Running head: BAYES FACTOR 1

© 2018, American Psychological Association. This paper is not the copy of

record and may not exactly replicate the final, authoritative version of the
article. Please do not copy or cite without authors' permission. The final article
will be available, upon publication, via its DOI: 10.1037/met0000201

A Tutorial on Testing Hypotheses Using the Bayes Factor

Herbert Hoijtink
Department of Methodology and Statistics, Utrecht University

Joris Mulder
Department of Methodology and Statistics, Tilburg University

Caspar van Lissa

Department of Methodology and Statistics, Utrecht University

Xin Gu
Department of Educational Psychology, East China Normal University

This paper has a rather long introduction. You can

skip it and start reading on page 10.

Author Note
BAYES FACTOR 2

Herbert Hoijtink, Department of Methodology and Statistics, Utrecht University,

P.O. Box 80140, 3508 TC, Utrecht, The Netherlands. E-mail: [email protected]. The first
author is supported by the Consortium on Individual Development (CID) which is funded
through the Gravitation program of the Dutch Ministry of Education, Culture, and Science
and the Netherlands Organization for Scientific Research (NWO grant number
024.001.003). Joris Mulder, Department of Methodology and Statistics, Tilburg University,
[email protected]. The second author is supported by a NWO Vidi Grant (452-17-006).
Caspar van Lissa, Department of Methodology and Statistics, Utrecht University. E-mail:
[email protected]. Xin Gu, Department of Educational Psychology, East China Normal
University, [email protected]. Earlier versions of this manuscript have been posted
with the bain package that can be obtained from
https://informative-hypotheses.sites.uu.nl/software/bain/.
BAYES FACTOR 3

Abstract

Learning about hypothesis evaluation using the Bayes factor could enhance psychological
research. In contrast to null-hypothesis significance testing: it renders the evidence in favor
of each of the hypotheses under consideration (it can be used to quantify support for the
null-hypothesis) instead of a dichotomous reject/do-not-reject decision; it can
straightforwardly be used for the evaluation of multiple hypotheses without having to
bother about the proper manner to account for multiple testing; and, it allows continuous
re-evaluation of hypotheses after additional data have been collected (Bayesian updating).
This tutorial addresses researchers considering to evaluate their hypotheses by means
of the Bayes factor. The focus is completely applied and each topic discussed is illustrated
using Bayes factors for the evaluation of hypotheses in the context of an ANOVA model,
obtained using the R package bain. Readers can execute all the analyses presented while
reading this tutorial if they download bain and the R-codes used. It will be elaborated in a
completely non-technical manner: what the Bayes factor is, how it can be obtained, how
Bayes factors should be interpreted, and what can be done with Bayes factors. After
reading this tutorial and executing the associated code, researchers will be able to use their
own data for the evaluation of hypotheses by means of the Bayes factor, not only in the
context of ANOVA models, but also in the context of other statistical models.
Keywords: bain, Bayes Factor, Bayesian Error Probabilities, Informative Hypotheses,
Posterior Probabilities.
BAYES FACTOR 4

A Tutorial on Testing Hypotheses Using the Bayes Factor

Introduction

Null hypothesis significance testing (NHST) is the dominant tool in psychological

research. It is used to test whether the null-hypothesis of no effect can be rejected based on
the observed data. This is done by comparing the p-value to a pre-specified significance
level. The popularity of NHST is surprising because in the last decades it has been heavily
criticised. For example, Cohen (1994) and Royal (1997) argue that the null-hypothesis is so
precise that it may never be true. However, Wainer (1999) provides examples where a
precise null-hypothesis provides a convincing description of the population of interest and
Jones and Tukey (2000) present "a sensible formulation of the significance test". The
bottom line is that the null hypothesis should not unthinkingly be used (as it often is), it
should only be used if it provides a plausible description of the population of interest.
Furthermore, Berger and Delampady (1987), Raftery (1995), Harlow, Mulaik, and Steiger,
(1997/2016), Wagenmakers (2007), and Masson (2011), criticized various aspects of (the
use of) NHST. This culminated in the recent attention for publication bias (Ioannides,
2005; Simons, Nelson, and Simonsohn, 2011; van Assen et al, 2014), and questionable
research practices (Fanelli, 2009; John, Loewenstein, and Prelec, 2012; Masicampo and
Lalande, 2012; Wicherts et al., 2016), which are all linked to the use of a pre-specified
significance level of, usually, .05.
Publication bias is the phenomenon that researchers whose research renders p < .05
while H0 is true (that is, a Type I error), will usually have their paper published, while
researchers who obtain p > .05 and do not reject the null-hypothesis will usually not have
their paper published. This is also known as the file-drawer problem: a fluke result gets
published while all the research showing that the result is false remains in the file-drawer.
Questionable research practices are the phenomenon that researchers use improper
methods to analyse their data with the goal to obtain a p-value smaller than .05. Examples
by which this can be achieved is: selective removal of outliers; testing six different
BAYES FACTOR 5

dependent variables and reporting only the significant results (without mentioning the
non-significant results nor applying a correction for capitalization on chance); post-hoc
(after collecting and looking at the data) selection of covariates, or collecting extra data
because the available data rendered a p-value that was only slightly larger than .05.

The consequences of publication bias and questionable research practices are shown
in the OSF "reproducibility project psychology" (https://osf.io/ezcuj/) where only
about 30% of 100 replication studies confirmed the results obtained by the original study
(Open Science Collaboration, 2015). An alternative for the use of threshold values (like an
alpha level of .05) is preregistration of research, as argued, for example, in Wagenmakers et
al. (2012). Ideally preregistration would entail that researchers write their paper before
collecting the data, that is, without data description, data analysis (but the analysis plan
should be in the paper), and conclusion. Based on this preregistration the journal will
decide whether the research is interesting enough to warrant publication (no threshold
values needed!). If the paper is accepted, the researchers collect the data, execute the
analyses, write a conclusion and their paper is ready to be published, irrespective of
whether the p value is smaller than .05 or not. Currently, preregistration can be done at,
for example, the Centre for Open Science at https://cos.io/rr/. There is also an
increasing number of journals that encourage preregistered research, an important example
is Psychological Science
(https://www.psychologicalscience.org/publications/psychological_science
/preregistration).

These developments led to a renewed attention for NHST and alternatives to NHST.
Wasserstein and Lazar (2016) highlighted when, why, and how p-values can properly be
used. Cumming (2012) advocates the use of confidence intervals which are summaries of
the information in the data with respect to the parameter of interest. The Bayesian
alternative for confidence intervals are credible intervals. The interested reader is referred
to Morey et al. (2016) for an evaluation and comparison of both types of intervals. In an
BAYES FACTOR 6

attempt to reduce the use of p-values Trafimov and Marks (2015) require researchers to use
descriptive statistics to present their data and more or less forbid the use of inductive
inferential methods (like p-values and confidence intervals). Benjamin et al. (2017) propose
to change the usual significance level of .05 to .005. One of their motivations is that this
level will reduce publication bias and is much harder to achieve using questionable research
practices. Also interesting is the revival of the Fisherian interpretation of the p-value
(Hurlbert and Lombardi, 2009), that is, use it as a measure of evidence against the
null-hypothesis without referring to a pre-specified significance level.

This tutorial will focus on still another alternative for NHST: Testing hypotheses
using the Bayes factor. Kass and Raftery (1995) revived the interest in the work of Jeffreys
(1961), and Klugkist, Laudy, and Hoijtink (2005) and Rouder et al. (2009) provided the
first implementations in software. As will be elaborated in this tutorial, hypothesis
evaluation using the Bayes factor has features that are valuable for psychological research.
First of all, it does not provide a dichotomous reject/do-not-reject decision with respect to
null-hypotheses. It renders the evidence in favor of each of the hypotheses under
consideration and can also be used to quantify the support in the data in favor of the
null-hypothesis. Secondly, it can be used for the evaluation of multiple hypotheses while
automatically accounting for the fact that not one but multiple hypotheses are evaluated.
Thirdly, while collecting data the support for the hypotheses of interest can continuously
be updated (Bayesian updating). When a research project is planned and executed, but
the support in the data for the hypotheses of interest is not convincing, within the
Bayesian paradigm it is proper to collect more data and to re-evaluate the hypotheses.
Fourth, not the Type I and Type II error probabilities are controlled, that is, how often is
the correct decision made if data are repeatedly sampled from the null and alternative
populations, respectively (note that, Type I and Type II errors are determined independent
of the observed data). What is controlled are the Bayesian error probabilities, that is, what
are the probabilities of making incorrect decisions based on the information in the observed
BAYES FACTOR 7

data (Bayesian error probabilities do not consider what happens if data are repeatedly
sampled from the null and alternative populations).

Of course the Bayes factor too is criticized. First of all, it does not control the Type I
and Type II errors (it controls the Bayesian error probabilities). However, the Bayesian
t-test can be specified such that it results in the smallest possible average of Type I and
Type II error probabilities (Gu, Hoijtink, and Mulder, 2016). Furthermore, using the
Bayesian t-test while updating renders compared to NHST the same or smaller Type I and
Type II error probabilities while needing smaller sample sizes (Schonbrodt et al, 2017).
Thus, although Bayes factors do not aim to control the Type I and Type II errors, this
does not imply that these are "out of control". Secondly, as is elaborated in Sellke, Bayarri,
and Berger (2001) and Mulder (2014), for the evaluation of simple null-hypotheses (like, a
mean is equal to zero) the Bayes factor tracks (is a transformation of) the p-value as a
measure of evidence against the null-hypothesis. However, this does not imply that
properties of the Bayes factor that are valuable for psychological research (shortly
elaborated in the previous paragraph) transfer to the p-value, nor that this holds for all
hypotheses that can be evaluated by both the p-value and the Bayes factor. Thirdly, as
will be elaborated in this tutorial, in order to be able to compute a Bayes factor a,
so-called, prior distribution has to be specified. The choice of the variance of this
distribution is subjective. Researchers who favor objective inferences may object to this
feature. However, as will be elaborated in this tutorial: for hypotheses specified using
equality constraints (like the null-hypothesis) a, so-called, sensitivity analysis can be used
to determine the influence of the prior variance on the resulting Bayes factors; and, for
informative hypotheses (Hoijtink, 2012) specified using only inequality constraints, the
prior variance does not influence the resulting Bayes factors.

There are a number of Bayes factors that can be used to quantify the evidence in the
data for a null and alternative hypothesis. The discussion will be limited to the three that
are implemented in software and can thus be used for psychological research. The
BAYES FACTOR 8

BayesFactor function from the R package (see, for the first paper about this package,
Rouder et al. 2009, and the website at
https://richarddmorey.github.io/BayesFactor/) follows in the tradition set by
Jeffreys (1961) and uses, so-called, Jeffreys-Zellner-Siow or g-priors (see, for example, Liang
et al., 2008), that is, default values for the variance of the prior distribution are proposed
that can be modified by the researcher to execute a sensitivity analysis. This package
enables the evaluation of null and alternative hypotheses in the context of analysis of
variance models, regression models, and contingency tables. The package BIEMS (see,
Mulder, Hoijtink, and, de Leeuw, 2012) and the website at
https://informative-hypotheses.sites.uu.nl/software/biems/ follows in the
tradition set by Berger and Pericchi (1996, 2004) and uses minimal training samples (a
small part of the observed data) to specify the variance of the prior distribution. This
package enables the evaluation of null, informative (such as, for example, directional
hypotheses like µ1 > µ2 > µ3 , that is, three means that are ordered from largest to
smallest), and alternative hypotheses in the context of the multivariate normal linear
model. The R function bain (Gu, 2016; Gu, Mulder, and Hoijtink, 2018; Hoijtink, Gu, and
Mulder, 2018; https://informative-hypotheses.sites.uu.nl/software/bain/) follows
in the tradition set by O’Hagan (1995) and uses a fraction of the information in the data to
specify the variance of the prior distribution. The package enables the evaluation of null,
informative, and alternative hypotheses in a wide range of models such as, for example, the
multivariate normal linear model, generalized linear models, random effects models, and
structural equation models (see, for example, Gu, Mulder, Decovic, and Hoijtink, 2014).
For hypotheses that can be evaluated by each of the three packages it has not yet been
thoroughly explored if the respective Bayes factors are the same. However, the few data
sets that the authors have thus far evaluated with two or more of the approaches, tended
to render relatively comparable Bayes factors.

