Structural Equation Modeling: A Multidisciplinary Journal

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Exploratory Factor Analysis (EFA) Programs in R

Lan Luo, Cara Arizmendi & Kathleen M. Gates

To cite this article: Lan Luo, Cara Arizmendi & Kathleen M. Gates (2019) Exploratory Factor
Analysis (EFA) Programs in R, Structural Equation Modeling: A Multidisciplinary Journal, 26:5,
819-826, DOI: 10.1080/10705511.2019.1615835

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Structural Equation Modeling: A Multidisciplinary Journal, 26: 819–826, 2019
Copyright © 2019 Taylor & Francis Group, LLC
ISSN: 1070-5511 print / 1532-8007 online
DOI: https://doi.org/10.1080/10705511.2019.1615835

SOFTWARE REVIEW

Exploratory Factor Analysis (EFA) Programs in R

Lan Luo, Cara Arizmendi, and Kathleen M. Gates
University of North Carolina at Chapel Hill

We provide a brief overview of two R packages that can conduct exploratory factor analysis
(EFA): psych and EFAutilities. After introducing EFA and the exemplar data used in this
paper we discuss best practices for EFA. Next, we describe the approaches used in the two
packages for EFA. During this explanation, we provide sample code and discuss the usage
and results of two empirical datasets. Finally, we highlight the similarities and distinctions of
each package on modeling EFA.

Keywords: Exploratory factor analysis, R software, exploratory factor analysis modeling

