Relevant bibliographies by topics / R packages

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  2. Dissertations / Theses
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  5. Conference papers
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Academic literature on the topic 'R packages'

Author: Grafiati
Published: 4 June 2021
Last updated: 12 February 2022

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Journal articles on the topic "R packages"

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Gonçalves, Emanuel, and Julio Saez-Rodriguez. "Cyrface: An interface from Cytoscape to R that provides a user interface to R packages." F1000Research 2 (September 19, 2013): 192. http://dx.doi.org/10.12688/f1000research.2-192.v1.

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There is an increasing number of software packages to analyse biological experimental data in the R environment. In particular, Bioconductor, a repository of curated R packages, is one of the most comprehensive resources for bioinformatics and biostatistics. The use of these packages is increasing, but it requires a basic understanding of the R language, as well as the syntax of the specific package used. The availability of user graphical interfaces for these packages would decrease the learning curve and broaden their application. Here, we present a Cytoscape plug-in termed Cyrface that allows Cytoscape plug-ins to connect to any function and package developed in R. Cyrface can be used to run R packages from within the Cytoscape environment making use of a graphical user interface. Moreover, it links the R packages with the capabilities of Cytoscape and its plug-ins, in particular network visualization and analysis. Cyrface’s utility has been demonstrated for two Bioconductor packages (CellNOptR and DrugVsDisease), and here we further illustrate its usage by implementing a workflow of data analysis and visualization. Download links, installation instructions and user guides can be accessed from the Cyrface homepage (http://www.ebi.ac.uk/saezrodriguez/cyrface/).
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Gonçalves, Emanuel, Franz Mirlach, and Julio Saez-Rodriguez. "Cyrface: An interface from Cytoscape to R that provides a user interface to R packages." F1000Research 2 (July 1, 2014): 192. http://dx.doi.org/10.12688/f1000research.2-192.v2.

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There is an increasing number of software packages to analyse biological experimental data in the R environment. In particular, Bioconductor, a repository of curated R packages, is one of the most comprehensive resources for bioinformatics and biostatistics. The use of these packages is increasing, but it requires a basic understanding of the R language, as well as the syntax of the specific package used. The availability of user graphical interfaces for these packages would decrease the learning curve and broaden their application. Here, we present a Cytoscape app termed Cyrface that allows Cytoscape apps to connect to any function and package developed in R. Cyrface can be used to run R packages from within the Cytoscape environment making use of a graphical user interface. Moreover, it can link R packages with the capabilities of Cytoscape and its apps, in particular network visualization and analysis. Cyrface’s utility has been demonstrated for two Bioconductor packages (CellNOptR and DrugVsDisease), and here we further illustrate its usage by implementing a workflow of data analysis and visualization. Download links, installation instructions and user guides can be accessed from the Cyrface’s homepage (http://www.ebi.ac.uk/saezrodriguez/cyrface/) and from the Cytoscape app store (http://apps.cytoscape.org/apps/cyrface).
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Schumacker, Randall. "Psychometric Packages in R." Measurement: Interdisciplinary Research and Perspectives 17, no. 2 (April 3, 2019): 106–12. http://dx.doi.org/10.1080/15366367.2018.1544434.

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Polanin, Joshua R., Emily A. Hennessy, and Emily E. Tanner-Smith. "A Review of Meta-Analysis Packages in R." Journal of Educational and Behavioral Statistics 42, no. 2 (November 30, 2016): 206–42. http://dx.doi.org/10.3102/1076998616674315.

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Meta-analysis is a statistical technique that allows an analyst to synthesize effect sizes from multiple primary studies. To estimate meta-analysis models, the open-source statistical environment R is quickly becoming a popular choice. The meta-analytic community has contributed to this growth by developing numerous packages specific to meta-analysis. The purpose of this study is to locate all publicly available meta-analytic R packages. We located 63 packages via a comprehensive online search. To help elucidate these functionalities to the field, we describe each of the packages, recommend applications for researchers interested in using R for meta-analyses, provide a brief tutorial of two meta-analysis packages, and make suggestions for future meta-analytic R package creators.
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Hraber, Peter. "Language games: Advanced R & R packages." Complexity 21, S2 (March 23, 2016): 635–40. http://dx.doi.org/10.1002/cplx.21780.

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Victor Oribamise, B., and Lauren L. Hulsman Hanna. "37 Sibs: an R toolkit for computation of relatedness measures using large pedigrees." Journal of Animal Science 98, Supplement_3 (November 2, 2020): 41–42. http://dx.doi.org/10.1093/jas/skaa054.074.