This tutorial will elaborate testing hypotheses using the Bayes factor. With the
BAYES FACTOR 9

exception of the specification of the prior distribution, what is written about the Bayes
factor applies to each of the implementations in BayesFactor, BIEMS, and bain. This
tutorial will be illustrated with the Bayes factor implemented in bain (and thus also
discuss the specification of the prior distribution in bain) because it is the most versatile of
the three packages: it can evaluate null, informative, and alternative hypotheses in a wide
range of statistical models, and can be used such that it renders inferences that are robust
with respect to outliers and distributional assumptions (Bosman, 2018). The audience for
this tutorial are researchers who want to use their data to evaluate the null and alternative
hypotheses and/or informative hypotheses. It will thoroughly be elaborated and illustrated
what can be done with Bayes factors. This tutorial does not contain any technical
background and formulas. The interested reader can follow up on the references given or
surf to the Bayes Factor, BIEMS, and bain websites to find the complete (technical)
background. To keep the exposition as simple and accessible as possible, all illustrations
concern hypotheses with respect to the means from an independent groups ANOVA.
However, hypothesis evaluation using the Bayes factor is by no means limited to ANOVAs.
In fact, using bain, hypothesis evaluation using the Bayes factor can be executed for many
statistical models that are of interest to psychological researchers. The bain package
contains many examples that, among others, elaborate its use in the context of, ANCOVA,
multiple regression, equivalence testing, logistic regression, and repeated measures analysis.
Instructions for the installation of bain, the annotated R code BFtutorial.R used to
create this tutorial, and the data used, can be obtained by downloading the latest version
from the bain website. Reading this tutorial in combination with executing parts of
BFtutorial.R will directly provide readers with hand-on experience.

This tutorial is organized as follows. First, the Bayes factor will be introduced,
followed by an application to the evaluation of null and alternative hypotheses.
Subsequently, properties of the Bayes factor will be highlighted and discussed. The tutorial
continues with the application of Bayes factor for the evaluation of informative hypotheses,
BAYES FACTOR 10

including an application to the evaluation of replication studies. The tutorial ends with a
description of the bain package and a short conclusion.

Introducing the Bayes Factor

In this section the Bayes factor will be introduced and an interpretation of the Bayes
factor in terms of Bayesian probabilities will be given. Among others, more examples
follow later in this tutorial, the Bayes factor can be used to test the null and alternative
hypotheses.

Definition: The Null and Alternative Hypotheses

The null-hypothesis is usually of the form

H0 : the effect is zero,

and the alternative hypothesis of the form

Ha : not H0 .

The effect may, for example, be a correlation, the differences between one or more pairs
of means, and one or more regression coefficients.

This tutorial will focus on the evaluation of hypotheses in the context of the ANOVA
model. With three groups it would hold that H0 : µ1 = µ2 = µ3 and Ha : not H0 . Note
once more, that it is not required to use the null-hypotheses (alternatives will be provided
later in this tutorial). It should only be used if it provides a plausible description of the
population of interest. Note furthermore, that, in this tutorial, Ha will be replaced by Hu ,
where the subscript u denotes that the means are unrestricted, that is, Hu : µ1 , µ2 , µ3 . The
difference between both representation is that the Ha explicitly excludes µ1 = µ2 = µ3
BAYES FACTOR 11

while Hu does not. In Bayesian statistics both representations are equivalent and will
1
render the same Bayes factors.

Definition: Bayes Factor

The Bayes Factor BF0u quantifies how much more likely the data are to be observed
under H0 than under Hu . Therefore, BF0u can be interpreted as the relative support
in the observed data for H0 versus Hu . If BF0u is 1, there is no preference for either
H0 or Hu . If BF0u is larger than 1, H0 is preferred. If BF0u is between 0 and 1, Hu is
preferred.

If, for example, BF0u = 4, the support in the observed data is 4 times larger for H0
than for Hu . The Bayes factor of Hu versus H0 , that is, reversing the order of the
hypotheses, is denoted by BFu0 = 1/BF0u . Therefore, BF0u = .1 implies that BFu0 = 10,
that is, the relative support in the data for Hu is 10 times larger than for H0 . The support
expressed by the Bayes factor is determined by balancing the relative fit and the relative
complexity of H0 versus Hu . A good hypothesis has a good fit, that is, it provides an
adequate description of the data at hand. Because better predictions can be derived from
more specific hypotheses, a good hypothesis is not unnecessarily complex, that is, it is
specific and parsimonious. Due to inclusion of the relative complexity the Bayes factor
functions as a so-called Occam’s razor, that is, when two hypotheses fit the data equally
well, the simples (least complex) hypothesis is preferred. Thus, if the observed effect is in
line with H0 , the more parsimonious hypothesis H0 wil be preferred over the more complex
hypothesis Hu . As is shown in, for example, Hoijtink (2012, pp. 59, Section 3.7.1), under
specific circumstances, the Bayes factor is equal to the following ratio: BF0u = f0 /c0 , where
f0 and c0 denote the relative fit and relative complexity of H0 versus Hu , respectively.
1
Bayes factors are computed by integrating so-called posterior and prior distributions with respect to
(parts of) Hu . Whether or not µ1 = µ2 = µ3 is included does not affect the outcome because, loosely
spoken, among the infinite number of possible combinations of values for µ1 , µ2 and µ3 that are in agreement
with Hu , µ1 = µ2 = µ3 has a "zero probability" of occurring.
BAYES FACTOR 12

Since fit and complexity of hypotheses (here H0 , which explains the subscript 0 in f0 and
c0 , later on for other hypotheses other subscripts will be used) are always determined
relative to Hu , the index u is implicit in the notation f0 and c0 . This expression of the
Bayes factor is known as the Savage-Dickey method (see, for example, Wagenmakers, et al,
2010 and Wetzels, Grasman, and Wagenmakers, 2010).

Using a simple example prior and posterior distributions, complexity and fit will now
be introduced. The interested reader is referred to Gu, Mulder, and Hoijtink (2018) and
Hoijtink, Gu, and Mulder (2018), for the complete statistical background. At the top of
Figure 1 three hypotheses corresponding to the (Bayesian) t-test are displayed: Hu : µ1 , µ2 ,
H1 : µ1 ≈ µ2 , and H2 : µ1 > µ2 . Note that, in order to make the exposition below accessible
and fitting for a tutorial, the exact equality in H0 is replaced by an approximate equality in
H1 which allows for small deviations from H0 (the difference between both means is less
than .2).

First of all, the posterior distribution of µ1 and µ2 has to be defined.

Definition: Posterior Distribution

The posterior distribution summarizes the information in the data and the prior dis-
tribution (see the next Definition) with respect to the population mean of each of the
groups in the ANOVA. The implementation in bain renders µg ∼ N (xg , σ̂ 2 /Ng ) for each
of g = 1, ..., G groups, where xg denotes the sample mean, σ̂ 2 the sample estimate of
the pooled within variance, and Ng the sample size in Group g.

The dashed circle in the top left hand figure in Figure 1 represents the posterior
distribution of µ1 and µ2 which is a bivariate normal distribution with N1 = N2 = 20,
x1 = .5, x2 = 0, and σ̂ 2 /Ng = .05 for g = 1, 2, that is, the posterior standard deviation is
about .22. It is a so-called 95% iso-density contour, that is, a two dimensional confidence
BAYES FACTOR 13

interval where both sample means determine the center and the corresponding posterior
standard deviations the radius (which is about 2 x .22 = .45). As can be seen, the data
indicate that it is most likely that both µ1 is positive and that µ2 is zero. As can also be
seen, this corresponds to Hu because there are no restrictions on both means. Note that,
bain cannot only be applied in the context of ANOVA, but in the context of a wide range
of statistical models. To achieve this, it works with a normal approximation of the
posterior distribution of only the parameters that are used to specify the hypotheses of
interest (see Gu, Mulder, Dekovic, and Hoijtink, 2014, Gu, Mulder, and Hoijtink, 2018,
and, Hoijtink, Gu, and Mulder, 2018, for the complete motivation and elaboration). For
the ANOVA model this implies that only the posterior distribution of the µ’s is used (the
within group variance σ 2 is integrated out) and their posterior is approximated by a
normal distribution.

Definition: Prior Distribution

When testing hypotheses using the Bayes factor, the prior distribution of the population
mean of each of the groups in the ANOVA is chosen such that it renders an adequate
quantification of the complexity (see the next Definition) of an hypothesis. The imple-
mentation in bain renders µg ∼ N (µB , 1/bg × σ̂ 2 /Ng ) for each of g = 1, ..., G groups.
This prior distribution has three important characteristics: i) the prior mean µB is
chosen such that it is located on the boundary of the hypotheses under consideration
(this is in line with Jeffreys, 1961, and holds also for the Bayes factors implemented
in BayesFactor and BIEMS); ii) it has the same shape (a normal distribution) as the
posterior distribution; and, iii) it is less informative than the posterior distribution due
to a larger variance obtained by multiplying the posterior variance with a fraction 1/bg .
The fraction bg (the fraction of information in the data used to specify the prior distri-
bution, O’Hagan, 1995) will further be discussed in the section dealing with "Sensitivity
Analysis".
BAYES FACTOR 14

The solid circle in the top left hand figure in Figure 1 represent the 95% iso-density
contours of the prior distribution of µ1 and µ2 . As can be seen the prior distribution is
centered on 0,0 (one of the values on the boundary of H1 , the approximation of H0 , and
H2 )2 , has the same shape as the posterior distribution, and has a larger variance than the
posterior distribution (1/bg × σ̂ 2 /Ng = 1 for g = 1, 2, that is, the prior standard deviation
equals 1 for each mean and the radius of the 95% isodensity contour is 2 x 1 = 2). As can
also be seen, this corresponds to Hu because there are no restrictions on both means.

Definition: Complexity

The complexity of an hypothesis is the proportion of the prior distribution that is

supported by the hypothesis at hand. The complexity has a value between 0 and 1
where smaller values denote a less complex, that is, more parsimonious, hypothesis.

As may be clear, H1 : µ1 ≈ µ2 is more specific (less complex) than H2 : µ1 > µ2 . As

can be seen on the top row of Figure 1, H1 (the area within the diagonal lines) supports
about 11% of the prior distribution (the solid circle) while H2 (the area below the diagonal
line) supports 50% of the prior distribution. This means that c1 = .11 and that c2 = .50,
that is, a small and larger relative complexity, respectively. Readers familiar with Akaike’s
information criterion (Akaike, 1974) and other information criteria (see, for example,
Burnham and Anderson, 2002) may be familiar with a quantification of complexity in
terms of the number of parameters in a model. As was illustrated, the quantification of
complexity in the Bayes factor has a different form.

2
Any other value on the boundary could also have been used. The interested reader is referred to Gu,
Mulder, and Hoijtink, 2018, for the technical elaboration.
BAYES FACTOR 15

Definition: Fit

The fit of an hypothesis is the proportion of the posterior distribution that is supported
by the hypothesis at hand. The fit has a value between 0 and 1 where larger values
denote a better fit.

As can be seen in the top row of Figure 1, about 15% of the posterior distribution is
supported by H1 (the area within the diagonal lines) and about 94% of the posterior
distribution is supported by H2 (the area below the diagonal line). This implies that
f1 = .15 and that f2 = .94. The fit and complexity values from Figure 1 can be used to
compute Bayes factors: BF1u = f1 /c1 = .15/.11 = 1.36, that is, the support in the data for
H1 is 1.36 times larger than the support for Hu ; and, BF2u = f2 /c2 = .94/.50 = 1.88, that
is, the support in the data for H2 is 1.88 times larger than for Hu . It is also possible to
compare H1 directly to H2 : BF12 = BF1u /BF2u = 1.36/1.88 = .72, that is, a slight
preference for H2 .

