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Deciding on Null Hypotheses using P-values or Bayesian alternatives: A simulation study.

Natural and social sciences seek to understand, explain and predict natural phenomena as well as to find socially relevant solutions to problems. To achieve its objectives, the scientific enterprise uses statistical analysis in combination with a specific form of reasoning based on deduction and induction. This interplay between deductive and inductive reasoning is considered the key core of statistical discovery in science (Box, 1976). However, some scholars think that the equilibrium between induction and deduction is unbalanced in favour of deductive reasoning procedures (Orlitzky, 2012). Additionally, it seems that statistical practise is becoming an automated process in which researchers tend to blindly use statistical knowledge to make decisions about their data (Gigerenzer, 1998, 2004).

The mainstream of statistical analysis is characterised by using the null hypothesis significance testing (NHST) procedure which have been the predominant option over the last 75 years. One of the key elements in the NHST scheme is the p-value as a tool to decide about the null hypothesis. But the p-value and its use have been extensively criticized, reviewed or questioned as an optimal model for making statistical decisions (i. e., Altman & Krzywinski, 2017a, 2017b; Bakan, 1966; Cohen, 1994; Dar, Serlin, & Omer, 1994; Halsey, Currant-Everett, Vowler, & Drummond, 2015; Nuzzo, 2014; Orlitzky, 2012; Rosnow & Rosenthal, 1989; Stern, 2016; Wagenmakers, 2007; Wasserstein & Lazar, 2016; Wilkinson & Task Force on Statistical Inference, 1999). There are several notable problems associated with p-values. Among the most prominent problems of p-value we could highlight that it is used in an all-or-nothing fashion to decide about statistical hypothesis (i. e., Masson, 2011; Stern, 2016) or that it has been understood as the probability that the null hypothesis is true (i. e., Cohen, 1994; Marden, 2000). In general, it seems that these problems with the p-value are generated at the educational context. For example, in a study carried out by Haller & Krauss (2002) it was shown that university students and professors shared similar misconceptions about the meaning and logic of the p-value.

The p-value is a conditional probability. Specifically, it is the probability of having observed the sample data, or some more extreme, if the null hypothesis was true. That is to say, P(D|[H.sub.0]). In frequentist terms, the p-value represents the number of times we would observe a sample statistic, or a more extreme one, in case the null hypothesis was true in population after we repeated one experiment many times under the same conditions. As a result, the lower the p-value the more unlikely would be the observed data in case the null hypothesis was true. That is the reason why the classical NHST is considered to not to provide information about the truth of the statistical hypothesis. As stated by Krzywinski & Altman (2013), this statistical viewpoint "does not tell us whether we are right. It tells us the chances of being wrong" (p. 809). The general recommendation is to use the p-value more sensibly avoiding misinterpretations, providing effect sizes, power and confidence interval estimations (i. e., Balluerka, Vergara, & Arnau, 2009; Gallistel, 2009; Wasserstein & Lazar, 2016; Wilkinson & Task Force on Statistical Inference, 1999). The controversy is currently so strong that the Basic and Applied Social Psychology journal (Trafimow, 2014) recommended their authors to use different statistical procedures to report their results. Finally, this journal decided to forbid any reference to the classical NHST procedure (Trafimow & Marks, 2015). However, as stated by Leek & Peng (2015) or Orlitzky (2012), the p-value issue is only the "tip of the iceberg" and prohibition is probably not the best solution.

