency allele that person has.

Author(s)
Claus Ekstrom <claus@rprimer.dk>

See Also
pedigree, kinship,

Examples

library(kinship2)
mydata <- data.frame(id=1:5,
dadid=c(NA, NA, 1, 1, 1),
momid=c(NA, NA, 2, 2, 2),
sex=c("male", "female", "male", "male", "male"),
famid=c(1,1,1,1,1))
relation <- data.frame(id1=c(3), id2=c(4), famid=c(1), code=c(1))
ped <- pedigree(id=mydata$id, dadid=mydata$dadid, momid=mydata$momid,
sex=mydata$sex, relation=relation)
segregate.genes(ped, c(.1, .3, .5))

sinv Invert a symmetric positive-definite matrix

Description
Inverts a symmetric positive-definite matrix without requiring the Matrix package.

Usage
sinv(obj)

Arguments
obj The symmetric positive-definite matrix
84 smokehealth

Details
This function does no error checking and it is up to the user to ensure that the input is indeed
symmetric, positive-definite, and a matrix.

Value
A matrix of the same size as the input object

Author(s)
Claus Ekstrom, <claus@rprimer.dk>.

Examples
m <- matrix(c(1, 0, .5, .5, 0, 1, .5, .5, .5, .5, 1, .5, .5, .5, .5, 1), 4)
sinv(m)

smokehealth Effect of smoking on self reported health

Description
Effect of smoking at 45 years of age on self reported health five years later. Data are on a sample of
males from the Glostrup survey.

Format
A table with daily smoking categories for the rows and self reported health five years later as the
columns.

Source
Data example found on the internet but originates from Svend Kreiner

Examples

data(smokehealth)
m <- smokehealth
m[,3] <- m[,3]+ m[,4]
m[4,] <- m[4,] + m[5,]
m <- m[1:4,1:3]
gkgamma(m)
chisq.test(m)
soccer 85

soccer Danish national soccer players

Description
Players on the Danish national soccer team. The dataset consists of all players who have been
picked to play on the men’s senior A-team, their position, date-of-birth, goals and matches.

Format
A data frame with 805 observations on the following 5 variables.

name a factor with names of the players

DoB a Date. The date-of-birth of the player
position a factor with levels Forward Defender Midfielder Goalkeeper
matches a numeric vector. The number of A matches played by the player
goals a numeric vector. The number of goals scored by the player in A matches

Source
Data collected from the player database of DBU on March 21st, 2014. See https://www.dbu.dk
for more information.

Examples

data(soccer)

birthmonth <- as.numeric(format(soccer$DoB, "%m"))

birthyear <- as.numeric(format(soccer$DoB, "%Y"))

superroot2 Gene expression data from two-color dye-swap experiment

Description
Gene expression levels from two-color dye-swap experiment on 6 microarrays. Arrays 1 and 2
represent the first biological sample (ie, the first dye swap), 3 and 4 the second, and arrays 5 and 6
the third.
86 tracemp

Format
A data frame with 258000 observations on the following 5 variables.
color a factor with levels green red representing the dye used for the gene expression
array a factor with levels 1 2 3 4 5 6 corresponding to the 6 arrays
gene a factor with 21500 levels representing the genes on the arrays
plant a factor with levels rnt wt for the two types of plants: runts and wild type
signal a numeric vector with the gene expression level (normalized but not log transformed)

Source
Data provided by Soren Bak <bak@life.ku.dk>.
Added by Claus Ekstrom <ekstrom@sund.ku.dk>

References
Morant, M. et al. (2010). Metabolomic, Transcriptional, Hormonal and Signaling Cross-Talk in
Superroot2. Molecular Plant. 3, p.192–211.

Examples

data(superroot2)
# Select one gene
g1 <- superroot2[superroot2$gene=="AT2G24000.1",]
model <- lm(log(signal) ~ plant + color + array, data=g1)
summary(model)

tracemp Fast computation of trace of matrix product

Description
Fast computation of the trace of the matrix product trace(t(A)

Usage
tracemp(A, B)

Arguments
A A matrix with dimensions n*k.
B A matrix with dimenions n*k.

Value
The trace of the matrix product
usd 87

Author(s)

Claus Ekstrom <claus@rprimer.dk>

Examples

A <- matrix(1:12, ncol=3)

tracemp(A, A)

usd Unbiased standard deviation

Description

This function computes the unbiased standard deviation of the values in x. If na.rm is TRUE then
missing values are removed before computation proceeds.

