Honoring the Lion: A Festschrift for Jan de Leeuw

This special volume celebrates the 20th anniversary of the Journal of Statistical Software (JSS) and is a Festschrift for its founding editor Jan de Leeuw. Jan recently retired from his long-held position as founding chair of the Department of Statistics at the University of California, Los Angeles. The contributions to this special volume look back at some of his research interests and accomplishments during the half-century that he has been active in psychometrics and statistics. In this introduction, the guest editors also reminisce on their own first encounters with Jan, ten years ago. Since that time JSS has solidified its place as a leading journal of computational statistics, a fact that has a lot to do with Jan's stewardship. We include a brief history of JSS

In and out of Madagascar : dispersal to peripheral islands, insular speciation and diversification of Indian Ocean daisy trees (Psiadia, Asteraceae)

This study was supported by the European Union’s HOTSPOTS Training Network (MEST-2005-020561)Madagascar is surrounded by archipelagos varying widely in origin, age and structure. Although small and geologically young, these archipelagos have accumulated disproportionate numbers of unique lineages in comparison to Madagascar, highlighting the role of waif-dispersal and rapid in situ diversification processes in generating endemic biodiversity. We reconstruct the evolutionary and biogeographical history of the genus Psiadia (Asteraceae), a plant genus with near equal numbers of species in Madagascar and surrounding islands. Analyzing patterns and processes of diversification, we explain species accumulation on peripheral islands and aim to offer new insights on the origin and potential causes for diversification in the Madagascar and Indian Ocean Islands biodiversity hotspot. Our results provide support for an African origin of the group, with strong support for non-monophyly. Colonization of the Mascarenes took place by two evolutionary distinct lineages from Madagascar, via two independent dispersal events, each unique for their spatial and temporal properties. Significant shifts in diversification rate followed regional expansion, resulting in co-occurring and phenotypically convergent species on high-elevation volcanic slopes. Like other endemic island lineages, Psiadia have been highly successful in dispersing to and radiating on isolated oceanic islands, typified by high habitat diversity and dynamic ecosystems fuelled by continued geological activity. Results stress the important biogeographical role for Rodrigues in serving as an outlying stepping stone from which regional colonization took place. We discuss how isolated volcanic islands contribute to regional diversity by generating substantial numbers of endemic species on short temporal scales. Factors pertaining to the mode and tempo of archipelago formation and its geographical isolation strongly govern evolutionary pathways available for species diversification, and the potential for successful diversification of dispersed lineages, therefore, appears highly dependent on the timing of arrival, as habitat and resource properties change dramatically over the course of oceanic island evolution.Publisher PDFPeer reviewe

Evolution of statistical analysis in empirical software engineering research: Current state and steps forward

Software engineering research is evolving and papers are increasingly based on empirical data from a multitude of sources, using statistical tests to determine if and to what degree empirical evidence supports their hypotheses. To investigate the practices and trends of statistical analysis in empirical software engineering (ESE), this paper presents a review of a large pool of papers from top-ranked software engineering journals. First, we manually reviewed 161 papers and in the second phase of our method, we conducted a more extensive semi-automatic classification of papers spanning the years 2001--2015 and 5,196 papers. Results from both review steps was used to: i) identify and analyze the predominant practices in ESE (e.g., using t-test or ANOVA), as well as relevant trends in usage of specific statistical methods (e.g., nonparametric tests and effect size measures) and, ii) develop a conceptual model for a statistical analysis workflow with suggestions on how to apply different statistical methods as well as guidelines to avoid pitfalls. Lastly, we confirm existing claims that current ESE practices lack a standard to report practical significance of results. We illustrate how practical significance can be discussed in terms of both the statistical analysis and in the practitioner's context.Comment: journal submission, 34 pages, 8 figure