One of the proposed alternatives to classic statistics based on NHST is to use Bayesian inference (i. e., Bakan, 1966; Balluerka et al., 2009; Cohen, 1994; Marden, 2000; Nuzzo, 2014; Stern, 2016; Trafimow & Marks, 2015; Wagenmakers, 2007; Wasserstein & Lazar, 2016). Bayesian statistic combines observed data with prior information about phenomena to make inferences by using the Bayes theorem. It is considered a common-sense approach to find evidences supporting statistical inferences (Anscombe, 1961; Bolstad, 2007; Edwards, Lindman, & Savage, 1963; Puga, Krzywinski, & Altman, 2015). Contrary to the p-value approximation, Bayesian statistics focuses on the probability of statistical hypothesis given sample data, P([H.sub.i]|D). Inside the Bayesian statistics framework, Bayes Factors have received plenty of attention as alternatives to the NHST procedure (i. e., Hoijtink, van Kooten, & Hulsker, 2016a, 2016b; Jarosz & Wiley, 2014; Morey & Rouder, 2011; Morey, Wagenmakers, & Rouder, 2016; Stern, 2016; Wagenmakers, 2007). In the context of null and alternative hypothesis tests, the Bayes Factor measures the amount of evidence favouring one hypothesis against another. For example, when we compute the Bayes Factor for [H.sub.0] to [H.sub.1] (B[F.sub.01]), we are finding the odds favouring the null hypothesis against the alternative [P([H.sub.0]|D) / P([H.sub.1]|D)]. Thus, the Bayes Factor represents how much likely is the null hypothesis given the observed data compared with the alternative one. In other words, "it is the factor by which prior odds is changed to the posterior odds" for an event (Bolstad, 2007, p. 70). As a result, the Bayes Factor is a quantitative measure informing about how the observed data have modified the odds of [H.sub.0] independently of its prior probability, P([H.sub.0]), (Held & Ott, 2018). When Bayes Factor equals one, data provide the same evidence for both hypothesis. However, when the B[F.sub.01] is higher than one, the null hypothesis is more probable than the alternative one. For example, if we observed a B[F.sub.01] = 5, we could conclude that the null hypothesis is five times more likely than the alternative.

Wagenmakers (2007), based on the model selection philosophy, proposed a method to compare the likelihood of the null and the alternative hypotheses using Bayes Factors. He suggested to use the Bayesian information criterion (BIC) to compute Bayes Factors for the null or the alternative hypothesis considering the variance components in linear models (Jarosz & Wiley, 2014; Masson, 2011). Wagenmakers' proposal has several advantages and weaknesses. The most striking advantage is that computations are relatively simple by taking the outputs from classical tests (i. e., t test or ANOVAs) provided by common statistical software. However, the main drawback of his proposal is that the resulting Bayes Factor takes into account a default prior information which is still object of hot discussions (i. e., Hoijtink et al., 2016a, 2016b; Morey et al., 2016; Stern, 2016). Another simple way to compute a Bayes Factor approximation is by using the p-value calibration introduced by Sellke, Bayarri, & Berger (2001). The Sellke et al. (2001) p-value calibration (also known as "Vovk-Sellke maximum p-ratio" or VS-MPR) is a function of the p-value and it is interpreted as the lower bound of the Bayes Factor (favouring [H.sub.0] to [H.sub.1]) for a wide range of different prior distributions (Altman & Krzywinski, 2017b). This calibration is simply computed by using the equation -e x p x ln(p), where p refers to the p-value.

Our objective is to compare the decisions about the null hypothesis by using the p-value at different classically applied cut-offs with the BIC-based and p-value based Bayes factors described above (we are not interested in the epistemological discussion about the truth of the null hypothesis but the interested reader can find some reflections about it in Cohen, 1994; Gallistell, 2009, or Orlitzky, 2013). We will simulate situations in which the null hypothesis holds and compare how these statistics orient the decision making about the null hypothesis. We expect the decisions based on Bayes Factor estimations to be more accurate than those made by using the p-value. If Bayesian alternatives to classical p-values are useful and more accurate to make decisions about null hypothesis, experimental and observational researchers would benefit from them when making statistical inferences in their research. More specifically, researchers would benefit from those tools helping them not to claim false statistical discoveries.

Method

Procedure

A million data sets were simulated using the native functions implemented in the R software for statistical computing (version 3.3.3 for Windows, R Core Team, 2017). Each data set consisted on two random samples (s1 and s2) taken from normally distributed populations with parameters N([micro] = 0, [sigma] = 1) in both cases. Ten different sample sizes were simulated (5, 10, 15, 20, 40, 70, 100, 250, 500 and 1000) and one hundred thousand data sets were simulated per sample size. Simulations were generated using random seeds to simplify replication and source code is available on the Puga and Ruiz-Ruano (2017) Open Science Framework project.

Data analysis

Exact p-values were extracted from the fitted linear model comparing (bilateral contrasts) sample means (s1 and s2) on each one of the simulated datasets. Dichotomic dummy variables were also generated to record situations in which the p-value was equal or lower than the normally used cut-offs (.05,.01,.005 and.001) to make decisions about the null hypothesis. The value.005 was included to take into account the recent suggestion to reduce the threshold to claim new discoveries by Benjamin et al. (2017).

