Signed August 2018
Naseem AlAidroos, PhD,
Christopher Fiacconi, PhD
Deborah Powell, PhD,
Harvey Marmurek, PhD,
Ian NewbyClark, PhD,
Jeffrey Spence, PhD,
David Stanley, PhD,
Lana Trick, PhD
Version: 2.00
This document is an organizational aid, and workbook, for students. We encourage students to take this document to meetings with their advisor and committee. This guide should enhance a committee’s ability to assess key areas of a student’s work.
In recent years a number of wellknown and apparently wellestablished findings have failed to replicate, resulting in what is commonly referred to as the replication crisis. The APA Publication Manual 6^{th}Edition notes that “The essence of the scientific method involves observations that can be repeated and verified by others.” (p. 12). However, a systematic investigation of the replicability of psychology findings published in Science revealed that over half of psychology findings do not replicate (see a related commentary in Nature). Even more disturbing, a Bayesian reanalysis of the reproducibility project showed that 64% of studies had sample sizes so small that strong evidence for or against the null or alternative hypotheses did not exist. Indeed, Morey and Lakens (2016) concluded that most of psychology is statistically unfalsifiable due to small sample sizes and correspondingly low power (see article). Our discipline’s reputation is suffering. News of the replication crisis has reached the popular press (e.g., The Atlantic, The Economist, Slate,Last Week Tonight).
An increasing number of psychologists have responded by promoting new research standards that involve open science and the elimination of Questionable Research Practices. The open science perspective is made manifest in the Transparency and Openness Promotion (TOP) guidelines for journal publications. These guidelines were adopted some time ago by the Association for Psychological Science. More recently, the guidelines were adopted by American Psychological Association journals (see details) and journals published by Elsevier (see details). It appears likely that, in the very near future, most journals in psychology will be using an open science approach. We strongly advise readers to take a moment to inspect the TOP Guidelines Summary Table.
A key aspect of open science and the TOP guidelines is the sharing of data associated with published research (with respect to medical research, see point #35 in the World Medical Association Declaration of Helsinki). This practice is viewed widely as highly important. Indeed, open science is recommended by all G7 science ministers. All TriAgency grants must include a datamanagement plan that includes plans for sharing: “research data resulting from agency funding should normally be preserved in a publicly accessible, secure and curated repository or other platform for discovery and reuse by others.” Moreover, a 2017 editorial published in the New England Journal of Medicineannounced that the International Committee of Medical JournalEditorsbelieves there is “an ethical obligation to responsibly share data.” As of this writing, 60% of highly ranked psychology journals require or encourage data sharing.
The increasing importance of demonstrating that findings are replicable is reflected in calls to make replication a requirement for the promotion of faculty (see details in Nature) and experts in open science are now refereeing applications for tenure and promotion (see details at the Center for Open Science and this article). Most dramatically, in one instance, a paper resulting from a dissertation was retracted due to misleading findings attributable to Questionable Research Practices. Subsequent to the retraction, the Ohio State University’s Board of Trustees unanimously revoked the PhD of the graduate student who wrote the dissertation (see details). Thus, the academic environment is changing and it is important to work toward using new best practices in lieu of older practices—many of which are synonymous with Questionable Research Practices. Doing so should help you avoid later career regrets and subsequent public mea culpas. One way to achieve your research objectives in this new academic environment is to incorporate replications into your research. Replications are becoming more common and there are even websites dedicated to helping students conduct replications (e.g., Psychology Science Accelerator) and indexing the success of replications (e.g.,Curate Science). You might even consider conducting a replication for your thesis (subject to committee approval).
As earlycareer researchers, it is important to be aware of the changing academic environment. Senior principal investigators may be reluctant to engage in open science (see this student perspective in a blog post and podcast) and research on resistance to data sharing indicates that one of the barriers to sharing data is that researchers do not feel that they have knowledge of how to share data online. This document is an educational aid and resource to provide students with introductory knowledge of how to participate in open science and online data sharing to start their education on these subjects.
In light of the changes in psychology, faculty members who teach statistics/methods have reviewed the literature and generated this guide for graduate students. The guide is intended to enhance the quality of student theses by facilitating their engagement in open and transparent research practices and by helping them avoid Questionable Research Practices, many of which are now deemed unethical and covered in the ethics section of textbooks.
This document is an informational tool.