Moving from the top row in Figure 1 to the bottom row shows the effect of increasing
the sample size to N = 64 per group. As can be seen in the left hand column, the prior
distribution remains unchanged, that is, it is independent of the sample size. As can also
be seen, a larger sample contains more information about µ1 and µ2 and therefore the
posterior distribution has a smaller variance (σ̂ 2 /Ng = .016 for g = 1, 2, that is, the
posterior standard deviation is about .125 in each group), that is, it is more precise. For
the larger sample size, f1 ≈ .00 and f2 ≈ 1.0. This renders BF1u = f1 /c1 = .00/.11 = 0,
BF2u = f2 /c2 = 1.0/.50 = 2, and, consequently, BF12 = BF1u /BF2u = 0/1 = 0, that is,
after observing more data H1 is zero times as likely as H2 . In summary, increasing the
sample size from 20 to 64 per group, lead to a considerable increase in the support for H2 .
BAYES FACTOR 16

Bayesian (Error) Probabilities

In the Bayesian framework the uncertainty about hypotheses is quantified using

Bayesian probabilities. On the one hand there are the prior probabilities P (H0 ) and
P (Hu ), that is, the probabilities of H0 and Hu before observing the data. On the other
hand there are the posterior probabilities P (H0 | data) and P (Hu | data), that is, the
probabilities of H0 and Hu after observing the data. Throughout this tutorial it will be
assumed that, before observing the data, H0 and Hu are equally likely. This translates into
equal prior probabilities: P (H0 ) = P (Hu ) = .53 . As far as known to the authors, this
choice is until now almost by default used by researchers. It is a reasonable choice, because
both H0 and Hu should be a priori plausible descriptions of the population of interest.
Nevertheless, further research into the specification of prior probabilities could be worth
while. It has to be stressed, that the computation of the Bayes factor does not depend on
the choice of the prior probabilities. These only play a role when the Bayes factor is
translated into posterior probabilities, that is, into Bayesian error probabilities.

Definition: Bayesian (Error) Probabilities

The Bayesian probabilities (Berger, 2003) P (H0 | data) and P (Hu | data) (also called
posterior probabilities) quantify the support for H0 and Hu , respectively, after observing
the data. Thus, P (H0 | data) can be seen as the Bayesian error probability when Hu is
selected as the preferred hypothesis, and P (Hu | data) is the Bayesian error probability
when H0 is selected as the preferred hypothesis. The ratio of these probabilities (the
posterior odds) can be computed using the BF and the prior odds via:

P (H0 |data) P (H0 )

= BF0u × , (1)
P (Hu |data) P (Hu )

3
Later in this paper more than two hypotheses will be considered at the same time. If there are three
hypotheses, the prior probabilities will be .33 each, if there ar four hypotheses, the prior probabilities will
be .25 each, etc.
BAYES FACTOR 17

where P (H0 ) and P (Hu ) denote the prior probabilities, that is, an evaluation of the
support for the hypotheses before observing the data.

As can be seen in Equation (1), the Bayes factor is used to update the information in
the prior probabilities with the information in the data rendering the posterior probabilities
P (H0 |data) and P (Hu |data) that quantify how plausible the hypotheses are after observing
the data. These probabilities can be interpreted as Bayesian error probabilities. If, for
example, BF0u = 4, the relative support in the data for H0 and Hu can be expressed as

P (H0 |data) .5
= 4 × = 4. (2)
P (Hu |data) .5

Combining this knowledge with the fact that posterior probabilities have to add up to 1.0
renders P (H0 |data) = .8 and P (Hu |data) = .2. If, subsequently, H0 is preferred, the
Bayesian error probability is .2 because there is still 20% chance that Hu is true.
Note that Bayesian probabilities are not classical probabilities. As an example let H0
state that the effect of a drug is zero. The classical probability that H0 is true is 1 or 0
because the hypothesis is either true or not. Note that, this classical probability is not the
p-value which is, in the Fisherian interpretation a measure of evidence against the
null-hypothesis (Hurlbert and Lombardi, 2009). Bayesian probabilities on the other hand
(whether prior or posterior probabilities), quantify one’s uncertainty about H0 and Hu . In
light of new information these probabilities can be updated (see later in this paper the
section about Bayesian updating), e.g., using new data to update prior probabilities into
posterior probabilities as is done in Equation 1.
Note furthermore, that the Type I and Type II error probabilities used in NHST are
not conditional on the data. If the t-test for the evaluation of one mean is executed with
α=.05 for two different data sets of the same size, the first may render a Cohen’s d of .2
with a p-value of .03 and the second a Cohen’s d of .8 with a p-value of .00. In both cases
H0 would be rejected with a significance level of .05 and the Type I error probabilities
would be equal to .05. This feels somewhat counterintuitive because an effect of .8 is much
BAYES FACTOR 18

more unlikely under H0 than an effect of .2 while the same error probability of .05 would
be reported (Berger, Brown, and Wolpert, 1994). Bayesian error probabilities, on the other
hand, are computed conditional on the information in the data. Since, if both data sets
have the same size, it is much less likely to observe a Cohen’s d of .8 than a Cohen’s d of .2
when H0 is true, the Bayesian error associated with a preference of Hu will be smaller for a
data set with a Cohen’s d of .8 (e.g., P (H0 | data) = .1 and P (Hu | data) = .9) than for a
data set with a Cohen’s d of .2 (e.g., P (H0 | data) = .3 and P (Hu | data) = .7).We view
this as an advantage of the Bayesian approach because the uncertainty about the
hypotheses is stated conditionally on the information in the observed data.

Evaluating the Null and Alternative Hypotheses using the Bayes Factor

This tutorial is illustrated using one of the studies from the OSF reproducibility
project psychology (Open Science Collaboration, 2015; https://osf.io/ezcuj/). Monin,
Sawyer, and Marquez (2008) investigate the attraction to "moral rebels", that is, persons
that take an unpopular but morally laudable stand. There are three groups in their
experiment: in Group 1 participants rate their attraction to "a person that is obedient and
selects an African American person from a police line up of three"; in Group 2 participants
execute a self-affirmation task intended to boost their self-confidence after which they rate
"a moral rebel who does not select the African American person"; and, in Group 3
participants execute a bogus writing task after which they rate "a moral rebel". The
authors expect that the attraction to moral rebels is higher in the group executing the
self-affirmation task (that boosts the confidence of the participants in that group) than in
the group executing the bogus writing task, possibly even higher than in the group that
rates the attraction of the obedient person. Their data will henceforth be referred to as the
Monin data. Corresponding to their study are the following null and alternative hypotheses
that will be used in this and the following sections:

H0 : µ1 = µ2 = µ3
BAYES FACTOR 19

Hu : µ1 , µ2 , µ3 ,

where, µ1 , µ2 , and µ3 denote the mean attractiveness scores in Groups 1, 2, and 3,

respectively.
The interested reader should now surf to https://informative-hypotheses.sites.
uu.nl/software/bain/ download and unzip the latest version of bain, read and execute
the installation instructions. Subsequently, BFtutorial.R can be opened in RStudio. Use
the cursor to select the lines corresponding to Tutorial Step 1 in BFtutorial.R. Clicking
the Run button will load the necessary R packages. Running Tutorial Step 2 will read the
data from monin.txt and holubar.txt (the latter will be introduced later in this paper).
Note that both data sets were recreated using the descriptives presented in Monin, Sawyer,
and Marquez (2008) and Holubar (2015), respectively (the code used can be found at the
end of BFtutorial.R). Running Tutorial Step 3 will render the descriptive statistics for
the Monin data that can be found in Results 1. Note furthermore, that small modifications
have been made to the bain output to make it correspond to the notation and labeling
used in this tutorial.

Results 1: Using describeBy to Obtain Descriptives for Monin

group n mean sd
1 19 1.88 1.38
2 19 2.54 1.95
3 29 0.02 2.38

Running Tutorial Step 4 will render the output presented in Results 2 obtained using
bain to evaluate H0 and Hu using the Bayes factor. This resulting Bayes factor is listed
under BF.c. As will be elaborated later in the paper, BF.c denotes the Bayes factor of a
hypothesis against its complement. For now it suffices to know that if a hypothesis is
specified using equality constraints (which is the case here) then the complement is
BAYES FACTOR 20

equivalent to Hu . As can be seen, BF0u = .001. The implication is that there is a 1000
times more support in the Monin data for Hu than for H0 . The posterior probabilities
(listed under PMPb) show that the Bayesian error associated with a preference for Hu is
only .001.

Results 2: Using bain to Obtain the Bayes Factor for the Monin Data

Hypothesis testing result

f= f>|= c= c>|= f c BF.c PMPa PMPb
H0 0.000 1.000 0.015 1.000 0.000 0.015 0.001 1.000 0.001
Hu . . . . . . . . 0.999

Properties of the Bayes Factor

This section will highlight various properties of the Bayes factor. The focus will be on
properties that are relevant for research psychologists evaluating hypotheses using data
from their domain of interest.

How Large Should the Bayes Factor Be?

A question that is often asked by researchers using the Bayes factor is how large it
should be in order to be able to draw decisive conclusions. More precisely they want to
know: how large should BF0u be in order to prefer H0 and how small should BF0u be in
order to prefer Hu ? Behind this question is a deeply ingrained need for a threshold value
that, like an α-level of .05 in NHST, can be used to decide which hypothesis should be
chosen. However, unlike NHST, the Bayes factor does not render a dichotomous (reject or
not reject H0 ) decision, it is a quantification of the support in the data for the hypotheses
under consideration. If BF0u is about 1, there is no preference for the null or alternative
hypothesis, that is, the Bayes factor can be indecisive and additional data are needed to
obtain more evidence about which hypothesis is likely to be true. It is clear and
BAYES FACTOR 21

undisputed that a BF0u of 100 (or .01) is not about 1, there is clear support for H0 (or
Hu ), and the Bayesian error probability is so small (.01), that for all practical purposes a
decisive conclusion can be made which hypothesis is the best. If BF0u is 10 (or .1), there
still is a preference for H0 (or Hu ) but with a Bayesian error probability of .09 the other
hypothesis can not yet be discarded. But if BF0u is 2 (or .5) it is not at all clear whether it
is wise to prefer H0 over Hu (or Hu over H0 ), because the Bayesian error probability is .33.
Consequently, for a proper interpretation of a Bayes factor formal threshold values are not
needed because the relative evidence for the hypotheses based on the Bayes factor speaks
for itself.

Based on the posterior probabilities of the hypotheses of interest, the same question
can be asked: when is a posterior probability large enough to "reject" a hypothesis.
However, here the same holds as for the Bayes factor, that is, the goal of Bayesian
hypothesis testing, is not to decide which hypotheses should be rejected or accepted after
observing the data. The goal is to quantify the uncertainty about the hypotheses using the
observed data. For example, when posterior probabilities of .97 and .03 are obtained for Hu
and H0 , one would conclude that there is strong evidence that Hu is true because there is
only a small posterior probability that H0 is true. However, in order to completely rule out
H0 , which can be done when its posterior probability is about zero, more data are needed.

When this is clear, researchers immediately have a new question: how large (or small,
but this distinction will be ignored in the remainder of this section) should the Bayes factor
be for a journal to accept my paper for publication? It is very unfortunate that threshold
values that can be used to answer this question have appeared in the literature. Sir Harold
Jeffreys, who originally proposed the Bayes factor (Jeffreys, 1961), used a BF0u larger than
3.2 as "positive" evidence in favor of H0 . He also proposed to use BF0u larger than 10 as
"strong" evidence. More recent, Kass and Raftery (1995) suggested to use larger than 3 and
larger than 20, respectively. One of the implications of these labels and numbers is that 3
might very well become the counterpart of .05 when using the Bayes factor. Then, as was
BAYES FACTOR 22

elaborated in the introduction for NHST, applications of hypotheses testing using the
Bayes factor would also become subject to phenomena like publication bias and
questionable research practices. It is preferable to preregister ones research, execute it, and
report the support for the hypotheses entertained in terms of the Bayes factor and
Bayesian error probabilities obtained without reference to a threshold value.