Two different Bayes Factors were computed. Firstly, the Wagenmakers (2007) BIC-based Bayes Factor was calculated from the variance components for each linear model comparing the two sample means. Secondly, the Sellke et al. (2001) p-value calibration (VS-MPR) was also computed. In this case, when p < 1/e, the value of the Bayesian calibration was coerced to 1, likewise it is done by JASP software (JASP Team, 2017). Both Bayes Factors were recorded to refer to evidences for the alternative hypothesis to the null (B[F.sub.10]) in order to simplify the comparison with p-values dummies. Although we are aware of the risks of using arbitrary cut-offs to interpret statistics in the context of statistical inference (see, for example, the discussion about that issue when considering the p-value in Rosnow & Rosenthal, 1989; or how Hoijtink et al., 2016, review this topic for Bayes Factors), we recoded both Bayes factors following the Jeffreys' (1948) labelled intervals. As a result, a B[F.sub.10] between 1 and 3 was considered anecdotal evidence for [H.sub.1] to [H.sub.0], from 3 to 10 was considered substantial, from 10 to 30 strong, from 30 to 100 very strong and higher than 100 decisive.

The R source code to perform all computations and recodifications is available on the Puga and Ruiz-Ruano (2017) Open Science Framework project.

Results

As can be seen in Table 1, the BIC-based Bayes Factor as well as the Vovk-Sellke Bayesian calibration produce the higher rates of correct inferences compared to the p-value. As expected, the error rate of the p-value is a function of the chosen cut-off point. The more restrictive the p-value, the less errors rejecting the [H.sub.0]. A similar trend is observed for Bayes factors, although a different behaviour is observed for BIC-based and p-value based Bayes Factor. Firstly, as can be seen in Table 1, whereas the Vovk-Sellke calibration produces a higher rate of anecdotal (33.02% of the times) evidence favouring [H.sub.1] against [H.sub.0] (which can be explained by the computation procedure, because when the p-value is higher than 1/e the value of this calibration is 1), the BIC-based Bayes Factor favours the alternative to the null 1.98% of the times. Secondly, the number of times (3.74%) that the VS-MPR finds substantial, strong, very strong or decisive evidences for [H.sub.1] to [H.sub.0] is always higher than those (0.27%) for the BIC-based Bayes Factor. If we consider the more restrictive decision point for both Bayes Factors, we can see that the BIC Bayes Factor only favours decisively the [H.sub.1] five times, whereas the Vovk-Sellke do the same in 467 times. Additionally, see Table 1, using the.001 cut-off for the p-value produces 977 erroneous rejections of the null hypothesis.

A closer look to the behaviour of both Bayes Factor estimations (Table 2) reveals that the BIC-based estimation tends to favour the [H.sub.0] against the [H.sub.1] when the p-value calibration finds substantial, strong, very strong or decisive evidences for [H.sub.1]. Thus, although there exists a positive relationship between both statistics (r =.62, 95% CI [.61,.62]), when the labels proposed by Jeffreys (1948) are used the concordance between them reduces (V =.33). Additionally, in Table 3 we can see that when the BIC Bayes Factor is categorised as anecdotal, the p-value still rejects the null hypothesis 12789 times at.05 cut-off, 3510 times at.01, 1736 at .005 and 301 times at.001 cut-off. However, when the Vovk-Sellke calibration considers a week or anecdotal evidence to [H.sub.1], only the p-value at level.05 would reject the null hypothesis 12699 times. On the other hand, if we consider the more restrictive p-value (.001), we see that the BIC-based Bayes Factor performs better than the Vovk-Sellke calibration. Considering a.001 cut-off, there are 977 cases in which the p-value rejects the [H.sub.0] whereas the BIC Bayes Factor favours [H.sub.0] or considers an anecdotal evidence favouring [H.sub.1] 445 times.

Table 4 shows that the more restrictive cut-off for p-value or label for Bayesian alternatives, the less evidence against the null for all sample sizes. As expected, the p-value shows a constant trend of errors as sample size g rows. T hat it is to say, independently of the sample size, the proportion of erroneously rejected null hypothesis is the same. The Bayesian p-value calibration follows the same trend but the number of errors reduces at different proportions depending on the Jeffreys' label considered. On the other hand, the error rate for the BIC Bayes Factor reduces as the sample size increases. So, the bigger the sample size the less probable the BIC Bayes Factor provides evidence favouring the alternative hypothesis. On average (Figure 1), and considering the Jeffreys' labels (1948), the Vovk-Sellke calibration always provides anecdotal evidences for [H.sub.1] to [H.sub.0] independently of sample size. On the contrary, the BIC-based Bayes Factor favours, on average, the null hypothesis for all sample sizes and its value decreases as sample size increases.

