Package ‘psy’

October 14, 2022

Title Various Procedures Used in Psychometrics
Version 1.2
Description Kappa, ICC, reliability coefficient, parallel analysis,
multi-traits multi-methods, spherical representation of a correlation matrix.
License GPL (>= 2)
Encoding UTF-8
RoxygenNote 7.1.2
NeedsCompilation no
Author Bruno Falissard [aut, cre]
Maintainer Bruno Falissard <[email protected]>
Repository CRAN
Date/Publication 2022-04-21 22:00:02 UTC

R topics documented:
ckappa . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
cronbach . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
ehd . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
expsy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
fpca . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
icc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
lkappa . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
mdspca . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
mtmm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
psy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
scree.plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
sleep . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
sphpca . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
wkappa . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Index 20

1
2 ckappa

ckappa Cohen’s Kappa for 2 raters

Description
Computes Cohen’s Kappa for agreement in the case of 2 raters. The diagnosis (the object of the
rating) may have k possible values.

Usage
ckappa(r)

Arguments
r n*2 matrix or dataframe, n subjects and 2 raters

Details
The function deals with the case where the two raters have not exactly the same scope of rating
(some software associate an error with this situation). Missing value are omitted.

Value
A list with :

$table the 2*k table of raw data (first rater in rows, second rater in columns)
$kappa Cohen’s Kappa

Author(s)
Bruno Falissard

References
Cohen, J. (1960), A coefficient of agreement for nominal scales, Educational and Psychological
measurements, 20, 37-46.

Examples
data(expsy)
## Cohen's kappa for binary diagnosis
ckappa(expsy[,c(12,14)])

##to obtain a 95%confidence interval:

#library(boot)
#ckappa.boot <- function(data,x) {ckappa(data[x,])[[2]]}
#res <- boot(expsy[,c(12,14)],ckappa.boot,1000)
## two-sided bootstrapped confidence interval of kappa
#quantile(res$t,c(0.025,0.975))
cronbach 3

## adjusted bootstrap percentile (BCa) confidence interval (better)

#boot.ci(res,type="bca")
##Cohen's kappa for non binary diagnosis
#ckappa(expsy[,c(11,13)])

cronbach Cronbach’s coefficient alpha

Description
Computes the Cronbach’s reliability coefficient alpha. This coefficient may be applied to a series of
items destinated to be aggregated in a single score. It estimates reliability in the framework of the
domain sampling model.

Usage
cronbach(v1)

Arguments
v1 n*p matrix or dataframe, n subjects and p items

Details
Missing value are omitted in a "listwise" way (all items are removed even if only one of them is
missing).

Value
A list with :

$sample.size Number of subjects under study

$number.of.items
Number of items of the scale or questionnaire
$alpha alpha

Author(s)
Bruno Falissard

References
Nunnaly, J.C., Bernstein, I.H. (1994), Psychometric Theory, 3rd edition, McGraw-Hill Series in
Psychology.
4 ehd

Examples
data(expsy)
cronbach(expsy[,1:10]) ## not good because item 2 is reversed (1 is high and 4 is low)
cronbach(cbind(expsy[,c(1,3:10)],-1*expsy[,2])) ## better

#to obtain a 95%confidence interval:

#datafile <- cbind(expsy[,c(1,3:10)],-1*expsy[,2])
#library(boot)
#cronbach.boot <- function(data,x) {cronbach(data[x,])[[3]]}
#res <- boot(datafile,cronbach.boot,1000)
#quantile(res$t,c(0.025,0.975)) ## two-sided bootstrapped confidence interval of Cronbach's alpha
#boot.ci(res,type="bca") ## adjusted bootstrap percentile (BCa) confidence interval (better)

ehd Depressive Mood Scale

Description
A data frame with 269 observations on the following 20 variables. Jouvent, R et al 1988 La clinique
polydimensionnelle de humeur depressive. Nouvelle version echelle EHD : Polydimensional rating
scale of depressive mood. Psychiatrie et Psychobiologie.