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Abstract Without appropriate relationships present in a given population, identifying dominance effects in the expression of desirable traits is challenging. Including non-additive effects is desirable to increase accuracy of breeding values. There is no current user-friendly tool package to investigate genetic relatedness in large pedigrees. The objective was to develop and implement efficient algorithms in R to calculate and visualize measures of relatedness (e.g., sibling and family structure, numerator relationship matrices) for large pedigrees. Comparisons to current R packages (Table 1) are also made. Functions to assign animals to families, summary of sibling counts, calculation of numerator relationship matrix (NRM), and NRM summary by groups were created, providing a comprehensive toolkit (Sibs package) not found in other packages. Pedigrees of various sizes (n = 20, 4,035, 120,000 and 132,833) were used to test functionality and compare to current packages. All runs were conducted on a Windows-based computer with an 8 GB RAM, 2.5 GHz Intel Core i7 processor. Other packages had no significant difference in runtime when constructing the NRM for small pedigrees (n = 20) compared to Sibs (0 to 0.05 s difference). However, packages such as ggroups, AGHmatrix, and pedigree were 10 to 15 min slower than Sibs for a 4,035-individual pedigree. Packages nadiv and pedigreemm competed with Sibs (0.30 to 60 s slower than Sibs), but no package besides Sibs was able to complete the 132,833-individual pedigree due to memory allocation issues in R. The nadiv package was closest with a pedigree of 120,000 individuals, but took 37 min to complete (13 min slower than Sibs). This package also provides easier input of pedigrees and is more encompassing of such relatedness measures than other packages (Table 1). Furthermore, it can provide an option to utilize other packages such as GCA for connectedness calculations when using large pedigrees.
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Astagneau, Paul C., Guillaume Thirel, Olivier Delaigue, Joseph H. A. Guillaume, Juraj Parajka, Claudia C. Brauer, Alberto Viglione, Wouter Buytaert, and Keith J. Beven. "Technical note: Hydrology modelling R packages – a unified analysis of models and practicalities from a user perspective." Hydrology and Earth System Sciences 25, no. 7 (July 8, 2021): 3937–73. http://dx.doi.org/10.5194/hess-25-3937-2021.

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Abstract. Following the rise of R as a scientific programming language, the increasing requirement for more transferable research and the growth of data availability in hydrology, R packages containing hydrological models are becoming more and more available as an open-source resource to hydrologists. Corresponding to the core of the hydrological studies workflow, their value is increasingly meaningful regarding the reliability of methods and results. Despite package and model distinctiveness, no study has ever provided a comparison of R packages for conceptual rainfall–runoff modelling from a user perspective by contrasting their philosophy, model characteristics and ease of use. We have selected eight packages based on our ability to consistently run their models on simple hydrology modelling examples. We have uniformly analysed the exact structure of seven of the hydrological models integrated into these R packages in terms of conceptual storages and fluxes, spatial discretisation, data requirements and output provided. The analysis showed that very different modelling choices are associated with these packages, which emphasises various hydrological concepts. These specificities are not always sufficiently well explained by the package documentation. Therefore a synthesis of the package functionalities was performed from a user perspective. This synthesis helps to inform the selection of which packages could/should be used depending on the problem at hand. In this regard, the technical features, documentation, R implementations and computational times were investigated. Moreover, by providing a framework for package comparison, this study is a step forward towards supporting more transferable and reusable methods and results for hydrological modelling in R.
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Mowinckel, Athanasia M., and Didac Vidal-Piñeiro. "Visualization of Brain Statistics With R Packages ggseg and ggseg3d." Advances in Methods and Practices in Psychological Science 3, no. 4 (November 30, 2020): 466–83. http://dx.doi.org/10.1177/2515245920928009.

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There is an increased emphasis on visualizing neuroimaging results in more intuitive ways. Common statistical tools for dissemination of these results, such as bar charts, lack the spatial dimension that is inherent in neuroimaging data. Here we present two packages for the statistical software R that integrate this spatial component. The ggseg and ggseg3d packages visualize predefined brain segmentations as 2D polygons and 3D meshes, respectively. Both packages are integrated with other well-established R packages, which allows great flexibility. In this Tutorial, we describe the main data and functions in the ggseg and ggseg3d packages for visualization of brain atlases. The highlighted functions are able to display brain-segmentation plots in R. Further, the accompanying ggsegExtra package includes a wider collection of atlases and is intended for community-based efforts to develop additional compatible atlases for ggseg and ggseg3d. Overall, the ggseg packages facilitate parcellation-based visualizations in R, improve and facilitate the dissemination of results, and increase the efficiency of workflows.
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Kyritsis, Konstantinos A., Bing Wang, Julie Sullivan, Rachel Lyne, and Gos Micklem. "InterMineR: an R package for InterMine databases." Bioinformatics 35, no. 17 (January 22, 2019): 3206–7. http://dx.doi.org/10.1093/bioinformatics/btz039.