In order to follow best practices, some first steps need to be followed. Here is a list of things to do:
We note that this document largely concerns confirmatory research (i.e., testing hypotheses). We by no means intend to devalue exploratory research. Indeed, it is one of the primary ways that hypotheses are generated for (possible) confirmation. Instead, we emphasize that it is important that you clearly indicate what of your research is exploratory and what is confirmatory. Be clear in your writing and in your preregistration plan. You should explicitly indicate which of your analyses are exploratory and which are confirmatory. Please note also that if you are engaged in exploratory research, then Null Hypothesis Significance Testing (NHST) should probably be avoided (see rationale in Gigerenzer (2004) and Wagenmakers et al., (2012)).
This document is structured around the stages of thesis work: hypothesizing, design, data collection, analyses, and reporting – consistent with the headings used by Wicherts et al. (2016).We also list the Questionable Research Practices associated with each stage and provide suggestions for avoiding them. We strongly advise going through all of these sections during thesis/dissertation proposal meetings because a priori decisions need to be made prior to data collection (including analysis decisions).
To help to ensure that the student has informed the committee about key decisions at each stage, there are check boxes at the end of each section.
Consultation and Help Line
Note that the Center for Open Science now has a help line (for individual researchers and labs) you can call for help with open science issues. They also have training workshops. Please see their website for details.
A common problem in psychology is specifying hypotheses in a vague way that makes it easier to engage in questionable research practices (also known as phacking). Indeed, Lakens (2017) noted that, “statistics teaching should focus less on how to answer questions and more on how to ask questions.” Consequently, we encourage you to ask your question in a manner that does not facilitate later phacking as described below.
When hypothesizing you should clearly specify both the direction and the magnitude of an effect. Avoid vague statements like, “there will be an interaction.” Instead, specify the exact pattern of the interaction: “For men, there will be a large effect of aggression (approx. d= 0.80), such that men in the high crowding condition will be more aggressive than men in the low crowding condition. For women, the effect of crowding will be smaller and negligible.” Note that sample size planning (e.g., power analysis) requires an effect size estimate, so why not incorporate that effect size into your hypothesis?
There are three primary approaches to specifying the effect size you expect for a hypothesis:
Researchers often use the effect size from a previous study(ies) to guide sample size analysis. Although common, this approach is problematic because the effect size likely will be a substantial overestimate, given the combined effects of sampling error and publication bias. In practice, published effect sizes tend to be double of those from replications (Reproducibility Project). Therefore, one approach is to use an expected effect size that is half the published effect size. Alternatively, you can use a safeguard approach to determining expected effect size. A safeguard approach involves using the lower bound of the effect size confidence interval, which is easy to calculate if not provided. You should also consult Anderson et al. (2017) for additional solutions to this issue, and associated software. Regardless, published effect sizes should not be used “as is” in power estimates given that they are likely overestimates that will result in underpowered studies. Even metaanalytic estimates of the literature are likely biased (e.g., egodepletion research). Consequently, if you choose this approach, you are well advised to use the lower bound of a metaanalytic effect size confidence interval following the safeguard strategy.
Another approach is to use small, medium, and large effect sizes. A common practice is to refer to Cohen’s standards for small, medium, and large (correlations .10, .30, .50, respectively; dvalues 0.20, 0.50, 0.80, respectively; partialeta squared .01, .06, .14, respectively). However, these classifications are controversial (Ellis, 2010, p. 40). In terms of historical context, these effect sizes are based on an evaluation of effects of a single volume (Volume 61) of the Journal of Abnormal and Social Psychology.
The problem with this approach is that what constitutes a small, medium or large effect size varies greatly with research context. More recent evaluations of effect sizes have been done that are more comprehensive in nature – and domain specific. Note that, due to publication bias, the effect size estimates below are likely overestimates. Moreover, it may be difficult to know how an effect size was calculated – so you may want to calculate it on your own from the summary statistics provided in the article.
Industrial Organizational Psychology. A review of approximately 150,000 focal and nonfocal relations over a 30year period revealed a median correlation of .16 with an interquartile range of .07 (25^{th}percentile) to .32 (75^{th}percentile; Bosco, Aguinis, Singh, Field, & Pierce, 2015). Thus, in IO Psychology, small, medium, and large correlations correspond to .07, .16, and .32.
Social Psychology.A review of 100 years of social psychological research revealed a mean correlation of .21, median correlation of .18, and a standard deviation of correlations across literatures of .15. (Richard, Bond, StokesZoota, 2003). Thus, in Social Psychology, small, medium, and large correlations could be approximated (using the SD) as .03, .18, and .33. Likewise, small, medium, and large dvalues correspond roughly to .06, .36, and .69.