Usage
data(ehd)

Format
This data frame contains the following columns:
e1 Observed painfull sadness
e2 Emotional hyperexpressiveness
e3 Emotional instability
e4 Observed monotony
e5 Lack spontaneous expressivity
e6 Lack affective reactivity
e7 Emotional incontinence
e8 Affective hyperesthesia
e9 Observed explosive mood
e10 Worried gesture
e11 Observed anhedonia
e12 Felt sadness
e13 Situational anhedonia
e14 Felt affective indifference
expsy 5

e15 Hypersensibility unpleasent events

e16 Sensory anhedonia
e17 Felt affective monotony
e18 Felt hyperemotionalism
e19 Felt irritability
e20 Felt explosive mood

Source
Jouvent, R et al 1988 La clinique polydimensionnelle de humeur depressive. Nouvelle version
echelle EHD : Polydimensional rating scale of depressive mood. Psychiatrie et Psychobiologie.

Examples
data(ehd)
str(ehd)

expsy Data set related to psychometry

Description
The expsy data frame has 30 rows and 16 columns with missing data. it1-it10 correspond to the
rating of 30 patients with a 10 items scale. r1, r2, r3 to the rating of item 1 by 3 different clinicians
of the same 30 patients. rb1, rb2, rb3 to the binary transformation of r1, r2, r3 (1 or 2 -> 0; and 3 or
4 -> 1) .

Usage
data(expsy)

Format
This data frame contains the following columns:
it1 a numeric vector corresponding to item 1 (rated from 1:low to 4:high)
it2 a numeric vector corresponding to item 2 (rated from 1:high to 4:low)
it3 a numeric vector corresponding to item 3 (rated from 1:low to 4:high)
it4 a numeric vector corresponding to item 4 (rated from 1:low to 4:high)
it5 a numeric vector corresponding to item 5 (rated from 1:low to 4:high)
it6 a numeric vector corresponding to item 6 (rated from 1:low to 4:high)
it7 a numeric vector corresponding to item 7 (rated from 1:low to 4:high)
it8 a numeric vector corresponding to item 8 (rated from 1:low to 4:high)
it9 a numeric vector corresponding to item 9 (rated from 1:low to 4:high)
6 fpca

it10 a numeric vector corresponding to item 10 (rated from 1:low to 4:high)

r1 a numeric vector corresponding to item 1 rated by rater 1
rb1 binary transformation of r1
r2 a numeric vector corresponding to item 1 rated by rater 2
rb2 binary transformation of r2
r3 a numeric vector corresponding to item 1 rated by rater 3
rb3 binary transformation of r3

Source
artificial data

Examples
data(expsy)
expsy[1:4,]

fpca Focused Principal Components Analysis

Description
Graphical representation similar to a principal components analysis but adapted to data structured
with dependent/independent variables

Usage
fpca(formula=NULL,y=NULL, x=NULL, data, cx=0.75, pvalues="No",
partial="Yes", input="data", contraction="No", sample.size=1)

Arguments
formula "model" formula, of the form y ~ x
y column number of the dependent variable
x column numbers of the independent (explanatory) variables
data name of datafile
cx size of the lettering (0.75 by default, 1 for bigger letters, 0.5 for smaller)
pvalues vector of prespecified pvalues (pvalues="No" by default) (see below)
partial partial="Yes" by default, corresponds to the original method (see below)
input input="Cor" for a correlation matrix (input="data" by default)
contraction change the aspect of the diagram, contraction="Yes" is convenient for large data
set (contraction="No" by default)
sample.size to be specified if input="Cor"
fpca 7

Details
This representation is close to a Principal Components Analysis (PCA). Contrary to PCA, cor-
relations between the dependent variable and the other variables are represented faithfully. The
relationships between non dependent variables are interpreted like in a PCA: correlated variables
are close or diametrically opposite (for negative correlations), independent variables make a right
angle with the origin. The focus on the dependent variable leads formally to a partialisation of the
correlations between the non dependent variables by the dependent variable (see reference). To
avoid this partialisation, the option partial="No" can be used. It may be interesting to represent
graphically the strength of association between the dependent variable and the other variables using
p values coming from a model. A vector of pvalue may be specified in this case.

Value
A plot (q plots in fact).

Author(s)
Bruno Falissard, Bill Morphey, Adeline Abbe

References
Falissard B, Focused Principal Components Analysis: looking at a correlation matrix with a par-
ticular interest in a given variable. Journal of Computational and Graphical Statistics (1999), 8(4):
906-912.