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Abstract Summary InterMineR is a package designed to provide a flexible interface between the R programming environment and biological databases built using the InterMine platform. The package offers access to the flexible query builder and the library of term enrichment tools of the InterMine framework, as well as interoperability with other Bioconductor packages. This facilitates automation of data retrieval tasks as well as downstream analysis with existing statistical tools in the R environment. Availability and implementation InterMineR is free and open source, released under the LGPL licence and available from the Bioconductor project and Github (https://bioconductor.org/packages/release/bioc/html/InterMineR.html, https://github.com/intermine/interMineR). Supplementary information Supplementary data are available at Bioinformatics online.
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Plummer, Martyn. "Portable C++ for R Packages." R Journal 3, no. 2 (2011): 60. http://dx.doi.org/10.32614/rj-2011-020.

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Dissertations / Theses on the topic "R packages"

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Hornik, Kurt. "Are There Too Many R Packages?" Austrian Statistical Society, c/o Bundesanstalt Statistik Austria, 2012. http://epub.wu.ac.at/3814/1/121Hornik.pdf.

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The number of R extension packages available from the CRAN repository has tremendously grown over the past 10 years. We look at this phenomenon in more detail, and discuss some of its consequences. In particular, we argue that the statistical computing community needs a more common understanding of software quality, and better domain-specific semantic resources.
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Rusch, Thomas, Patrick Mair, and Reinhold Hatzinger. "Psychometrics With R: A Review Of CRAN Packages For Item Response Theory." WU Vienna University of Economics and Business, 2013. http://epub.wu.ac.at/4010/1/resrepIRThandbook.pdf.

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In this paper we review the current state of R packages for Item Response Theory (IRT). We group the available packages based on their purpose and provide an overview of each package's main functionality. Each of the packages we describe has a peer-reviewed publication associated with it. We also provide a tutorial analysis of data from the 1990 Workplace Industrial Relation Survey to show how the breadth and exibility of IRT packages in R can be leveraged to conduct even challenging item analyses with versatility and ease. These items relate to the type of consultations that are carried out in a firm when major changes are implemented. We first use unidimensional IRT models just to discover that they fit do not fit well. We then use nonparametric IRT to explore the possible causes for the scaling problem. Based on the results from the exploration, we finally use a two-dimensional model on a subset of the original items to achieve a good fit with a sensible interpretation, namely that there are two types of consultations a firm may engage in: consultations with workers/representatives from the firm and with official union representatives. The different items relate mostly to one of these dimensions and firms can be scaled well along these two dimensions.
Series: Discussion Paper Series / Center for Empirical Research Methods
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Granato, Italo Stefanine Correia. "snpReady and BGGE: R packages to prepare datasets and perform genome-enabled predictions." Universidade de São Paulo, 2018. http://www.teses.usp.br/teses/disponiveis/11/11137/tde-21062018-134207/.