Cognitive Neuroscience.A review of approximately 10,000 cognitive neuroscience articles revealed an interquartile range of d= 0.34 (25^{th}percentile) to d= 1.22 (75^{th}percentile; Szucs & Ioannidis, 2017). Thus, in cognitive neuroscience a small effect size is d= 0.34 and a large effect size is d= 1.22.
Clinical Child and Adolescent Psychology.To our knowledge, this field has not undertaken a selfstudy and so we suggest that student researchers in this area use the effect sizes from the analysis of the I/O or Social Psychology fields, which are comparable.
This approach is favoured among some statisticians in psychology due to the fact that the researcher must make it clear the direction and size of the effect in which he/she is interested. For example, let’s say that you set the minimum effect size of interest as a dvalue of 0.80 and use this value in your sample size analysis. In doing so, you are saying that a dvalue of 0.75 (or anything below 0.80) is not of theoretical importance or interest. Moreover, you are saying that if you obtain an effect of d= 0.75 you are “ok” with it being nonsignificant due to its lack of theoretical importance. This approach gives the researcher the greatest a prioriflexibility in determining what effect sizes are of interest.
One solution to the problem of hypothesizing after results are known is the preregistration of hypotheses. This practice prevents researchers from conducting exploratory analyses and later reporting them as confirmatory. As noted above, preregistration of hypotheses before data collection is becoming increasingly important – and a requirement for journals using Level 3 of the TOP guidelines. Note that preregistration of associated data analysis plans is also important. It is discussed in the analysis section of this document.
The committee meeting in which you obtain approval of your thesis is, effectively, a process in which you preregister your thesis hypotheses with the committee. Why not go the extra step and register your hypotheses with the Open Science Foundation (https://osf.io) or at As Predicted (https://aspredicted.org)?
These four links may be of interest: OSF 101, Preregistration: A Plan, Not a Prison, Open Science Knowledge Base, and the Open Science Training Handbook.
_____ The student created directional hypotheses.
_____ The student indicated what effect size should be expected for each hypothesis.
_____ The student explicitly indicated which analyses will be exploratory.
The key issue here is making decisions that reduce unnecessary complexity in data collection, to limit flexibility during analysis, and evaluation of hypotheses (i.e., confirmatory research). Including multiple measures of the same variable (predictor or dependent variables) in confirmatory research allows for researcher flexibility during the analysis stage. If multiple measures are used as operationalizations of the same construct, be sure to clearly indicate a priori which onewill be used to evaluate the hypothesis. Switching the measure that is used to evaluate a hypothesis negates the validity of the hypothesis test. Using a measure to evaluate the question underlying a hypothesis that is not specified a priori results in substantially increased Type I error rates. This type of analysis is best considered exploratory – rather than an evaluation of the hypothesis. This same reasoning applies to the use of covariates. It can be challenging to achieve the sample size required to properly power a study. Consequently, you might want to consider programs such as Study Swap as a means of obtaining your requisite sample size. Note that given that most psychology studies typically have statistical power of less than .50, looking at the sample size of a previous study to set your sample size is generally discouraged.
You may find it helpful to read Maxwell and Kelley (2011) prior to planning your sample size:
Maxwell, S. E., & Kelley, K. (2011). Ethics and sample size planning. Handbook of ethics in quantitative methodology, 159184.
A critical aspect of design is determining the sample size that will be used. There are two general approaches:
1) Dynamically setting sample size (i.e., optional stopping)
2) Setting the sample size in advance
One approach is to set the sample size dynamically. One periodically examines their data during data collection, and data collection stops when some criterion is achieved (e.g., statistical significance). Historically, this approach has been problematic because it substantially increases Type I errors. Indeed, some authors have noted that, with this optional stopping approach, researchers can always obtain a significant pvalue (see Wagenmakers, 2007). Correspondingly, optional stopping (without correction/adjustment) has been classified as a Questionable Research Practice (see Wicherts et al., 2016).
Fortunately, statistical approaches have been devised that allow researchers to use optional stopping (dynamic sample sizes) without engaging in a Questionable Research Practice. One advantage of these approaches is that they do not rely on analyzing power a priori, which can be difficult to estimate accurately. Note, however, that power analyses should still be conducted for other reasons, such as assessing the feasibility of your study given time or financial constraints.