Examples
data(sleep)
fpca(Paradoxical.sleep~Body.weight+Brain.weight+Slow.wave.sleep+Maximum.life.span+
Gestation.time+Predation+Sleep.exposure+Danger,data=sleep)
fpca(y="Paradoxical.sleep",x=c("Body.weight","Brain.weight","Slow.wave.sleep",
"Maximum.life.span","Gestation.time","Predation","Sleep.exposure","Danger"),data=sleep)

## focused PCA of the duration of paradoxical sleep (dreams, 5th column)

## against constitutional variables in mammals (columns 2, 3, 4, 7, 8, 9, 10, 11).
## Variables inside the red cercle are significantly correlated
## to the dependent variable with p<0.05.
## Green variables are positively correlated to the dependent variable,
## yellow variables are negatively correlated.
## There are three clear clusters of independent variables.

corsleep <- as.data.frame(cor(sleep[,2:11],use="pairwise.complete.obs"))

fpca(Paradoxical.sleep~Body.weight+Brain.weight+Slow.wave.sleep+Maximum.life.span+
Gestation.time+Predation+Sleep.exposure+Danger,
data=corsleep,input="Cor",sample.size=60)

## when missing data are numerous, the representation of a pairwise correlation

## matrix may be preferred (even if mathematical properties are not so good...)

numer <- c(2:4,7:11)

8 icc

l <- length(numer)
resu <- vector(length=l)
for(i in 1:l)
{
int <- sleep[,numer[i]]
mod <- lm(sleep$Paradoxical.sleep~int)
resu[i] <- summary(mod)[[4]][2,4]*sign(summary(mod)[[4]][2,1])
}
fpca(Paradoxical.sleep~Body.weight+Brain.weight+Slow.wave.sleep+Maximum.life.span+
Gestation.time+Predation+Sleep.exposure+Danger,
data=sleep,pvalues=resu)
## A representation with p values
## When input="Cor" or pvalues="Yes" partial is turned to "No"

mod <- lm(sleep$Paradoxical.sleep~sleep$Body.weight+sleep$Brain.weight+

sleep$Slow.wave.sleep+sleep$Maximum.life.span+sleep$Gestation.time+
sleep$Predation+sleep$Sleep.exposure+sleep$Danger)
resu <- summary(mod)[[4]][2:9,4]*sign(summary(mod)[[4]][2:9,1])
fpca(Paradoxical.sleep~Body.weight+Brain.weight+Slow.wave.sleep+Maximum.life.span+
Gestation.time+Predation+Sleep.exposure+Danger,
data=sleep,pvalues=resu)
## A representation with p values which come from a multiple linear model
## (here results are difficult to interpret)

icc Intraclass correlation coefficient (ICC)

Description

Computes the ICC of several series of measurements, for example in an interrater agreement study.
Two types of ICC are proposed: consistency and agreement.

Usage

icc(data)

Arguments

data n*p matrix or dataframe, n subjects p raters

Details

Missing data are omitted in a listwise way. The "agreement" ICC is the ratio of the subject variance
by the sum of the subject variance, the rater variance and the residual; it is generally prefered. The
"consistency" version is the ratio of the subject variance by the sum of the subject variance and the
residual; it may be of interest when estimating the reliability of pre/post variations in measurements.
lkappa 9

Value
A list with :

$nb.subjects number of subjects under study

$nb.raters number of raters
$subject.variance
subject variance
$rater.variance
rater variance
$residual residual variance
$icc.consistency
Intra class correlation coefficient, "consistency" version
$icc.agreement Intra class correlation coefficient, "agreement" version

Author(s)
Bruno Falissard

References
Shrout, P.E., Fleiss, J.L. (1979), Intraclass correlation: uses in assessing rater reliability, Psycho-
logical Bulletin, 86, 420-428.

Examples
data(expsy)
icc(expsy[,c(12,14,16)])

#to obtain a 95%confidence interval:

#library(boot)
#icc.boot <- function(data,x) {icc(data[x,])[[7]]}
#res <- boot(expsy[,c(12,14,16)],icc.boot,1000)
#quantile(res$t,c(0.025,0.975)) # two-sided bootstrapped confidence interval of icc (agreement)
#boot.ci(res,type="bca") # adjusted bootstrap percentile (BCa) confidence interval (better)

lkappa Light’s kappa for n raters

Description
Computes Light’s Kappa for agreement in the case of n raters. The diagnosis (the object of the
rating) may have k possible values (ordered or not).