programs in R

Factor analysis is generally used to explore the under-
lying correlations and structure of a set of measured
variables (Brown, 2001, p. 184). It is used very often
in fields that frequently encourage and analyze latent
constructs, such as psychology and sociology. Factor
analysis itself generally appears in the form of either
exploratory factor analysis (EFA) or confirmatory factor
analysis (CFA). EFA allows the observed (i.e., measured)
variables to be associated with any and multiple latent
factors, whereas CFA imposes restrictions regarding
which variables load onto which factors. CFA requires
a priori knowledge regarding the theoretical structure
whereas EFA aims to identify this structure in a data-
driven manner. This paper focuses on EFA and evaluates
the primary approaches available for conducting this
analysis within the R software framework (R Core
Team, 2018).
EFA is a useful method to describe the shared varia-
bility among measured variables, and to investigate
potential underlying latent factors through measurable
variables. It is useful for data reduction and to uncover
unknown patterns of relations. EFA is also especially
Correspondence should be addressed to Lan Luo, University of North
Carolina at Chapel Hill, 342 Davie Hall, Chapel Hill, NC 27599.
E-mail: lanl27@live.unc.edu
Color versions of one or more of the figures in the article can be found
online at www.tandfonline.com/hsem.
useful and convenient when one has tried a variety of
hypothesized CFA models but none of the proposed
models fit well. By giving the model a high level of
flexibility, it is able to provide insights that could lead
researchers to better measurements of the underlying
constructs, in turn influencing the inferences made from
the analysis. Because of the highly flexible nature of
EFA, open-source software, such as R, is a good plat-
form with which to perform EFA analysis. This paper
provides overviews of two packages in R that offer
specific functions for EFA: psych package (Revelle,
2018) and EFAutilities package (Zhang, Jiang, Hattori,
& Trichtinger, 2018). In the following, we first describe
the illustrative data used throughout the paper, then
insights into the options and methods available in the
two R packages, followed by a comparison and discus-
sion of the output and results.
ILLUSTRATIVE DATA
We will use two empirical data sets to illustrate the
functionality of psych and EFAutilities. One is from the
classic Holzinger and Swineford study (Holzinger &
Swineford, 1939, N = 301), used in many articles and
books on Structural Equation Modeling (SEM) and factor
analysis (e.g., Jöreskog, 1971; Mulaik, 2009, p. 341;
Tucker & Lewis, 1973) as well as in some manuals for
820 LUO ET AL.
related software packages (e.g., lavaan; Rosseel, 2012).
It consists of mental ability scores of seventh- and
eighth-grade students from two different schools. The
proposed three latent variables for mental ability are
visual ability, textual ability, and speed. The original
dataset has scores derived from 26 test questions, but
a smaller subset with only 9 test questions is more
widely used in the literature (e.g. Jöreskog, 1969). The
dataset used in this article is the above-mentioned 9-item
data and can be accessed in the data object
“HolzingerSwindeford1939” provided by the lavaan
package (Rosseel, 2012).
The code to select the subset used in this article is as
follows:
library(“lavaan”)
data(“HolzingerSwineford1939”)
variables1 <- c("x1", "x2", "x3", "x4",
"x5", "x6", "x7", "x8", "x9") H1939Xs <-
HolzingerSwineford1939[variables1]
To better examine how EFA is computed across
packages, we will also use the Composite Scores of the
Chinese Personality Assessment Inventory (CPAI537; N =
537), provided by the EFAutilities package. This is a part of
a large survey on marital satisfaction (Luo et al., 2008). The
original dataset consists of data from participants of 537
urban Chinese couples in their first year of marriage, and
the subset used in this article includes 28 composite scores
of the CPAI (Cheung et al., 1996) for the wives only. This
dataset has a sample size only slightly larger than that of
HolzingerSwineford1939 but contains around three times
the number of variables. By including a more complex
dataset, there is a greater probability of observing the
potential differences in both model results and computa-
tional time between different packages.
BEST PRACTICES FOR EFA
Before evaluating the packages is it important to under-
stand the best practices and current recommendations
regarding EFA. This provides a baseline from which to
investigate the extent to which each package contains
options that allow the user to adjust parameters and criteria
based on emerging research. Two primary issues are of
concern when conducting EFA: determining the number
of factors and selecting the final structure for how the
measured variables relate to the factors.
When little is known in substantive areas, EFA can pro-
vide insight to underlying patterns in the data (Bollen, 1989,
p. 228). Primarily, EFA provides a suggested number of
latent factors (Zwick & Velicer, 1986). A number of methods
exist for selecting the number of factors in EFA. Some of the
more straightforward approaches are the Kaiser rule (1960),
the scree test (Cattell, 1966), and Horn’s parallel analysis
(1965). Each of these methods utilizes a stopping rule deter-
mining the number of latent factors based on the eigenvalues
for the correlation matrix, which can be represented visually
on a scree plot. Researchers are usually recommended to not
use one approach as the single cut-off criterion. For example,
Ruscio and Roche (2012) noted that Kaiser rule has the
tendency to over-extract factors. The root-mean-square
error of approximation (RMSEA; Browne & Cudeck,
1992), another method to determine the number of factors,
is an estimate of model misfit per degree of freedom in the
population. Akaike’s information criterion (AIC; Akaike,
1973) and Bayesian information criterion (BIC; Schwarz,
1978) are two other methods that are based on model like-
lihood, prioritizing parsimony. Different methods may arrive
at different optimal numbers of factors. Deciding which
solution is best is left up to the researcher, either by exploring
multiple solutions to find consensus or subjective selection.
It is suggested that the researcher should consider the reason-
able number of factors that are worthwhile to retain, and not
focus on getting the “correct” number of factors for the
“true” model, which many researchers have suggested that
in most cases doesn’t exist (e.g. Cattell, 1966; MacCallum,
2003). The two packages being discussed here provide dif-
ferent criteria. The psych package offers three approaches to
calculate the number of factors: Very Simple Structure
(Revelle & Rocklin, 1979), Minimum Average Partial cor-
relation (Velicer, 1976), and parallel analysis criteria (fa.
parallel). EFAutilities offers the Kaiser rule.
The literature on selecting the final structure is a bit less
clear and homogeneous. Typically, in practice researchers
will consider an observed variable as loading on a given
latent factor if the standardized factor loading is above
a certain threshold. In practice, this threshold varies and is
largely related to the sample size (Stevens, 2002).
Tabachnick and Fidell (2007) provided a rule of thumb
that for a sample size of 300, a statistically meaningful
factor loading would need to be above .32. Peterson
(2000) conducted a meta-analysis and found that the most
common cutoff value is .40; it is not only the value that
one-third of the studies used but also the average cutoff
value.
R PACKAGES FOR EFA
This section provides an overview of the fa() function
available in the psych package (Revelle, 2018) and the
efa() function from the EFAutilities package (Zhang
et al., 2018). Other EFA-related functions (e.g. plotting
functions) included in those packages will also be
 EFA R PROGRAMS 821

discussed. Overviews will focus on both the default

function, computation, and results obtained when apply-
ing the two functions to the HolzingerSwineford1939 and
CPAI537 data. Differences and similarities between the
functions will then be discussed.