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The use of molecular markers allows an increase in efficiency of the selection as well as better understanding of genetic resources in breeding programs. However, with the increase in the number of markers, it is necessary to process it before it can be ready to use. Also, to explore Genotype x Environment (GE) in the context of genomic prediction some covariance matrices needs to be set up before the prediction step. Thus, aiming to facilitate the introduction of genomic practices in the breeding program pipelines, we developed two R-packages. The former is called snpReady, which is set to prepare data sets to perform genomic studies. This package offers three functions to reach this objective, from organizing and apply the quality control, build the genomic relationship matrix and a summary of a population genetics. Furthermore, we present a new imputation method for missing markers. The latter is the BGGE package that was built to generate kernels for some GE genomic models and perform predictions. It consists of two functions (getK and BGGE). The former is helpful to create kernels for the GE genomic models, and the latter performs genomic predictions with some features for GE kernels that decreases the computational time. The features covered in the two packages presents a fast and straightforward option to help the introduction and usage of genome analysis in the breeding program pipeline.
O uso de marcadores moleculares permite um aumento na eficiência da seleção, bem como uma melhor compreensão dos recursos genéticos em programas de melhoramento. No entanto, com o aumento do número de marcadores, é necessário o processamento deste antes de deixa-lo disponível para uso. Além disso, para explorar a interação genótipo x ambiente (GA) no contexto da predição genômica, algumas matrizes de covariância precisam ser obtidas antes da etapa de predição. Assim, com o objetivo de facilitar a introdução de práticas genômicas nos programa de melhoramento, dois pacotes em R foram desenvolvidos. O primeiro, snpReady, foi criado para preparar conjuntos de dados para realizar estudos genômicos. Este pacote oferece três funções para atingir esse objetivo, organizando e aplicando o controle de qualidade, construindo a matriz de parentesco genômico e com estimativas de parâmetros genéticos populacionais. Além disso, apresentamos um novo método de imputação para marcas perdidas. O segundo pacote é o BGGE, criado para gerar kernels para alguns modelos genômicos de interação GA e realizar predições genômicas. Consiste em duas funções (getK e BGGE). A primeira é utilizada para criar kernels para os modelos GA, e a última realiza predições genômicas, com alguns recursos especifico para os kernels GA que diminuem o tempo computacional. Os recursos abordados nos dois pacotes apresentam uma opção rápida e direta para ajudar a introdução e uso de análises genômicas nas diversas etapas do programa de melhoramento.
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Kozinski, Lukasz. "Constant protectionism in the financial meltdown: are national stimulas packages new forms of protection alongside currency devaluation?" Thesis, McGill University, 2011. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=104530.

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Deriving from research of the two North American economies, the study investigated the nature and makeup of various stimulus policies enacted by the respective governments in response to the recent financial crisis. Specific attention was given to identifying the most significant industry recipients of stimulus offerings. World Trade Organization (WTO) dispute histories for the American and Canadian economies were investigated to find parallels between recent fiscal stimulus offerings amongst various industry beneficiaries and past instances of international trade disputes. Evidence of national stimulus packages being new sources of protection for traditional recipients was discovered. American WTO disputes targeting important stimulus recipients during the crisis period underlined international identification of that country's fiscal policies as protectionist in several economic sectors. Periods of American Dollar depreciation are thought to have exacerbated recent international reactions. No such marked parallel in recent disputes was found for Canada, though it is believed that clear Canadian Dollar appreciation over the past two years is the explanatory factor for this reserved international reaction. Stimulus in conjunction with depreciation, it would seem have been accepted to a lesser degree than stimulus alone. Central, however, is the finding that stimulus packages for both nations were found to focus on industries historically inclined on protectionism.
Émanant de la recherche sur les deux economies Nord-Américaines, l'étude a investigué la composition de plusieurs projets de stimule fiscal de ces deux nations en réponse à la crise financière récente. Plus précisement, la recherche a visé les industries et secteurs économiques les plus affectés par les offres de stimule des gouvernments Canadien et Americain. L'histoire des disputes précédentes à l'Organisation Mondiale du Commerce (OMC) du Canada et des États-Unis à été investigué afin de pouvior identifier des parallèles entre les bénéficiers des stimules contemporains et des tendances de protéctionisme chez ces deux economies dans le passé. Des preuves signifiantes de nouvelles sources de protection des industries nationaux ont été découvertes. Plusieures disputes dans l'OMC contre les industries Américaines qui ont réçu des niveau de stimule importantes pendants la crise ont soulignés le charactère protectioniste des project fiscaux proposés par ce pays. La dévaluation en valeur du Dollar Américain est presumée d'être la cause des réactions négatives internationals. Le stimule Canadien n'a pas crée une reaction internationale aussi marquée mais l'appréciation soulignée du Dollar Canadien pendants les deux dernières années est presumée d'être la raison de ce restraint des partenaires d'échange international du Canada. L'application des stimules économiques en conjunction avec une chute de valeur de la monnaie nationale n'a pas donc été acceptée au même niveau que les stimules seulements. Néamoins, et au centre de cette invéstigation, les projects de stimules fiscaux proposés part les deux économies ont été démasquées pour être des nouvelles sources de protéction pour des récipients historiquement protéctionistes.
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Dehghannya, Jalal. "Mathematical modeling of airflow, heat and mass transfer during forced convection cooling of produce in ventilated packages." Thesis, McGill University, 2008. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=115663.