Usage

usd(x, na.rm = FALSE)

Arguments

x a numeric vector or an R object but not a factor coercible to numeric by as.double(x)

na.rm logical. Should missing values be removed?

Details

Like var this uses denominator n - 1. The standard deviation of a length-one or zero-length vector
is NA.

Value

A scalar

Examples
sd(1:5)
usd(1:5)
88 wallyplot.default

wallyplot.default Plots a Wally plot

Description
Produces a 3x3 grid of residual- or qq-plots plots from a lm object. One of the nine subfigures is
the true residual plot/qqplot while the remaining are plots that fulfill the assumptions of the linear
model

Usage
## Default S3 method:
wallyplot(
x,
y = x,
FUN = residualplot,
hide = TRUE,
simulateFunction = rnorm,
model = NULL,
...
)

## S3 method for class 'lm'

wallyplot(
x,
y = x,
FUN = residualplot,
hide = TRUE,
simulateFunction = lmsimresiduals,
...
)

wallyplot(
x,
y = x,
FUN = residualplot,
hide = TRUE,
simulateFunction = rnorm,
...
)

Arguments
x a numeric vector of x values, or an lm object.
y a numeric vector of y values of the same length as x or a n * 9 matrix of y values
- one column for each of the nine plots to make. The first column is the one
corresponding to the results from the dataset
wallyplot.default 89

FUN a function that accepts an x, y and ... argument and produces a graphical model
validation plots from the x and y values.
hide logical; if TRUE (the default) then the identity of the true residual plot is hidden
until the user presses a key. If FALSE then the true residual plot is shown in the
center.
simulateFunction
The function used to produce y values under the null hypothesis. Defaults to
rnorm
model Optional input to simulateFunction
... Other arguments passed to the plot function FUN

Details
Users who look at residual plots or qqnorm plots for the first time often feel they lack the experience
to determine if the residual plot is okay or if the model assumptions are indeed violated. One way
to convey "experience" is to plot a series of graphical model validation plots simulated under the
model assumption together with the corresponding plot from the real data and see if the user can
pinpoint one of them that looks like an odd-one-out. If the proper plot from the real data does not
stand out then the assumptions are not likely to be violated.
The Wallyplot produces a 3x3 grid of plots from a lm object or from a set of pairs of x and y values.
One of the nine subfigures is the true plot while the remaining are plots that fulfill the assumptions
of the linear model. After the user interactively hits a key the correct residual plot (correponding to
the provided data) is shown.
The plotting function can be set using the FUN argument which should be a function that accepts x,
y and ... arguments and plots the desired figure. When y is a single vector the same length as x
then the function simulateFunction is used to generate the remaining y values corresponding the
situations under the null.
For a description of the features of the default residual plot see the help page for residualplot.

Author(s)
Claus Ekstrom <claus@rprimer.dk>

References
Ekstrom, CT (2014) Teaching ’Instant Experience’ with Graphical Model Validation Techniques.
Teaching Statistics (36), p 23-26

Examples

## Not run:
data(trees)
res <- lm(Volume ~ Height + Girth, data=trees)
wallyplot(res)

# Create a grid of QQ-plot figures

90 write.xml

# Define function to plot a qq plot with an identity line

qqnorm.wally <- function(x, y, ...) { qqnorm(y, ...) ; abline(a=0, b=1) }
wallyplot(res, FUN=qqnorm.wally, main="")

# Define function to simulate components+residuals for Girth

cprsimulate <- function(n) {rnorm(n)+trees$Girth}
# Create the cpr plotting function
cprplot <- function(x, y, ...) {plot(x, y, pch=20, ...) ;
lines(lowess(x, y), lty=3)}
# Create the Wallyplot
wallyplot(trees$Girth, trees$Girth+rstudent(res), FUN=cprplot,
simulateFunction=cprsimulate, xlab="Girth")

## End(Not run)

write.xml Write a data frame in XML format

Description
Writes the data frame to a file in the XML format.

Usage
write.xml(data, file = NULL, collapse = TRUE)

Arguments
data the data frame object to save
file the file name to be written to.
collapse logical. Should the output file be collapsed to make it fill less? (Defaults to
TRUE)

Details
This function does not require the XML package to be installed to function properly.