Learning Large-Scale Bayesian Networks with the sparsebn Package

Learning graphical models from data is an important problem with wide applications, ranging from genomics to the social sciences. Nowadays datasets often have upwards of thousands---sometimes tens or hundreds of thousands---of variables and far fewer samples. To meet this challenge, we have developed a new R package called sparsebn for learning the structure of large, sparse graphical models with a focus on Bayesian networks. While there are many existing software packages for this task, this package focuses on the unique setting of learning large networks from high-dimensional data, possibly with interventions. As such, the methods provided place a premium on scalability and consistency in a high-dimensional setting. Furthermore, in the presence of interventions, the methods implemented here achieve the goal of learning a causal network from data. Additionally, the sparsebn package is fully compatible with existing software packages for network analysis.Comment: To appear in the Journal of Statistical Software, 39 pages, 7 figure

Technical Debt Prioritization: State of the Art. A Systematic Literature Review

Background. Software companies need to manage and refactor Technical Debt issues. Therefore, it is necessary to understand if and when refactoring Technical Debt should be prioritized with respect to developing features or fixing bugs. Objective. The goal of this study is to investigate the existing body of knowledge in software engineering to understand what Technical Debt prioritization approaches have been proposed in research and industry. Method. We conducted a Systematic Literature Review among 384 unique papers published until 2018, following a consolidated methodology applied in Software Engineering. We included 38 primary studies. Results. Different approaches have been proposed for Technical Debt prioritization, all having different goals and optimizing on different criteria. The proposed measures capture only a small part of the plethora of factors used to prioritize Technical Debt qualitatively in practice. We report an impact map of such factors. However, there is a lack of empirical and validated set of tools. Conclusion. We observed that technical Debt prioritization research is preliminary and there is no consensus on what are the important factors and how to measure them. Consequently, we cannot consider current research conclusive and in this paper, we outline different directions for necessary future investigations

Does “Evaluating Journal Quality and the Association for Information Systems Senior Scholars Journal Basket…” Support the Basket with Bibliometric Measures?

We re-examine “Evaluating Journal Quality and the Association for Information Systems Senior Scholars Journal Basket…” by Lowry et al. (2013). They sought to use bibliometric methods to validate the Basket as the eight top quality journals that are “strictly speaking, IS journals” (Lowry et al., 2013, pp. 995, 997). They examined 21 journals out of 140 journals considered as possible IS journals. We also expand the sample to 73 of the 140 journals. Our sample includes a wider range of approaches to IS, although all were suggested by IS scholars in a survey by Lowry and colleagues. We also use the same sample of 21 journals in Lowry et al. with the same methods of analysis so far as possible. With the narrow sample, we replicate Lowry et al. as closely as we can, whereas with the broader sample we employ a conceptual replication. This latter replication also employs alternative methods. For example, we consider citations (a quality measure) and centrality (a relevance measure in this context) as distinct, rather than merging them as in Lowry et al. High centrality scores from the sample of 73 journals do not necessarily indicate close connections with IS. Therefore, we determine which journals are of high quality and closely connected with the Basket and with their sample. These results support the broad purpose of Lowry et al., finding a wider set of high quality and relevant journals than just MISQ and ISR, and find a wider set of relevant, top quality journals

Effect of jumbo squid (Dosidicus gigas) skin extract on the microbial activity in chilled mackerel (Scomber scombrus)

6 páginas, 4 tablas, 2 figurasDuring the industrial processing of jumbo squid (Dosidicus gigas), large amounts of by-products containing biological active compounds are generated. In this study, aqueous solutions including acetic acid-ethanol extracts of jumbo squid skin (JSS) were tested at three different concentrations as icing media. The effects of the JSS extracts on the quality evolution of chilled mackerel (Scomber scombrus) were monitored. A significant inhibition (p < 0.05) of microbial activity was determined in the fish batch corresponding to the icing condition including the highest JSS concentration. Additionally, fish specimens corresponding to batches including any of the JSS concentrations tested showed lower (p < 0.05) proteolytic counts and pH values than control mackerel. Sensory analysis revealed a marked shelf life extension in chilled mackerel stored in ice including the highest JSS concentration; specimens from such batch were found to be still acceptable after 13 days of storage, while all other mackerel batches were rejectable. The marked microbial activity inhibition observed could be explained on the basis of the presence in ice of lipophilic compounds obtained by acetic acid-ethanol extraction of JSSThis work was supported by the CONACYT-Mexico grant 154046 and the Consejo Superior de Investigaciones Científicas (CSIC) through Research Project PIE 201370E001Peer reviewe