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Forced convection cooling process is the most widely used method of cooling to extend shelf life of horticultural produce after harvest. However, heterogeneous cooling of produce inside different parts of ventilated packages is a serious problem. Therefore, it is essential to design packages that facilitate air circulation throughout the entire package to provide uniform cooling. Selection of appropriate combinations of air temperature and velocity for a given vent design is currently done largely by experimental trial and error approach. A more logical approach in designing new packages, to provide uniform cooling, is to develop mathematical models that would be able to predict package performance without requiring costly experiments.
In this study, mathematical models of simultaneous airflow, heat and mass transfer during forced convection cooling process were developed and validated with experimental data. The study showed that produce cooling is strongly influenced by different ventilated package designs. Generally, cooling uniformity was increased by increasing number of vents from 1 (2.4% vent area) to 5 (12.1% vent area). More uniform produce cooling was obtained at less cooling time when vents were uniformly distributed on package walls with at least 4.8% opening areas. Aerodynamic studies showed that heterogeneity of airflow distribution during the process is strongly influenced by different package vent configurations. The highest cooling heterogeneity index (108%) was recorded at 2.4% vent area whereas lowest heterogeneity index (0%) was detected in a package with 12.1% vent area.
The magnitudes of produce evaporative cooling (EC) and heat generation by respiration (HG) as well as the interactive effects of EC, HG and package vent design on produce cooling time were also investigated. Considerable differences in cooling times were obtained with regard to independent and simultaneous effects of EC and HG in different package vent configurations. Cooling time was increased to about 47% in a package with 1 vent compared to packages with 3 and 5 vents considering simultaneous effects of EC and HG. Therefore, the effects of EC and HG can be influential in designing the forced-air precooling system and consequently, in the accurate determination of cooling time and the corresponding refrigeration load.
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Lee, Harry B. "A comparative analysis of lectures versus interactive computer-assisted learning packages for the teaching and learning of anatomy by tertiary students." Curtin University of Technology, Faculty of Education, 1996. http://espace.library.curtin.edu.au:80/R/?func=dbin-jump-full&object_id=11232.

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The primary aim of this study was to validate interactive computer-assisted learning packages (ICALP) in a self operated computer controlled educational resource (SOCCER) to undergraduate (UG) physiotherapy students of anatomy. The development of ICALP, Test and FeedBack items for SOCCER are described, as well as the mechanism of delivery with continuous positive reinforcement to randomly selected students. To meet this requirement, a computer managed learning environment (CMLE) was established to affirm the value of ICALP and SOCCER materials to replace traditional lectures in anatomy. Quantitative data is given to verify this hypothesis during the education of UG physiotherapy students of anatomy. Throughout 1992, the UG population was randomly divided into Lecture and ICALP groups, with mutual exclusion of each to the other, for ten areas of study. These results were validated by re-application to the succeeding UG population in 1993. The secondary aim of this study was in two-parts. Firstly, to verify that ICALP materials can be applied to transfer 2-D cognitive anatomical information in a self-paced format of autonomous learning. Secondly, to investigate a premise that previously acquired 2-D anatomical information may be transferred into a 3-D psycho-motor skill. Ample data is given to verify the first hypothesis, with sufficient evidence to support the second. The subsidiary aim of this study compared the educational and administrative cost-effectiveness of ICALP and SOCCER with traditional lectures used in anatomy. Evidence is given to demonstrate that the time saved in lectures can be replaced by a lecture-seminar approach to problem-based learning to empower UG2 students to achieve at a level beyond that which would normally be expected. Sufficient data is provided to affirm the cost-benefits of ICALP and SOCCER to academic staff, individual students, and ++
administrators. The untested belief held by schools of anatomy that high ranking pre-entrants in English, English Literature, and Human Biology, are more likely to transpose 2-D anatomical information into a 3-D skill than high ranking pre-entrants in Mathematics, Chemistry and Physics was also investigated. Scrutiny of these data could not determine any discriminatory differences of ability to succeed in UG anatomy by either of these two categories.
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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.
Series: Research Report Series / Department of Statistics and Mathematics
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Privé, Florian. "Genetic risk score based on statistical learning Efficient analysis of large-scale genome-wide data with two R packages: bigstatsr and bigsnpr Efficient implementation of penalized regression for genetic risk prediction Making the most of Clumping and Thresholding for polygenic scores." Thesis, Université Grenoble Alpes (ComUE), 2019. http://www.theses.fr/2019GREAS024.