There are two common optionalstopping approaches:
1) Use inferential statistics that directly compare the null and alternative hypotheses, such as the Bayes factor (Rouder, 2014; Schönbrodt & Wagenmakers, 2018; although see de Heide & Grünwald, 2017). The idea here is that you stop data collection as soon as your data provide strong evidence in favour of either the null or alternative, thus avoiding bias for one conclusion over the other.
2) Optional stopping techniques that involve ‘paying a price’. The simplest version is deciding on the number of times you will peek at your data in advance (e.g., 3) and then applying a Bonferonni correction (alpha / # of peeks) each time you look, instead of alpha equal to .05. Two key articles to read are Lakens (2014) and Sagarin, Ambler, and Lee (2014) that provide less conservative approaches to this problem. Be sure to read these articles and decide determine number of times you will peek at your data before you begin data collection. You might even consider preregistering the number of times you will peek at your data with this approach.
The key to setting sample sizes in advance is to keep in mind that you do not set the sample size for the design(e.g., 2x2 ANOVA). Instead, you determine the desired sample size for each hypothesis.
There are two approaches to settings sample sizes in advance.
In reality, you should probably use both approaches (pvalue and confidence interval) to make the most informed sample size plan. Detailed information on both approaches is provided below. We recognize that, following data collection, the obtained sample sizeis often smaller than the desired sample size. Therefore, to appropriately interpret pvalues, you should calculate power after you have finished data collection based on your obtained sample size. Note this is not post hoc power. That is, this power calculation is notbased on the effect sizes you obtain in your study. Rather, the calculation is based on the effect sizes you specified prior to data collection. This power calculation will allow you and your committee to appropriately interpret your results.
You may also want to calculate the positive predictive value (see description and calculator) which indicates, given a significant pvalue, the probability that the alternative hypothesis is true (details below).
A common problem faced by graduate students is that a thesis must sometimes be submitted/presented prior to the end of data collection. This can be problematic, because it could appear that you are using an optional stopping approach even if that was not your intent. One way to avoid concerns with this course of action is to preregister your planned sample size on the Open Science Foundation website and also preregister that you may need to present a thesis based on a subset of the data prior to end of data collection. Using this approach, you can continue to collect data after you set aside a subset of it to be used for a thesis. Note, you are not stopping data collection  simply setting aside a subset of the data to be used for your thesis. Preregistration and openness make this a viable approach.
Regardless of whether you are using a confidence interval or pvalue approach, you will need to have an expected effect size (see calculation details) for each hypothesis. Your expected effect size might be a specific correlation or standardized mean difference (i.e., dvalue). A critical concern is how to pick your expected effect size – see the Hypothesis section of this document in which we outline several strategies.
Example. A past study found d= 0.70, n1=80, n2=80 (relevant to our hypothesis 1) and r= .40, N= 120 (relevant to our hypothesis 2). We use a safeguard power approach from this single study and determine expected effect size. Confidence intervals were not reported in the original article. We assume CI’s were not reported in the original article and we use the software R to determine the confidence intervals for the effects d= .70, 95% CI[0.38, 1.02] and r= .40, 95%[.26, .52]. Thus, our conservative dvalue and correlation expected population effect sizes are 0.38 and .26, respectively.
R code for confidence intervals (assuming psychand MBESSpackages are installed):
> library(MBESS)
> ci.smd(smd = 0.70, n.1 = 80, n.2 = 80)
> library(psych)
> r.con(r = .40, n = 160)
Two tables are illustrated below that should be presented to your committee.
Desired Sample Size Planning:

a priori expected 
Desired power 
Overall Sample Size 
Hypothesis 1 
d=.38 
.80 
220 (110 per group) 
Hypothesis 2 
r=.26 
.80 
113 



Desired N = 220(i.e., pick the higher N) 
R code for sample size (assuming pwrpackage is installed):
> library(pwr)
> pwr.t.test(d=.38, power=.80)
> pwr.r.test(r=.26, power=.80)
Actual Power Using Obtained Sample Size:

a priori expected 
Obtained overall sample size 
Power based on expected effect size and obtained sample size 
Hypothesis 1 
d=.38 
150 (75 per group) 
.64 
Hypothesis 2 
r=.26 
150 
.90 
etc 



R code for actual power estimate (assuming pwrpackage is installed):
> library(pwr)
> pwr.t.test(d = 0.38, n = 75)
> pwr.r.test(r = .26, n = 150)
Calculating positive predictive value based on power
If you report a pvalue that is significant, a key question is whether the significant pvalue reflects a “true positive.” That is, it would be informative to know the probability that a significant effect reflects a true effect. The number that conveys this information is called positive predictive value (PPV). To understand why most research conclusions in psychology are incorrect and how PPV works, see this video. To calculate PPV for a hypothesis, you need to know alpha (e.g., .05), actual (not desired) power (e.g., .80), and the probability the hypothesis is true. Johnson et al. (2017) found, “the probability that the proportion of experimental hypotheses tested in psychology are false likely exceeds 90%” (p.1). This finding suggests that a .10 value for the “% of true a priori hypothesis” in the link below.
