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1
Theußl, Stefan, Uwe Ligges, and Kurt Hornik. "Prospects and Challenges in R Package Development." Institute for Statistics and Mathematics, WU Vienna University of Economics and Business, 2010. http://epub.wu.ac.at/866/1/document.pdf.
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R, a software package for statistical computing and graphics, has evolved into the lingua franca of (computational) statistics. One of the cornerstones of R's success is the decentralized and modularized way of creating software using a multi-tiered development model: The R Development Core Team provides the "base system", which delivers basic statistical functionality, and many other developers contribute code in the form of extensions in a standardized format via so-called packages. In order to be accessible by a broader audience, packages are made available via standardized source code repositories. To support such a loosely coupled development model, repositories should be able to verify that the provided packages meet certain formal quality criteria and "work": both relative to the development of the base R system as well as with other packages (interoperability). However, established quality assurance systems and collaborative infrastructures typically face several challenges, some of which we will discuss in this paper.<br>Series: Research Report Series / Department of Statistics and Mathematics
2
Guy, Abel. "fanplot: An R Package for Visualising Sequential Distributions." The R Foundation for Statistical Computing, 2015. http://epub.wu.ac.at/5910/1/Abel_2015_RJ_fanplot%2DAn%2DR%2DPackage.pdf.
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Fan charts, first developed by the Bank of England in 1996, have become a standard method for visualising forecasts with uncertainty. Using shading fan charts focus the attention towards the whole distribution away from a single central measure. This article describes the basics of plotting fan charts using an R add-on package alongside some additional methods for displaying sequential distributions. Examples are based on distributions of both estimated parameters from a time series model and future values with uncertainty.
3
Kastner, Gregor. "Heavy-Tailed Innovations in the R Package stochvol." WU Vienna University of Economics and Business, 2015. http://epub.wu.ac.at/4918/1/heavytails.pdf.
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We document how sampling from a conditional Student's t distribution is implemented in stochvol. Moreover, a simple example using EUR/CHF exchange rates illustrates how to use the augmented sampler. We conclude with results and implications. (author's abstract)
4
Randahl, David. "Raoul: An R-Package for Handling Missing Data." Thesis, Uppsala universitet, Statistiska institutionen, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-297051.
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Hornik, Kurt, and Bettina Grün. "topicmodels: An R Package for Fitting Topic Models." American Statistical Association, 2011. http://epub.wu.ac.at/3987/1/topicmodels.pdf.
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Topic models allow the probabilistic modeling of term frequency occurrences in documents.
The fitted model can be used to estimate the similarity between documents as
well as between a set of specified keywords using an additional layer of latent variables
which are referred to as topics. The R package topicmodels provides basic infrastructure
for fitting topic models based on data structures from the text mining package tm. The
package includes interfaces to two algorithms for fitting topic models: the variational
expectation-maximization algorithm provided by David M. Blei and co-authors and an
algorithm using Gibbs sampling by Xuan-Hieu Phan and co-authors.
6
Karatzoglou, Alexandros, Alex Smola, Kurt Hornik, and Achim Zeileis. "kernlab - An S4 package for kernel methods in R." Institut für Statistik und Mathematik, WU Vienna University of Economics and Business, 2004. http://epub.wu.ac.at/1048/1/document.pdf.
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kernlab is an extensible package for kernel-based machine learning methods in R. It takes advantage of R's new S4 object model and provides a framework for creating and using kernel-based algorithms. The package contains dot product primitives (kernels), implementations of support vector machines and the relevance vector machine, Gaussian processes, a ranking algorithm, kernel PCA, kernel CCA, and a spectral clustering algorithm. Moreover it provides a general purpose quadratic programming solver, and an incomplete Cholesky decomposition method. (author's abstract)<br>Series: Research Report Series / Department of Statistics and Mathematics
7
Buder, Thomas, Andreas Deutsch, Michael Seifert, and Anja Voss-Böhme. "CellTrans: An R Package to Quantify Stochastic Cell State Transitions." Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2017. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-230144.
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Many normal and cancerous cell lines exhibit a stable composition of cells in distinct states which can, e.g., be defined on the basis of cell surface markers. There is evidence that such an equilibrium is associated with stochastic transitions between distinct states. Quantifying these transitions has the potential to better understand cell lineage compositions. We introduce CellTrans, an R package to quantify stochastic cell state transitions from cell state proportion data from fluorescence-activated cell sorting and flow cytometry experiments. The R package is based on a mathematical model in which cell state alterations occur due to stochastic transitions between distinct cell states whose rates only depend on the current state of a cell. CellTrans is an automated tool for estimating the underlying transition probabilities from appropriately prepared data. We point out potential analytical challenges in the quantification of these cell transitions and explain how CellTrans handles them. The applicability of CellTrans is demonstrated on publicly available data on the evolution of cell state compositions in cancer cell lines. We show that CellTrans can be used to (1) infer the transition probabilities between different cell states, (2) predict cell line compositions at a certain time, (3) predict equilibrium cell state compositions, and (4) estimate the time needed to reach this equilibrium. We provide an implementation of CellTrans in R, freely available via GitHub (https://github.com/tbuder/CellTrans).
8
de, Leeuw Jan, and Patrick Mair. "Simple and Canonical Correspondence Analysis Using the R Package anacor." Foundation for Open Access Statistics, 2009. http://dx.doi.org/10.18637/jss.v031.i05.
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This paper presents the R package anacor for the computation of simple and canonical correspondence analysis with missing values. The canonical correspondence analysis is specified in a rather general way by imposing covariates on the rows and/or the columns of the two-dimensional frequency table. The package allows for scaling methods such as standard, Benzécri, centroid, and Goodman scaling. In addition, along with well-known two- and three-dimensional joint plots including confidence ellipsoids, it offers alternative plotting possibilities in terms of transformation plots, Benzécri plots, and regression plots.
9
Hahsler, Michael, Kurt Hornik, and Christian Buchta. "Getting Things in Order: An Introduction to the R Package seriation." American Statistical Association, 2008. http://epub.wu.ac.at/4003/1/things.pdf.
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Seriation, i.e., finding a suitable linear order for a set of objects given data and a loss or merit function, is a basic problem in data analysis. Caused by the problem's combinatorial nature, it is hard to solve for all but very small sets. Nevertheless, both exact solution methods and heuristics are available. In this paper we present the package seriation which provides an infrastructure for seriation with R. The infrastructure comprises data
structures to represent linear orders as permutation vectors, a wide array of seriation methods using a consistent interface, a method to calculate the value of various loss and merit functions, and several visualization techniques which build on seriation. To illustrate how easily the package can be applied for a variety of applications, a comprehensive collection of examples is presented.
10
Feinerer, Ingo, Christian Buchta, Wilhelm Geiger, Johannes Rauch, Patrick Mair, and Kurt Hornik. "The textcat Package for n-Gram Based Text Categorization in R." American Statistical Association, 2013. http://epub.wu.ac.at/3985/1/textcat.pdf.
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Identifying the language used will typically be the first step in most natural language
processing tasks. Among the wide variety of language identification methods discussed
in the literature, the ones employing the Cavnar and Trenkle (1994) approach to text
categorization based on character n-gram frequencies have been particularly successful.
This paper presents the R extension package textcat for n-gram based text categorization
which implements both the Cavnar and Trenkle approach as well as a reduced n-gram
approach designed to remove redundancies of the original approach. A multi-lingual
corpus obtained from the Wikipedia pages available on a selection of topics is used to
illustrate the functionality of the package and the performance of the provided language
identification methods. (authors' abstract)
11
Hahsler, Michael, Kurt Hornik, and Christian Buchta. "Getting Things in Order: An Introduction to the R package seriation." Department of Statistics and Mathematics, WU Vienna University of Economics and Business, 2007. http://epub.wu.ac.at/852/1/document.pdf.