Usage
lkappa(r, type="Cohen", weights="squared")
10 lkappa

Arguments

r m*n matrix, m subjects and n raters

type type="Cohen" for a categorical diagnosis. If not, the diagnosis is supposed to be
ordered
weights weights="squared" for a weighted kappa with squared weights. If not, weigths
are computed with absolute values.

Details

Light’s Kappa is equal to the mean of the n(n-1)/2 kappas obtained from each pair of raters. Missing
values are omitted locally when considering each pair of raters. If type="Cohen" the diagnosis is
considered as a categorical variable. If not, the diagnosis is considered as an ordered variable and
weigthed kappa’s are computed. In this last situation, the type of weights that is used (squared or
absolute values) is given by the variable weigths.

Value

kappa (mean of the n(n-1)/2 kappas obtained from each pair of raters)

Author(s)

Bruno Falissard

References

Conger, A.J. (1980), Integration and generalisation of Kappas for multiple raters, Psychological
Bulletin, 88, 322-328.

Examples

data(expsy)
lkappa(expsy[,c(11,13,15)]) # Light's kappa for non binary diagnosis
lkappa(expsy[,c(12,14,16)]) # Light's kappa for binary diagnosis
lkappa(expsy[,c(11,13,15)], type="weighted") # Light's kappa for non binary ordered diagnosis

#to obtain a 95%confidence interval:

#library(boot)
#lkappa.boot <- function(data,x) {lkappa(data[x,], type="weighted")}
#res <- boot(expsy[,c(11,13,15)],lkappa.boot,1000)
#quantile(res$t,c(0.025,0.975)) # Bootstrapped confidence interval of Light's kappa
#boot.ci(res,type="bca") # adjusted bootstrap percentile (BCa) confidence interval
mdspca 11

mdspca Graphical representation of a correlation matrix using a Principal

Component Analysis

Description
Similar to many routines, the interest is in the possible representation of both variables and subjects
(and by the way categorical variables) with active and supplementary points. Missing data are
omitted.

Usage
mdspca(datafile, supvar="no", supsubj="no", namesupvar=colnames(supvar,do.NULL=FALSE),
namesupsubj=colnames(supsubj, do.NULL=FALSE), dimx=1, dimy=2, cx=0.75)

Arguments
datafile name of datafile
supvar matrix corresponding to supplementary variables (if any), supvar="no" by de-
fault
supsubj matrix corresponding to supplementary subjects (if any), supsubj="no" by de-
fault
namesupvar names of the points corresponding to the supplementary variables
namesupsubj names of the points corresponding to the supplementary subjects
dimx rank of the component displayed on the x axis (1 by default)
dimy rank of the component displayed on the y axis (2 by default)
cx size of the lettering (0.75 by default, 1 for bigger letters, 0.5 for smaller)

Value
A diagram (two diagrams if supplementary subjects are used)

Author(s)
Bruno Falissard

Examples
data(sleep)

mdspca(sleep[,c(2:5,7:11)])
## three consistent groups of variables, paradoxical sleep (in other words: dream)
## is negatively correlated with danger

mdspca(sleep[,c(2:5,7:11)],supvar=sleep[,6],namesupvar="Total.sleep",supsubj=sleep[,1],
namesupsubj="",cx=0.5)
12 mtmm

## Total.sleep is here a supplementary variable since it is deduced

## from Paradoxical.sleep and Slow.wave.sleep
## The variable Species is displayed in the subject plane,
## Rabbit and Cow have a high level of danger

mtmm Multitrait Multimethod approach of scale validation

Description
This function is destinated to assess the convergent and discriminant validity of subscales of a given
scale. Items belonging to the same subscale should correlate highly amongst themselves. Items
belonging to different subscales should not correlate highly. This approach is simpler and more ro-
bust than confirmatory factor analysis (CFA). It can be interesting to verify (at least approximately)
the proposed structure of an existing instrument in a new population. Most psychometricians will
however prefer CFA.

