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Data analysis and statistics for geography, environmental science, and engineering
This practical, classroom-tested textbook helps readers learn quantitative methodology, including how to implement advanced analysis methods using an open-source software platform. Based on the author's many years of teaching undergraduate and graduate students in several countries, the book brings together principles of statistics and probability, multivariate analysis, and spatial analysis methods applied to a variety of geographical and environmental models. Theory is accompanied by practical hands-on computer exercises, progressing from easy to difficult. The text also presents a review of mathematical methods, making the book self-contained.
eBook
Structural equation modeling : applications using Mplus
A reference guide for applications of SEM using Mplus Structural Equation Modeling: Applications Using Mplus is intended as both a teaching resource and a reference guide. Written in non-mathematical terms, this book focuses on the conceptual and practical aspects of Structural Equation Modeling (SEM). Basic concepts and examples of various SEM models are demonstrated along with recently developed advanced methods, such as mixture modeling and model-based power analysis and sample size estimate for SEM. The statistical modeling program, Mplus, is also featured and provides researchers with a flexible tool to analyze their data with an easy-to-use interface and graphical displays of data and analysis results. Key features: Presents a useful reference guide for applications of SEM whilst systematically demonstrating various advanced SEM models, such as multi-group and mixture models using Mplus. Discusses and demonstrates various SEM models using both cross-sectional and longitudinal data with both continuous and categorical outcomes. Provides step-by-step instructions of model specification and estimation, as well as detail interpretation of Mplus results. Explores different methods for sample size estimate and statistical power analysis for SEM. By following the examples provided in this book, readers will be able to build their own SEM models using Mplus. Teachers, graduate students, and researchers in social sciences and health studies will also benefit from this book.
eBook
Variability in the analysis of a single neuroimaging dataset by many teams
Data analysis workflows in many scientific domains have become increasingly complex and flexible. Here we assess the effect of this flexibility on the results of functional magnetic resonance imaging by asking 70 independent teams to analyse the same dataset, testing the same 9 ex-ante hypotheses
1
. The flexibility of analytical approaches is exemplified by the fact that no two teams chose identical workflows to analyse the data. This flexibility resulted in sizeable variation in the results of hypothesis tests, even for teams whose statistical maps were highly correlated at intermediate stages of the analysis pipeline. Variation in reported results was related to several aspects of analysis methodology. Notably, a meta-analytical approach that aggregated information across teams yielded a significant consensus in activated regions. Furthermore, prediction markets of researchers in the field revealed an overestimation of the likelihood of significant findings, even by researchers with direct knowledge of the dataset
2
–
5
. Our findings show that analytical flexibility can have substantial effects on scientific conclusions, and identify factors that may be related to variability in the analysis of functional magnetic resonance imaging. The results emphasize the importance of validating and sharing complex analysis workflows, and demonstrate the need for performing and reporting multiple analyses of the same data. Potential approaches that could be used to mitigate issues related to analytical variability are discussed.
The results obtained by seventy different teams analysing the same functional magnetic resonance imaging dataset show substantial variation, highlighting the influence of analytical choices and the importance of sharing workflows publicly and performing multiple analyses.
Journal Article
diaPASEF: parallel accumulation–serial fragmentation combined with data-independent acquisition
Data-independent acquisition modes isolate and concurrently fragment populations of different precursors by cycling through segments of a predefined precursor
m/z
range. Although these selection windows collectively cover the entire
m/z
range, overall, only a few per cent of all incoming ions are isolated for mass analysis. Here, we make use of the correlation of molecular weight and ion mobility in a trapped ion mobility device (timsTOF Pro) to devise a scan mode that samples up to 100% of the peptide precursor ion current in
m/z
and mobility windows. We extend an established targeted data extraction workflow by inclusion of the ion mobility dimension for both signal extraction and scoring and thereby increase the specificity for precursor identification. Data acquired from whole proteome digests and mixed organism samples demonstrate deep proteome coverage and a high degree of reproducibility as well as quantitative accuracy, even from 10 ng sample amounts.
diaPASEF makes use of the correlation between the ion mobility and the
m
/
z
of peptides to trap and release precursor ions in a TIMS-TOF mass spectrometer for an almost complete sampling of the precursor ion beam with data-independent acquisition.
Journal Article
Eleven grand challenges in single-cell data science
The recent boom in microfluidics and combinatorial indexing strategies, combined with low sequencing costs, has empowered single-cell sequencing technology. Thousands—or even millions—of cells analyzed in a single experiment amount to a data revolution in single-cell biology and pose unique data science problems. Here, we outline eleven challenges that will be central to bringing this emerging field of single-cell data science forward. For each challenge, we highlight motivating research questions, review prior work, and formulate open problems. This compendium is for established researchers, newcomers, and students alike, highlighting interesting and rewarding problems for the coming years.
Journal Article