Pełny tekst źródłaStreszczenie:
Seriation, i.e., finding a linear order for a set of objects given data and a loss or merit function, is a basic problem in data analysis. Caused by the problem's combinatorial nature, it is hard to solve for all but very small sets. Nevertheless, both exact solution methods and heuristics are available. In this paper we present the package seriation which provides the infrastructure for seriation with R. The infrastructure comprises data structures to represent linear orders as permutation vectors, a wide array of seriation methods using a consistent interface, a method to calculate the value of various loss and merit functions, and several visualization techniques which build on seriation. To illustrate how easily the package can be applied for a variety of applications, a comprehensive collection of examples is presented.<br>Series: Research Report Series / Department of Statistics and Mathematics
12
Jot, Sapan. "pcaL1: An R Package of Principal Component Analysis using the L1 Norm." VCU Scholars Compass, 2011. http://scholarscompass.vcu.edu/etd/2488.
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Principal component analysis (PCA) is a dimensionality reduction tool which captures the features of data set in low dimensional subspace. Traditional PCA uses L2-PCA and has much desired orthogonality properties, but is sensitive to outliers. PCA using L1 norm has been proposed as an alternative to counter the effect of outliers. The R environment for statistical computing already provides L2-PCA function prcomp(), but there are not many options for L1 norm PCA methods. The goal of the research was to create one R package with different options of PCA methods using L1 norm. So, we choose three different L1-PCA algorithms: PCA-L1 proposed by Kwak [10], L1-PCA* by Brooks et. al. [1], and L1-PCA by Ke and Kanade [9]; to create a package pcaL1 in R, interfacing with C implementation of these algorithms. An open source software for solving linear problems, CLP, is used to solve the optimization problems for L1-PCA* and L1-PCA. We use this package on human microbiome data to investigate the relationship between people based on colonizing bacteria.
13
Philipp, Michel, Thomas Rusch, Kurt Hornik, and Carolin Strobl. "Measuring the Stability of Results from Supervised Statistical Learning." WU Vienna University of Economics and Business, 2017. http://epub.wu.ac.at/5398/1/Report131.pdf.
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Stability is a major requirement to draw reliable conclusions when
interpreting results from supervised statistical learning. In this
paper, we present a general framework for assessing and comparing the
stability of results, that can be used in real-world statistical
learning applications or in benchmark studies. We use the framework to
show that stability is a property of both the algorithm and the
data-generating process. In particular, we demonstrate that unstable
algorithms (such as recursive partitioning) can produce stable results
when the functional form of the relationship between the predictors
and the response matches the algorithm. Typical uses of the framework
in practice would be to compare the stability of results generated by
different candidate algorithms for a data set at hand or to assess the
stability of algorithms in a benchmark study. Code to perform the
stability analyses is provided in the form of an R-package.<br>Series: Research Report Series / Department of Statistics and Mathematics
14
Kastner, Gregor. "Dealing with Stochastic Volatility in Time Series Using the R Package stochvol." Foundation for Open Access Statistics, 2016. http://epub.wu.ac.at/4890/1/v69i05.pdf.
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The R package stochvol provides a fully Bayesian implementation of heteroskedasticity modeling within the framework of stochastic volatility. It utilizes Markov chain Monte Carlo (MCMC) samplers to conduct inference by obtaining draws from the posterior distribution of parameters and latent variables which can then be used for predicting future volatilities. The package can straightforwardly be employed as a stand-alone tool; moreover, it allows for easy incorporation into other MCMC samplers. The main focus of this paper is to show the functionality of stochvol. In addition, it provides a brief mathematical description of the model, an overview of the sampling schemes used, and several illustrative examples using exchange rate data. (author's abstract)
15
Hornik, Kurt, and Bettina Grün. "movMF: An R Package for Fitting Mixtures of von Mises-Fisher Distributions." American Statistical Association, 2014. http://epub.wu.ac.at/4893/1/v58i10.pdf.
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Finite mixtures of von Mises-Fisher distributions allow to apply model-based clustering methods to data which is of standardized length, i.e., all data points lie on the unit sphere. The R package movMF contains functionality to draw samples from finite mixtures of von
Mises-Fisher distributions and to fit these models using the expectation-maximization algorithm
for maximum likelihood estimation. Special features are the possibility to use
sparse matrix representations for the input data, different variants of the expectationmaximization
algorithm, different methods for determining the concentration parameters
in the M-step and to impose constraints on the concentration parameters over the components.
In this paper we describe the main fitting function of the package and illustrate its
application. In addition we compare the clustering performance of finite mixtures of
von Mises-Fisher distributions to spherical k-means. We also discuss the resolution of
several numerical issues which occur for estimating the concentration parameters and for
determining the normalizing constant of the von Mises-Fisher distribution. (authors' abstract)
16
Zhu, Hongxu. "AN R PACKAGE FOR FITTING DIRICHLET PROCESS MIXTURES OF MULTIVARIATE GAUSSIAN DISTRIBUTIONS." Case Western Reserve University School of Graduate Studies / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=case155752396390554.
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Downey, Sean S., Guowei Sun, and Peter Norquest. "alineR: an R Package for Optimizing Feature-Weighted Alignments and Linguistic Distances." R FOUNDATION STATISTICAL COMPUTING, 2017. http://hdl.handle.net/10150/625224.
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Linguistic distance measurements are commonly used in anthropology and biology when quantitative and statistical comparisons between words are needed. This is common, for example, when analyzing linguistic and genetic data. Such comparisons can provide insight into historical population patterns and evolutionary processes. However, the most commonly used linguistic distances are derived from edit distances, which do not weight phonetic features that may, for example, represent smaller-scale patterns in linguistic evolution. Thus, computational methods for calculating feature-weighted linguistic distances are needed for linguistic, biological, and evolutionary applications; additionally, the linguistic distances presented here are generic and may have broader applications in fields such as text mining and search, as well as applications in psycholinguistics and morphology. To facilitate this research, we are making available an open-source R software package that performs feature-weighted linguistic distance calculations. The package also includes a supervised learning methodology that uses a genetic algorithm and manually determined alignments to estimate 13 linguistic parameters including feature weights and a skip penalty. Here we present the package and use it to demonstrate the supervised learning methodology by estimating the optimal linguistic parameters for both simulated data and for a sample of Austronesian languages. Our results show that the methodology can estimate these parameters for both simulated and real language data, that optimizing feature weights improves alignment accuracy by approximately 29%, and that optimization significantly affects the resulting distance measurements. Availability: alineR is available on CRAN.
18
Zeileis, Achim, Mark A. van de Wiel, Kurt Hornik, and Torsten Hothorn. "Implementing a Class of Permutation Tests: The coin Package." American Statistical Association, 2008. http://epub.wu.ac.at/4004/1/class.pdf.
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The R package coin implements a unified approach to permutation tests providing a
huge class of independence tests for nominal, ordered, numeric, and censored data as well
as multivariate data at mixed scales. Based on a rich and
exible conceptual framework
that embeds different permutation test procedures into a common theory, a computational
framework is established in coin that likewise embeds the corresponding R functionality
in a common S4 class structure with associated generic functions. As a consequence,
the computational tools in coin inherit the
exibility of the underlying theory and conditional
inference functions for important special cases can be set up easily. Conditional
versions of classical tests|such as tests for location and scale problems in two or more
samples, independence in two- or three-way contingency tables, or association problems
for censored, ordered categorical or multivariate data|can easily be implemented as special
cases using this computational toolbox by choosing appropriate transformations of
the observations. The paper gives a detailed exposition of both the internal structure of
the package and the provided user interfaces along with examples on how to extend the
implemented functionality. (authors' abstract)
19
Hothorn, Torsten, Kurt Hornik, de Wiel Mark A. van, and Achim Zeileis. "Implementing a Class of Permutation Tests: The coin Package." Department of Statistics and Mathematics, WU Vienna University of Economics and Business, 2007. http://epub.wu.ac.at/408/1/document.pdf.