Online PPV Calculator
Johnson, V. E., Payne, R. D., Wang, T., Asher, A., & Mandal, S. (2017). On the reproducibility of psychological science. Journal of the American Statistical Association, 112(517),110.
A good approach to setting sample size in advance is to set the required sample size based on the precision you desire in the confidence interval. A good rule of thumb is ensuring the uncertainty in the data is not larger than the effect you are studying. This means the width of a confidence interval (upper bound – lower bound) should not be larger than the effect size (at a bare minimum). Consider the following scenario: You work in a literature with extraordinarily strong effect sizes and your expected effect size is d = 0.38. You would want to set a sample size so that the confidence interval around a dvalue of this magnitude is not larger than 0.38. You can do this easily in R with the MBESS package. You simply type the command below (after the package is installed):
R code for sample sized based on confidence interval (assuming MBESSpackage is installed):
> library(MBESS)
> ss.aipe.smd(delta=.38, conf.level=.95, width=.38)
> ss.aipe.R2(Population.R2 = .26^2, width = .26^2, p=1)
Note 1: We use commands based on regression R^{2}to plan for correlation sample size. So, we need to use ^2 to indicate the value is squared in the ss.aipe.R2 command above. As well, be aware that p = 1 in the above ss.aipe.R2 commands indicates that the number of predictors is 1.
Note 2: The MBESS package can plan for confidence interval precision for more complex designs – see the documentation. The BUCSS package has many helpful tools for sample size planning especially if you have a withinparticipant ANOVA design. The web apps on the corresponding website Designing Experiments may also be of interest.
Note 3. GPOWERcan also be useful in many scenarios. However, be sure to read the related article in Behavior Research Methodsfor details on how to effectively use GPOWER as well as the follow up articleon correlation and regression designs.
Note 4. Jake Westfall has a number of online power calculators that are helpful: power analysis for crossed random effects, power analysis with two random factors (crossed or nested), and power analysis for general ANOVA designs. This is an excellent source for power analyses for repeated measures designs. Also consider the R package, longpower, for power analyses for repeated measures designs.
Note 5. In terms of Confirmatory Factor Analysis, examine the simsem R package and how it can be used to calculate power under different simulation conditions.
Note 6. If you are using multilevel or nested data the powerlmm R package may for your sample size planning.
We offer a general check list and then an additional checklist for students using dynamic sample size setting.
General:
_____ The student presented a clear rationale and estimate for each expected effect size.
_____ Prior to data collection, the student conducted a thorough power analysis, and has either calculated the needed sample size or committed to a particular “optional stopping” data collection approach.
_____ After data collection, the student is prepared to calculate the observed power (based on expected effect size and obtained sample size) as well as an estimated positive predictive value for each hypothesis.
_____ Correspondingly, the informational value of the study has been discussed with respect to the decision to conduct it.
_____ Estimates of the sample sizes that are needed for confidence intervals that are no larger than the expected effect size were presented for each hypothesis.
_____ The student indicated a commitment to the specific measure that will operationalize each construct with respect to hypothesis testing. (A change of dependent measure for any hypothesis following data collection makes that analysis an example of cherrypicking results and therefore exploratory rather than confirmatory; which implies pvalues should not be used.)
_____ The student agreed to include all studies conducted as part of the thesis regardless of whether they supported the hypotheses proposed.
_____ Be sure to indicate your intention to share your data in a repository when applying for Research Ethics Board clearance. Wording in the consent form is particularly important in this regard.
Additional: If using the dynamic sample size / optional stopping approach:
_____ The student discussed the advantages and disadvantages of dynamically setting sample size and the approaches for correction.
_____ The student indicated the number of times he/she will peek at the data.
_____ The student indicated the correction approach for peeking that will be used (sequential analysis, paugmented, other).