Discussion

Our results show that Bayesian alternatives are more accurate to make decisions about the null hypothesis than the traditionally used p-values thresholds when there is no difference between two sets of observations. Therefore, from a practical or applied point of view, we could consider these alternatives as useful tools for researchers to avoid false discoveries claims. In a current situation in which replication is viewed as a problem threatening science reputation (i. e., Baker, 2016; Munafo et al., 2014, 2017; Nuzzo, 2015), statistical tools with these properties will help researchers when making statistical inferences. We have also observed that, although the Vovk-Sellke p-value calibration is better than the p-value to orient researchers' decisions about the null hypothesis, the BIC-based Bayes Factor is more accurate in the situations we simulated. Our results show that the BIC Bayesian alternative works better as sample size becomes bigger. We also note that using the recently proposed (Benjamin et al., 2017).005 cut-off for p-value still produces about six times more false discoveries than using the.001 cut-off. In any case, we agree Trafimow & Erap (2017) who suggest that using any arbitrary thresholds to control Type I is a matter which deserves careful discussion.

Given that as sample size grows lower p-values are expected for small effect sizes (i. e., Marden, 2000; Morey & Rouder, 2011; Wagenmakers, 2007), future works should study whether our results hold at different effect sizes. An additional limitation of our study is we did not use Bayes Factors sensitive to prior distributions so future studies should address this issue.

There is not a commonly accepted alternative to the NHST procedure despite critics. Our data suggest that a Bayesian approach to statistical inference could be a good alternative. As Wagenmakers (2007) note, a feasible alternative to the classic NHST procedure should satisfy the following requirements: a) the approach should only depend on observed data, b) results must be independent of researchers' intentions, c) the procedure must orient statistical decisions considering both null and alternative hypothesis, e) it should be easy to calculate, and f) it must be an objective procedure. The BIC-based approach to statistical inference we tested in this paper is possibly a good starting point with a great compromise between all these requirements. Although implementing such an innovation is not easy, we agree that the change should begin at educational level (Bolstad, 2007; Orlitzky, 2012). Bayesian statistics provides researchers the information they need when deciding about statistical hypothesis (Cohen, 1994) so introducing it in educational programs will be helpful for scientific progress. Unfortunately, it is relatively uncommon to see Bayesian contents in the syllabus of degrees or postgraduate programs in psychology. For example, Ord, Ripley, Hook, & Erspamer (2016) reported that Bayesian statistics is rarely presented in the APA-accredited doctoral programs in clinical and counselling psychology.

In our opinion, the use of the p-values as critical elements for decision making should be deinstitutionalized as suggested by Orlitzky (2012). Instead of banning or rejecting them at all (Trafimow & Marks, 2015), we agree Marden (2000) not to forget p-values and "not discard the p-value all together, but just be careful" (p. 1319). We think Bayes factors should be used as complements not as a simple alternative because the statistical inference can be enriched by using both approaches simultaneously. As suggested before, the progressive introduction of Bayesian inference in the mainstream of resea rch practise is not easy and some disagreements should be fixed in the go (see, for example, Hoijtink et al., 2016). In any case, the evolution of personal computers allows nowadays the implementation of sophisticated analysis based on the subjective approach to statistical inference (Fienberg, 2006) in a similar vein the linear models are now plausible compared to the past (Cohen, Cohen, West, & Aiken, 2003) so time will tell whether Bayesian statistics becomes a key element into the researchers' toolkit.

Acknowledgements

JLP was supported by grant PSI2014-53427-P from Ministry of Economy and Competitiveness (FEDER funding) and grant 19267/PI/14 from Fundacion Seneca.

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Ana Maria Ruiz-Ruano Garcia and Jorge Lopez Puga

UCAM Universidad Catolica de Murcia

Corresponding author: Jorge Lopez Puga

Facultad de Ciencias de la Salud

UCAM Universidad Catolica de Murcia

30107 Murcia (Spain)

e-mail: jpuga@ucam.edu

Received: August 22, 2017 * Accepted: November 29, 2017

doi: 10.7334/psicothema2017.308
Table 1
Number of times that the BIC-based Bayes Factor (B[F.sub.10]), Vovk
-Sellke maximum p-ratio (VS-MP[R.sub.10]), and p-value favours
decisions towards the alternative hypothesis or the null (Favours to
[H.sub.0])

                       B[F.sub.10]  VS-MP[R.sub.10]  p-value lower
                                                     than...