Pełny tekst źródłaStreszczenie:
The R package coin implements a unified approach to permutation tests providing a huge class of independence tests for nominal, ordered, numeric, and censored data as well as multivariate data at mixed scales. Based on a rich and flexible conceptual framework that embeds different permutation test procedures into a common theory, a computational framework is established in coin that likewise embeds the corresponding R functionality in a common S4 class structure with associated generic functions. As a consequence, the computational tools in coin inherit the flexibility of the underlying theory and conditional inference functions for important special cases can be set up easily. Conditional versions of classical tests - such as tests for location and scale problems in two or more samples, independence in two- or three-way contingency tables, or association problems for censored, ordered categorical or multivariate data - can be easily be implemented as special cases using this computational toolbox by choosing appropriate transformations of the observations. The paper gives a detailed exposition of both the internal structure of the package and the provided user interfaces.<br>Series: Research Report Series / Department of Statistics and Mathematics
20
Kleiber, Christian, Kurt Hornik, Friedrich Leisch, and Achim Zeileis. "strucchange: An R Package for Testing for Structural Change in Linear Regression Models." American Statistical Association, 2002. http://epub.wu.ac.at/4001/1/strucchange.pdf.
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This paper reviews tests for structural change in linear regression models from the
generalized fluctuation test framework as well as from the F test (Chow test) framework.
It introduces a unified approach for implementing these tests and presents how these ideas
have been realized in an R package called strucchange. Enhancing the standard significance
test approach the package contains methods to fit, plot and test empirical fluctuation
processes (like CUSUM, MOSUM and estimates-based processes) and to compute, plot and
test sequences of F statistics with the supF, aveF and expF test. Thus, it makes powerful
tools available to display information about structural changes in regression relationships
and to assess their significance. Furthermore, it is described how incoming data can be
monitored.
21
Zeileis, Achim, Friedrich Leisch, Kurt Hornik, and Christian Kleiber. "strucchange. An R package for testing for structural change in linear regression models." SFB Adaptive Information Systems and Modelling in Economics and Management Science, WU Vienna University of Economics and Business, 2001. http://epub.wu.ac.at/1124/1/document.pdf.
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This paper introduces ideas and methods for testing for structural change in linear regression models and presents how these have been realized in an R package called strucchange. It features tests from the generalized fluctuation test framework as well as from the F test (Chow test) framework. Extending standard significance tests it contains methods to fit, plot and test empirical fluctuation processes (like CUSUM, MOSUM and estimates-based processes) on the one hand and to compute, plot and test sequences of F statistics with the supF, aveF and expF test on the other. Thus, it makes powerful tools available to display information about structural changes in regression relationships and to assess their significance. Furthermore it is described how incoming data can be monitored online.<br>Series: Report Series SFB "Adaptive Information Systems and Modelling in Economics and Management Science"
22
Mair, Patrick, and Reinhold Hatzinger. "Extended Rasch Modeling: The eRm Package for the Application of IRT Models in R." Department of Statistics and Mathematics, WU Vienna University of Economics and Business, 2007. http://epub.wu.ac.at/332/1/document.pdf.
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Item response theory models (IRT) are increasingly becoming established in social science research, particularly in the analysis of performance or attitudinal data in psychology, education, medicine, marketing and other fields where testing is relevant. We propose the R package eRm (extended Rasch modeling) for computing Rasch models and several extensions. A main characteristic of some IRT models, the Rasch model being the most prominent, concerns the separation of two kinds of parameters, one that describes qualities of the subject under investigation, and the other relates to qualities of the situation under which the response of a subject is observed. Using conditional maximum likelihood (CML) estimation both types of parameters may be estimated independently from each other. IRT models are well suited to cope with dichotomous and polytomous responses, where the response categories may be unordered as well as ordered. The incorporation of linear structures allows for modeling the effects of covariates and enables the analysis of repeated categorical measurements. The eRm package fits the following models: the Rasch model, the rating scale model (RSM), and the partial credit model (PCM) as well as linear reparameterizations through covariate structures like the linear logistic test model (LLTM), the linear rating scale model (LRSM), and the linear partial credit model (LPCM). We use an unitary, efficient CML approach to estimate the item parameters and their standard errors. Graphical and numeric tools for assessing goodness-of-fit are provided. (author's abstract)<br>Series: Research Report Series / Department of Statistics and Mathematics
23
Mair, Patrick, Eva Hofmann, Kathrin Gruber, Reinhold Hatzinger, Achim Zeileis, and Kurt Hornik. "Motives for Participation in Open-Source Software Projects: A Survey among R Package Authors." WU Vienna University of Economics and Business, 2014. http://epub.wu.ac.at/4135/1/Report126.pdf.
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One of the cornerstones of the R system for statistical computing is the
multitude of contributed packages making an extremely broad range of
statistical techniques and other quantitative methods freely available. This
study investigates which factors are the crucial determinants responsible for
the participation of the package authors in the R project. For this purpose a
survey was conducted among R package authors, collecting data on different
types of participation in the R project, three psychometric scales (hybrid
forms of motivation, work design characteristics, and values), as well as
various specie-demographic factors. These data are analyzed using item
response theory and generalized linear models, showing that the most important
determinants for participation are a hybrid form of motivation and the
knowledge characteristics of the work design. Other factors are found to have
less impact or influence only specific aspects of participation. (authors' abstract)<br>Series: Research Report Series / Department of Statistics and Mathematics
24
Chuová, Trang. "Analýza výrobního sortimentu firmy KEB-EGE spol.s r. o." Master's thesis, Vysoká škola ekonomická v Praze, 2011. http://www.nusl.cz/ntk/nusl-113608.
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My diploma thesis is dedicated to the analysis of the product assortment of the KEB-EGE ltd. company that concentrates on producing autodiagnostics and steel constructions. The theoretical part involves basic marketing terms and the practical part introduces the company itself, its customers, competition and suppliers, the analysis of the company macro environment and the analysis of the marketing mix as for its four tools, which is product, price, distribution and marketing communication.
25
Hornik, Kurt, Duncan Murdoch, and Achim Zeileis. "Who Did What? The Roles of R Package Authors and How to Refer to Them." WU Vienna University of Economics and Business, 2011. http://epub.wu.ac.at/3269/1/Report114.pdf.
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Computational infrastructure for reprenting persons and citations has been available in R for several years, but has been restructured through enhanced classes "person" and "bibentry" in recent versions of R. The new features include support for the specification of the roles of package authors (e.g.,maintainer, author, contributor, translator, etc.) and more flexible formatting/printing tools among various other improvements. Here, we introduce the new classes and their methods and indicate how this functionality is employed in themanagement of R packages. Specifically, we show how the authors of R packages can be specified along with their roles in package 'DESCRIPTION' and/or 'CITATION' files and the citations produced from it. (author's abstract)<br>Series: Research Report Series / Department of Statistics and Mathematics
26
Hornik, Kurt, Duncan Murdoch, and Achim Zeileis. "Who Did What? The Roles of R Package Authors and How to Refer to Them." The R Foundation for Statistical Computing, 2012. http://epub.wu.ac.at/6395/1/RJ%2D2012%2D009.pdf.
Pełny tekst źródłaStreszczenie:
Computational infrastructure for representing
persons and citations has been available
in R for several years, but has been restructured
through enhanced classes "person" and
"bibentry" in recent versions of R. The new
features include support for the specification of
the roles of package authors (e.g. maintainer,
author, contributor, translator, etc.) and more
flexible formatting/printing tools among various
other improvements. Here, we introduce
the new classes and their methods and indicate
how this functionality is employed in the management
of R packages. Specifically, we show
how the authors of R packages can be specified
along with their roles in package ´DESCRIPTION´
and/or ´CITATION´ files and the citations produced
from it.