Value
None

Author(s)
Claus Ekstrom, <claus@rprimer.dk> based on previous work by Duncan Temple Lang.
write.xml 91

Examples

## Not run:
data(trees)
write.xml(trees, file="mydata.xml")

## End(Not run)
Index

∗ ~htests ∗ htest
feature.test, 27 drop1.geeglm, 22
∗ datagen drop1.geem, 23
age, 6 gkgamma, 33
auc, 7 power_binom_test, 55
clipit, 12 power_mcnemar_test, 56
common.shared, 18 power_prop_test, 58
extended.shared, 25 power_t_test, 60
founder.shared, 30 prepost.test, 61
plr, 54 QIC.geeglm, 63
rmvt.pedigree, 74 ∗ iplot
rmvtnorm.pedigree, 75 col.alpha, 15
segregate.genes, 82 col.shade, 15
∗ datasets col.tint, 16
bdstat, 8 panel.hist, 52
bees, 9 panel.r2, 53
clotting, 13 wallyplot.default, 88
earthquakes, 24 ∗ manip
greenland, 35 adaptive.weights, 4
categorize, 11
happiness, 35
expand_table, 25
icecreamads, 39
fac2num, 27
kwdata, 40
loadRData, 41
lifeexpect, 41
lower.tri.vector, 42
matched, 43
monte_carlo_chisq_test, 46
nh4, 47
round_percent, 79
picea, 54
scorefct, 81
qpcr, 65
screen_variables, 81
rainman, 66 ∗ models
smokehealth, 84 geekin, 31
soccer, 85 ∗ package
superroot2, 85 MESS, 44
∗ file ∗ print
sinv, 83 ht, 37
write.xml, 90 ∗ univar
∗ hplot cmd, 14
residual_plot, 71 ∗ utilities
residualplot.default, 69 ordered.clusters, 48
rnorm_perfect, 76
rootonorm, 77 adaptive.weights, 4

92
INDEX 93

add_torows, 5 icecreamads, 39
age, 6 integrate, 8
approx, 8
as.POSIXlt, 6 ks_cumtest, 39
auc, 7 kwdata, 40

bdstat, 8 lifeexpect, 41
bees, 9 load, 42
bin, 10 loadRData, 41
binom.test, 56 lower.tri, 43
lower.tri.vector, 42
categorize, 11
chisq.test, 34, 62 matched, 43
clipit, 12 maximum_subarray, 44
clotting, 13 mcnemar.test, 58
cmd, 14 MESS, 44
col.alpha, 15 MESS-package (MESS), 44
col.shade, 15 mfastLmCpp, 45
monte_carlo_chisq_test, 46
col.tint, 16
colCumSum, 17
nh4, 47
common.shared, 18
conditional_rowMeans, 19 ordered.clusters, 48
cor.test, 49
cumsumbinning, 20 p.adjust, 49
pairwise.cor.test, 49
dCor, 21 pairwise_combination_indices, 50
dCov, 21 pairwise_Schur_product, 51
drop1, 22, 24 panel.hist, 52
drop1.geeglm, 22 panel.r2, 53
drop1.geem, 23 par, 80
duplicated, 48 picea, 54
plr, 54
earthquakes, 24 power.prop.test, 59, 61
expand_table, 25 power.t.test, 59, 61
extended.shared, 25 power_binom_test, 55
power_mcnemar_test, 56
fac2num, 27 power_prop_test, 58, 61
feature.test, 27 power_t_test, 59, 60
filldown, 29 predict, 71, 73
founder.shared, 30 prepost.test, 61
print.geekin (geekin), 31
geekin, 31
ginv, 64 qdiag, 63
gkgamma, 33 QIC (QIC.geeglm), 63
greenland, 35 QIC.geeglm, 63
qpcr, 65
happiness, 35 quadform, 66
ht, 37
hwe_frequencies, 38 rainman, 66
94 INDEX

repmat, 68
residual_plot, 71
residualplot, 89
residualplot (residualplot.default), 69
residualplot.default, 69
rmvt.pedigree, 74
rmvtnorm.pedigree, 75
rnorm_perfect, 76
rootogram (rootonorm), 77
rootonorm, 77
round_percent, 79
rstandard, 71, 73
rud, 80

scorefct, 81
screen_variables, 81
segregate.genes, 82
sinv, 83
smokehealth, 84
soccer, 85
solve, 64
splinefun, 8
superroot2, 85

tracemp, 86

usd, 87

wallyplot (wallyplot.default), 88
wallyplot.default, 88
write.xml, 90