Usage
mtmm(datafile,x,color=FALSE,itemTot=FALSE,graphItem=FALSE,stripChart=FALSE,namesDim=NULL)

Arguments
datafile name of datafile
x a list of variable names (as many elements as there are subscales)
color boxplot are in colour: FALSE = colourless just in grey and white (by default),
TRUE = with colours
itemTot if TRUE, for subscale i (i=1,...,n), boxplot of Pearson’s correlations between
total score of subscale i and the items of subscale j (j=1,...n). If j=i, the item is
omited in the computation of the total score. If FALSE, for subscale i (i=1,...,n),
boxplot of Pearson’s correlations between the items of subscale i and the items
of subscale j (j=1,...n)
graphItem if TRUE represents graphically each correlation
stripChart if TRUE, dot charts are preferred to boxplots. Used with small number of items
namesDim Labels foreach boxplots

Value
For subscale i (i=1,...,n), displays the n boxplots of the distributions of the Pearson’s correlations
between items of subscale i and items of subscale j (j=1,...,n). If j=i, the correlation of a given item
with itself is ommited. Boxplot for i=j (grey by default) should be above boxplots for i!=j. Likewise,
the correlation of an item with the global score of its subscale should be above its correlations with
the global score of the other subscales.
psy 13

Author(s)
Adeline Abbe

Examples

data(ehd)

par(mfrow=c(1,5))
mtmm(ehd,list(c("e15","e18","e19","e20"),c("e4","e5","e6","e14","e17"),c("e11","e13","e16")
,c("e1","e10","e12"),c("e2","e3","e7","e8","e9")))

# Boxplots of the distributions of the Pearson's correlations between total score of

# subscale i and the items of subscale j
par(mfrow=c(1,5))
mtmm(ehd,list(c("e15","e18","e19","e20"),c("e4","e5","e6","e14","e17"),c("e11","e13","e16")
,c("e1","e10","e12"),c("e2","e3","e7","e8","e9")))

# Pearson's correlations between total score of subscale i and all items

par(mfrow=c(3,2))
mtmm(ehd,list(c("e15","e18","e19","e20"),c("e4","e5","e6","e14","e17"),c("e11","e13","e16")
,c("e1","e10","e12"),c("e2","e3","e7","e8","e9")),graphItem=TRUE)

psy Various procedures used in psychometry

Description
Kappa, Intra class correlation coefficient, Cronbach alpha, Scree plot, Multitraits multimethods,
Spherical representation of a correlation matrix

Details

Package: psy
Type: Package
Version: 1.0
Date: 2009-12-23
License: free
LazyLoad: yes

Author(s)
Bruno Falissard <[email protected]>
14 scree.plot

References
Falissard B, A spherical representation of a correlation matrix, Journal of Classification (1996),
13:2, 267-280.
Horn, JL (1965) A Rationale and Test for the Number of Factors in Factor Analysis, Psychometrika,
30, 179-185.
Mammals: Ecological and Constitutional Correlates, by Allison, T. and Cicchetti, D. (1976) Sci-
ence, November 12, vol. 194, pp.732-734
Jouvent, R et al 1988 La clinique polydimensionnelle de humeur depressive. Nouvelle version
echelle EHD : Polydimensional rating scale of depressive mood. Psychiatrie et Psychobiologie.

Examples
data(sleep)
sphpca(sleep[,c(2:5,7:11)])
data(expsy)
scree.plot(expsy[,1:10],simu=20,use="P")
data(ehd)
par(mfrow=c(1,5))
mtmm(ehd,list(c("e15","e18","e19","e20"),c("e4","e5","e6","e14","e17"),c("e11","e13","e16")
,c("e1","e10","e12"),c("e2","e3","e7","e8","e9")))

scree.plot Screeplot of eigenvalues, simulated data are available

Description
Graphical representation of the eigenvalues of a correlation/covariance matrix. Usefull to determine
the dimensional structure of a set of variables. Simulation are proposed to help the interpretation.

Usage
scree.plot(namefile, title = "Scree Plot", type = "R", use = "complete.obs", simu = "F")

Arguments
namefile dataset
title Title
type type="R" to obtain the eigenvalues of the correlation matrix of dataset, type="V"
for the covariance matrix, type="M" if the input data is directly the matrix,
type="E" if the input data are directly the eigenvalues
use omit missing values by default, use="P" to analyse the pairwise correlation/covariance
matrix
simu simu=p to add p screeplots of simulated random normal data (same number of
patients and variables as in the original data set, same pattern of missing data if
use="P")
sleep 15

Details
Simulations lead sometimes to underestimate the actual number of dimensions (as opposed to
Kayser rule: eigen values superior to 1). Basically, simu=20 is enough.