27
Tremblay, Serge 1961. "A microcomputer software package to design agricultural drainage plans /." Thesis, McGill University, 1987. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=63911.
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28
Ryan, Niamh Margaret. "The design and application of SuRFR : an R package to prioritise candidate functional DNA sequence variants." Thesis, University of Edinburgh, 2016. http://hdl.handle.net/1842/22916.
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Genetic analyses such as linkage and genome wide association studies (GWAS) have been extremely successful at identifying genomic regions that harbour genetic variants contributing to complex disorders. Over 90% of disease-associated variants from GWAS fall within non-coding regions (Maurano et al., 2012). However, pinpointing the causal variants has proven a major bottleneck to genetic research. To address this I have developed SuRFR, an R package for the ranked prioritisation of candidate causal variants by predicted function. SuRFR produces rank orderings of variants based upon functional genomic annotations, including DNase hypersensitivity signal, chromatin state, minor allele frequency, and conservation. The ranks for each annotation are combined into a final prioritisation rank using a weighting system that has been parametrised and tested through ten-fold cross-validation. SuRFR has been tested extensively upon a combination of synthetic and real datasets and has been shown to perform with high sensitivity and specificity. These analyses have provided insight into the extent to which different classes of functional annotation are most useful for the identification of known regulatory variants: the most important factor for identifying a true variant across all classes of regulatory variants is position relative to genes. I have also shown that SuRFR performs at least as well as its nearest competitors whilst benefiting from the advantages that come from being part of the R environment. I have applied SuRFR to several genomics projects, particularly the study of psychiatric illness, including genome sequencing of a large Scottish family with bipolar disorder. This has resulted in the prioritisation of such variants for future study.
29
Zhang, Jiaqi. "A Comparison of Propensity Score Matching Methods in R with the MatchIt Package: A Simulation Study." University of Cincinnati / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1367938207.
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30
Brett, Craig 1965. "An interval mathematics package for computer-aided design in electromagnetics /." Thesis, McGill University, 1990. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=59532.
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Recent developments in CAD for electromagnetic devices have utilized knowledge-based programming techniques to simplify the task of design process automation. The ultimate goal is to duplicate the role an expert designer performs in synthesizing devices such as transformers, motors, and actuators.<br>A missing quality from these CAD systems is a convenient representation of design space. Interval mathematics is proposed as a means of dealing with this elusive representation. The present work details an interval mathematics package that allows the user to put practical limits on certain parameters enabling the program to deduce the valid design space of the device. This facility permits the system to recognize and eliminate impossible designs and to guide the novice designer through the true search space. Intervals may also be used in other types of expert knowledge such as if-then rules and heuristic "rules of thumb" derived from years of design experience.
31
Almeida, Bernardo Simons de. "A visualização de dados nas lotas da Docapesca." Master's thesis, Instituto Superior de Economia e Gestão, 2020. http://hdl.handle.net/10400.5/21032.
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Mestrado em Métodos Quantitativos para a Decisão Económica e Empresarial<br>Na segunda década do século XXI, assistiu-se a um crescimento exponencial dos dados criados diariamente. Consequentemente, a visualização de dados é cada vez mais relevante no contexto empresarial, revelando-se cada vez mais essencial para a tomada de decisões e planeamento de estratégias de negócio.
Este trabalho foi realizado, em conjunto com a Docapesca, com a finalidade de criar um dashboard capaz de analisar os dados específicos relativos ao pescado transacionado nas lotas em Portugal num determinado período (Entre 2009 e 2018). Com uma abordagem metodológica orientada para a data visualization, foi possível elaborar um dashboard com as propriedades indicadas para o que foi solicitado.
Foi possível implementar a revisão da literatura, criando um dashboard atendendo ao que foi referido anteriormente.<br>The second decade of the 21st century saw an exponential growth in the data created daily. Consequently, data visualization is increasingly relevant in the business context, proving to be increasingly essential for decision making and business strategy planning.
In association with Docapesca, this work was carried out with the purpose of creating a dashboard capable of analyzing the specific data related to fish traded at auction in Portugal in a given period (Between 2009 and 2018). With a methodological approach oriented to data visualization, it was possible to elaborate a dashboard with the properties indicated for what was requested.
Despite not being implemented, the final assessment was positive and allowed conclusions to be drawn that were correct in relation to the data under study.<br>info:eu-repo/semantics/publishedVersion
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Hu, Yang. "Extreme Value Mixture Modelling with Simulation Study and Applications in Finance and Insurance." Thesis, University of Canterbury. Mathematics and Statistics, 2013. http://hdl.handle.net/10092/8538.
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Extreme value theory has been used to develop models for describing the distribution of rare events. The extreme value theory based models can be used for asymptotically approximating the behavior of the tail(s) of the distribution function. An important challenge in the application of such extreme value models is the choice of a threshold, beyond which point the asymptotically justified extreme value models can provide good extrapolation. One approach for determining the threshold is to fit the all available data by an extreme value mixture model.
This thesis will review most of the existing extreme value mixture models in the literature and implement them in a package for the statistical programming language R to make them more readily useable by practitioners as they are not commonly available in any software. There are many different forms of extreme value mixture models in the literature (e.g. parametric, semi-parametric and non-parametric), which provide an automated approach for estimating the threshold and taking into account the uncertainties with threshold selection.
However, it is not clear that how the proportion above the threshold or tail fraction should be treated as there is no consistency in the existing model derivations. This thesis will develop some new models by adaptation of the existing ones in the literature and placing them all within a more generalized framework for taking into account how the tail fraction is defined in the model. Various new models are proposed by extending some of the existing parametric form mixture models to have continuous density at the threshold, which has the advantage of using less model parameters and being more physically plausible. The generalised framework all the mixture models are placed within can be used for demonstrating the importance of the specification of the tail fraction. An R package called evmix has been created to enable these mixture models to be more easily applied and further developed. For every mixture model, the density, distribution, quantile, random number generation, likelihood and fitting function are presented (Bayesian inference via MCMC is also implemented for the non-parametric extreme value mixture models).
A simulation study investigates the performance of the various extreme value mixture models under different population distributions with a representative variety of lower and upper tail behaviors. The results show that the kernel density estimator based non-parametric form mixture model is able to provide good tail estimation in general, whilst the parametric and semi-parametric forms mixture models can give a reasonable fit if the distribution below the threshold is correctly specified. Somewhat surprisingly, it is found that including a constraint of continuity at the threshold does not substantially improve the model fit in the upper tail. The hybrid Pareto model performs poorly as it does not include the tail fraction term. The relevant mixture models are applied to insurance and financial applications which highlight the practical usefulness of these models.
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Mair, Patrick, Eva Hofmann, Kathrin Gruber, Reinhold Hatzinger, Achim Zeileis, and Kurt Hornik. "What Drives Package Authors to Participate in the R Project for Statistical Computing? Exploring Motivation, Values, and Work Design." National Academy of Sciences, 2015. http://epub.wu.ac.at/4702/1/cranpnas.pdf.
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One of the cornerstones of the R system for statistical computing is the multitude of packages contributed by numerous package authors. This makes an extremely broad range of statistical techniques and other quantitative methods freely available. So far no empirical study has investigated psychological factors that drive authors to participate in the R project. This article presents a
study of R package authors, collecting data on different types of participation (number of packages, participation in mailing lists, participation in conferences), three psychological scales (types of motivation, psychological values, and work design characteristics), as well as various sociodemographic factors. The data are
analyzed using item response models and subsequent generalized linear models, showing that the most important determinants for participation are a hybrid form of motivation and the social characteristics of the work design. Other factors are found to have less impact or influence only specific aspects of participation. (authors' abstract)
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Landry, Guillaume. "ImaSim, a simulation software package for the teaching of medical x-ray imaging." Thesis, McGill University, 2009. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=67028.