Anecdotal               19766       330182
Substantial              2391        29810           .05     50083
Strong                    257         5648           .01     10052
Very Strong                38         1459           .005     5020
Decisive                    5          467           .001      977
Favours to [H.sub.0]   977543       632434                  933868
Hit rate                   99.73        96.26                   93.39

Note: The hit rate score for Bayes Factors was computed taking into
account that an anecdotal evidence for [H.sub.1] to [H.sub.0] can be
considered as an acceptable decision in this context

Table 2

Contingency table comparing the BIC-based Bayes Factor (B[F.sub.10])
and Vovk-Sellke maximum p-ratio (VS-MP[R.sub.10]) classifications

                                     VS-MP[R.sub.10]
B[F.sub.10]  Anecdotal  Substantial  Strong           Very Strong

Anecdotal      8990      8020        2148             492
Substantial       0       905         891             431
Strong            0         0          14             126
Very Strong       0         0           0               0
Decisive          0         0           0               0
< 1          321192     20885        2595             410

B[F.sub.10]  Decisive     < 1

Anecdotal    116             0
Substantial  164             0
Strong       117             0
Very Strong   38             0
Decisive       5             0
< 1           27        632434

Note: < 1 indicates the number of times favouring the null hypothesis

Table 3
Comparison between the BIC-based Bayes Factor (B[F.sub.10]), Vovk
-Sellke maximum p-ratio (VS-MP[R.sub.10]), and p-value

                              p <.05   p <.01  p <.005  p <.001  Total

Anecdotal    B[F.sub.10]      12789     3521   1736     301      18347
             VS-MP[R.sub.10]  12699        0      0       0      12699
Substantial  B[F.sub.10]       2391     1728   1259     331       5709
             VS-MP[R.sub.10]  29810     2478      0       0      32288
Strong       B[F.sub.10]        257      257    257     158        929
             VS-MP[R.sub.10]   5648     5648   3094       0      14390
Very Strong  B[F.sub.10]         38       38     38      38        152
             VS-MP[R.sub.10]   1459     1459   1459     510       4887
Decisive     B[F.sub.10]          5        5      5       5         20
             VS-MP[R.sub.10]    467      467    467     467       1868
< 1          B[F.sub.10]      34603     4503   1725     144      40975
             VS-MP[R.sub.10]      0        0      0       0          0
Total                         50083    10052   5020     977      66132

Note: < 1 indicates the number of times favouring the null hypothesis

Table 4
Number of times the BIC-based Bayes Factor (B[F.sub.10]), the Vovk
-Sellke maximum p-ratio (VS-MP[R.sub.10]), and the p-value find
evidence against the null hypothesis as a function of sample size

                                                          n
                                    5     10    15    20    40    70

                       .05          5040  5000  4897  5004  5093  5085
p-value lower than...  .01           942  1002  1010  1023   982   999
                       .005          473   510   491   520   485   508
                       .001           94   106    84   102    94   103
                       Substantial  1412   442   243   160    62    41
                       Strong        159    60    13    14     7     2
B[F.sub.10]            Very Strong    31     3     1     2     1     0
                       Decisive        3     2     0     0     0     0
                       Substantial  3083  2991  2924  3027  3048  2999
                       Strong        521   560   557   573   571   574
VS-MP[R.sub.10]        Very Strong   123   137   147   148   142   142
                       Decisive       56    62    34    52    44    55

                                    100   250   500   1000

                       .05          4993  5019  4940  5012
p-value lower than...  .01          1030  1010  1009  1045
                       .005          533   490   501   509
                       .001          107    96    94    97
                       Substantial    19     5     5     2
                       Strong          2     0     0     0
B[F.sub.10]            Very Strong     0     0     0     0
                       Decisive        0     0     0     0
                       Substantial  2941  2958  2908  2931
                       Strong        586   559   577   570
VS-MP[R.sub.10]        Very Strong   166   148   143   163
                       Decisive       38    41    40    45
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Author:Garcia, Ana Maria Ruiz-Ruano; Puga, Jorge Lopez
Publication:Psicothema
Date:Jan 1, 2018
Words:4781
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