With respect to random assignment, it is not only important to commit to true random assignment when possible (i.e., by using a random number generator), but it is also important to keep in mind that the goal of random assignment (i.e., equivalence of participants between conditions on all nuisance factors) can be achieved only with much higher sample sizes than previously thought (see article and reflection). The threats to experimental integrity by not blinding participants and/or experimenters are well known (i.e., demand character and inadvertent direction of participants’ responding). Performing anyoperation on data in a nonblinded manner could inflate the Type I error rate. As Wagenmakers and others have made clear, it is paramount that there be no possibility of stopping based on observed results. Doing so willinflate the Type I error rate – unless appropriate mitigation procedures are used (e.g., paugmented, sequential analysis, or by using a Bayesian statistical approach).
_____ The student thoroughly discussed design considerations and reasoning with the committee.
_____ The student agreed to create power estimates following data collection (see previous section)
_____ The student discussed a data sharing plan with the committee.
_____ The ethics application form appropriately reflects the data sharing strategy on the Informed Consentpage (if relevant).
All of the above practices inappropriately (and arguably unethically) allow researchers to make analysis decisions based on the nature of the data obtained. You can avoid these QRPs by constructing a formal data analysis planthat concretely addresses all decisions. For example, if you plan to conduct a moderated multiple regression analysis, you should specify (prior to data collection) what alternative procedure you will use if you violate the assumptions of regression (e.g., high reliability of predictors, multivariate normality of errors, etc.). Likewise, if you plan to use a covariate in your regression, you should specify (prior to data collection), not only what the covariate is, but what alternative procedure you will use if the covariate interacts with another predictor. The principle behind doing so is that the researcher will have a clear record of their analysis intentions prior to data collection so that they can demonstrate researcher flexibility was not used during analyses. Some data analysis plans go so far as to have blank templates for the tables and graphs that will be used in the final thesis. Ideally, the data analysis plan is stored before data collection in a repository such as the Open Science Foundation. As per point 3 above, it is crucial to evaluate the assumptions under your analyses (see Osborne, 2017)
When interpreting data, a common practice is to use pvalues. If reporting pvalues, report them exactly and do not round down to meet significance. For example, do not round .054 to .05 (doing so avoids Questionable Research Practice #5). Unfortunately, pvalues are poorly understood by psychological researchers. Indeed, approximately 80% of psychology professors do not understand the correct interpretation of pvalues (Haller & Kraus, 2002; Kline, 2009, pp. 120, 125). A correct definition of a pvalue is available in Kline (2009)—be sure to consult this reference. In addition, there is a long history of criticism of the Null Hypothesis Significance Testing Process (NHSTP) that questions the value of the practice (e.g., Cohen, 1994; Cumming, 2008). Indeed, although most journals accept pvalues, some have banned them (see Woolston, 2015).
In addition, the American Statistical Association has issued a statement with a few key points about pvalues (see below). These points were designed to provide “principles to improve the conduct and interpretation of quantitative science.” Context for these points is also available.
“pvalues do not measure the probability that the studied hypothesis is true, or the probability that the data were produced by random chance alone”
“By itself, a pvalue does not provide a good measure of evidence regarding a model or hypothesis.”
“A pvalue, or statistical significance, does not measure the size of an effect or the importance of a result.”
“Scientific conclusions and business or policy decisions should not be based only on whether a pvalue passes a specific threshold.”
The consequence of these truths is that a thesis based exclusively or primarily on pvalues does not represent good science.
How should student researchers proceed in light of these truths? One promising approach is captured in the quotation below from the Executive Director of the American Statistical Association:
“In the post p<0.05 era, scientific argumentation is not based on whether a pvalue is small enough or not. Attention is paid to effect sizes and confidence intervals. Evidence is thought of as being continuous rather than some sort of dichotomy.”
Ron Wasserstein,
Executive Director,
American Statistical Association, 2016
(Read the complete interview)
The recommendation of the Executive Director of the American Statistical Associations to interpret data using effect sizes and confidence intervals is consistent with APA task force on statistical significance (see PDF links at bottom of the task force webpage). The APA task force report stated “Always present effect sizes for primary outcomes” and “Interval estimates should be given for any effect sizes involving principal outcomes” (p. 599, Wilkinson, 1999). The 2016 American Statistical Association position goes beyond this by suggesting that confidence intervals and effect sizes should be the primary means of interpretation.
