This note summarizes developments of the genepop software since its first description in 1995, and in particular those new to version 4.0: an extended input format, several estimators of neighbourhood size under isolation by distance, new estimators and confidence intervals for null allele frequency, and less important extensions to previous options. genepop now runs under Linux as well as under Windows, and can be entirely controlled by batch calls.

genepop'007: a complete re-implementation of the genepop software for Windows and Linux

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Modern Applied Statistics With S

1. Introduction and Overview. 2. Detecting Influential Observations and Outliers. 3. Detecting and Assessing Collinearity. 4. Applications and Remedies. 5. Research Issues and Directions for Extensions. Bibliography. Author Index. Subject Index.

Regression Diagnostics: Identifying Influential Data and Sources of Collinearity

B-splines are attractive for nonparametric modelling, but choosing the optimal number and positions of knots is a complex task. Equidistant knots can be used, but their small and discrete number allows only limited control over smoothness and fit. We propose to use a relatively large number of knots and a difference penalty on coefficients of adjacent B-splines. We show connections to the familiar spline penalty on the integral of the squared second derivative. A short overview of B-splines, of their construction and of penalized likelihood is presented. We discuss properties of penalized B-splines and propose various criteria for the choice of an optimal penalty parameter. Nonparametric logistic regression, density estimation and scatterplot smoothing are used as examples. Some details of the computations are presented.

/pdf/flexible-smoothing-with-b-splines-and-penalties-aqyuxvm7bh.pdf

Flexible smoothing with B-splines and penalties

Aspect] is a simple and practical aspect-oriented extension to Java With just a few new constructs, AspectJ provides support for modular implementation of a range of crosscutting concerns. In AspectJ's dynamic join point model, join points are well-defined points in the execution of the program; pointcuts are collections of join points; advice are special method-like constructs that can be attached to pointcuts; and aspects are modular units of crosscutting implementation, comprising pointcuts, advice, and ordinary Java member declarations. AspectJ code is compiled into standard Java bytecode. Simple extensions to existing Java development environments make it possible to browse the crosscutting structure of aspects in the same kind of way as one browses the inheritance structure of classes. Several examples show that AspectJ is powerful, and that programs written using it are easy to understand.

An overview of AspectJ

Bootstrap confidence intervalsCommentCommentCommentCommentRejoinder

A number of effective error detection tools have been built in recent years to check if a program conforms to certain design rules. An important class of design rules deals with sequences of events asso-ciated with a set of related objects. This paper presents a language called PQL (Program Query Language) that allows programmers to express such questions easily in an application-specific context. A query looks like a code excerpt corresponding to the shortest amount of code that would violate a design rule. Details of the tar-get application's precise implementation are abstracted away. The programmer may also specify actions to perform when a match is found, such as recording relevant information or even correcting an erroneous execution on the fly.We have developed both static and dynamic techniques to find solutions to PQL queries. Our static analyzer finds all potential matches conservatively using a context-sensitive, flow-insensitive, inclusion-based pointer alias analysis. Static results are also use-ful in reducing the number of instrumentation points for dynamic analysis. Our dynamic analyzer instruments the source program to catch all violations precisely as the program runs and to optionally perform user-specified actions.We have implemented the techniques described in this paper and found 206 errors in 6 large real-world open-source Java applica-tions containing a total of nearly 60,000 classes. These errors are important security flaws, resource leaks, and violations of consis-tency invariants. The combination of static and dynamic analysis proves effective at addressing a wide range of debugging and pro-gram comprehension queries. We have found that dynamic analysis is especially suitable for preventing errors such as security vulner-abilities at runtime.