fa() in the psych package

The psych package (Revelle, 2018) is a large package
written initially with personality, psychometric theory,
and experimental psychology researchers in mind. In
addition to providing basic descriptive statistics, it con-
tains functions for multivariate analysis and scale con-
struction, using multiple methods such as factor analysis,
principal component analysis, and cluster analysis. We
focus on the fa() function which provides exploratory
factor analysis results. Complementary graphing func-
tions will be introduced as the function is applied to
the sample datasets.
Usage of fa() is shown below with all arguments are set
to the default:
fa(r,nfactors=1,n.obs = NA,n.iter=1, rota-
te="oblimin", scores="regression",
residuals=FALSE, SMC=TRUE, covar=
FALSE,missing=FALSE,impute="median",
min.err = 0.001, max.iter = 50,
symmetric=TRUE, warnings=TRUE,
fm="minres", alpha=.1,p=.05,oblique.
scores=FALSE,np.obs=NULL,
use="pairwise",cor="cor", correct=.5,
weight=NULL,..)
Most of the arguments can be left to the default in
most cases other than the first two. The r argument
indicates the dataset being analyzed, and number of
factors is specified using nfactors. Factor rotation type
and criterion are integrated in the argument, rotate, and
the default is (oblique) oblimin. The argument, fm,
indicates the factoring method; options include but are
not restricted to minimum residual, which is the default
method, ordinary least squares, maximum likelihood,
and alpha factor analysis.
This package offers a few ways in which the number
of factors can be decided. One can use fa() to select the
number of factors by iteratively running the function
with increasing factor numbers up to the maximum num-
ber of factors that can be fit before the model is satu-
rated. From these results, researchers can compare fit
values such as the RMSEA and BIC across the number
of factors. An alternative approach provided within the
psych package is to use the fa.parallel() function to
obtain the suggested number of factors, as well as the
number of components. To use fa.parallel, first, the
number of factors is calculated:
FIGURE 1 H1939 data parallel analysis scree plots by psych.
fa.parallel(H1939Xs, fm="ml", main=
"H1939 Parallel Analysis Scree Plots")
fa.parallel(CPAI537, fm="ml",
main=" CPAI537 Parallel Analysis Scree
Plots ")
The essential arguments for fa.parallel() are the dataset
to be estimated and the factoring method. For consistency,
we used maximum likelihood as the factoring method, as it
is also used in fa() in the following. The method used here
is Horn’s (1965) parallel analysis, which the authors stated
as an equally compelling procedure. The output gives you
both textual outputs of the suggested number of factors and
components and a scree plot (Figures 1 and 2) of the
successive eigenvalues. The suggested number of factors
or components (which is not considered here) to extract is
provided and is based on comparing the scree of factors of
the observed data with that of a random data matrix the
same size as the original data. The scree plots, however, do
not contain any suggestions, and thus can be used to deter-
mine the number of factors using other alternatives.
Once the number of suggested factor is determined
using fa.parallel, EFA can be conducted with the fa()
function shown below to arrive at the model structure:
#M1 is generated for later graphing func-
tion reference
M1 <- fa (H1939Xs, nfactors=3, rotate="o-
blimin", fm="ml)
fa (CPAI537, nfactors=5, rotate="obli-
min", fm="ml)
Multiple graphing options are included in the psych
package, and here we introduce the graphing functions
822 LUO ET AL.

FIGURE 2 CPAI537 data parallel analysis scree plots by psych.

most related to EFA. Using the HolzingerSwineford1939

data:
#IV correlation plot on the observed data
cor.plot(H1939Xs, numbers=T, upper=F,
diag=F,
main="H1939data correlation", cex=.7)
#heatmap of the loadings
cor.plot(M1, numbers=T, upper=T, diag=T,
main="H1939data Heatmap")
#factor loadings visual presentation
fa.diagram(M1, main=" H1939data")
The independent variables correlation plot (Figure 3) is
a useful visualization of the data before one moves on to do
the actual EFA; it gives researchers a general idea what the
results of EFA might look like. The heatmap (Figure 4) con-
tains the loadings of variables on all latent factors. The factor
loadings graph (Figure 5) is a simpler representation; it shows
what is the factor that each variable is loaded on the most.

efa() in the EFAutilities package
The EFAutilities package (Zhang et al., 2018), as indicated by
the package name, is a small R package specifically designed
for modeling EFA. It computes standard errors for parameter
estimates, factor loadings, and correlations under various
conditions (e.g., rotation). EFAutilities uses a different default
FIGURE 3 H1939 data independent variables correlation graph by
psych.
rotation, CF-varimax, from psych’s default, oblique oblimin,
although the other possible options in both packages largely
overlap. It also contains two datasets, one of which as

