Multidimensional scaling
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The Decoding Toolbox (TDT): a versatile software package for multivariate analyses of functional imaging data Open
The multivariate analysis of brain signals has recently sparked a great amount of interest, yet accessible and versatile tools to carry out decoding analyses are scarce. Here we introduce The Decoding Toolbox (TDT) which represents a user-…
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Visualizing Psychological Networks: A Tutorial in R Open
Networks have emerged as a popular method for studying mental disorders. Psychopathology networks consist of aspects (e.g., symptoms) of mental disorders (nodes) and the connections between those aspects (edges). Unfortunately, the visual …
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The trouble with stress: A flexible method for the evaluation of nonmetric multidimensional scaling Open
Nonmetric multidimensional scaling (NMDS) is a powerful statistical tool which enables complex multivariate data sets to be visualized in a reduced number of dimensions. Users typically evaluate the fit of an NMDS ordination via ordination…
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Carving out OPE space and precise O(2) model critical exponents Open
We develop new tools for isolating CFTs using the numerical bootstrap. A “cutting surface” algorithm for scanning OPE coefficients makes it possible to find islands in high-dimensional spaces. Together with recent progress in large-scale s…
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Scaling diffraction data in the <i>DIALS</i> software package: algorithms and new approaches for multi-crystal scaling Open
In processing X-ray diffraction data, the intensities obtained from integration of the diffraction images must be corrected for experimental effects in order to place all intensities on a common scale both within and between data collectio…
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Value tradeoffs propel and inhibit behavior: Validating the 19 refined values in four countries Open
We assess the predictive and discriminant validity of the basic values in the refined Schwartz value theory by examining how value tradeoffs predict behavior in Italy, Poland, Russia, and the USA. One thousand eight hundred and fifty‐seven…
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Scaling Up Open
Survey measures of gender have been critiqued for failing to reflect the diversity of the population. Conventionally, respondents to national surveys are categorized as female or male. Calls for improvement have centered on adding addition…
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Unsupervised topological alignment for single-cell multi-omics integration Open
Motivation Single-cell multi-omics data provide a comprehensive molecular view of cells. However, single-cell multi-omics datasets consist of unpaired cells measured with distinct unmatched features across modalities, making data integrati…
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Psychological responses to natural patterns in architecture Open
In the following experiments, we examined whether perceptions of naturalness in architecture are linked to objective visual patterns, and we investigated how natural patterns influence aesthetic evaluations of architectural scenes. Experim…
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What Is Meditation? Proposing an Empirically Derived Classification System Open
Meditation is an umbrella term, which subsumes a huge number of diverse practices. It is still unclear how these practices can be classified in a reasonable way. Earlier proposals have struggled to do justice to the diversity of meditation…
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Goodness-of-Fit Assessment in Multidimensional Scaling and Unfolding. Open
Judging goodness of fit in multidimensional scaling requires a comprehensive set of diagnostic tools instead of relying on stress rules of thumb. This article elaborates on corresponding strategies and gives practical guidelines for resear…
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Scaling Properties of Dimensionality Reduction for Neural Populations and Network Models Open
Recent studies have applied dimensionality reduction methods to understand how the multi-dimensional structure of neural population activity gives rise to brain function. It is unclear, however, how the results obtained from dimensionality…
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Using Joint Scaling Methods to Study Ideology and Representation: Evidence from Latin America Open
In this article, I use joint scaling methods and similar items from three large-scale surveys to place voters, parties, and politicians from different Latin American countries on a common ideological space. The findings reveal that ideolog…
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Assessing similarity of <i>n‐</i>dimensional hypervolumes: Which metric to use? Open
Aim The n ‐dimensional hypervolume framework ( Glob. Ecol. Biogeogr. [2014] 23 :595–609) implemented through the R package 'hypervolume' is being increasingly used in ecology and biogeography. This approach offers a reliable means for comp…
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Nostalgia’s place among self-relevant emotions Open
How is nostalgia positioned among self-relevant emotions? We tested, in six studies, which self-relevant emotions are perceived as most similar versus least similar to nostalgia, and what underlies these similarities/differences. We used m…