/pdf/finding-application-errors-and-security-flaws-using-pql-a-2w29bix4m3.pdf

Finding application errors and security flaws using PQL: a program query language

SUMMARY We propose a single unifying approach to bootstrap resampling, applicable to a very wide range of statistical problems. It enables attention to be focused sharply on one or more characteristics which are of major importance in any particular problem, such as coverage error or length for confidence intervals, or bias for point estimation. Our approach leads easily and directly to a very general form of bootstrap iteration, unifying and generalizing present disparate accounts of this subject. It also provides simple solutions to relatively complex problems, such as a suggestion by Lehmann (1986) for 'conditionally' short confidence intervals. We set out a single unifying principle guiding the operation of bootstrap resampling, applicable to a very wide range of statistical problems including bias reduction, shrinkage, hypothesis testing and confidence interval construction. Our principle differs from other approaches in that it focuses attention directly on a measure of quality or accuracy, expressed in the form of an equation whose solution is sought. A very general form of bootstrap iteration is an immediate consequence of iterating the empirical solution to this equation so as to improve accuracy. When employed for bias reduction, iteration of the resampling principle yields a competitor to the generalized jackknife, enabling bias to be reduced to arbitrarily low levels. When applied to confidence intervals it produces the techniques of Hall (1986) and Beran (1987). The resampling principle leads easily to solutions of new, complex problems, such as empirical versions of confidence intervals proposed by Lehmann (1986). Lehmann argued that an 'ideal' confidence interval is one which is short when it covers the true parameter value but not necessarily otherwise. The resampling principle suggests a simple empirical means of constructing such intervals. Section 2 describes the general principle, and ? 3 shows how it leads naturally to bootstrap iteration. There we show that in many problems of practical interest, such as bias reduction and coverage-error reduction in two-sided confidence intervals, each iteration reduces error by the factor n-1, where n is sample size. In the case of confidence intervals our result sharpens one of Beran (1987), who showed that coverage error is reduced by the factor n-2 in two-sided intervals. The main exception to our n-1 rule is coverage error of one-sided intervals, where error is reduced by the factor n-A at each iteration. Our approach to bootstrap iteration serves to unify not just the philosophy of iteration for different statistical problems, but also different techniques of iteration for the same

https://www.jstor.org/stable/info/2336307

On bootstrap resampling and iteration

Econometric studies have highlighted factors that appear to explain the differential effects of information technology (IT) on productivity at the firm level. Central to these explanations is the concept of organizational transformation; that value realization from IT depends on time-consuming investments in organizational change and results in new, often intangible, organizational assets. The aim of this study was to further investigate the concept of IT-enabled organizational transformation as a component of the value realized from IT at the firm level. Survey data was analyzed from respondents from 1050 businesses of varying sizes and across industries. Transformational benefits were found to exist as a distinct benefit category and to be closely related to other forms of IT-generated business benefits. They were also an important component of overall IT business value. Qualitative data illustrated these findings and pointed to possible complex causal relationships in the generation of IT value. The findings have implications for models of IT business value generation and for managerial practice.

The transformational dimension in the realization of business value from information technology

Cross-site scripting (XSS) and SQL injection errors are two prominent examples of taint-based vulnerabilities that have been responsible for a large number of security breaches in recent years. This paper presents QED, a goal-directed model-checking system that automatically generates attacks exploiting taint-based vulnerabilities in large Java web applications. This is the first time where model checking has been used successfully on real-life Java programs to create attack sequences that consist of multiple HTTP requests.

QED accepts any Java web application that is written to the standard servlet specification. The analyst specifies the vulnerability of interest in a specification that looks like a Java code fragment, along with a range of values for form parameters. QED then generates a goal-directed analysis from the specification to perform session-aware tests, optimizes to eliminate inputs that are not of interest, and feeds the remainder to a model checker. The checker will systematically explore the remaining state space and report example attacks if the vulnerability specification is matched.

QED provides better results than traditional analyses because it does not generate any false positive warnings. It proves the existence of errors by providing an example attack and a program trace showing how the code is compromised. Past experience suggests this is important because it makes it easy for the application maintainer to recognize the errors and to make the necessary fixes. In addition, for a class of applications, QED can guarantee that it has found all the potential bugs in the program. We have run QED over 3 Java web applications totaling 130,000 lines of code. We found 10 SQL injections and 13 cross-site scripting errors.

/pdf/automatic-generation-of-xss-and-sql-injection-attacks-with-58t5qrvyed.pdf

Michael A. Martin

Papers

Bootstrap confidence intervalsCommentCommentCommentCommentRejoinder

Finding application errors and security flaws using PQL: a program query language

On bootstrap resampling and iteration

The transformational dimension in the realization of business value from information technology

Automatic generation of XSS and SQL injection attacks with goal-directed model checking