The Bayes Factor can be Used to Quantify Support for the Null Hypothesis

NHST is focussed on the null hypothesis. The outcome can be that H0 is rejected or
that it is not rejected. The outcome cannot be that H0 is accepted (see, for example,
Wagenmakers, 2007). When H0 and Hu are evaluated using the Bayes factor, both
hypotheses have an equal standing, that is, neither has the role of the traditional null or
alternative hypotheses, they are simply two hypotheses. The probability of observing the
data is computed given each hypothesis and translated into the Bayes factor. This implies
that the Bayes factor may result in a preference of H0 over Hu (if the probability of the
data given H0 is the largest) as well as a preference of Hu over H0 (if the probability of the
data given Hu is the largest). For the Monin data BF0u = .001, that is, Hu is preferred over
H0 . However, had BF0u = 50, H0 would have received 50 times more support than Hu .

The Bayes Factor Selects the best of the Hypotheses Under Consideration

The Bayes factor selects the best of the hypotheses under consideration. For the
Monin data this implies that irrespective of whether the data favour H0 or Hu , it may be
that both hypotheses provide an inadequate description of the population from which the
data were sampled. It is very well possible that there are other hypotheses (that were not
considered) for which the support in the data is (much) larger. Consider again, the Monin
data that provide 1000 times more support for Hu than for H0 . What this tells us, is that
the three population means are very likely not equal to each other. It does not tell us if all
the means are different or that there is a pair among them that is the same. This can be
BAYES FACTOR 23

addressed by the following set of hypotheses which constitute the Bayesian counterpart of a
pairwise comparison of means analysis:

H0 : µ1 = µ2 = µ3

Hu1 : µ1 = µ2 , µ3

Hu2 : µ1 = µ3 , µ2

Hu3 : µ2 = µ3 , µ1

Hu : µ1 , µ2 , µ3 .

Executing Tutorial Step 5 renders the output presented in Results 3. In the column
labeled BF.c each hypothesis is tested against Hu . Note once more, to avoid confusion,
that BF.c denotes the Bayes factor of a hypothesis against its complement (discussed later
in this paper). For now it suffices to know that if a hypothesis is specified using only
equality constraints (which holds for H0 , Hu1 , Hu2 , and Hu3 ) then the complement is
equivalent to Hu . As can be seen, BF0u is still .001, that is, the support for Hu is still 1000
times larger than for H0 . However, it can now also be seen that the support for Hu1 is 3.22
times larger than the support for Hu . Stated otherwise, compared to Hu1 both H0 and Hu
are relatively inadequate hypotheses and if only these two are considered, the best of two
relatively inadequate hypotheses will be preferred. Once the other hypotheses are added, it
becomes clear that Ha1 is the preferred hypothesis. Note that, the Bayes factor and
posterior probabilities can be computed from the numbers listed under f and c, e.g., for
Hu1 , BF.c = .367/.114 = 3.216 and BF.c = .754/.235 = 3.216. A further elaboration of the
numbers that can be found in the bain output will follow in the section dealing with
informative hypotheses.

Results 3: The Best of the Hypotheses under Consideration

Hypothesis testing result

BAYES FACTOR 24

f= f>|= c= c>|= f c BF.c PMPa PMPb

H0 0.000 1.000 0.015 1.000 0.000 0.015 0.001 0.000 0.000
Hu1 0.367 1.000 0.114 1.000 0.367 0.114 3.216 0.985 0.754
Hu2 0.005 1.000 0.114 1.000 0.005 0.114 0.045 0.014 0.011
Hu3 0.000 1.000 0.114 1.000 0.000 0.114 0.001 0.000 0.000
Hu . . . . . . . . 0.235

What is illustrated, is that the posterior probabilities renders the degree of support in
the data for the hypotheses under consideration. They cannot be used to detect the truth
with respect to the population of interest because there may be hypotheses that are
superior to the hypotheses under consideration. What is obtained is not the truth but the
best hypothesis from the set of hypotheses under consideration which will only survive
until a better hypothesis is conceived and evaluated.

The Costs of Evaluating More than Two Hypotheses

As was highlighted in the previous section, it is straightforward to evaluate more than

two hypotheses using the Bayes factor. However, there is a price to pay. When only H0
and Hu were considered, the Bayesian error probability associated with a preference of Hu
was .001 (see, Results 2). When five hypotheses were considered, the Bayesian error
associated with a preference of Hu1 was equal to 0 + .011 + 0 + .235 = .246 (the sum of
the posterior probabilities of the other hypotheses, see Results 3), that is, the larger the
number of hypotheses under consideration, the larger the probability of preferring the
wrong hypothesis. Therefore, one should only include hypotheses that are plausible and
represent the main (competing) expectations with respect to the research question at hand.

Bayesian Updating as an Alternative for Sample Size Determination

When using the Bayes factor, it would be useful to know the sample size needed to
achieve Bayesian error probabilities of a specified size. However, as to yet, there are only a
BAYES FACTOR 25

few papers on this topic (see, for example, De Santis, 2004, and Klugkist et al., 2014) and
software for sample size determination is lacking.

An alternative for sample size determination is Bayesian updating (Rouder, 2014;

Schonbrodt, et al., 2017). Bayesian updating resembles NHST based sequential data
analysis (see, for example, Demets and Lan, 1994). The basic idea is to collect an initial
batch of data, compute the p-value to evaluate H0 , if necessary collect more data,
recompute the p-value, and to repeat the process until either the p-value is below the
α-level chosen, or the process has been repeated a pre-specified number of times. Sequential
data analysis requires careful planning because, in order to avoid an inflated overall α-level,
the α-level per test has to be adjusted for the number of times a p-value is computed.

The Bayesian approach does not focus on the α-level. The focus of Bayesian
updating is to achieve decisive evidence towards one of the hypotheses such that competing
hypotheses can be ruled out with small enough Bayesian error probabilities, that is, with
small enough probabilities of making an erroneous decision given the data that are
currently available. This implies that after the collection of additional data both Bayes
factor and posterior probabilities can without further ado be recomputed and evaluated.
Consider, for example, the evaluation of H0 , Hu1 , Hu2 , Hu3 , and Hu presented in Results 3.
As can be seen the support for Hu1 is at least three times larger than the support for each
of the other hypotheses. This is not overwhelming support, because a choice in favor of
Hu1 is still associated with a Bayesian error probability of .246. If additional data are
collected, more information becomes available, which, if consistent with the information in
the first batch of data, will increase the Bayes factor in favor of Hu1 and reduce the
Bayesian error probability. It may also happen that the additional data provide less
support for Hu1 , which will lead to a reduction in the size of the Bayes factor in favor of
Hu1 and to an increased Bayesian error probability if H1u would be selected.

As is highlighted by Rouder (2014), the stopping rule is optional, that is, additional
data can be collected as often as is deemed necessary. If only H0 and Hu would be under
BAYES FACTOR 26

investigation, this implies that one can start with only a few persons, compute BF0u , add a
few persons, recompute BF0u , and continue until the Bayes factor is large enough (support
for H0 ), small enough (support for Hu ), or stabilizes around one (no preference for either
H0 or Hu ). Such a procedure is in many cases a viable alternative for sample size
calculations before the data are collected. An illustration is presented in Results 4 that can
be obtained by running Tutorial Step 6. It concerns updating of BF0u using the Monin
data, starting with an initial sample size of two per group and using increments of one
person per group.

Results 4: Bayesian Updating

Updating BF0u using the Monin data. Initial sample size equal to 2 per group, 1
person per group increments until a final sample size of 19 per group.
0.4
0.3
BF0u
0.20.1
0.0

5 10 15
N per Group

As can be seen, based on 19 persons per group it seems that BF0u = .04 which
indicates a preference for Hu . If a smaller value of the Bayes factor is deemed necessary
more persons should be collected. Note that, the Bayes factor has a different size from the
BAYES FACTOR 27

one reported in Results 3 because here only the first 19 of the 29 persons in Group 3 have
been used.

Sequential evaluation of H0 , Hu1 , Hu2 , Hu3 , and Hu by means of posterior probabilities

is presented in Results 5 and can be obtained by running Tutorial Step 7. As can be seen,
around the 17th person matters are rather clear, that is, Hu1 is the preferred hypothesis,
but Hu can not yet be excluded. Continuation is only warranted if the Bayesian error
probabilities are not yet deemed small enough. As is also illustrated in Results 5, it is not a
good idea to base results on too few persons per group. Stopping after, for example, the
8th person would have lead to a preference for Hu2 instead of Hu1 . It is therefore
recommended to always continue until each line (whether representing a Bayes factor or a
posterior probability) is showing a stable increasing or decreasing trend (as is almost the
case in Results 5, only the line for Hu does not yet show a stable trend).

We illustrated Bayesian updating using existing data. If the data still have to be
collected, researchers should consider the guidelines presented in Rouder (2014),
Schonbrodt, et al. (2017), and Schonbrodt and Wagenmakers (in press). First of all,
determine the desired degree of evidence, that is, be explicit about the stopping rule. In
other words, once the lines in plots like Results 4 and 5 show stable trends, at which size of
the Bayes factor or the largest posterior probability will the updating process be stopped.
Secondly, decide on the size of an initial batch of persons before computing Bayes factors
and posterior probabilities for the first time. For the Bayesian t-test, Rouder (2014),
Schonbrodt, et al. (2017), and Schonbrodt and Wagenmakers (in press), advise to start
with an initial batch of 20 persons per group. Together with the requirement that the
Bayes factor and posterior probabilities should show stable trends when updating (do not
stop the updating process after adding one person to each group), this will provide some
protection against stopping the updating process too soon because a small sample may
paint an inaccurate picture of the population of interest. Generalizing the advise for the
Bayesian t-test, an initial batch of 20 persons per group can also be used when updating in
BAYES FACTOR 28

the context of a Bayesian ANOVA. However, attention for the application of Bayesian
updating is relatively recent and the subject of ongoing research. For other designs and
analyses as to yet only common sense is available to determine the size of the initial batch
of persons. The interested reader is referred to Schonbrodt and Wagenmakers (in press).
Their Bayesian design analysis will, very likely, in the future be generalized beyond the
context of the Bayesian t-test. Thirdly, decide on the maximum number of persons that can
be obtained (one may not be able to continue sampling indefinitely due to time and money
restrictions, or because the number of persons with a certain characteristic is limited).
Fourth, present the choices made in a preregistration of the research project at hand.

Results 5: Bayesian Updating of Posterior Probabilities

Analysis of the Monin data. Initial sample size equal to 2 per group, 1 person per
group increments until a final sample size of 19 per group.
1.0

H0
0.8

Hu1

Hu2
posterior probabilities

Hu3
0.6

Hu
0.4 0.2
0.0

5 10 15
N per Group
BAYES FACTOR 29

Sensitivity Analysis

As was elaborated when discussing the complexity of the null-hypothesis, to compute

the Bayes factor, the variance of the prior distribution for each of the means appearing in
the hypotheses has to be specified. In bain the prior variance is computed using a fraction
of the information in the data for each group mean (O’Hagan, 1995; De Santis and
Spezzaferri, 2001; Mulder, 2014). More specifically, as was highlighted in the definition of
the prior distribution, for an ANOVA, the variance of the prior distribution for each of the
means is
1 σ̂ 2
× , (3)
bg Ng
where σ̂ 2 denotes the estimated residual variance of an ANOVA, there are g = 1, ..., G
groups, where G denotes the number of groups, J denotes the number of constraints used
J
to specify the null hypothesis, and bg = G
× N1g is a fraction of the information with respect
to µg in the data for Group g. Note that, the total information is contained in Ng
observations, and that bg is a fraction of this information (see, Gu, Mulder, and Hoijtink,
2018, and, Hoijtink, Gu, and Mulder, 2018, for the details and further elaborations). The
idea of using a fraction of the information in the data to specify the prior variance is
well-established. The interested reader is referred to Spiegelhalter and Smith (1982),
Raftery (1995), Berger and Pericchi (1996, 2004), and Mulder et al. (2010, 2012, 2014).
The idea ensures that the prior variance is neither too small nor too large but tailored to
the uncertainty of the means in the data set at hand using a fraction of the information in
the data corresponding to a so-called minimal training sample.