Value
a plot

Author(s)
Bruno Falissard

References
Horn, JL (1965) A Rationale and Test for the Number of Factors in Factor Analysis, Psychometrika,
30, 179-185. Cattell, RB (1966) The scree test for the number of factors. Multivariate Behavioral
Research, 1, 245-276.

Examples
data(expsy)
scree.plot(expsy[,1:10],simu=20,use="P") #no obvious structure with such a small sample

sleep Ecological and Constitutional Data in Mammals

Description
Data from which conclusions were drawn in the article Mammals: Ecological and Constitutional
Correlates, by Allison, T. and Cicchetti, D. (1976) Science, November 12, vol. 194, pp.732-734

Usage
data(sleep)

Format
This data frame contains the following columns:

Species a factor with levels

Body.weight a numeric vector, body weight in kg
Brain.weight a numeric vector, Brain weight in g
Slow.wave.sleep a numeric vector, nondreaming sleep (hrs/day)
Paradoxical.sleep a numeric vector, dreaming sleep (hrs/day)
Total.sleep a numeric vector, nondreaming + "dreaming" (hrs/day)
Maximum.life.span a numeric vector (in years)
16 sphpca

Gestation.time a numeric vector (in days)

Predation a numeric vector, Predation index (1 min - 5 max)
Sleep.exposure a numeric vector, Sleep exposure index (1 min - 5 max)
Danger a numeric vector, Overall danger index (1 min - 5 max)

Source
http://lib.stat.cmu.edu/datasets/sleep

References
Mammals: Ecological and Constitutional Correlates, by Allison, T. and Cicchetti, D. (1976) Sci-
ence, November 12, vol. 194, pp.732-734

Examples
data(sleep)
str(sleep)

sphpca Spherical Representation of a Correlation Matrix

Description
Graphical representation of a correlation matrix, similar to principal component analysis (PCA) but
the mapping is on a sphere. The information is close to a 3d PCA, the picture is however easier to
interpret since the variables are in fact on a 2d map.

Usage
sphpca(datafile, h=0, v=0, f=0, cx=0.75, nbsphere=2, back=FALSE, input="data",
method="approx", maxiter=500, output=FALSE)

Arguments
datafile name of datafile
h rotation of the sphere on a horizontal plane (in degres)
v rotation of the sphere on a vertical plane (in degres)
f rotation of the sphere on a frontal plane (in degres)
cx size of the lettering (0.75 by default, 1 for bigger letters, 0.5 for smaller)
nbsphere two by default: front and back
back "FALSE" by default: the back sphere is not seen through
input "data" by default: raw data are analysed, if not "data": correlation matrix is
expected
sphpca 17

method "approx" by default: the estimation is based on a principal component analysis

approximation. If "exact" the "approx" estimation is optimized (may be compu-
tationaly consumming). if "rscal" a multidimensional scaling approach is used:
distances between points on the sphere are optimized so that they represent at
best the original correlations. The scaling that is used leads to angles on the
sphere proportional to correlation between variables
maxiter maximum number of iterations in the optim process
output FALSE by default: if TRUE and method="rscal" numerical results are proposed

Details
There is an isophormism between a correlation matrix and points on the unit hypersphere of Rn. It
can be shown that a 3d spherical representation of a correlation matrix is statistically and cognitively
interesting (see reference). The default option method="approx" is based on a principal components
approximation (see reference). It is fast and gives rather good results. If method="exact" the rep-
resentation is sligthly improved in terms of fit (the sphere minimizes the sum of squared distances
between the original variables on the hypersphere and their projections on the sphere). The op-
tion method="rscal" optimizes the representation of correlations between variables with distances
between points (in a least squares sense). For convenience, the scaling of points on the sphere
is chosen so that angles between points are linearly related to correlations between variables (this
is not the case on the hypersphere were d=[2*(1-r)]^0.5). For method="exact" or method="rscal"
computations may be rather lengthy (and not sensible for more than 20-40 variables). The sphere
may be rotated to help in visualising most of variables on a same side (front for example). By
default, the back of the sphere (right plot) is not seen showing through.