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The goal of this project is to enhance the teaching and the self study of diagnostic and radiotherapy x-ray imaging by creating an interactive educational software package, ImaSim, based on a simulation environment. Various imaging modalities found in a radiology or radiation oncology department have been included. ImaSim aims at faithfully reproducing the physics behind these modalities while keeping the operation simple and straightforward. Photons simulated fall into the energy range encompassing radiology and radiation oncology. The user can interactively vary many parameters related to image formation. ImaSim enables a user to quickly demonstrate and study principles associated with the creation of a radiological image in a classroom or in a self-learning setting. Many imaging phenomena can be studied with the aid of ImaSim. This work, by rendering accurate image creation easily accessible, has the potential to enhance textbook based teaching and heighten student interest in medical photon imaging.<br>L'objectif de ce projet consiste en l'amélioration de l'enseignement de l'imagerie médicale par la création d'un logiciel interactif, ImaSim, basé sur un environnement de simulation. La plupart des modalités d'imagerie médicale propres à un département de radiologie ou radio oncologie se retrouvent dans ImaSim. ImaSim vise à préserver une utilisation simple tout en modélisant adéquatement les aspects physiques associés aux modalités d'imagerie. Les photons générés tombent dans la gamme d'énergie propre à la radiologie et à la radio oncologie. Plusieurs paramètres liés à la formation d'images peuvent être variés interactivement par l'utilisateur. ImaSim permet donc d'étudier les principes associés à la création d'une image radiologique. Plusieurs phénomènes peuvent êtres étudiés à l'aide d'ImaSim. Ce projet a le potentiel de complémenter l'enseignement traditionnel de l'imagerie médicale.
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Gauthier, Laurent. "Development and use of a database and program package for farm production management." Thesis, McGill University, 1986. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=74030.
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Yamamoto, Ayako. "Validation of new operational package for the Lagrangian diagnosis of stratosphere-troposphere exchange." Thesis, McGill University, 2012. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=106407.
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A new tool for the Lagrangian diagnosis of stratosphere-troposphere exchange (STE) was developed for Environment Canada and became operational in July 2010, providing unique, high-resolution daily forecasts of STE over the globe. This thesis offers a comprehensive validation of these STE forecasts in the context of an ozonesonde balloon campaign conducted at three locations in Eastern Canada from 12 July to 4 August 2010. The STE forecasts are calculated using a Lagrangian kinematic trajectory methodology based on the high-resolution global GEM model forecasts at Environment Canada. Both observations and the STE forecasts during this period showed much larger frequency of stratospheric air intrusions deep into the troposphere at all locations compared to past studies. The STE dataset compares reasonably well with the observations above 500 hPa, yet is found to underestimate the frequency of events reaching below 700 hPa level. Sources of error can possibly be introduced by (1) errors in the 6-day global GEM forecasts, (2) errors in the identification of air with stratospheric origin in observations, and/or (3) the lack of convective and turbulent mixing representation in the trajectory model. Despite these large sources of errors, the STE forecasts turn out to be one of the best datasets available for the STE studies, being useful to estimate the currently controversial STE contribution to the tropospheric ozone budget in the free troposphere as well as in the boundary layer.<br>Un nouvel outil de diagnostic d'échange stratosphère-troposphère (STE) a été développé pour Environment Canada et est devenu opérationnel en Juillet 2010, fournissant des prévisions quotidiennes de haute résolution à l'échelle globale. Cette thèse offre une validation complète des prévisions STE dans le contexte d'une campagne de ballons-sondes mesurant l'ozone, conduite à trois localisations dans l'Est du Canada du 12 Juillet au 4 Août 2010. Les prévisions STE sont calculées avec une méthode cinématique de trajectoires Lagrangiennes basée sur la sortie du modèle global à haute résolution GEM d'Environment Canada. Les observations et résultats du modèle montrent une fréquence d'intrusions profondes d'air stratosphérique bien plus grande que dans les études précédentes. Les données STE correspondent relativement bien aux observations au dessus de 500 hPa, mais elles sous-estiment la fréquence des évènements attaignant 700 hPa. Les sources d'erreurs sont possiblement: (1) des erreurs dans la prévision de GEM, (2) des erreurs dans l'identification de parcelle d'air d'origine stratosphérique et/ou (3) le manque de convection et de turbulence dans le modèle de trajectoire. Malgré ces sources d'erreurs, les données d'intrusions s'avèrent être une des meilleures sources disponible pour, entre autres, estimer la présente et controversée contribution stratosphérique au budget total d'ozone de la troposphère.
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Tawy, Gwenllian Fflur. "Development and validation of a functional outcome measure package for total knee arthroplasty." Thesis, University of Strathclyde, 2017. http://digitool.lib.strath.ac.uk:80/R/?func=dbin-jump-full&object_id=30377.
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Functional improvement is an important outcome following total knee arthroplasty (TKA). According to recent research, three-dimensional motion analysis is the most scientific method of measuring dynamic knee function. Nevertheless, current protocols are too time consuming and complicated for routine clinical use. This study developed a clinic-appropriate motion capture system, and investigated the feasibility of its use in a clinical environment. A compact motion capture system (Dimensions: 3.5(L)x2.1(H)x1.1(W)m) and bespoke cluster-based biomechanical model were developed. Assessments for quantifying knee range of motion (ROM), knee strength, gait kinematics, and gait stability were incorporated into the software. Most results were reported in real-time. Validation studies of the assessments against clinical standard tools showed few clinically significant differences between the results, suggesting that the assessments could be used as accurate and reliable alternatives to the traditional tools. The system was then used clinically to report the functional outcome of Medacta GMK Sphere TKA patients. Patients underwent functional testing pre-, 6-weeks, and 1-year post-operatively. Average recorded assessment time was 16.8±2.4 minutes. On average, knee ROM, gait kinematics, spatio-temporal parameters of gait and gait stability improved post-operatively. Knee strength decreased over the first year however, suggesting that TKA patients require strength training post operatively in order to optimise functional outcome. The results reported in this trial were generally consistent with the current literature, implying that the system returned valid data for this patient cohort,and that the Medacta GMK Sphere TKA was successful at improving knee function, especially in frontal and transverse planes during gait. To conclude, this thesis has shown that motion capture technology can feasibly be used in the clinical environment to assess the function of TKA patients in an acceptable clinical time frame. The system developed and presented here can therefore justifiably be used clinically to better report the functional outcome of TKA.
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Younkin, Samuel G. "The Linkage Disequilibrium LASSO for SNP Selection in Genetic Association Studies." Case Western Reserve University School of Graduate Studies / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=case1291219489.
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Kherrazi, Soufiane. "Les pratiques de contrôle managérial dans le contexte de l’innovation collaborative : le cas des consortiums de R&D européens sponsorisés." Thesis, université Paris-Saclay, 2020. http://www.theses.fr/2020UPASI004.