The evaluation of H0 and Hu using the Monin data presented in Results 2 was based
2 1
on bg = 3
× Ng
which renders a prior variance of 6.125 for each of the groups because
σ̂ 2 = 4.085. However, consider once more, the middle figure in the top row of Figure 1. The
complexity of H1 (as an approximation of H0 ) was .11. Now imagine that the prior
distribution (the solid circle) has a larger variance (the radius of the circle becomes larger).
Then the prior distribution will be more spread out, and the proportion supported by H1
BAYES FACTOR 30

will become smaller, e.g. .01. Hence, the larger the prior variance, the smaller the relative
complexity of H1 . As a consequence BF1u = f1 /c1 will become larger. In Figure 1 with the
smaller prior variance it was .15/.11=1.36, with the larger prior variance it could have been
.15/.01=15. The same holds for H0 (of which H1 is a close approximation) but the technical
elaboration needed to show that would not be fitting for a tutorial. Stated otherwise, when
the null hypothesis is evaluated (the elaboration in this section holds for all hypotheses
specified using (about) equality constraints) Bayes factor is sensitive to the choice of bg .

A so-called sensitivity analysis can be used to determine the effect of this choice on
the outcomes. A simple sensitivity analysis is obtained running Tutorial Step 8a where the
Monin data are analyzed using fractions bg , 2 × bg , and 3 × bg for the specification of the
prior variance. As will be seen for the Monin data, BF0u = .001 irrespective of the choice of
the fraction. In other words, the results are robust with respect to reasonable choices of the
fraction of information and the corresponding prior variance. However, executing the
sensitivity analysis with the Holubar data that will be introduced later in this tutorial (run
Tutorial Step 8b), will show that although the conclusions are in the same direction (H0 is
the preferred hypothesis), the size of the Bayes factor and the Bayesian error probabilities
do to some extent depend on the fraction chosen. For fractions of bg , 2 × bg , and 3 × bg ,
BF0u will be 5.02, 2.51, and 1.67, respectively.

In our experiences so far, usually roughly the same conclusion is obtained if

sensitivity analyses are executed, but there is no guarantee that this will always be the
case. As default it is preferred to use a prior variance based on the fraction bg because that
renders the largest prior variance and therefore the largest support for H0 . In an era of
heightened awareness of publication bias, sloppy science, and irreplicability of research
results, researchers should be conservative, that is, convincing evidence is needed before
another hypothesis is preferred over H0 . However, it is up to the users of bain to decide if
they want to follow this preference or if they want to execute a sensitivity analysis.
BAYES FACTOR 31

Outliers and Model Assumptions

There has been a fair amount of literature on the effect of outliers and violation of
model assumptions on NHST in the context of ANOVA. An outlier is a person whose score
on the dependent variable is quite different from the scores of the other persons in the
group. ANOVA assumptions that received attention are: the score of each person should
be independent of the score of the other persons; within each group the scores have to be
normally distributed; and, each group should have the same residual variance. Various
approaches to detect violations of model assumptions have been proposed, the interested
reader is referred to Miller (1998) for an elaborate overview. These approaches can be used
both when NHST and Bayes factors are used for hypotheses evaluation.

When Bayes factors are used for hypotheses evaluation, the presence of outliers is
equally detrimental as when NHST is used. To illustrate this, two outliers with scores of 9
and 10 on attraction, respectively, were added to Group 3. Running Tutorial Step 9
rendered Results 6. As can be seen, due to the presence of two outliers, BF0u changed from
.001 to .921, which changed the conclusion from "quite some evidence in favor of Hu " to
"hardly any evidence in favor of Hu ". There is one study in the context of ANOVA into the
effect of violation of the assumption of homogeneous variances on hypotheses evaluation by
means of the Bayes factor (Van Rossum, van de Schoot, and Hoijtink, 2013). Although
further study is definitely needed, it appears that the Bayes factor, like NHST, is robust if
the violations are not too extreme (the ratio of the smallest to largest sample size is smaller
than 1:4, and the ratio of smallest too largest within group variance is smaller than 1:10).

Because, similar as NHST, the Bayes factor depends on the employed statistical
model, it is likely that the Bayes factor is also sensitive to model violations. Therefore,
researchers are well advised to consider the following courses of action. Define what are
considered to be outliers in a preregistration of your research. Subsequently, two courses of
action are open when it turns out that the data contain outliers. First of all, outliers can
be removed from the data before executing the desired analyses. Secondly, so-called, robust
BAYES FACTOR 32

inference (see, for example, Wilcox, 2017) can be used, that is, use statistical approaches
that are not sensitive to the presence of outliers (a simple example is using the median
instead of the mean). Recently, robust Bayes factors hypothesis evaluation in the context
of the ANOVA model has become available. The interested reader is referred to Bosman
(2018) which can be obtained from the bain website. The independence assumption is, for
example, violated if persons are organized within, so called, level two units, like children
within class rooms, patients within therapists, and employees within companies. In such
cases the ANOVA model can be replaced by a multi-level model (Hox, 2010). Define in a
preregistration what are considered to be unequal variances and if this happens to be the
case in your data use the ANOVA equivalent of an unequal variances t-test (Derrick, Toher,
and White 2016; an example of a unequal variances Bayesian t-test is contained in the bain
package). Define in a preregistration what is considered to be a violation of the normality
assumption and if this happens to be the case in your data use a robust Bayes factor.

Results 6: The Effect of Two Outliers

Hypothesis testing result

f= f>|= c= c>|= f c BF.c PMPa PMPb
H0 0.009 1.000 0.009 1.000 0.009 0.009 0.921 1.000 0.479
Hu . . . . . . . . 0.521

Evaluating Competing Informative Hypotheses using the Bayes factor

So far the focus has been on the evaluation of the null and alternative hypotheses. As
was elaborated in the introduction, the null hypothesis should not "unthinkingly" be used,
but only if it provides a plausible description of the population of interest. Furthermore,
the evaluation of H0 and Hu in this tutorial highlighted that if Hu is the preferred
BAYES FACTOR 33

hypothesis, not a lot is learned, that is, "something is going on, but it is unclear what".
There is evidence that differences between means are present, but it is unclear between
which means and in which direction. In that sense testing H0 against Hu may not be very
informative. This can be remedied by using and evaluating informative hypotheses
(Hoijtink, 2012), that is, hypotheses that represent the expectations that researchers have.
These may be of the kind "something is going on and I expect it to be like this" or "either
this or that is going on". The formulation and evaluation of informative hypotheses will be
elaborated in this section.

Definition: Informative Hypotheses

Informative hypotheses specify the expected relations between (combinations of) pa-
rameters (e.g., means) and may include effect sizes. In an ANOVA context, that is, the
comparison of two or more independent means, the main building blocks are:

Block 1: equality and order constraints between parameters. This results in constraints
of the form µ1 < µ2 , µ1 = µ2 , and µ1 > µ2 , that is, the mean of Group 1 is smaller
than, equal to, and larger than the mean of Group 2, respectively.

Block 2: equality and order constraints between combinations of parameters. This

results in contraints of, for example, the form µ1 −µ2 > µ3 −µ4 , or µ1 +µ2 > µ3 +µ4 .

Block 3: effect sizes. For example, µ1 > µ2 + .2σ̂, that is, the mean of Group 1 is at
least .2 standard deviations larger than the mean of Group 2.

Block 4: range constraints. These can, for example, replace the traditional null and
alternative hypothesis, e.g., H0 : |µ1 − µ2 | < .2σ̂ versus Hu : |µ1 − µ2 | > .2σ̂, where
H0 states that the difference between both means is smaller than .2 standard
deviations (that is, smaller than a Cohen’s, 1992, d of .2) and Hu states that the
BAYES FACTOR 34

difference is larger than .2 standard deviations.

Using these building blocks hypotheses can be constructed. Examples are:

H1 : µ1 > µ2 > µ3 , that is, a complete ordering of means

H2 : µ1 > µ2 & µ1 > µ3 , that is, an incomplete ordering of means

H3 : µ11 − µ12 > µ21 − µ22 & µ11 > µ12 & µ11 > µ21 , where the indices refer to four means
organized in a 2 × 2 factorial design, that is, a precise directional description of an
interaction effect

H4 : µ1 > µ2 + .2σ̂ & µ1 > µ3 + .2σ̂, that is, the first mean is at least .2 standard
deviations larger than the second and third means.

The interested reader is referred to Hoijtink (2012) for a more elaborate discussion and
illustrations (also outside the context of ANOVA models) of informative hypotheses. Note
that, using p-values (Silvapulle and Sen, 2004) one informative hypothesis can be
compared to either the null or the alternative hypothesis. The comparison of two
competing informative hypotheses can not be done with p-values. However, as will be
shown in the next section using the Monin data, this can be done using the Bayes factor
(with and without the inclusion of the null and unconstrained hypotheses).

Analysis of the Monin Data Using Informative Hypotheses

Given the goal of their experiment, it may very well have been that Monin, Sawyer,
and Marques (2008) had the following hypotheses in mind:

H1 : µ1 > µ2 > µ3 , that is, the attractiveness of the obedient person (Group 1) is higher
than of the moral rebel with self affirmation (Group 2), which is in turn higher than
the moral rebel with bogus writing task (Group 3).
BAYES FACTOR 35

H2 : µ1 > µ2 = µ3 , that is, the attractiveness of the obedient person (Group 1) is higher
than of the moral rebel (Groups 2 and 3), irrespective of the experimental
manipulation used to self affirm the participants in Group 2.

H3 : µ1 = µ2 > µ3 , that is, after self affirmation the attractiveness of the moral rebel
(Group 1) is equal to the attractiveness of the obedient person (Group 2) and both
are more attractive than the moral rebel after a bogus writing task (Group 3).

Hu : anything can be going on, that is, the means are unconstrained.

Running Tutorial Step 10 to evaluate these hypotheses renders the output displayed in
Results 7. As can be seen in the column labeled PMPb, H3 has the highest posterior model
probability (.769) and is therefore the best of the set of hypotheses under consideration.
However, since a preference for H3 comes with Bayesian error probabilities of .11 and .12,
for H1 and Hu , respectively, these hypotheses can not yet be ignored.

Results 7: Evaluating Informative Hypotheses using the Monin Data

Hypothesis testing result

f= f>|= c= c>|= f c BF.c PMPa PMPb
H1 1.000 0.156 1.000 0.168 0.156 0.168 0.921 0.127 0.112
H2 0.000 0.942 0.114 0.500 0.000 0.057 0.001 0.000 0.000
H3 0.367 1.000 0.114 0.500 0.367 0.057 6.433 0.873 0.769
Hu . . . . . . . . 0.120

BF-matrix
H1 H2 H3
H1 1.000 635.530 0.145
BAYES FACTOR 36

H2 0.002 1.000 0.000

H3 6.889 4378.362 1.000

Results 7 will now be used to further elaborate on the information that can be found
in the output from bain.
1. If a hypothesis is specified only using inequality constraints (that is, smaller than
and larger than), the column labeled BF.c contains the Bayes factor of the hypothesis at
hand versus its complement Hc , that is, not the inequality constrained hypothesis at hand.
The complement of H1 : µ1 > µ2 > µ3 contains any set of restrictions between the means
that is not H1 . As can be seen BF1c = .921, which implies that there is about equal
support for both hypotheses in the data.
2. If a hypothesis is specified using equality constraints, possibly in addition to
inequality constraints, BF.c = BF.u , that is, the complement hypothesis is equivalent to the
unconstrained hypothesis because the probability that a precise equality constraint hold
equals zero under the unconstrained hypothesis. As can be seen in the column labeled BF.c
(for these hypotheses the label could also have been BF.u) the support in the data for H3
is 6.4 times larger than for Hu .
3. The second table in Results 7 contains the Bayes factors between pairs of
informative hypotheses. For example, BF12 = 635.5 which implies that the support in the
data is 635.5 times larger for H1 than for H2 . It can also be seen that BF31 = 6.8 which
implies that the support in the data is 6.8 times larger for H3 than for H1 . Note that,
BFii0 = BFiu /BFi0 u . For example, BF32 = 6.433/.00148 = 4378.36 (note that in the bain
output .00148 is rounded to .001). However, since for H1 BF1c is presented instead of BF1u ,
BF31 can not directly be computed using the Bayes factors in the column labeled BF.c.
4. The posterior probabilities displayed in the column labeled PMPb are obtained
including Hu in the set of hypotheses under investigation. They show at a glance that with
a posterior probability of .769 H3 is the hypothesis receiving the most support and that a
preference for H3 comes with an error probability of .112 + 0 + .120=.232. Another name
BAYES FACTOR 37

for Hu , which is always included under PMPb, is the "fail safe hypothesis", if none of the
informative hypotheses are supported by the data, both the Bayes factors and posterior
probabilities will express a preference for Hu .
5. The posterior probabilities displayed in the column labeled PMPa are obtained
ignoring Hu . These posterior probabilities are used if the goal is to determine which of two
or more informative hypotheses is the best.
6. The columns labeled f and c contain the relative fit and relative complexity of each
hypothesis. These numbers are of interest for more technically oriented users and not for
those who use bain to evaluate hypotheses. Nevertheless, a few examples will be presented.
For example, BF3u = f3 /c3 = .367/.057 = 6.433; and,
BF1c = (f1 /c1 )/((1 − f1 )/(1 − c1 )) = (.156/.168)/(.844/.832) = .921. The numbers in the
first four columns are the fits and complexities dissected into parts belonging to the equality
and inequality constraints, respectively. These numbers have not and will not be discussed
in this tutorial. The interested reader is referred to Gu, Mulder, and Hoijtink (2018).