Confidence intervals can be constructed using raw data units (e.g., CI around a mean or mean difference) or around a standardized effect size (e.g., r or d). A survey of researchers indicated that researchers frequently fail to understand what is conveyed by a confidence interval (Cummings, Williams & Fidler, 2004; also see this document by Howell). Consequently, it may be helpful to review how to interpret confidence intervals “by eye” (Cumming & Finch, 2005; for standard error whiskers see Cumming, Fidler, & Vaux, 2007). In most cases, if dealing with the difference between means, it’s easier to interpret a confidence interval for the difference (e.g., dvalue with CI), rather than the two means.
In short, a confidence interval can be interpreted as a plausible estimate of the range of populationlevel effects that could have caused the sample effect (see Cumming & Finch, 2005). Population values closer to the middle of the confidence interval are somewhat more likely than those at the extremes. In using confidence intervals, there is a temptation to use them merely as a proxy for significance testing (i.e., in a dichotomous way). This practice is illadvised. Nevertheless, there is a tendency to do so, as indicated in the article “Editors can lead researchers to confidence intervals but can’t make them think: Statistical reform lessons from medicine” by Fidler et al. (2004). That is, many researchers, when switching to confidence intervals, make the error of trying to use them to provide dichotomous evidence (i.e., reject/fail to reject the null hypothesis) rather than continuous evidence. Continuous evidence requires researchers to think about the full range of the confidence interval when interpreting their findings.
We suggest using confidence intervals as the primary basis for your conclusions. When making scientific or applied conclusions ask yourself: “are my conclusions consistent with the full range of effect sizes in the confidence interval?” If not, revise your conclusions.
It can be difficult to know what to focus on when reporting confidence intervals. If an effect is significant, it makes sense to discuss the (absolute magnitude) lower bound of the confidence interval to indicate how small the effect could be. Conversely, it makes sense to discuss the (absolute magnitude) upper bound of the confidence interval to indicate how large the (nonsignificant) effect could be.
In some instances, the confidence interval may be sufficiently wide that few meaningful conclusions appear possible (e.g., the plausible population effect size ranges from near zero to large). In this event, the primary conclusion may be that a larger sample size is needed in that research domain. We provide example text for reporting confidence intervals in the next section.
In addition to statistical significance, there is an increasing emphasis on the practical significance of findings (e.g., How many fewer days does a major depressive episode last given a certain treatment versus control?). Here is a great example of how to investigate practical significance in the context of testing for an interaction using regression.
_____ The student has presented the committee with a data analysis planthat addresses each of the above points.
_____ This data analysis plan for confirmatory hypothesis testing must be completed prior to data collection.
_____ The data analysis plan clearly indicates the specific analysis that will be used for each hypothesis.
_____ Where relevant, the data analysis plan clearly indicates how the assumptions will be assessed for each hypothesis test and handled if violated.
_____ The data analysis plan clearly indicates how problematic outliers (i.e., points of influence) will be dealt with.
_____ The data analysis plan clearly indicates a strategy for handling missing data in analyses (e.g., pairwise deletion, listwise deletion, etc).
_____ In the event that covariates are to be included in any analysis, the specific covariates for each hypothesis test are mentioned in the predata collection analysis plan.
_____ Confidence intervals will be reported for all tests.
_____ Consider avoiding pvalues when conducting exploratory analyses.
_____ Consistent with the TriAgency position on data management, uploading analysis scripts, descriptions of variables in the data file (i.e., data code book), and the data to an open access platform (e.g., osf.io) was considered.
Many of the above concerns can be mitigated simply by following the TriAgency recommendations for data sharing and management. Beginning in the fall of 2017, all TriAgency grants must include a datamanagement plan: “research data resulting from agency funding should normally be preserved in a publicly accessible, secure and curated repository or other platform for discovery and reuse by others.” Providing a codebook along with your data is a good idea, and see these practical tips for ethical data sharing.
As noted elsewhere, the American Statistical Association states that scientific conclusions should not be based on pvalues alone. Consequently, effect sizes (raw or standardized) with confidence intervals should be reported for each hypothesis. According to Cumming & Finch (2001) a confidence interval can be interpreted as a plausible range of population effect sizes that could have produced the effect observed in the sample. Be sure to visualize your effect size before writing about it to avoid over interpretation of results (see links for dvalues and correlations).