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Le génotypage devient de moins en moins cher, rendant les données de génotypes disponibles pour des millions d’individus. Par ailleurs, l’imputation permet d’obtenir l’information génotypique pour des millions de positions de l’ADN, capturant l’essentiel de la variation génétique du génome humain. Compte tenu de la richesse des données et du fait que de nombreux traits et maladies sont héréditaires (par exemple, la génétique peut expliquer 80% de la variation de la taille dans la population), il est envisagé d’utiliser des modèles prédictifs basés sur l’information génétique dans le cadre d’une médecine personnalisée.Au cours de ma thèse, je me suis concentré sur l’amélioration de la capacité prédictive des modèles polygéniques. Les modèles prédictifs faisant partie d’une analyse statistique plus large des jeux de données, j’ai développé des outils permettant l’analyse exploratoire de grands jeux de données, constitués de deux packages R/C++ décrits dans la première partie de ma thèse. Ensuite, j’ai développé une implémentation efficace de larégression pénalisée pour construire des modèles polygéniques basés sur des centaines de milliers d’individus génotypés. Enfin, j’ai amélioré la méthode appelée “clumpingand thresholding”, qui est la méthode polygénique la plus largement utilisée et qui estbasée sur des statistiques résumées plus largement accessibles par rapport aux données individuelles.Dans l’ensemble, j’ai appliqué de nombreux concepts d’apprentissage statistique aux données génétiques. J’ai utilisé du “extreme gradient boosting” pour imputer des variants génotypés, du “feature engineering” pour capturer des effets récessifs et dominants dans une régression pénalisée, et du “parameter tuning” et des “stacked regres-sions” pour améliorer les modèles polygéniques prédictifs. L’apprentissage statistique n’est pour l’instant pas très utilisé en génétique humaine et ma thèse est une tentative pour changer cela
Genotyping is becoming cheaper, making genotype data available for millions of indi-viduals. Moreover, imputation enables to get genotype information at millions of locicapturing most of the genetic variation in the human genome. Given such large data andthe fact that many traits and diseases are heritable (e.g. 80% of the variation of heightin the population can be explained by genetics), it is envisioned that predictive modelsbased on genetic information will be part of a personalized medicine.In my thesis work, I focused on improving predictive ability of polygenic models.Because prediction modeling is part of a larger statistical analysis of datasets, I de-veloped tools to allow flexible exploratory analyses of large datasets, which consist intwo R/C++ packages described in the first part of my thesis. Then, I developed someefficient implementation of penalized regression to build polygenic models based onhundreds of thousands of genotyped individuals. Finally, I improved the “clumping andthresholding” method, which is the most widely used polygenic method and is based onsummary statistics that are widely available as compared to individual-level data.Overall, I applied many concepts of statistical learning to genetic data. I used ex-treme gradient boosting for imputing genotyped variants, feature engineering to cap-ture recessive and dominant effects in penalized regression, and parameter tuning andstacked regressions to improve polygenic prediction. Statistical learning is not widelyused in human genetics and my thesis is an attempt to change that
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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.
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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.
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Books on the topic "R packages"

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Hölzer, Michael. Quality management with SAP R/3: Making it work for your business. Harlow: SAP Press/Addison-Wesley, 2001.

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García Martínez, Constantino Antonio, Abraham Otero Quintana, Xosé A. Vila, María José Lado Touriño, Leandro Rodríguez-Liñares, Jesús María Rodríguez Presedo, and Arturo José Méndez Penín. Heart Rate Variability Analysis with the R package RHRV. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-65355-6.

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Baio, Gianluca, Andrea Berardi, and Anna Heath. Bayesian Cost-Effectiveness Analysis with the R package BCEA. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-55718-2.

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Teufel, T. SAP Business one. Boston, MA: Thomson/Course Technology, 2005.

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Tim, Rhodes, and Davis Jeff, eds. Sams teach yourself SAP in 24 hours. Indianapolis, Ind: Sam Pub., 2008.

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Danielle, Larocca, ed. Sams teach yourself SAP in 24 hours. 2nd ed. Indianapolis, Ind: Sams, 2006.

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Inc, BIEC International, and Indonesia. Direktorat Bina Program Penyiapan Pemukiman., eds. Phase IIIA, final report, Sukaraja WPP XIVa SKP D1 (R): Phase IIIA studies of transmigration settlements development in West Kalimantan (package C). [Jakarta?]: China Engineering Consultants, Inc. in association with BIEC International Inc., 1988.