Considerations When Evaluating Informative Hypotheses

There are a few things to consider when evaluating informative hypotheses:

1. All that has been said about Bayes factor, posterior probabilities, and Bayesian
error probabilities in the context of the evaluation of the null and alternative hypotheses,
also applies to the evaluation of informative hypotheses.
2. It may be that none of the informative hypotheses provides an adequate
description of the population of interest. If that happens, the Bayes factor will prefer the
best of a set of inadequate hypotheses. This can be avoided in two manners. First of all, if
all informative hypotheses are inadequate (the restrictions used to construct the hypothesis
are not supported by the data), the Bayes factor will prefer Hu . Secondly, if an informative
hypothesis Hi is constructed using only inequality constraints, its complement Hc will be
preferred if the constraints used to formulate Hi are not supported by the data.
BAYES FACTOR 38

3. Keep the set of competing informative hypotheses as small as possible. If there are
three means in an experiment, than, using equality and inequality constraints, many
hypotheses can be constructed, e.g., H1 : µ1 > µ2 > µ3 , H2 : µ1 = µ2 , µ3 , etc. If all these
hypotheses are formulated and evaluated, the Bayes factor will select the hypothesis that
best describes the data and not, as it should be, the hypothesis that best describes the
population from which the data were sampled. This would be antithetical to the goals of
science. Researchers should evaluate a set of a priori formulated plausible theory based
hypotheses and should not go on a quest for the hypothesis that best described the data.
Nothing will be learned by choosing this "best" hypothesis, because the Bayesian error
probability associated with a preference for this "best" hypothesis will be huge (cf. the
section on the costs of evaluating more than two hypotheses presented earlier in this
tutorial).
4. The informative hypotheses under consideration have to be compatible (Mulder,
Hoijtink, and Klugkist, 2010; Gu, Mulder, and Hoijtink, 2018). It is important to note that
bain will give a warning if hypotheses are not compatible. A precise definition of
compatibility will not be given here, only a few common examples of compatible and
incompatible hypotheses will be presented. For example, H0 : µ1 = µ2 = µ3 ,
H1 : µ1 > µ2 > µ3 , and H2 : µ1 < µ2 , µ3 are compatible because replacement of each "," and
inequality constraint by an equality constraint renders two constraints: µ1 = µ2 and
µ2 = µ3 . Since there is a solution to these equations, e.g., µ1 = µ2 = µ3 = 0, the hypotheses
under consideration are compatible. Analogously, H1 : µ1 − µ2 > µ3 − µ4 and
H2 : µ1 + µ2 > µ3 + µ4 are compatible. If the inequality is replaced by an equality, two
equation result: µ1 − µ2 = µ3 − µ4 and µ1 + µ2 = µ3 + µ4 . Again there is a solution to
these equation, e.g., each mean is equal to 0, and therefore, both hypothesis are
compatible. However, H1 : µ1 = 0 and H2 : µ1 > .5 are not compatible. Replacing the
inequality by an equality renders two equations: µ1 = 0 and µ1 = .5, for which a solution
does not exist. Hypotheses have to be compatible, because the solution to the equations
BAYES FACTOR 39

renders the mean of the prior distribution under Hu (see the left hand figure in the top row
of Figure 1). If a solution cannot be obtained, the prior distribution cannot be specified
and bain cannot be used for the joint evaluation of the hypotheses of interest. Each
hypothesis (e.g., H1 : µ1 = 0 and H2 : µ1 > .5) can be evaluated independently, but the
resulting Bayes factors are not comparable because the unconstrained prior distribution is
different for each hypothesis.

Sensitivity Analysis for Inequality Constrained Hypotheses

When evaluating hypotheses specified using only inequality constraints, the Bayes
factor and posterior probabilities are not sensitive with respect to fraction of information in
the data for each group used to specify to prior variance (Mulder, 2014). This is illustrated
when running Tutorial Step 11. Using subsequently fractions bg , 2 × bg , and 3 × bg , the
variances of the prior distributions of the means become 6.125, 3.062, and 2.042,
respectively. However, this does not lead to different Bayes factors for H1 : µ1 > µ2 > µ3
versus its complement. Displayed in Results 8 are the testing results that are obtained for
each fraction, that is, the results are the same. The implication is that in the case of
inequality constrained hypotheses there is no discussion about which fraction to use (any
value goes) and a sensitivity analysis is never needed.

Results 8: Sensitivity Analysis: Results Obtained Using Fractions bg , 2 × bg ,

and 3 × bg , to Specify the Variance of the Prior Distribution

Hypothesis testing result

f= f>|= c= c>|= f c BF.c PMPa PMPb
H1 1.000 0.156 1.000 0.168 0.156 0.168 0.921 1.000 0.483
Hu . . . . . . . . 0.517
BAYES FACTOR 40

Using Bayes Factor for Replication Research

The lack of reproducibilty of psychological research can be addressed by the

execution of replication studies. If a replication study finds the same results as the original
study, the empirical basis for the result is fortified. As is exemplified by the Open Science
Foundation Reproducibility Project Psychology (https://osf.io/ezcuj/), replication
research is currently receiving a lot of attention. The interested reader is referred to
Anderson and Maxwell (2015) and Simonsohn (2015) for methodology for the evaluation of
replication studies. In this section, it will first of all be elaborated how the Bayes factor
can be used in the context of replication studies if the focus is on H0 and Hu (see also, Etz
and Vandekerckhove, 2016). Subsequently, the potential of informative hypotheses for the
evaluation of replication studies will be highlighted.

Using the Bayes Factor to Evaluate H0 and Hu in a Replication Study

Holubar (2015) replicated the study by Monin, Sawyer, and Marques (2008).
Running Tutorial Step 12a renders the descriptives presented in Results 9. As can be seen,
the differences between the means are smaller than the differences between the means from
the Monin data presented in Results 1.

Results 9: Using describeBy to Obtain Descriptives for Holubar

group n mean sd
1 20 0.98 1.20
2 27 0.02 1.88
3 28 0.27 1.72

Running Tutorial Step 12b renders Results 10 which shows that the Bayes factor
resulting from the analysis of the Holubar data is 5.02 in favor of H0 . The Bayes factor
BAYES FACTOR 41

resulting from the analysis of the Monin data was .001 in favor of Hu . Although this is not
a formal evaluation of the replication study, a comparison of the size of both Bayes factors
(one larger than 1, one substantially smaller than 1) suggests that the results obtained
using the Monin data were not replicated using the Holubar data. In other situations,
however, it may very well be less easy to determine from a comparison of the size of both
Bayes whether the results of an original study were successfully replicated or not. In the
next section a better founded procedure to evaluate replication studies will be proposed: i)
translate the results of the original study in an informative hypothesis; followed by ii) use
the data from the replication study to evaluate this informative hypothesis.

Results 10: Using bain to Obtain Bayes Factor for Holubar

Hypothesis testing result

f= f>|= c= c>|= f c BF.c PMPa PMPb
H0 0.111 1.000 0.022 1.000 0.111 0.022 5.023 1.000 0.834
Hu . . . . . . . . 0.166

Evaluating Replication Studies by Means of Informative Hypotheses

As was elaborated when introducing informative hypotheses, the null-hypothesis may

not be the hypothesis that represents the expectations that researchers have. In the context
of replication studies it is almost certain that the null-hypothesis does not represent the
results obtained by the authors of the original study. Monin, Sawyer, and Marquez (2008)
did not find that "nothing is going on", they found that after self affirmation the
attractiveness of the moral rebel is equal to the attractiveness of the obedient person and
both are more attractive than the moral rebel after a bogus writing task. It will now be
shown that informative hypotheses can be used to represent the results of an original
study, which can subsequently be re-evaluated using the results from a replication study.
BAYES FACTOR 42

Procedure: Evaluating Replication Studies by Means of Informative Hy-

potheses

Step 1. Translate the main results of the original study into an informative hypothesis
Horiginal . In the context of ANOVA models, three building blocks can be used

Block 1. If the original study concluded that two means are equal, use equality
constraints like, for example, µ1 = µ2

Block 2. If the original study concluded that a mean is larger or smaller than
another mean, use inequality constraints like, for example, µ1 > µ2 and
µ1 < µ2

Block 3. If the original study concluded that a mean is, say, (at least) .2 standard
deviations larger than another mean, use components like µ1 = µ2 + .2σ̂ or
µ1 > µ2 + .2σ̂.

Step 2. Choose as competing hypotheses H0 : all the means are equal and Hc : not Horiginal ,
that is, the complement of Horiginal .

Applying the procedure from the box above to the replication of Monin, Sawyer, and
Marquez (2008) by Holubar (2015) rendered the following hypotheses:

H0 : µ1 = µ2 = µ3

Horiginal : µ1 = µ2 > µ3

Hc : not Horiginal , which in this case is equal to Hu because Horiginal contains an

equality constraint.

Evaluating these hypotheses using the Holubar data and bain (execute Tutorial Step 12c)
rendered Results 11. As can be seen, the Bayes factor favors H0 over Horiginal and Hc ,
BAYES FACTOR 43

that is, the hypothesis derived from the results of the original study by Monin, Sawyer, and
Marques (2008) is not corroborated by Holubar (2015). Note that, the Bayesian error
associated with a preference of H0 is .298, which is quite large, implying that the other
hypotheses can not yet be disqualified. Collecting and processing more data by means of
Bayesian updating might render smaller Bayesian error probabilities. Note furthermore,
that the approach presented in this section is only one aspect of the proper evaluation of
replication studies. The interested reader is referred to https://osf.io/3s2zd/ for a
discussion of Holubar (2015) by the first author of Monin, Sawyer, and Marquez (2008).

Results 11: Replicating Monin, Sawyer, and Marquez (2008) using the Hol-
ubar data

Hypothesis testing result

f= f>|= c= c>|= f c BF.c PMPa PMPb
H0 0.111 1.000 0.022 1.000 0.111 0.022 5.023 0.816 0.702
Horiginal 0.120 0.655 0.138 0.500 0.079 0.069 1.134 0.184 0.158
Hu . . . . . . . . 0.140

The bain Package

All the Bayes factors presented in this tutorial have been computed with the R
package bain. In this section it will be elaborated which models can be handled by bain.
The reader is referred to the bain package in which elaborations and instructive examples
are given of how bain should be instructed if ANOVA models and other models are used.
It will be elaborated how the results obtained with bain should be reported, and future
developments will shortly be discussed.
BAYES FACTOR 44

Which Statistical Models Can be Handled

bain can be used for the evaluation of null, alternative, and informative hypotheses
by means of the Bayes factor in the context of a wide range of statistical models like, for
example, (repeated measures) ANOVA, ANCOVA, (logistic regression), multilevel
modeling, and structural equation modeling (see for an example, Gu, Mulder, Dekovic, and
Hoijtink, 2014). For applications beyond ANOVA the bain contains many examples
containing a description of the model, instructive examples of hypotheses, and annotated R
code showing how to execute the analyses. It concerns: the Bayesian independent groups
(with unequal within group variances) t-test; ANOVA; ANCOVA; multiple regression;
equivalence testing, multiple group logistic regression; multiple regression when the data
contain missing values (Hoijtink, Gu, Mulder, and Rosseel, 2018); repeated measures in a
within-between design; and hypothesis evaluation using a robust Bayes factor in the context
of ANOVA. The whole range of models for which the bain R package can be used for
Bayesian hypothesis evaluation is still being explored. In the future instructive examples
with respect to additional models and applications will be added to the bain package.

