Phaser is a program for phasing macromolecular crystal structures by both molecular replacement and experimental phasing methods. The novel phasing algorithms implemented in Phaser have been developed using maximum likelihood and multivariate statistics. For molecular replacement, the new algorithms have proved to be significantly better than traditional methods in discriminating correct solutions from noise, and for single-wavelength anomalous dispersion experimental phasing, the new algorithms, which account for correlations between F+ and F−, give better phases (lower mean phase error with respect to the phases given by the refined structure) than those that use mean F and anomalous differences ΔF. One of the design concepts of Phaser was that it be capable of a high degree of automation. To this end, Phaser (written in C++) can be called directly from Python, although it can also be called using traditional CCP4 keyword-style input. Phaser is a platform for future development of improved phasing methods and their release, including source code, to the crystallographic community.

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Phaser crystallographic software

An essential textbook for any student or researcher in biology needing to design experiments, sample programs or analyse the resulting data The text begins with a revision of estimation and hypothesis testing methods, covering both classical and Bayesian philosophies, before advancing to the analysis of linear and generalized linear models Topics covered include linear and logistic regression, simple and complex ANOVA models (for factorial, nested, block, split-plot and repeated measures and covariance designs), and log-linear models Multivariate techniques, including classification and ordination, are then introduced Special emphasis is placed on checking assumptions, exploratory data analysis and presentation of results The main analyses are illustrated with many examples from published papers and there is an extensive reference list to both the statistical and biological literature The book is supported by a website that provides all data sets, questions for each chapter and links to software

/pdf/experimental-design-and-data-analysis-for-biologists-8ybva8d53x.pdf

Experimental Design and Data Analysis for Biologists

https://www.wsl.ch/staff/niklaus.zimmermann/papers/ecomod135_147.pdf

Predictive habitat distribution models in ecology

Kernel methods provide a powerful and unified framework for pattern discovery, motivating algorithms that can act on general types of data (e.g. strings, vectors or text) and look for general types of relations (e.g. rankings, classifications, regressions, clusters). The application areas range from neural networks and pattern recognition to machine learning and data mining. This book, developed from lectures and tutorials, fulfils two major roles: firstly it provides practitioners with a large toolkit of algorithms, kernels and solutions ready to use for standard pattern discovery problems in fields such as bioinformatics, text analysis, image analysis. Secondly it provides an easy introduction for students and researchers to the growing field of kernel-based pattern analysis, demonstrating with examples how to handcraft an algorithm or a kernel for a new specific application, and covering all the necessary conceptual and mathematical tools to do so.

/pdf/kernel-methods-for-pattern-analysis-3ta60xrj0i.pdf

Kernel Methods for Pattern Analysis

Predicting the distribution of endangered species from habitat data is frequently perceived to be a useful technique. Models that predict the presence or absence of a species are normally judged by the number of prediction errors. These may be of two types: false positives and false negatives. Many of the prediction errors can be traced to ecological processes such as unsaturated habitat and species interactions. Consequently, if prediction errors are not placed in an ecological context the results of the model may be misleading. The simplest, and most widely used, measure of prediction accuracy is the number of correctly classified cases. There are other measures of prediction success that may be more appropriate. Strategies for assessing the causes and costs of these errors are discussed. A range of techniques for measuring error in presence/absence models, including some that are seldom used by ecologists (e.g. ROC plots and cost matrices), are described. A new approach to estimating prediction error, which is based on the spatial characteristics of the errors, is proposed. Thirteen recommendations are made to enable the objective selection of an error assessment technique for ecological presence/absence models.

https://www.cambridge.org/core/services/aop-cambridge-core/content/view/S0376892997000088

A review of methods for the assessment of prediction errors in conservation presence/absence models

(2005). Applied Multivariate Statistical Analysis. Technometrics: Vol. 47, No. 4, pp. 517-517.

Applied Multivariate Statistical Analysis

(1996). A Step-by-Step Approach to Using the SAS™ System for Factor Analysis and Structural Equation Modeling. Technometrics: Vol. 38, No. 3, pp. 296-297.

Charles E. Heckler

Papers

Applied Multivariate Statistical Analysis

A Step-by-Step Approach to Using the SAS™ System for Factor Analysis and Structural Equation Modeling

Applied Discriminant Analysis

Correspondence Analysis and Data Coding With Java and R

Introduction to Mixed Modelling. Beyond Regression and Analysis of Variance, by Nicholas W. Galwey