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An Assessment of the Exporting Literature: Using Theory and Data to Identify Future Research Directions Open
Exporting research is an established facet of the field of international marketing. That stated, the radical increase in recent export activity necessitates a sustained research effort devoted to the topic. In this article, the authors pro…
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Recovering a Basic Space from Issue Scales in<i>R</i> Open
basicspace is an R package that conducts Aldrich-McKelvey and Blackbox scaling to recover estimates of the underlying latent dimensions of issue scale data. We illustrate several applications of the package to survey data commonly used in …
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PDBFlex: exploring flexibility in protein structures Open
The PDBFlex database, available freely and with no login requirements at http://pdbflex.org, provides information on flexibility of protein structures as revealed by the analysis of variations between depositions of different structural mo…
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Cleavage Identities in Voters’ Own Words: Harnessing Open‐Ended Survey Responses Open
Fundamental transformations of underlying cleavage structures in advanced democracies should become evident in new collective identities. This article uses quantitative text analysis to investigate how voters describe their ingroups and ou…
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Cluster Correspondence Analysis Open
A method is proposed that combines dimension reduction and cluster analysis for categorical data by simultaneously assigning individuals to clusters and optimal scaling values to categories in such a way that a single between variance maxi…
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Reliable Multi-Fractal Characterization of Weighted Complex Networks: Algorithms and Implications Open
Through an elegant geometrical interpretation, the multi-fractal analysis quantifies the spatial and temporal irregularities of the structural and dynamical formation of complex networks. Despite its effectiveness in unweighted networks, t…
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More on Multidimensional Scaling and Unfolding in <i>R</i>: <b>smacof</b> Version 2 Open
The smacof package offers a comprehensive implementation of multidimensional scaling (MDS) techniques in R. Since its first publication (De Leeuw and Mair 2009b) the functionality of the package has been enhanced, and several additional me…
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Analysis of haplotype networks: The randomized minimum spanning tree method Open
Haplotype network construction is a widely used approach for analysing and visualizing the relationships among DNA sequences within a population or species. This approach has some problems such as how to quantify alternative links among se…
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Robust Analysis of Phylogenetic Tree Space Open
Phylogenetic analyses often produce large numbers of trees. Mapping trees’ distribution in “tree space” can illuminate the behavior and performance of search strategies, reveal distinct clusters of optimal trees, and expose differences bet…
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Expanding the Map of Intrinsic and Extrinsic Aspirations Using Network Analysis and Multidimensional Scaling: Examining Four New Aspirations Open
Life goals or aspirations can be distinguished as intrinsic or extrinsic, with different implications for well-being. In this study we used network analysis to reexamine this intrinsic-extrinsic distinction, illustrating how novel candidat…
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The Behavioral Space of Zebrafish Locomotion and Its Neural Network Analog Open
How simple is the underlying control mechanism for the complex locomotion of vertebrates? We explore this question for the swimming behavior of zebrafish larvae. A parameter-independent method, similar to that used in studies of worms and …
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The immutability of valence and arousal in the foundation of emotion. Open
Over the past century, great debate has ensued regarding the fundamental properties of emotions. The idea that 2 properties-valence and arousal-are critical for emotion and psychologically irreducible has had substantial staying power in t…
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Application of Exploratory Data Analyses opens a new perspective in morphology-based alpha-taxonomy of eusocial organisms Open
This article introduces a new application of the Exploratory Data Analysis (EDA) algorithms Ward's method, Unweighted Pair Group Method with Arithmetic Mean (UPGMA), K-Means clustering, and a combination of Non-Metric Multidimensional Scal…
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How to normalize metatranscriptomic count data for differential expression analysis Open
Background Differential expression analysis on the basis of RNA-Seq count data has become a standard tool in transcriptomics. Several studies have shown that prior normalization of the data is crucial for a reliable detection of transcript…
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2D Representation of Transcriptomes by t-SNE Exposes Relatedness between Human Tissues Open
The GTEx Consortium reported that hierarchical clustering of RNA profiles from 25 unique tissue types among 1641 individuals accurately distinguished the tissue types, but a multidimensional scaling failed to generate a 2D projection of th…