Reporting the Results of Analyses with the bain Package

The box below presents the information that should be presented in a research
report. Subsequently, an example, reporting the replication of Monin, Sawyer, and
Marques (2008) by Holubar (2015) will be given in Results 13.

Procedure: Reporting Research Results

The following information should be provided when reporting the results of Bayesian
evaluation of null, alternative, and informative hypotheses.
1. Present the variables of interest.
2. Present the statistical model used.
3. Explain which model parameters are being tested in the hypotheses.
BAYES FACTOR 45

4. Present estimates of the model parameters, their covariance matrix (per group),
and the sample size (per group). This information can be found in the bain output
before the Bayes factors and posterior probabilities are printed (see Results 12 obtained
after running Tutorial Step 12c). Comparing Results 13 with Results 12 will show where
the relevant numbers can be found in the bain output.
5. Present the hypotheses of interest.
6. Present and interpret the Bayes factors and the posterior probabilities, that is,
report on the Bayesian error probabilities. Comparing Results 13 with Results 11 will
show where the relevant numbers can be found in the bain output.

Results 12: Replicating Monin, Sawyer, and Marquez (2008) using the Hol-
ubar data

Choice of b
J 2
N 20 27 28
b 0.033 0.025 0.024

Estimates and covariance matrix of parameters

Estimates
0.98 0.02 0.27
Posterior Covariance Matrix
[,1] [,2] [,3]
[1,] 0.138 0.000 0.000
[2,] 0.000 0.102 0.000
[3,] 0.000 0.000 0.099
BAYES FACTOR 46

Results 13: Reporting the Replication of Monin, Sawyer, and Marquez

(2008) using the Holubar data

The variable of interest is attractiveness measured in three groups: 1 - obedient, 2 -

moral rebel with self-affirmation, and 3 - moral rebel with bogus writing task. An
analysis of variance model is used to estimate the mean attractiveness in each of the
three groups. The results are displayed in the table below.

Group Average Variance of Average Sample Size

obedient .98 .138 20

self-affirmation .02 .102 27
bogus writing task .27 .099 28

Three hypotheses will be evaluated:

H0 : µ1 = µ2 = µ3

Horiginal : µ1 = µ2 > µ3

Hu : µ1 , µ2 , µ3 .

The Bayes factors versus Hu and the posterior probabilities (computed assuming equal
prior probabilities) are displayed in the table below.

Hypothesis BF.a posterior probability

H0 5.02 .70
Horiginal 1.13 .16
Hu .14

As can be seen, H0 is supported more than both Horiginal and Hu . The Bayesian error
probability associated with preferring H0 equals .30.
BAYES FACTOR 47

Future Developments

The development of bain has not reached the end of the line. In the future new
applications will be added to the bain package. Two research projects are currently being
executed. As discussed earlier in this tutorial, the first concerns robust Bayes factors, that
is, robust with respect to the presence of outliers and distributional assumptions. This is
relatively straightforward to implement in the bain framework. All that needs to be done is
replace the parameter estimates and their covariance matrix by their robust counterparts.
One example concerning robust Bayes factors for hypothesis evaluation in the context of
ANOVA models can be found in the bain package (Bosman, 2018). The second project
concerns sample size calculations for Bayesian hypothesis testing. It is expected that in the
summer of 2019 an example concerning sample size calculations when executing the
Bayesian t-test will be added to the bain website. Examples concerning ANOVA,
ANCOVA, and multiple regression are also envisaged. Other topics that deserve further
attention, either by the bain team or by other researchers are: the specification of prior
probabilities beyond the current "default" that a priori each hypothesis is equally likely (for
example, if H0 states that extra sensory perception does not exists while H1 states that
extrasensory perception does exist, it may not be sensible to assign equal prior model
probabilities to both hypotheses); further development and study of Bayesian updating;
and, the specification of prior distributions other than the approach currently implemented.

Furthermore, the Bayesian t-tests, ANOVA, ANCOVA, and multiple regression

(including the option to evaluate informative hypotheses) available in bain are currently
being implemented in JASP (https://jasp-stats.org/). JASP allows users that are not
familiar with the R package (for example bachelor students in the social and behavioral
sciences) to use packages like bain and also Bayesfactor because it has an intuitive
interface which makes it very easy to use.
BAYES FACTOR 48

Conclusion

A core feature of this tutorial, is that hypotheses with respect to the same set of
parameters (in this tutorial hypotheses with respect to population means) are evaluated
using the Bayes factor. However, in principle, the Bayes factor can also be used in other
situations. Examples are: determining whether an auto-regressive model provides a better
description of longitudinal data than a growth curve model; determining the optimal
number of factors in an exploratory factor analysis; and, determining whether or not a data
point is an outlier. The presentation in this tutorial does not cover those situations and
explanations, interpretations, and applications may be markedly different.

This tutorial was illustrated using the R package bain. However, theory, definitions,
and procedures presented to a large extend also apply if other software packages are used
to compute Bayes factors for the evaluation of null, informative, and alternative
hypotheses. The package BIEMS (Mulder, Hoijtink, and de Leeuw, 2012) that can be found
at https://informative-hypotheses.sites.uu.nl/software/biems/ can be used to
evaluate null, alternative, and informative hypotheses in the context of the multivariate
normal linear model (encompassing, for example, analyses of variance models and linear
regression). The BayesFactor package, see, for example, Rouder et al. (2009), can be
found at https://richarddmorey.github.io/BayesFactor/ and can be used for the
evaluation of null and alternative hypotheses in two and more group analyses of variance,
multiple regression, and contingency tables. The interested reader is furthermore referred
to Boing-Messing et al. (2017), who present an R package that can be used for the
evaluation of hypotheses with respect to variances, Mulder (2016) for a package addressing
correlations, and Dittrich, Leenders, and Mulder (2017) for a package addressing network
autorcorrelations.

Although quite some ground was covered in this tutorial, there will without doubt be
readers with remaining questions or applications that have not been covered. Those
readers are welcome to address their queries to the bain team.
BAYES FACTOR 49

References

Akaike, H. (1974), A new look at the statistical model identification. IEEE Transactions
on Automatic Control, 19, 716âĂŞ723. doi:10.1109/TAC.1974.1100705, MR 0423716.

Anderson, S. F., and Maxwell, S. E. (2016). There’s more than one way to conduct a
replication study: Beyond statistical significance. Psychological Methods, 21, 1-12.
http://dx.doi.org/10.1037/met0000051

Benjamin, D.J., Berger, J.O., Johannesson, M., Nosek, B.A., Wagenmakers, E.-J., ..., and,
Morgan, S.L. (2017). Redefine statistical significance. Nature Human Behaviour, 2(1)
(pp. 6-10), ISSN 2397-3374, Springer Nature, doi:10.1038/s41562-017-0189-z

Berger, J.O. and Delampady, M. (1987). Testing precise hypotheses. Statistical Science,
2, 317-335. http://dx.doi.org/10.1214/ss/1177013238

magentaBerger, J.O., Brown, L.D., and Wolpert, R.L. (1994). A unified conditional
frequentist and Bayesian test for fixed and sequential hypothesis testing. The Annals
of Statistics, 22, 1787-1807. http://dx.doi.org/10.1214/aos/1176325757

Berger, J.O. and Pericchi, L.R. (1996). The intrinsic Bayes factor for model selection and
prediction. Journal of the American Statistical Association, 91, 109-122. DOI:
10.1080/01621459.1996.10476668

Berger, J.O. and Pericchi, L.R. (2004). Training samples in objective Bayesian model
selection. The Annals of Statistics, 32, 841-869. DOI:10.1214/009053604000000229

Berger, J.O. (2003). Could Fisher, Jeffreys and Neyman have agreed on Testing?
Statistical Science, 18, 1-32. http://dx.doi.org/10.1214/ss/1056397485

Burnham, K.P. and Anderson, D.R. (2002). Model Selection and Multimodal Inference: A
Practical InformationTheoretic Approach. New York: Springer.
BAYES FACTOR 50

Boing-Messing, F., van Assen, M.A.L.M., Hofman, A.D., Hoijtink, H., and Mulder, J.
(2017). Bayesian evaluation of constrained hypotheses on variances of multiple
independent groups. Psychological Methods, 22, 262-287.
http://dx.doi.org/10.1037/met0000116

Bosman, M. (2018). Robust Bayes factors for Bayesian ANOVA: Overcoming adverse
effects of non-normality and outliers. Master Thesis, Methodology and Statistics for
the Behavioural, Biomedical and Social Sciences. Utrecht University, the
Netherlands. Downloadable via
https://informative-hypotheses.sites.uu.nl/software/bain/ Example 9.

Cohen, J. (1992). A power primer. Psychological Bulletin, 112, 155-159.

http://dx.doi.org/10.1037/0033-2909.112.1.155

Cohen, J. (1994). The earth is round, p<.05. American Psychologist, 49, 997-1003.
http://dx.doi.org/10.1037/0003-066X.49.12.997

Cumming, G. (2012). Understanding the New Statistics, Effect Sizes, Confidence

Intervals, and Meta-Analysis. New York: Routledge.

Demets, D.L., Lan, K.K.G. (1994). Interim analysis: The alpha spending function
approach. Statistics in Medicine. 13, 1341-1352.
http://dx.doi.org/10.1002/sim.4780131308

Derrick, B., Toher, D., and White, P. (2016). Why Welchs test is Type I error robust.
The Quantitative Methods for Psychology, 12, 30-38.
http://dx.doi.org/10.20982/tqmp.12.1.p030

De Santis, F. (2004). Statistical evidence and sample size determination for Bayesian
hypotheses testing. Journal of Statistical Planning and Inference, 124, 121-144.
http://dx.doi.org/10.1016/S0378-3758(03)00198-8
BAYES FACTOR 51

De Santis, F. and Spezzaferri, F. (2001). Consistent fractional Bayes factor for nested
normal linear models. Journal of Statistical Planning and Inference, 97,, 305-321.
http://dx.doi.org/10.1016/S0378-3758(00)00240-8

Dittrich, D., Leenders, R. T. A. J., and Mulder, J. (2017). Network autocorrelation

modeling: A Bayes factor approach for testing (multiple) precise and interval
hypotheses. Sociological Methods and Research. DOI: 10.1177/0049124117729712

Etz, A. and Vandekerckhove, J. (2016). A Bayesian perspective on the reproducibilty

project: psychology. PLOS ONE, 11, 2.
http://dx.doi.org/10.1371/journal.pone.0149794

Fanelli, D. (2009). How many scientists fabricate and falsify research? A systematic
review and meta-analysis of survey data. PloS ONE, 4, e5738.
http://dx.doi.org/10.1371/journal.pone.0005738

Furr, R.M. and Rosenthal, R. (2003). Repeated-measures contrasts for multiple pattern
hypotheses. Psychological Methods, 8, 275-293.
http://dx.doi.org/10.1037/1082-989X.8.3.275

Gelman, A., Carlin, J.B., Stern, H.S., Dunson, D.B., Vehtari, A., and Rubin, D.B. (2013).
Bayesian Data Analysis. Boca Raton: Chapman and Hall/CRC.