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Reconnaissance and outline planning and preparation of SP structure plans for transm[i]g[r]ation settlements development Irian Jaya (package J), phase II, final report: SKP Bupul E, WPP XXIII b. [Jakarta]: Republic of Indonesia, Departemen Transmigrasi, Direktorat Jenderal Penyiapan Pemukiman, Direktorat Bina Program, 1987.

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R Packages: Organize, Test, Document, and Share Your Code. O'Reilly, 2015.

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Foundations Of Statistical Algorithms With References To R Packages. Taylor & Francis Ltd, 2013.

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Book chapters on the topic "R packages"

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Zucchini, Walter, Iain L. MacDonald, and Roland Langrock. "R packages." In Hidden Markov Models for Time Series, 123–30. Second edition / Walter Zucchini, Iain L. MacDonald, and Roland Langrock. | Boca Raton : Taylor & Francis, 2016. | Series: Monographs on statistics and applied probability ; 150 | “A CRC title.”: Chapman and Hall/CRC, 2017. http://dx.doi.org/10.1201/b20790-8.

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Arnold, Taylor, and Lauren Tilton. "R Packages." In Quantitative Methods in the Humanities and Social Sciences, 179–82. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-20702-5_11.

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Campbell, Matthew. "Custom R Packages." In Learn RStudio IDE, 113–24. Berkeley, CA: Apress, 2019. http://dx.doi.org/10.1007/978-1-4842-4511-8_10.

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Stowell, Sarah. "Add-On Packages." In Using R for Statistics, 185–92. Berkeley, CA: Apress, 2014. http://dx.doi.org/10.1007/978-1-4842-0139-8_12.

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Monogan, James E. "Obtaining R and Downloading Packages." In Use R!, 1–11. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-23446-5_1.

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Campbell, Matthew. "Essential R Packages: Tidyverse." In Learn RStudio IDE, 63–72. Berkeley, CA: Apress, 2019. http://dx.doi.org/10.1007/978-1-4842-4511-8_6.

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Monogan, James E. "Using Packages to Apply Advanced Models." In Use R!, 127–55. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-23446-5_8.

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Wiley, Matt, and Joshua F. Wiley. "Writing Packages." In Advanced R 4 Data Programming and the Cloud, 129–80. Berkeley, CA: Apress, 2020. http://dx.doi.org/10.1007/978-1-4842-5973-3_6.

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Wiley, Matt, and Joshua F. Wiley. "Installing Packages and Using Libraries." In Beginning R 4, 21–31. Berkeley, CA: Apress, 2020. http://dx.doi.org/10.1007/978-1-4842-6053-1_2.

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Quicke, Donald, Buntika A. Butcher, and Rachel Kruft Welton. "Principal components analysis." In Practical R for biologists: an introduction, 194–99. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789245349.0194.

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Abstract This chapter focuses on how to conduct a principal components analysis. To conduct principal components analysis, R has two similar built-in functions prcomp and princomp in the default stats package. Other implementations can be found in various downloadable packages, e.g. the function PCA from the package FactoMineR, the function dudi.pca from the package ade4 and the function acp from the package amap. The functions prcomp and princomp employ different calculation methods but in practice the results they return will be almost identical.
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Conference papers on the topic "R packages"

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Vidoni, Melina. "Evaluating Unit Testing Practices in R Packages." In 2021 IEEE/ACM 43rd International Conference on Software Engineering (ICSE). IEEE, 2021. http://dx.doi.org/10.1109/icse43902.2021.00136.

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Decan, Alexandre, Tom Mens, Maelick Claes, and Philippe Grosjean. "On the Development and Distribution of R Packages." In ECSAW '15: 2015 European Conference on Software Architecture Workshops. New York, NY, USA: ACM, 2015. http://dx.doi.org/10.1145/2797433.2797476.

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Cho, Wonhee, Yoojin Lim, Hwangro Lee, Mohan Krishna Varma, Moonsoo Lee, and Eunmi Choi. "Big Data Analysis with Interactive Visualization using R packages." In the 2014 International Conference. New York, New York, USA: ACM Press, 2014. http://dx.doi.org/10.1145/2640087.2644168.

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"Self-Admitted Technical Debt in R Packages: An Exploratory Study." In 2021 IEEE/ACM 18th International Conference on Mining Software Repositories (MSR). IEEE, 2021. http://dx.doi.org/10.1109/msr52588.2021.00030.