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Cette recherche aborde la question du contrôle managérial (CM) de l'innovation collaborative. Elle se propose de contribuer à la littérature sur le CM en tenant compte à la fois des perspectives de contingence et de consistance interne pour examiner la mise en place du CM, en particulier dans le contexte des consortiums de R&D. L'ouverture des frontières de la R&D n’est pas sans conséquences sur le design et l'efficacité du CM. Elle implique des défis particuliers et soulève des tensions spécifiques entre les exigences de contrôle et les besoins d’innovation. Sur la base d'une enquête quantitative auprès de 232 firmes impliquées dans des consortiums européens de R&D sponsorisés et mobilisant une modélisation par équations structurelles, nous concevons un modèle de CM inter-firme permettant de soutenir l'innovation collaborative.Nos résultats montrent que l'écosystème de l'innovation joue un rôle essentiel en tant qu'élément institutionnel façonnant le design du CM. Nous mettons en évidence également sur la base de nos résultats que l'approche package est plus appropriée que l'approche système dans le contexte de l’innovation collaborative et permet, en outre, d’envisager plusieurs configurations du CM. Ces dernières sont amenées à s’ajuster en fonction des changements de l’environnement et de l’incertitude technologique. Les résultats font ressortir, enfin, les effets modérateurs des risques relationnels qui peuvent renforcer ou affaiblir l’efficacité du package de CM. L’efficacité du package semble être, en conséquence, liée à son « adéquation » avec le contexte de la collaboration plutôt qu'à sa « cohérence interne »<br>This research addresses the issue of management control (MC) of collaborative innovation. It attempts to fill this gap in MC literature by considering both contingency and internal consistency perspectives to examine the MC setting, especially in the context of R&D consortia. Opening the boundaries of R&D has implications for the MC design and effectiveness. It involves particular challenges and raises specific tensions of competing demands between control and innovation. Based on a quantitative survey of 232 firms involved in sponsored European R&D consortia and using the structural equation modeling method, we design an interfirm MC model to support collaborative innovation. Our results show that the innovation ecosystem plays a critical role as an institutional element shaping the MC design. We also infer based on our findings that the package approach is more suitable than the system one to set up control practices within a collaborative innovation context. Thus, the package allows several configurations of MC to face environment change and technological uncertainty. We highlight also the moderating effects of relational risks that may strengthen or damp the benefits of the MC package. Accordingly, the package’s effectiveness seems to be related to its “fit” with the collaboration context rather than its “internal consistency”
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Khalid, Madihah. "Enhancing the mathematical achievement of technical education students in Brunei Darussalam using a teaching and learning package." Curtin University of Technology, Science and Mathematics Education Centre, 2004. http://espace.library.curtin.edu.au:80/R/?func=dbin-jump-full&object_id=15984.
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Mathematics plays a key role in many of today’s most secure and financially rewarding careers. In almost every sector of the economy, a substantial core of mathematics is needed to prepare students both for work and for higher education. The impact of computers and information technology in areas as diverse as manufacturing and advertising means that understanding mathematics becomes more important because it provides students with basic prerequisites in other useful areas such as problem-solving. Technical students in Brunei are trained with the skills needed in the world of industry and commerce to become competent workers and many of them continue to pursue higher education. They need the right balance of mathematics that can prepare them for both purposes. Considered to be academically weak, and coming from the system (high schools) whose teaching approaches benefit abstract learners, these students need to be motivated and have their interest in mathematics nurtured. This study is an attempt to improve the mathematical skills of technical students in Brunei by developing a teaching and learning package that can be used by mathematics instructors with their students. The package was designed to provide student-centred instruction and focuses on the learning environment aspects of “Teacher Support”, “Innovation”, “Cooperation”, “Task Orientation” and “Relevance”. These learning environment aspects were incorporated into each category of the ARCS motivational model (Keller, 1983b) for the purpose of enhancing motivation. It was anticipated that students’ mathematical understanding and attitude would be improved when their learning environment and thus their motivation was enhanced.<br>When the package was implemented among a group of technical students, they experienced an approach to the teaching of mathematics that shifted from instruction fostering the procedures of practice and memorisation toward instruction that emphasised mathematical inquiry and conceptual understanding. Integrated curricula and cooperative learning techniques were used to link both the mathematics understanding of materials and their composition to the application of materials in the world of work. The use of technology to pursue mathematical investigations by way of learning aids was encouraged because the impact of technology on education today cannot be ignored. A group of students from two classes were involved in the implementation of the package to determine its effectiveness, for a duration of eight weeks. By applying the pre-experimental design methodology to the study, pre-test and post-test were used to measure students’ cognitive and affective changes. Mathematics proficiency in the categories of procedural skills, conceptual understanding and problem solving abilities were measured and examined by comparing students’ pre- and post-test results. Other forms of assessment such as projects and graded class-work (and homework) and also the communication that took place between the students during discussions were analysed to further validate their mathematical understanding. The learning environment and attitude factors mentioned were identified and validated through surveys, observations and interviews. A learning environment instrument called the College Classroom Environment Inventory (CCEI) was adapted for the purpose of measuring students’ perception of the learning environment.<br>Another instrument named the Attitude Towards Mathematics survey was designed to measure students’ attitude towards mathematics. Both instruments were created, validated and then used to measure students’ affective changes (before and after package implementation) and thus evaluate the efficacy of the package. Besides the quantitative data obtained, the qualitative data from observations and interviews was used to confirm, explain and verify results. The results obtained from this study demonstrated students’ improved cognitive outcome in all areas of mathematical proficiency measured. As for the affective outcome, there were improvements in students’ perception of the classroom environment and also in the attitude category of “Importance” where more post-test than pre-test students agreed on the importance of mathematics in everyday life. The result also indicated associations between cognitive outcomes and a number of the learning environment scales. Students who experienced the package also demonstrated better mathematical understanding compared to those who did not. Students, instructors, curriculum developers and administrators should benefit from the results of this study. The study also provides a starting point for more research of this kind to be carried out for the benefit of technical students in Brunei in particular, and for mathematics students generally.
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Bogered, Gustaf, and Christian Rundquist. "Management Control Systems as a Package and the Impact on Organizational Ambidexterity : A Case Study of a R&D Organization in a Swedish Medical Technology Company." Thesis, Linköpings universitet, Företagsekonomi, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-131052.
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Background: The idea of MCSs operating together in a package is not a new concept. However, not many empirical studies have been made where MCSs have been studied as a package despite studies showing the importance in doing so. The assessment of the performance implications of MCSPs has traditionally been limited to financial measures. Theory suggests that the performance of a MCSP ought to be assessed on a broader scale than conventional output measures. Organizational ambidexterity has been positively associated with a broad variety of performance measures and thus it is used as an assessment tool in this study in response to the need for performance measurement on a broader scale than financial output. Purpose: The purpose of this study is to describe the MCSP in two different phases in the case organization and assess how the MCSP in these two phases promotes the organization’s ability to achieve organizational ambidexterity. Methodology: This study uses a qualitative research strategy and is limited to a single case study in a R&D organization within a Swedish medical technology company. Semistructured qualitative interviews have been used to collect empirical data. Conclusion: The MCSP in the two phases is composed of different MCSs that were found to be used differently. Within the MCSP in both phases, several linkages were revealed between control elements and that some MCSs function to achieve the purposes of other MCSs. This study further concludes that the MCSP of the current phase was found to promote organizational ambidexterity better than the MCSP in the previous phase due to it promoting a better balance between exploitation and exploration.
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Liu, Hangcheng. "EXAMINING THE CONFIRMATORY TETRAD ANALYSIS (CTA) AS A SOLUTION OF THE INADEQUACY OF TRADITIONAL STRUCTURAL EQUATION MODELING (SEM) FIT INDICES." VCU Scholars Compass, 2018. https://scholarscompass.vcu.edu/etd/5565.
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Structural Equation Modeling (SEM) is a framework of statistical methods that allows us to represent complex relationships between variables. SEM is widely used in economics, genetics and the behavioral sciences (e.g. psychology, psychobiology, sociology and medicine). Model complexity is defined as a model’s ability to fit different data patterns and it plays an important role in model selection when applying SEM. As in linear regression, the number of free model parameters is typically used in traditional SEM model fit indices as a measure of the model complexity. However, only using number of free model parameters to indicate SEM model complexity is crude since other contributing factors, such as the type of constraint or functional form are ignored.