Gelman, A. and Stern, H. (2006). The difference between "significant" and "not
significant" is not itself statistically significant. The American Statistician, 60,
328-331. http://dx.doi.org/10.1198/000313006X152649

Gu, X., Mulder. J., Dekovic, M., and Hoijtink, H. (2014). Bayesian evaluation of
inequality constrained hypotheses. Psychological Methods, 19, 511-527. DOI:
10.1037/met0000017
BAYES FACTOR 52

Gu, X. (2016). Bayesian Evaluation of Informative Hypotheses. Doctoral Dissertation,

University Utrecht.
https://informative-hypotheses.sites.uu.nl/books-and-theses/

Gu. X., Hoijtink, H., and Mulder, J. (2016). Error probabilities in default Bayesian
hypothesis testing. Journal of Mathematical Psychology, 72, 130-143.
http://dx.doi.org/10.1016/j.jmp.2015.09.001

Gu, X., Mulder, J., and Hoijtink, H. (2018). Approximated adjusted fractional Bayes
factors: A general method for testing informative hypotheses. British Journal of
Mathematical and Statistical Psychology. http://dx.doi.org/10.1111/bmsp.12110

Harlow, L.L., Mulaik, S.A., and Steiger, J.H. (1997/2016). What if there were no
Significance Tests. New York: Routledge.

Hoijtink, H. (2012). Informative Hypotheses. Theory and Practice for Behavioral and
Social Scientists. Boca Raton: Chapman and Hall/CRC.

Hoijtink H., Gu, X., and Mulder, J. (2018). bain, multiple group Bayesian evaluation of
informative hypotheses. British Journal of Mathematical and Statistical Psychology.
DOI: 10.1111/bmsp.12145

Hoijtink, H., Gu, X., Mulder, J., and Rosseel, Y. (2018). Computing Bayes factors from
data with missing values. Psychological Methods.

Holubar, T. (2015). Replication of "The rejection of moral rebels", study 4 by Monin,

Sawyer, and Marques (2008, JPSP). https://osf.io/ezcuj/

Hox, J.J. (2010). Multilevel Analysis. Techniques and Applications. Oxford: Routledge.

Hurlbert, S.H. and Lombardi, C.M. (2009). Final collapse of the Neyman-Pearson
decision theoretic framework and rise of the neoFisherian. Annales Zoologici Fennici,
46, 311-349. ISSN 1797-2450 (online)
BAYES FACTOR 53

John, L.K., Loewenstein, G., and Prelec, D. (2012). Measuring the prevalence of
questionable research practices with incentives for truth telling. Psychological
Science, 23, 524-532. http://dx.doi.org/10.1177/0956797611430953

Ioannides, J.P.A. (2005). Why most published research findings are false. PLoS Medicine,
2, e124. http://dx.doi.org/10.1371/journal.pmed.0020124

Jeffreys, H. (1961). Theory of Probability. Oxford: Clarendon Press.

Jones, L.V. and Tukey, J.W. (2000) A sensible formulation of the significance test.
Psychological Methods, 5, 411-414. http://dx.doi.org/10.1037/1082-989X.5.4.411

Kass, R.E. and Raftery, A.E. (1995). Bayes Factors. Journal of the American Statistical
Association, 90, 773-795. http://dx.doi.org/10.1080/01621459.1995.10476572

Klugkist, I., Laudy, O., and Hoijtink, H. (2005). Inequality constrained analysis of
variance: A Bayesian approach. Psychological Methods, 10, 477-493.
http://dx.doi.org/10.1037/1082-989X.10.4.477

Klugkist, I., Post, L., HaarHais, F., and van Wesel, F. (2014). Confirmatory methods, or
huge samples, are required to obtain power for the evaluation of theories. Open
Journal for Statistics, 4, 710-725. http://dx.doi.org/10.4236/ojs.2014.49066

Liang, F., Paulo, R., Molina, G., Clyde, M., and Berger, J. (2008). Mixtures of g priors
for Bayesian variable selection. Journal of the American Statistical Association, 103,
410-423. doi: 10.1198/016214507000001337

Masicampo, E.J. and Lalande, D.R. (2012). A peculiar prevalence of p values just below
.05. The quarterly journal of experimental psychology, 65, 2271-2279.
http://dx.doi.org/10.1080/17470218.2012.711335

Masson, M.E. (2011). A tutorial on a practical Bayesian alternative to null-hypothesis

significance testing. Behavioral Research Methods, 43, 679-690. doi:
BAYES FACTOR 54

10.3758/s13428-010-0049-5

Miller, R. (1998). Beyond ANOVA: Basics of Applied Statistics. Boca Raton: Chapman
and Hall/CRC.

Monin, B, Sawyer, P.J., and Marquez, M.J. (2008). The rejection of moral rebels:
resenting those who do the right thing. Journal of Personality and Social Psychology,
95, 76-93. http://dx.doi.org/10.1037/0022-3514.95.1.76

Morey, R. D., Hoekstra, R.,Rouder, J. N., Lee, M. D., and, Wagenmakers, E.-J. (2016).
The fallacy of placing confidence in confidence intervals. Psychonomic Bulletin &
Review. 23, 103-123. doi:10.3758/s13423-015-0947-8

Mulder, J., Hoijtink, H., and Klugkist, I. (2010). Equality and Inequality Constrained
Multivariate Linear Models: Model Selection Using Constrained Posterior Priors.
Journal of Statistical Planning and Inference, 140, 887-906.
http://dx.doi.org/10.1016/j.jspi.2009.09.022

Mulder, J. (2014). Prior adjusted default Bayes factors for testing (in)equality
constrained hypotheses. Computational Statistics and Data Analysis, 71, 448-463.
http://dx.doi.org/10.1016/j.csda.2013.07.017

Mulder, J. (2016). Bayes factors for testing order-constrained hypotheses on correlations.

Journal of Mathematical Psychology, 72, 104-115.
http://dx.doi.org/10.1016/j.jmp.2014.09.004

Mulder, J., Hoijtink, H., and de Leeuw, C. (2012). BIEMS: A Fortran 90 program for
calculating Bayes factors for inequality and equality constrained models. Journal of
Statistical Software, 46, 2. http://dx.doi.org/10.18637/jss.v046.i02

O’Hagan, A. (1995). Fractional Bayes factors for model comparison (with discussion).
Journal of the Royal Statistical Society. Series B, 57, 99-138.
BAYES FACTOR 55

http://www.jstor.org/stable/2346088

Open Science Collaboration. (2015). Estimating the reproducibility of psychological

science. Science, 349, 6251. http://dx.doi.org/10.1126/science.aac4716

Raftery, A.E. (1995). Bayesian model selection in social research. Sociological

Methodology, 25, 111-163. http://dx.doi.org/10.2307/271063

Rouder, J. N., Speckman, P. L., Sun, D., Morey, R. D., and Iverson, G. (2009). Bayesian
t-tests for accepting and rejecting the null hypothesis. Psychonomic Bulletin &
Review, 16, 225-237. http://dx.doi.org/10.3758/PBR.16.2.225

Rouder, J. N. (2014). Optional stopping: No problem for Bayesians. Psychonomic

Bulletin & Review, 21, 301-308. http://dx.doi.org/10 .3758/s13423-014-0595-4

Royal, R. (1997). Statistical Evidence. A Likelihood Paradigm. New York: Chapman and
Hall/CRC.

Schonbrodt, F.D., Wagenmakers, E-J., Zehetleitner, M., and Perugini, M. (2017).

Sequential hypothesis testing with Bayes factors: Efficiently testing mean differences.
Psychological Methods, 22, 322-339. http://dx.doi.org/10.1037/met0000061

Schonbrodt, F.D. and Wagenmakers, E.-J. (in press). Bayes factor design analysis:
Planning for compelling evidence. Psychonomic Bulletin & Review.

Sellke, T., Bayarri, M.J., and Berger, J.O. (2001). Calibration of p values for testing
precise null hypotheses. The American Statistician, 55, 62-71.
http://dx.doi.org/10.1198/000313001300339950

Silvapulle, M. and Sen, P. (2004). Constrained Statistical Inference; Order, Inequality, and
Shape Constraints. New York: NY: Wiley.

Simons, J.P., Nelson, L.D., and Simonsohn, U. (2011). False-positive psychology.

Psychological Science, 22, 1359-1366. http://dx.doi.org/10.1177/0956797611417632
BAYES FACTOR 56

Simonsohn, U. (2015). Small telescopes: Detectability and the evaluation of replication

results. Psychological Science, 26, 559-569.
http://dx.doi.org/10.1177/0956797614567341

Spiegelhalter, D.J. and Smith, A.F.M. (1982). Bayes factors for linear and log-linear
models with vague prior information. Journal of the Royal Statistical Society. Series
B, 44, 377-387. http://www.jstor.org/stable/2345495

Trafimow, D. and Marks, M. (2015). Editorial. Basic and Applied Social Psychology, 37,
1-2. http://dx.doi.org/10.1080/01973533.2015.1012991

Van Assen, M.A.L.M., Van Aert, R.C.M., Nuijten, M.B., and Wicherts, J.M. (2014). Why
publishing everything is more effective than selective publishing of statistically
significant results. PLoS One, 9, e84896.
http://dx.doi.org/10.1371/journal.pone.0084896

Van Buuren, S. (2012). Flexible Imputation of Missing Data. Boca Raton: Chapman and
Hall/CRC.

Van Rossum, M., van de Schoot, R., and Hoijtink, H. (2013). Is the hypothesis correct or
is it not. Bayesian evaluation of one informative hypothesis for ANOVA.
Methodology, 9, 13-22. https://doi.org/10.1027/1614-2241/a000050

Wagenmakers, E-J. (2007). A practical solution to the pervasive problems of p values.

Psychonomic Bulletin & Review, 15, 779-804. http://dx.doi.org/10.3758/BF03194105

Wagenmakers, E-J., Lodewyckx, T., Kuriyal, H., and Grasman, R. (2010). Bayesian
hypothesis testing for psychologists: A tutorial on the Savage-Dickey method.
Cognitive Psychology, 60, 158-189. doi:10.1016/j.cogpsych.2009.12.001

Wagenmakers E-J., Wetzels, R., Borsboom, D., van der Maas,H.L.J. and Kievit, R.A.
(2012). An agenda for purely confirmatory research. Perspectives on Psychological
BAYES FACTOR 57

Science, 7, 632-638. DOI: 10.1177/1745691612463078

Wainer, H. (1999). One cheer for null hypothesis significance testing. Psychological
Methods, 4, 212-213. http://dx.doi.org/10.1037/1082-989X.4.2.212

Wasserstein, R.L. and Lazar, N.A. (2016). The ASA’s statement on p-values: context,
process, and purpose. The American Statistician, 70, 129-133. DOI:
10.1080/00031305.2016.1154108

Wetzels, R., Grasman, R.P.P.P., and Wagenmakers, E-J. (2010). An encompassing prior
generalization of the Savage-Dickey density ratio. Computational Statistics and Data
Analysis, 54, 2094-2102. http://dx.doi.org/10.1016/j.csda.2010.03.016

Wicherts, J.M., Veldkamp, L.S., Augusteijn, H.E.M., Bakker, M., van Aert, R.C.M., and
van Assen, A.L.M. (2016). Degrees of freedom in planning, analyzing, and reporting
psychological studies; A checklist to avoid p-hacking. Frontiers in Psychology, 7,
1832. http://dx.doi.org/10.3389/fpsyg.2016.01832

Wilcox, R. R. (2017). Introduction to Robust Estimation and Hypothesis Testing, 4th

Edition. New York: Academic Press.
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Hu: µ1 , µ2 H1: µ1 ≈ µ2 H2: µ1 > µ2

µ2 µ2 µ2

N = 20 1 1 1
per group
1 2 3 µ1 1 2 3 µ1 1 2 3 µ1
-1 -1 -1

µ2 µ2 µ2

N = 64 1 1 1
per group
1 2 3 µ1 1 2 3 µ1 1 2 3 µ1
-1 -1 -1

Figure 1 . An illustration of prior and posterior distribution, complexity and fit. The areas

within the solid circle located within the diagonal band in the middle two figures and below

the diagonal in the right hand figures are the complexities of H1 and H2 , respectively. The

corresponding areas within the dashed circle are the fits for H1 (middle two figures within

the diagonal band) and H2 (right hand figures below the diagonal band), respectively.