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Lin, Po-Yao, M. C. Yew, S. S. Yeh, S. M. Chen, C. H. Lin, C. S. Chen, C. C. Hsieh, et al. "Reliability Performance of Advanced Organic Interposer (CoWoS®-R) Packages." In 2021 IEEE 71st Electronic Components and Technology Conference (ECTC). IEEE, 2021. http://dx.doi.org/10.1109/ectc32696.2021.00125.

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Nishiyama, Keita, and Takahiro Sato. "Technical Report on the Creation of Interactive Graphs for Fact Books using R and R Packages." In 2019 8th International Congress on Advanced Applied Informatics (IIAI-AAI). IEEE, 2019. http://dx.doi.org/10.1109/iiai-aai.2019.00081.

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Korkmaz, Gizem, Claire Kelling, Carol Robbins, and Sallie A. Keller. "Modeling the Impact of R Packages Using Dependency and Contributor Networks." In 2018 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM). IEEE, 2018. http://dx.doi.org/10.1109/asonam.2018.8508255.

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Plotog, I., P. Svasta, J. Villain, Z. Illyefalvi-Vitez, A. Pietrikova, M. Branzei, F. Miculescu, et al. "HISOLD 4P Q&R, COST project for solder material innovations and solder joint properties assessment." In 2009 15th International Symposium for Design and Technology of Electronics Packages (SIITME). IEEE, 2009. http://dx.doi.org/10.1109/siitme.2009.5407395.

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Codabux, Zadia, Melina Vidoni, and Fatemeh H. Fard. "Technical Debt in the Peer-Review Documentation of R Packages: a rOpenSci Case Study." In 2021 IEEE/ACM 18th International Conference on Mining Software Repositories (MSR). IEEE, 2021. http://dx.doi.org/10.1109/msr52588.2021.00032.

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Zanella, Gianluca, and Charles Z. Liu. "A Social Network Perspective on the Success of Open Source Software: The Case of R Packages." In Hawaii International Conference on System Sciences. Hawaii International Conference on System Sciences, 2020. http://dx.doi.org/10.24251/hicss.2020.058.

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Reports on the topic "R packages"

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Baker, J., S. Yee, and L. Brand. Analysis of Illinois Home Performance with ENERGY STAR(R) Measure Packages. Office of Scientific and Technical Information (OSTI), September 2013. http://dx.doi.org/10.2172/1096668.

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Buffleben, George M., Timothy J. Shepodd, and Paul J. Nigrey. Evaluation of SAES COMBOGETTER(r) for Use in Nuclear Material Transportation Packages. Office of Scientific and Technical Information (OSTI), January 2001. http://dx.doi.org/10.2172/781980.

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Nash, Edward John, Aiva Jasilioniene, Evgueni M. Andreev, and Kryštof Zeman. A collection of "R" packages for the production of period fertility tables and some summary fertility indicators. Rostock: Max Planck Institute for Demographic Research, February 2011. http://dx.doi.org/10.4054/mpidr-tr-2011-001.

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Castleton, Karl J., Gene Whelan, and Bonnie L. Hoopes. FRAMES Software System: Linking to the Statistical Package R. Office of Scientific and Technical Information (OSTI), December 2006. http://dx.doi.org/10.2172/944521.

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Gu, Jiaying, and Roger Koenker. Rebayes: an R package for empirical bayes mixture methods. The IFS, August 2017. http://dx.doi.org/10.1920/wp.cem.2017.3717.

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Nash, Edward John, Aiva Jasilioniene, and Evgueni M. Andreev. An "R" package for the production of cohort fertility tables. Rostock: Max Planck Institute for Demographic Research, November 2010. http://dx.doi.org/10.4054/mpidr-tr-2010-007.

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Fernandez-Val, Ivan, Michael Lipsitz, Alexandre Belloni, and Victor Chernozhukov. Quantreg.nonpar: an R package for performing nonparametric series quantile regression. The IFS, June 2017. http://dx.doi.org/10.1920/wp.cem.2017.2917.

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Cortez, Paulo. A tutorial on using the rminer R package for data mining tasks. University of Minho, July 2015. http://dx.doi.org/10.21814/1822.36210.

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Jdanov, Dmitri A., and Edward John Nash. An "R" package for the production of a Lexis database of fertility data. Rostock: Max Planck Institute for Demographic Research, May 2011. http://dx.doi.org/10.4054/mpidr-tr-2011-003.

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Spindler, Martin, Victor Chernozhukov, and Philipp Bach. Valid simultaneous inference in high-dimensional settings (with the HDM package for R). The IFS, June 2019. http://dx.doi.org/10.1920/wp.cem.2019.3019.

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