To solve this problem, a special technique, Confirmatory Tetrad Analysis (CTA) is examined. A tetrad refers to the difference in the products of certain covariances (or correlations) among four random variables. A structural equation model often implies that some tetrads should be zero. These model implied zero tetrads are called vanishing tetrads. In CTA, the goodness of fit can be determined by testing the null hypothesis that the model implied vanishing tetrads are equal to zero. CTA can be helpful to improve model selection because different functional forms may affect the model implied vanishing tetrad number (t), and models not nested according to the traditional likelihood ratio test may be nested in terms of tetrads.
In this dissertation, an R package was created to perform CTA, a two-step method was developed to determine SEM model complexity using simulated data, and it is demonstrated how the number of vanishing tetrads can be helpful to indicate SEM model complexity in some situations.
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Chan, John Tak Yan. "An interactive computer graphics package for power system analysis based on two-dimensional projections on the voltge space /." Thesis, McGill University, 1987. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=63787.
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Kärcher, Karsten. "Reinventing the package holiday business : new information and communication technologies in the British and German tour operator sectors." Thesis, University of Strathclyde, 1996. http://oleg.lib.strath.ac.uk:80/R/?func=dbin-jump-full&object_id=25330.
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Tour operators and travel agents are threatened with disintermediation in the travel and tourism industry, especially as a consequence of altered customer demand and new information and communication technologies which foster direct bookings. In this thesis, however, it is argued that major European tour operators are reinventing their business activities to adapt to these changes and to secure their strategic position in the package holiday business. These tour operators are in particular developing and implementing new information and communication technology strategies to support both their production and distribution of holiday packages and, moreover, to enable them to automatically assemble and market individually tailored holidays. Data to support this argument was gained from an extensive empirical survey in Britain and Germany. A total of 44 tour operators were interviewed in Britain and Germany, which controlled over 65% of their respective national market shares. The interviewed tour operators also included ten of the top twelve European tour operator groups. Leading tour operator associations and charter airlines were interviewed in addition. This research provides a detailed insight into the tour operator sector, particularly in Britain and Germany, thus contributing to research in the travel and tourism industry. Moreover, a theoretical framework is developed and proposed, largely based on industrial organisation and new institutional economics literature. The application of this framework in this thesis for the study of the package holiday business contributes to travel and tourism research, and provides a useful methodology for the study of a sector or industry.
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Yarar, Nadine [Verfasser], Ulrich R. [Akademischer Betreuer] Orth, and Robert [Gutachter] Mai. "Research on food healthiness : Supporting decisions on public health, package design, and everyday consumption situations / Nadine Yarar ; Gutachter: Robert Mai ; Betreuer: Ulrich R. Orth." Kiel : Universitätsbibliothek Kiel, 2017. http://d-nb.info/1223394204/34.
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Carse, Bruce. "Biomechanical data in the design process : a study of the hands and wrists of older adults during package opening." Thesis, University of Strathclyde, 2010. http://oleg.lib.strath.ac.uk:80/R/?func=dbin-jump-full&object_id=12824.
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Guitton, Yann. "Diversité des composés terpéniques volatils au sein du genre Lavandula : aspects évolutifs et physiologiques." Phd thesis, Université Jean Monnet - Saint-Etienne, 2010. http://tel.archives-ouvertes.fr/tel-00675866.
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La production de lavande concoure au rayonnement de la région Rhône-Alpes. Les applications de l'huile essentielle (HE) de lavande reposent sur la culture de 3 espèces (L. aangustifolia, L. latifolia et L. stoechas et d'un hybride L. x intermedia) aux chémotypes marqués. Le genre Lavandula est un modèle idéal pour comprendre la structuration et l'origine de la diversité des composés organiques volatils (COV) en particulier des terpènes. Les lavandes ont l'avantage d'avoir une aire de distribution large avec des régions bioclimatiques différentes, un nombre d'espèces limité (39) ayant des caractéristiques morphologiques et écologiques variées. Pour caractériser la diversité des COV accumulés dans les espèces du genre et envisager leur évolution, nous avons analysé (GC-MS) les COV de 29 espèces (certaines pour la première fois). Comme souvent chez les plantes, la production de COV dans les inflorescences de lavande est soumise à une régulation spatio-temporelle. L'émission différentielle de COV au cours du temps chez L. angustifolia a été relevée par les agriculteurs qui ont observé une qualité d'HE différente suivant la maturité des inflorescences au moment de la récolte. Pour modéliser ces variations et les corréler avec des étapes du développement de la plante, nous avons analysé, au niveau chimique (GC-FID) et moléculaire (qPCR), les variations temporelles des principaux COV dans les feuilles et les inflorescences (plusieurs années et cultivars). En amont de ces recherches sur les COV du genre Lavandula, différent outils de bioinformatique ont été développés. En particulier, le module " MSeasy " qui permet d'automatiser le rapatriement de données de GC-MS. Ceci constitue un pré-requis pour utiliser la lavande comme modèle d'étude des COV chez les Lamiacées
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Liu, Meng. "A PREDICTIVE PROBABILITY INTERIM DESIGN FOR PHASE II CLINICAL TRIALS WITH CONTINUOUS ENDPOINTS." UKnowledge, 2017. http://uknowledge.uky.edu/epb_etds/15.
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Phase II clinical trials aim to potentially screen out ineffective and identify effective therapies to move forward to randomized phase III trials. Single-arm studies remain the most utilized design in phase II oncology trials, especially in scenarios where a randomized design is simply not practical. Due to concerns regarding excessive toxicity or ineffective new treatment strategies, interim analyses are typically incorporated in the trial, and the choice of statistical methods mainly depends on the type of primary endpoints. For oncology trials, the most common primary objectives in phase II trials include tumor response rate (binary endpoint) and progression disease-free survival (time-to-event endpoint). Interim strategies are well-developed for both endpoints in single-arm phase II trials.
The advent of molecular targeted therapies, often with lower toxicity profiles from traditional cytotoxic treatments, has shifted the drug development paradigm into establishing evidence of biological activity, target modulation and pharmacodynamics effects of these therapies in early phase trials. As such, these trials need to address simultaneous evaluation of safety as well as proof-of-concept of biological marker activity or changes in continuous tumor size instead of binary response rates.
In this dissertation, we extend a predictive probability design for binary outcomes in the single-arm clinical trial setting and develop two interim designs for continuous endpoints, such as continuous tumor shrinkage or change in a biomarker over time. The two-stage design mainly focuses on the futility stopping strategies, while it also has the capacity of early stopping for efficacy. Both optimal and minimax designs are presented for this two-stage design. The multi-stage design has the flexibility of stopping the trial early either due to futility or efficacy. Due to the intense computation and searching strategy we adopt, only the minimax design is presented for this multi-stage design. The multi-stage design allows for up to 40 interim looks with continuous monitoring possible for large and moderate effect sizes, requiring an overall sample size less than 40. The stopping boundaries for both designs are based on predictive probability with normal likelihood and its conjugated prior distributions, while the design itself satisfies the pre-specified type I and type II error rate constraints. From simulation results, when compared with binary endpoints, both designs well preserve statistical properties across different effect sizes with reduced sample size. We also develop an R package, PPSC, and detail it in chapter four, so that both designs can be freely accessible for use in future phase II clinical trials with the collaborative efforts of biostatisticians. Clinical investigators and biostatisticians have the flexibility to specify the parameters from the hypothesis testing framework, searching ranges of the boundaries for predictive probabilities, the number of interim looks involved and if the continuous monitoring is preferred and so on.
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Yan, Donglin. "Bivariate Generalization of the Time-to-Event Conditional Reassessment Method with a Novel Adaptive Randomization Method." UKnowledge, 2018. https://uknowledge.uky.edu/epb_etds/18.