FIGURE 4 H1939 data EFA heatmap by psych.
FIGURE 5 H1939 data EFA factor loadings graph by psych.
EFA R PROGRAMS 823
introduced earlier (CPAI537) is one of the two sample data-
sets in this article for demonstration.
Sample code, in which each argument is set to the
default, to use the efa() function is as follows:
efa(x=NULL, factors=NULL, covmat=NULL,
n.obs=NULL, dist='normal',
fm='ols', rtype='oblique', rotation=
'CF-varimax',
normalize=FALSE, maxit=1000, geomin.
delta=NULL,
MTarget=NULL, MWeight=NULL, PhiWeight
= NULL,
PhiTarget = NULL, useorder=FALSE,
se='information', LConfid=c(0.95,0.90),
CItype='pse',
Ib=2000, mnames=NULL, fnames=NULL,
merror='YES',
wxt2 = 1e0)
The only essential argument required here is x. One can use
the defaults or specify for each of the remaining arguments. The
argument, x, is the dataset that is to be analyzed and should be
a n -by-p matrix where n is the number of observations and p is
the number of observed variables. The argument, factors, is
where the users indicate the number of factors. If not specified
by the researcher, the suggested number of factors will be
calculated using the Kaiser rule (1960), which equals to the
number of eigenvalues of the correlation matrix larger than one.
This is different from the methods used in psych that are
described above. EFAutilities was designed to not contain any
alternatives to calculate the number of factors, and users are
encouraged to select the number of factors not relying on one
single method but based on other relevant statistics such as
standard errors (Zhang, 2014). The argument, se, is the method
for calculating standard errors for rotated factor loadings and
factor correlations, which are not calculated by most factor
analysis programs but need to be taken account of for effective
use of EFA (Zhang, 2014). The default factor rotation type is
oblique as determined by rtype; the other type is orthogonal
which is rarely used in EFA. The default factor rotation criterion
is CF-varimax as indicated by the rotation argument; other
options exist.
To better understand how efa() works, it is also used to
analyze the two demonstration datasets. Code is shown in
the following (most default arguments are omitted):
#for HolzingerSwineford1939
efa(x=H1939Xs, fm="ml", rtype="oblique",
rotation="CF-quartimax")
#for CPAI537
efa (CPAI537, rtype="oblique", fm="ml",
rotation="CF-quartimax")
The different options and default for factor rotation
criteria and factoring methods are summarized in Table 1.
824 LUO ET AL.

TABLE 1
Factor Rotation and Factoring Method Options

Available
argument fa() efa()

Factor N/A, it is incorporated in factor rotation criteria Oblique (default), orthogonal

rotation
type
Factor Oblique: “oblimin” (default), “promax”, “simplimax”, “CF-varimax” (default), “CF-quartimax”, “CF-equamax”, “CF-facparsim”,
rotation “bentlerQ”, “geominQ”, “biquartimin” and “cluster” “CF-parsimax”, “target”, “goemin”, and “xtarge” (for oblique rotation only)
criteria Orthogonal: “none”, “varimax”, “quartimax”, “bentlerT”,
“equamax”, “varimin”, “geominT” and “bifactor”
Factoring “minres” (default), “uls”, “ols”, “wls”, “gls”, “pa”, “ml”, “ols” (default) and “ml”
method “minchi”, “minrank”, “old.min”, and “alpha”

COMPARISONS: ESTIMATES AND rbenchmark package (Kusnierczyk, 2012). The psych

COMPUTATIONAL TIME package appears to be faster in arriving at EFA solu-
tions. Additionally, the number of factors selected was
In order to compare the estimates obtained using the the same. The model structures are also identical; with
two packages, the models were run using the same the common cut off point of .4, we still arrive at the
methods: maximum likelihood factoring method, obli- same model structures and factor loading estimates as
que rotation method, and oblimin and CF-quartimax shown in Table 4. The two packages evidenced overall
rotation criterion, which are considered to be equivalent agreement in the solutions.
for oblique rotation (Zhang et al., 2018). The following
tables represent the correlations of calculated latent
factors as a representative of parameter estimates in
the output (Table 2) and suggested number of factors DISCUSSION
as well as computational time (Table 3). We see that the
estimates for the correlation among factors are identical With the increasing number of psychometric methods,
after rounding (Table 2). The precision differs between EFA has come under great scrutiny. A primary critique
the packages (psych to the hundredths place and is that it does not allow researchers to constrain specific
EFAutilities to the thousandths by default) and the aspects of the model (Bollen, 1989) even if certain
values are presented as they are provided by the observed variables are thought to relate onto the same
packages. Computational time (Table 3) was calculated construct. Additional critiques come in the form of
as the average time of 1000 repeats using the Gorsuch’s (1983, p. 393) who argued that CFA is usually
more powerful and should be preferred over EFA when
possible. However, it is not always possible to rely on
TABLE 2
CFA, and EFA can be useful as a first step before using
Latent Factor Correlations (Cor)
CFA. For this reason, we evaluated the functionality of
H1939 H1939 H1939 CPAI537 CPAI537 CPAI537 currently available EFA packages.
Package Cor(r1, Cor(r1, Cor(r2, Cor(r1, Cor(r1, Cor(r2, The fa() function in psych and efa() function in the
name r2) r3) r3) r2) r5) r3) EFAutilities package use somewhat similar syntax. For
psych .22 .33 .27 .35 −.09 .08
EFAutilities .216 .326 .270 .354 −.086 .078
TABLE 4
H1939 Model Structure and Estimates

