Gov 1005: Data David Kane
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Navigating the R Package Universe by Julia Silge, John C
CONTRIBUTED RESEARCH ARTICLES 558 Navigating the R Package Universe by Julia Silge, John C. Nash, and Spencer Graves Abstract Today, the enormous number of contributed packages available to R users outstrips any given user’s ability to understand how these packages work, their relative merits, or how they are related to each other. We organized a plenary session at useR!2017 in Brussels for the R community to think through these issues and ways forward. This session considered three key points of discussion. Users can navigate the universe of R packages with (1) capabilities for directly searching for R packages, (2) guidance for which packages to use, e.g., from CRAN Task Views and other sources, and (3) access to common interfaces for alternative approaches to essentially the same problem. Introduction As of our writing, there are over 13,000 packages on CRAN. R users must approach this abundance of packages with effective strategies to find what they need and choose which packages to invest time in learning how to use. At useR!2017 in Brussels, we organized a plenary session on this issue, with three themes: search, guidance, and unification. Here, we summarize these important themes, the discussion in our community both at useR!2017 and in the intervening months, and where we can go from here. Users need options to search R packages, perhaps the content of DESCRIPTION files, documenta- tion files, or other components of R packages. One author (SG) has worked on the issue of searching for R functions from within R itself in the sos package (Graves et al., 2017). -
Downloaded from Ensembl V41 (6), All
IN SILICO APPROACHES TO INVESTIGATING MECHANISMS OF GENE REGULATION by SHANNAN JANELLE HO SUI B.Sc., The University of British Columbia, 2000 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in THE FACULTY OF GRADUATE STUDIES (Genetics) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) March 2008 © Shannan Janelle Ho Sui, 2008 Abstract Identification and characterization of regions influencing the precise spatial and temporal expression of genes is critical to our understanding of gene regulatory networks. Connecting transcription factors to the cis-regulatory elements that they bind and regulate remains a challenging problem in computational biology. The rapid accumulation of whole genome sequences and genome-wide expression data, and advances in alignment algorithms and motif-finding methods, provide opportunities to tackle the important task of dissecting how genes are regulated. Genes exhibiting similar expression profiles are often regulated by common transcription factors. We developed a method for identifying statistically over- represented regulatory motifs in the promoters of co-expressed genes using weight matrix models representing the specificity of known factors. Application of our methods to yeast fermenting in grape must revealed elements that play important roles in utilizing carbon sources. Extension of the method to metazoan genomes via incorporation of comparative sequence analysis facilitated identification of functionally relevant binding sites for sets of tissue-specific genes, and for genes showing similar expression in large-scale expression profiling studies. Further extensions address alternative promoters for human genes and coordinated binding of multiple transcription factors to cis-regulatory modules. Sequence conservation reveals segments of genes of potential interest, but the degree of sequence divergence among human genes and their orthologous sequences varies widely. -
R Generation [1] 25
IN DETAIL > y <- 25 > y R generation [1] 25 14 SIGNIFICANCE August 2018 The story of a statistical programming they shared an interest in what Ihaka calls “playing academic fun language that became a subcultural and games” with statistical computing languages. phenomenon. By Nick Thieme Each had questions about programming languages they wanted to answer. In particular, both Ihaka and Gentleman shared a common knowledge of the language called eyond the age of 5, very few people would profess “Scheme”, and both found the language useful in a variety to have a favourite letter. But if you have ever been of ways. Scheme, however, was unwieldy to type and lacked to a statistics or data science conference, you may desired functionality. Again, convenience brought good have seen more than a few grown adults wearing fortune. Each was familiar with another language, called “S”, Bbadges or stickers with the phrase “I love R!”. and S provided the kind of syntax they wanted. With no blend To these proud badge-wearers, R is much more than the of the two languages commercially available, Gentleman eighteenth letter of the modern English alphabet. The R suggested building something themselves. they love is a programming language that provides a robust Around that time, the University of Auckland needed environment for tabulating, analysing and visualising data, one a programming language to use in its undergraduate statistics powered by a community of millions of users collaborating courses as the school’s current tool had reached the end of its in ways large and small to make statistical computing more useful life. -
BUSMGT 7331: Descriptive Analytics and Visualization