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Phase I clinical trials in oncology aim to evaluate the toxicity risk of new therapies and identify a safe but also effective dose for future studies. Traditional Phase I trials of chemotherapies focus on estimating the maximum tolerated dose (MTD). The rationale for finding the MTD is that better therapeutic effects are expected at higher dose levels as long as the risk of severe toxicity is acceptable. With the advent of a new generation of cancer treatments such as the molecularly targeted agents (MTAs) and immunotherapies, higher dose levels no longer guarantee increased therapeutic effects, and the focus has shifted to estimating the optimal biological dose (OBD). The OBD is a dose level with the highest biologic activity with acceptable toxicity. The search for OBD requires joint evaluation of toxicity and efficacy. Although several seamleass phase I/II designs have been published in recent years, there is not a consensus regarding an optimal design and further improvement is needed for some designs to be widely used in practice.
In this dissertation, we propose a modification to an existing seamless phase I/II design by Wages and Tait (2015) for locating the OBD based on binary outcomes, and extend it to time to event (TITE) endpoints. While the original design showed promising results, we hypothesized that performance could be improved by replacing the original adaptive randomization stage with a different randomization strategy. We proposed to calculate dose assigning probabilities by averaging all candidate models that fit the observed data reasonably well, as opposed to the original design that based all calculations on one best-fit model. We proposed three different strategies to select and average among candidate models, and simulations are used to compare the proposed strategies to the original design. Under most scenarios, one of the proposed strategies allocates more patients to the optimal dose while improving accuracy in selecting the final optimal dose without increasing the overall risk of toxicity.
We further extend this design to TITE endpoints to address a potential issue of delayed outcomes. The original design is most appropriate when both toxicity and efficacy outcomes can be observed shortly after the treatment, but delayed outcomes are common, especially for efficacy endpoints. The motivating example for this TITE extension is a Phase I/II study evaluating optimal dosing of all-trans retinoic acid (ATRA) in combination with a fixed dose of daratumumab in the treatment of relapsed or refractory multiple myeloma. The toxicity endpoint is observed in one cycle of therapy (i.e., 4 weeks) while the efficacy endpoint is assessed after 8 weeks of treatment. The difference in endpoint observation windows causes logistical challenges in conducting the trial, since it is not acceptable in practice to wait until both outcomes for each participant have been observed before sequentially assigning the dose of a newly eligible participant. The result would be a delay in treatment for patients and undesirably long trial duration. To address this issue, we generalize the time-to-event continual reassessment method (TITE-CRM) to bivariate outcomes with potentially non-monotonic dose-efficacy relationship. Simulation studies show that the proposed TITE design maintains similar probability in selecting the correct OBD comparing to the binary original design, but the number of patients treated at the OBD decreases as the rate of enrollment increases.
We also develop an R package for the proposed methods and document the R functions used in this research. The functions in this R package assist implementation of the proposed randomization strategy and design. The input and output format of these functions follow similar formatting of existing R packages such as "dfcrm" or "pocrm" to allow direct comparison of results. Input parameters include efficacy skeletons, prior distribution of any model parameters, escalation restrictions, design method, and observed data. Output includes recommended dose level for the next patient, MTD, estimated model parameters, and estimated probabilities of each set of skeletons. Simulation functions are included in this R package so that the proposed methods can be used to design a trial based on certain parameters and assess performance. Parameters of these scenarios include total sample size, true dose-toxicity relationship, true dose-efficacy relationship, patient recruit rate, delay in toxicity and efficacy responses.
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Costa, Gildete Fernandes da. "Aspectos lingu?stico-ergon?micos em r?tulos: avalia??o da linguagem verbo-visual de r?tulos de embalagens para alimentos achocolatados." Universidade Federal do Rio Grande do Norte, 2011. http://repositorio.ufrn.br:8080/jspui/handle/123456789/15021.
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Previous issue date: 2011-12-12<br>We have been living in a world of packed products. The package and the labels support the companies to communicate with the customers in addition to give protection, storage and convenience in proportion to the products that move in the price list. The labels mainly add up a value which helps the companies differ their products and increase the value of the brands among the final customers. However, the information given in the label are not clear sometimes. It displays a verbal-visual defective language resulted from a poor visibility, legibleness and comprehensibleness of the verbal and visual marks. The aim of this research is to verify, according to the costumers‟ view, the level of the clarity in the informative texts, harmony and ergonomic conformity of the package labels in the chocolate powder of the Claralate brand, considering the linguistic aspects presented on the labels. The criteria to evaluate the chocolate package selected were based on the linguistic field: the organization and the structure of the text derided from the classification of the textual genre; the clarity and the comprehension of the language utilized on those labels. From the ergonomic view, the informative and ergonomic conformity, based on the following requirements: legibility, symbols, characters, reading fields and intermission of the written lines. Therefore, the research done july 2007 and added july 2011 had a structured questionnaire in the interview put to the 118 customers of the chocolate package that go shopping in one of the two supermarkets in Floriano, Piau? S?o Jorge and/or Super Quaresma. The main results of the investigation show that the linguistic aspects in the informative texts of the labels provide the customers‟ expectancy partially, while the consideration of the informative ergonomic analyzed can contribute to the improvement of the information and consequent visual progress of those, on the labels of chocolate package investigated. As recommendation towards the maker of the product, the outcome of the research indicates: harmonize the proportion of the letters and numbers; enlarge the letters size; make the visual information more comprehensive determined by the reading field; put the expiry date in a better visual place<br>Vivemos num mundo de produtos embalados. A embalagem e os r?tulos ajudam as empresas a se comunicarem com os consumidores e a fornecerem prote??o, armazenagem e conveni?ncia, ? medida que os produtos se movimentam na cadeia de valor. Especialmente os r?tulos adicionam um valor que auxilia as empresas a diferenciar seus produtos e a aumentar o valor da marca entre os consumidores finais. Por?m, muitas vezes, as informa??es contidas nos r?tulos das embalagens n?o s?o claras, apresentando uma linguagem verbo-visual deficiente resultante da m? visibilidade, legibilidade e compreensibilidade de signos verbais e visuais. O objetivo dessa pesquisa ? verificar, na vis?o dos consumidores, o n?vel de clareza dos textos informativos, harmonia e conformidade ergon?mica do r?tulo de embalagem do achocolatado em p? Claralate , considerando os aspectos lingu?sticos e ergon?micos presentes no r?tulo do produto. Os crit?rios para avalia??o da embalagem do achocolatado selecionado foram do ponto de vista lingu?stico: a organiza??o e estrutura??o dos textos a partir da classifica??o do g?nero textual; a clareza e compreens?o da linguagem utilizada no r?tulo. Do ponto de vista da ergonomia, a conformidade ergon?mica informacional, com base nos requisitos: legibilidade, s?mbolos, caracteres, campo de leitura e espa?amento de linhas. Para tanto, a pesquisa de campo realizada em julho de 2007 e, ampliada em julho de 2011, utilizou um question?rio estruturado na entrevista a 118 consumidores de achocolatados que realizam suas compras em um dos dois supermercados de Floriano-Pi. S?o Jorge e/ou Super Quaresma. Os principais resultados da investiga??o mostram que os aspectos lingu?sticos presentes nos textos informativos do r?tulo atendem parcialmente ?s expectativas dos consumidores, enquanto a considera??o dos requisitos ergon?micos informacionais analisados podem vir a contribuir para o aperfei?oamento das informa??es e consequente melhoria visual destas, no r?tulo de embalagem do achocolatado investigado. Como recomenda??o ? fabricante do produto, o resultado da pesquisa aponta: Harmonizar a propor??o das letras e algarismos; Aumentar o tamanho das letras; Tornar melhor compreensiva a informa??o visual determinada pelos campos de leitura; Colocar a data de validade em local de melhor destaque