Reproducibility of science p-values and multiplicity software

The fickle p value generates irreproducible results. Graphpad prism 7 statistics guide multiplicity adjusted. Multiplicity and reproducibility in scientific studies summer 2006 1. The reproducibility of research and the misinterpretation.

Pvalues and multiplicity published scientific findings seem to be increasingly failing efforts at replication. It does not offer to explain the assumptions behind methods, nor does it flag delicate or dubious assumptions. Similarly, a lower statistical threshold higher pvalue requires a. Is software reproducibility possible and practical. The controversy surrounding significance testing and p values is not new see. While these will be briefly discussed, the talk will focus on the alltoocommon misuse of pvalues and failure to properly account for multiplicities as two likely major contributors to the lack of reproducibility. The connections of 1 with bahadur efficiency are discussed in lambert and hall 1982 but are not relevant to our work. Reproducible results define the very core of scientific integrity in modern research. Niss is hosting a third webinar that will focus on the use of pvalues in making decisions. This blog is based on part of a talk i gave in january 2017, and the thinking behind it, in turn, is based on my view of a series of recent talks and blogs, and how they might be fit together. Berger, reproducibility of science, pvalues and multiplicity, sbss webinar, oct 4, 2012. Fighting or embracing multiplicity in neuroimaging.

If, as in colquhoun, this is done by simulation, one has to look at a narrow band of pvalues around the observed value, say pvalues that lie between 0. It is called the multiple testing multiple comparison or multiplicity issue in. Objectives concerns over multiplicities in statistical analysis and reproducibility of scientific experiments are becoming increasingly prominent in almost every scientific discipline, as experimental and computational capabilities have vastly increased in recent years. The nsf has developed a reproducibility framework to define and enhance the confidence in and reliability of science and engineering research. Reproducibility is a defining feature of science, but the extent to which it characterizes current research is unknown. Reproducibility is generated by two separate laboratories running the test and is therefore also called interlaboratory precision. The value of each adjusted p value depends on the entire family. The american statistical association asa has released a statement on statistical significance and pvalues with six principles underlying the ation of the pvalue.

The authors of the august 2015 study, estimating the reproducibility of psychological science, set out to assess the rate and predictors of reproducibility in the field of psychology. Replicability is affected by rapidly changing standards, researcher degrees of freedom, and possible bugs or errors in code, whether introduced by software developers or. To avoid this, they recommend evaluation of the evidence either study provides to a hypothesis. Inferential misinterpretations associated with use of pvalues, both significant and not. Reproducibility is the closeness of the agreement between the results of measurements of the same measurand carried out with same methodology described in the corresponding scientific evidence e. The bayesian approaches to both testing and multiplicity will be highlighted as possible general solutions to the problem. The reproducibility of scientific findings has been called into question. Flickr, lendingmemo concerns about widespread misunderstanding and misuse of pvalues in science have prompted the american statistical association asa to issue its firstever policy statement about the proper use of the statistical tool. Open licensing and science policy columbia university. Multiplicity corrections in the context of principled subgroup search will be illustrated using the family of sides subgroup identification based on differential effect search methods. Upenn postselection inference for models that are approximations 2011 9 36. On march 7, the organization released a set of six principles on the power and limitations of the pvalue.

In other words, when we emphasize the importance of reproducibility in all scientific. For the miller data, using the mojirsheibani and tibshirani 1996 bootstrap methodology, the 90% bounds are 0. Goodman, a comment on replication, pvalues and evidence. This hidden multiplicity is rarely acknowledged in scientific papers. The adjusted p value for one particular comparison would have a different value if there were a different number of comparisons or if the data in the other comparisons were. However, a major cause of this lack of repeatability is not being considered. Postselection inference for models that are approximations. Researchers announce master plan for better science. Multiplicity and reproducibility in scientific studies. This is undoubtedly due to many sources, including specifics of individual scientific cultures and overall scientific biases such as publication bias. A bayesian perspective, forthcoming in the journal of management, 2014. Statistical inference and the replication crisis springerlink. Just as prediction bounds for a new response variable provide an indication of the range of likely values, prediction bounds for p new provide a range of likely values for replicate p values. Significance thresholds and two sorts of reproducibility.