Value
A plot. If method="rscal" and output=TRUE, a list with :
$stress.before.optim
Stress before optimization. The stress is equal to the sum of squares of differ-
ences between distances on the 3d sphere and distances on the hypersphere.
$stress.after.optim
Stress after optimization.
$convergence If 0, convergence is OK. If not, maxiter may be increased.
$correlations Correlation matrix of variables (Pearson).
$residuals Differences between observed correlations (hypersphere) and correlations esti-
mated from points on the 3d sphere.
$mean.abs.resid
Mean of absolute values of residuals.

Author(s)
Bruno Falissard

References
Falissard B, A spherical representation of a correlation matrix, Journal of Classification (1996),
13:2, 267-280.
18 wkappa

Examples
data(sleep)
sphpca(sleep[,c(2:5,7:11)])
## spherical representation of ecological and constitutional correlates in mammals

sphpca(sleep[,c(2:5,7:11)],method="rscal",output=TRUE)
## idem, but optimizes the representation of correlations between variables with distances
## between points

corsleep <- as.data.frame(cor(sleep[,c(2:5,7:11)],use="pairwise.complete.obs"))

sphpca(corsleep,input="Cor")
sphpca(corsleep,method="rscal",input="Cor")
## when missing data are numerous, the representation of a pairwise correlation
## matrix may be preferred (even if mathematical properties are not so good...)

sphpca(corsleep,method="rscal",input="Cor",h=180,f=180,nbsphere=1,back=TRUE)
## other option of presentation

##
# library(polycor)
# sleep$Predation <- as.ordered(sleep$Predation)
# sleep$Sleep.exposure <- as.ordered(sleep$Sleep.exposure)
# sleep$Danger <- as.ordered(sleep$Danger)
# corsleeph <- as.data.frame(hetcor(sleep[,c(2:5,7:11)])$correlations)
# sphpca(corsleeph,input="Cor",f=180)
# sphpca(corsleeph,method="rscal",input="Cor",f=180)
## --> Correlations between discrete variables may appear shoking to some statisticians (?)
## --> Representation of polychoric/polyserial correlations could be prefered in this situation

wkappa weighted Kappa for 2 raters

Description

Computes a weighted Kappa for agreement in the case of 2 raters. The diagnosis (the object of the
rating) may have k possible ordered values.

Usage

wkappa(r,weights="squared")

Arguments

r n*2 matrix or dataframe, n subjects and 2 raters

weights weights="squared" to obtain squared weights. If not, absolute weights are com-
puted (see details)
wkappa 19

Details
Diagnoses have to be coded by numbers (ordered naturally). For weigths="squared", weights are
related to squared differences between rows and columns indices (in this situation wkappa is close
to an icc). For weights!="squared", weights are related to absolute values of differences between
rows and columns indices. The function is supposed to deal with the case where the two raters have
not exactly the same scope of rating. Missing value are omitted.

Value
A list with :
$table the 2*k table of raw data (first rater in rows, second rater in columns)
$weights "squared" or "absolute"
$kappa Weighted Kappa

Author(s)
Bruno Falissard

References
Cohen, J. Weighted kappa: nominal scale agreement with provision for scaled disagreement or
partial credit. Psychological Bulletin 70 (1968): 213-220.

Examples
data(expsy)
wkappa(expsy[,c(11,13)]) # weighted kappa (squared weights)

#to obtain a 95%confidence interval:

#library(boot)
#wkappa.boot <- function(data,x) {wkappa(data[x,])[[3]]}
#res <- boot(expsy[,c(11,13)],wkappa.boot,1000)
#quantile(res$t,c(0.025,0.975)) # two-sided bootstrapped confidence interval of weighted kappa
#boot.ci(res,type="bca") # adjusted bootstrap percentile (BCa) confidence interval (better)
Index

∗ datasets
ehd, 4
expsy, 5
sleep, 15
∗ multivariate
fpca, 6
mdspca, 11
scree.plot, 14
sphpca, 16
∗ package
psy, 13
∗ univar
ckappa, 2
cronbach, 3
icc, 8
lkappa, 9
wkappa, 18

ckappa, 2
cronbach, 3

ehd, 4
expsy, 5

fpca, 6

icc, 8

lkappa, 9

mdspca, 11
mtmm, 12

psy, 13

scree.plot, 14
sleep, 15
sphpca, 16

wkappa, 18

20