Exploratory analysis should be reported as exploratory. Because pvalues are only meaningful with an a priori hypothesis, they should not be reported with exploratory analyses (see details in Gigerenzer (2004) and Wagenmakers et al., (2012)). Rather, exploratory analyses should be seen as an empirical process for generating hypotheses to be tested in a subsequent study. Confidence intervals are still appropriate with exploratory analyses.
Many psychology papers have reporting errors that substantially change interpretation of results. A review of 28 years of pvalues (over 250,000 pvalues) revealed that the test statistic (e.g., t(28) = 2.60) is inconsistent with the reported
pvalue (e.g., p = .0147) more than 50% of the time (Nuijten, Hartgerink, van Assen, Epskamp, & Wicherts, 2015). Interestingly, willingness to share data appears to be associated with fewer statistical reporting errors (Wicherts, Bakker, & Molenaar, 2011). Fortunately, errors can be detected easily with an automated process. A PDF of a thesis can be checked at http://statcheck.io/. Note that some journals (e.g., Psychological Science) are now using statcheck on all nondesk rejected articles as part of the review process.
You will likely find the article "Writing Empirical Articles: Transparency, Reproducibility, Clarity, and Memorability" a helpful resource.
In addition, the American Psychological Association has issued new Journal Article Reporting Standards (JARS). We strongly recommend that you read the article and follow its prescriptions.
Example Text:
Below is example text for correlations and dvalues from the Cumming & CalinJageman (2016) textbook. We suggest using a similar style, but also adding pvalues to the text (and of course ensuring APAstyle).
Cumming, G., & CalinJageman, R. (2016). Introduction to the new statistics: Estimation, open science, and beyond. Routledge.
“The correlation between wellbeing and selfesteem was r= .35, 95% CI[.16, .53], N = 95. Relative to other correlates of wellbeing that have been reported, this is a fairly strong relationship. The CI, however, is somewhat long and consistent with anywhere from a weak positive to a very strong positive relationship.” (pp. 324325)
The correlation between wellbeing and gratitude was r= .35, 95% CI [.11, .69], N = 20. The CI is quite long. These data are only sufficient to rule out a strong negative relationship between these variables.” (p. 325)
“Motor skill for men (M = 33.8%, s = 12.8%, n = 62) was a little higher than for women (M = 29.7% s = 15.8%, n = 89). The difference in performance may seem small in terms of raw scores (M_{mean} M_{women}= 4.0%, 95% CI [.7, 8.8]), but the standardized effect size was moderate (d_{unbiased}= 0.28, 95% Ci [.05, 0.61]) relative to the existing literature. However, both CIs are quite long, and are consistent with anywhere from no advantage up to a large advantage for men. More data are required to estimate more precisely the degree to which ender might be related to motor skill.”(p. 188)
Considering and reporting power, positive predictive values, and confidence intervals for all hypothesis tests help to facilitate a method of reporting that draws attention to the statistical inference limitations of a study. In the past, it was common for authors to be in a scenario associated with low power, low positive predictive values, and wide confidence intervals, but not report these statistics and correspondingly draw overly strong conclusions. The process we have outlined in this document is designed to provide readers of your thesis with a realistic view of the inferential limitations of your study and allow them to fairly consider the informational value of the study and other hypotheses. This is consistent with the Canadian Psychological Association’s Ethics Guidelines presented below.
Acknowledge the limitations, and not suppress disconfirming evidence, of their own and their colleagues’ methods, findings, interventions, and views, and acknowledge alternative hypotheses and explanations.
Evaluate how their own experiences, attitudes, culture, beliefs, values, individual differences, specific training, external pressures, personal needs, and historical, economic, and political context might influence their activities and thinking, integrating this awareness into their attempts to be as objective and unbiased as possible in their research, service, teaching, supervision, employment, evaluation, adjudication, editorial, and peer review activities.
__ The student used http://statcheck.io/ on the thesis document and provided the committee with the resulting report.
__ The student reported confidence intervals and effect sizes.
__ Interpretation of results was based on the full range of the confidence interval – which conveys the uncertainty of the effect size estimate. Do recognize the center of the confidence interval is more likely than the extremes.
__ Applied recommendations were only made in a manner consistent with the full range of the confidence interval. In particular, keep in mind the lowerbound of the confidence interval.
__ Student has clearly identified exploratory analyses and avoided reporting pvalues for these analyses.
__ Only a priori confirmatory hypotheses were reported as confirmatory.
__ All analyses conducted were reported.
__ All studies conducted were reported.