TABLE 3 Item name Factor 1 Factor 2 Factor 3

Suggested Number of Factors and Computational Time (CT)
Item 1 .60 .19 .03
CT: CT: Item 2 .51 .04 −.12
H1939 CPAI537 number number Item 3 .69 −.07 .02
number number of of CT: CT: Item 4 .02 .84 .01
Package of of factors factors EFA EFA Item 5 −.07 .89 .01
name factors factors H1939 CPAI537 H1939 CPAI537 Item 6 .08 .81 −.01
Item 7 −.15 .04 .72
psych 3 5 .430 .732 0.118 1.004 Item 8 .10 −.03 .70
EFAutilities 3 5 N/A N/A 1.778 4.733 Item 9 .37 .04 .46

both efa() and fa(), the amount of minimum input from
the user for this demonstration was the same: dataset
being analyzed, number of factors (for fa() only), factor
extraction methods, and rotation methods. Although
they have different default arguments (e.g. default rota-
tion criterion for fa is oblimin and for efa is CF-
varimax; possible options for the main arguments are
also shown in Table 1), they produce identical results
when set to use the same methods for modeling and
rotation, with output differences almost only due to
rounding. psych and both EFAutilities demonstrated to
be very useful and powerful packages for EFA.
The biggest difference between the two packages on
EFA is probably the method to determine the number
of factors. Indeed, there are a variety of methods to do
so; although one will usually get very similar suggested
number of factors regardless of the method, there are
times they will suggest different values. The psych
package provides more flexibility in terms of options
for deciding the number of factors. It offers three
approaches to arriving at the suggested number of
latent factors. The EFAutilities package offers only
one option for identifying the number of factors. The
easy to use efa() function calculates the number of
factors using the Kaiser method. This difference
reflects the preferences of the package authors.
Although the EFAutilities package does not offer
alternative approaches calculating the number of fac-
tors, it offers four methods to calculate standard errors
for rotated factor loadings and factor correlations,
which have been suggested as more justifiable in mak-
ing EFA decisions (Cudeck & O’Dell, 1994). Standard
errors in EFA can facilitate both other EFA decisions
(e.g. the number of factors to retain) and the presenta-
tion of the final model structure (Zhang, 2014).
However, standard errors in EFA have not been routi-
nely examined, likely due to both the difficulty in their
estimation and researchers’ unawareness of their avail-
ability. By providing the option to calculate standard
errors in EFAutilities, their usage is encouraged in
arriving the final model structure.
Computational time was calculated using rbenchmark
(Kusnierczyk, 2012). The computational time is the average
of 1000 runs. The fa function was faster than the efa function
for both the datasets, and the difference is larger when the
sample size increases. It is also not surprising that both func-
tions took a longer time to process when the dataset is larger.
Although it is unwise to conclude based on only two datasets,
the results here suggests that as the sample size and number of
variables being assessed increase, efa(), compared to fa(), will
likely take a longer time to process.
In closing, the two packages are similar in that they arrive
at the same solution when argument options are set to be
equivalent and run on commonly used exemplar data where
EFA R PROGRAMS 825
factor structures are clear. However, they offer differences that
users should be mindful of when selecting an approach. In
practice, FA rarely is conducted as solely exploratory or solely
confirmatory but often falls somewhere in between these
extremes. With this in mind, researchers can also utilize
other packages, such as lavaan (Rosseel, 2012) to perform
FA and adjust models in an exploratory manner. Multiple
packages and software can also be used simultaneously to
better provide insights on how the model can be improved and
better specified, which goes along with the intentions with
which when EFA is typically conducted.
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