Skip to main content center for methods in implementation and prevention science cmips. This reading list was compiled from the hard labors of many other people, especially those who posted their syllabi on the osf open and reproducible methods site the selection and organization of these readings was intended as a resource for our current 2018 graduate course on reproducibility and replicability, which means we focused primarily on. We conclude that bems p values do not indicate evidence in favor of precognition. R eproducibility is one of the buzziest terms in science today. Prognostic value and reproducibility of pretreatment ct. In 2017 the asa published the statement, the asas statement on pvalues. Pdf estimating the reproducibility of psychological science. The framework suggests a disciplinespecific approach to improving research rigor and transparency. All replications follow predefined analysis plans publicly posted prior to the replications, and have a statistical. A manifesto for reproducible science nature human behaviour. Key facts about multiplicity adjusted p values a separate adjusted p values is computed for each comparison in a family of comparisons. Misleading pvalues showing up more often in biomedical journal articles, study finds mar 15, 2016 poor transparency and reporting jeopardize the reproducibility of science.

Department of statistical science duke university reproducibility of science. Since that time, many statisticians have been thinking and writing about alternatives to the traditional pvalue. A major problem is that we tend to take small pvalues at face value, but mistrust results with. Highlights for social and behavioral scientists concerns about the reproducibility and replicability of research results have been expressed in both scientific and popular media. Reproducibility may be influenced by software development and change over time, a problem that is greatly compounded by the rising dependency between software packages. The reliability and reproducibility of science are under scrutiny. The pvalue as a measure of statistical significance evidence against a. Statistics is the main inferential tool used in science and medicine. Asa statement on pvalues derived from and brought even greater attention to the overall problem. Metaresearch for evaluating reproducibility in ecology and. With multiplicity being inevitable, practices to control experimentwise type i. If, as in colquhoun, this is done by simulation, one has to look at a narrow band of p values around the observed value, say p values that lie between 0. Standard methods of distribution are used for others to access the software.

Reproducibility of texture features was evaluated using concordance correlation coefficients ccc. As these concerns came to light, congress requested that the national academies of sciences, engineering, and. Reproducibility has become a new catchword, with a subtle distinction from replication. Reproducibility is a measure of the method s sensitivity to laboratory changes. Ultimately, inferential reproducibility might be an unattainable ideal, and in some situations not even a desirable one, because differences between scientists and their interpretations of a single or multiple studies are the means through which weaknesses or gaps in the evidence base are identified and science progresses. It remains that the complexity of software and flexibility of choices in tuning parameters can. Unfortunately, reproducibility of results is actually becoming increasingly more difficult, owing to the variety of ways of approaching analysis and incapability of data structures and file types. American statistical association releases statement on.

We show that oscs article contains three major statistical errors and, when corrected, provides no evidence of a replication crisis. However, it is possible to post the data and the computer software used to analyze it online, so that others can verify the results. It is about setting up all your processes in a way that is repeatable preferably by a computer and well documented. John snows identification of links between cholera and water supply 17, paul brocas work on.

This is a guide to make scientific research more easily communicated and performed by using tools that promote reproducibility. Although concern over the reproducibility of scientific results is not itself new, largescale metaresearch projects aimed at directly evaluating the reproducibility of entire fields of research are a relatively new and growing phenomenon. Under the conventional paradigm, most software implementations do. While this multiple testing problem is well known and studied, it continues to be both a theoretical and practical problem. The terms reproducibility crisis and replication crisis gained currency in conversation and in print over the last decade e. A framework for ongoing and future national science foundation activities to improve reproducibility, replicability, and robustness in funded research. We conducted replications of 100 experimental and correlational studies. Unfortunately, there is a shortage of replication studies available for this study to analyze. Stark i agree with the spirit of the asa pvalue statement, but i disagree with some of the content, for instance. Most philosophies of science agree that it is a core component of scientific theory testing schmidt 2009. Software software provided here has been supported by the following grants. If two studies identify the same finding as statistically significant with pvalues p1. Reproducibility in functional neuroimaging studies.

One factor influencing reproducibility is the simultaneous testing of multiple hypotheses, which entails false positive findings unless the analyzed pvalues are carefully corrected. Indeed, the evidence is consistent with the opposite conclusion that the reproducibility of psychological science is quite high and, in fact, statistically indistinguishable from 100%. With multiplicity being inevitable, practices to control experiment wise type i. Today, the reproducibility of scientific finding under the responsible. Evidence of an increasing lack of reproducibility of science. Reproducibility is a best practice in data science as well as in scientific research, and in a lot of ways, comes down to having a software engineering mentality. In the era of big data and expensive science, it isnt always possible to replicate an experiment. P values linked to null hypothesis significance testing nhst is the most widely. What have we not learnt from millions of scientific papers with p. Open licensing and science policy victoria stodden. Perspective from the literature on the role of expert judgment in. A hallmark of scientific creativity is the ability to see novel and unexpected patterns in data. Statistical software does not help you know what to compute, nor how to interpret the result.