BUSMGT 7331: Descriptive Analytics and Visualization Spring 2019, Term 1 January 7, 2019 Instructor: Hyunwoo Park (https://fisher.osu.edu/people/park.2706) Office: Fisher Hall 632 Email: [email protected] Phone: 614-292-3166 Class Schedule: 8:30am-12:pm Saturday 1/19, 2/2, 2/16 Recitation/Office Hours: Thursdays 6:30pm-8pm at Gerlach 203 (also via WebEx) 1 Course Description Businesses and organizations today collect and store unprecedented quantities of data. In order to make informed decisions with such a massive amount of the accumulated data, organizations seek to adopt and utilize data mining and machine learning techniques. Applying advanced techniques must be preceded by a careful examination of the raw data. This step becomes increasingly important and also easily overlooked as the amount of data increases because human examination is prone to fail without adequate tools to describe a large dataset. Another growing challenge is to communicate a large dataset and complicated models with human decision makers. Descriptive analytics, and visualizations in particular, helps find patterns in the data and communicate the insights in an effective manner. This course aims to equip students with methods and techniques to summarize and communicate the underlying patterns of different types of data. This course serves as a stepping stone for further predictive and prescriptive analytics. 2 Course Learning Outcomes By the end of this course, students should successfully be able to: • Identify various distributions that frequently occur in observational data. • Compute key descriptive statistics from data. • Measure and interpret relationships among variables. • Transform unstructured data such as texts into structured format. -
Introduction to Data Science for Transportation Researchers, Planners, and Engineers
Portland State University PDXScholar Transportation Research and Education Center TREC Final Reports (TREC) 1-2017 Introduction to Data Science for Transportation Researchers, Planners, and Engineers Liming Wang Portland State University Follow this and additional works at: https://pdxscholar.library.pdx.edu/trec_reports Part of the Transportation Commons, Urban Studies Commons, and the Urban Studies and Planning Commons Let us know how access to this document benefits ou.y Recommended Citation Wang, Liming. Introduction to Data Science for Transportation Researchers, Planners, and Engineers. NITC-ED-854. Portland, OR: Transportation Research and Education Center (TREC), 2018. https://doi.org/ 10.15760/trec.192 This Report is brought to you for free and open access. It has been accepted for inclusion in TREC Final Reports by an authorized administrator of PDXScholar. Please contact us if we can make this document more accessible: [email protected]. FINAL REPORT Introduction to Data Science for Transportation Researchers, Planners, and Engineers NITC-ED-854 January 2018 NITC is a U.S. Department of Transportation national university transportation center. INTRODUCTION TO DATA SCIENCE FOR TRANSPORTATION RESEARCHERS, PLANNERS, AND ENGINEERS Final Report NITC-ED-854 by Liming Wang Portland State University for National Institute for Transportation and Communities (NITC) P.O. Box 751 Portland, OR 97207 January 2017 Technical Report Documentation Page 1. Report No. 2. Government Accession No. 3. Recipient’s Catalog No. NITC-ED-854 4. Title and Subtitle 5. Report Date Introduction to Data Science for Transportation Researchers, Planners, and Engineers January 2017 6. Performing Organization Code 7. Author(s) 8. Performing Organization Report No. Liming Wang 9. -
6:30 PM Grand Ballroom Foyer
Printable Program Printed on: 09/23/2021 Wednesday, May 29 Registration SDSS Hours Wed, May 29, 7:00 AM - 6:30 PM Grand Ballroom Foyer SC1 - Welcome to the Tidyverse: An Introduction to R for Data Science Short Course Wed, May 29, 8:00 AM - 5:30 PM Grand Ballroom E Instructor(s): Garrett Grolemund, RStudio Looking for an effective way to learn R? This one day course will teach you a workflow for doing data science with the R language. It focuses on using R's Tidyverse, which is a core set of R packages that are known for their impressive performance and ease of use. We will focus on doing data science, not programming. You'll learn to: * Visualize data with R's ggplot2 package * Wrangle data with R's dplyr package * Fit models with base R, and * Document your work reproducibly with R Markdown Along the way, you will practice using R's syntax, gaining comfort with R through many exercises and examples. Bring your laptop! The workshop will be taught by Garrett Grolemund, an award winning instructor and the co-author of _R for Data Science_. SC2 - Modeling in the Tidyverse Short Course Wed, May 29, 8:00 AM - 5:30 PM Grand Ballroom F Instructor(s): Max Kuhn, RStudio The tidyverse is an opinionated collection of R packages designed for data science. All packages share an underlying design philosophy, grammar, and data structures. In the last two years, a suite of tidyverse packages have been created that focus on modeling. This course walks through the process of modeling data using these tools. -
Patent Landscape Report: Marine Genetic Resources
Patent Landscape Report: Marine Genetic Resources The WIPO patent landscape report project is based on the Development Agenda project DA_19_30_31_01 “Developing Tools for Access to Patent Information” described in document CDIP/4/6, adopted by the Committee on Development and Intellectual Property (CDIP) at its fourth session held from November 16 to November 20, 2009. The purpose of each report is three fold : • It attempts to research and describe the patterns of patenting and innovation activity related to specific technologies in various domains such as health, food and agriculture, climate change related technologies, and others. • WIPO attempts to collaborate for each report with institutional partners (IGOs, NGOs, public institutions of Member States) working in the respec- tive field and having an interest in a specific topic. The collaborative work in the planning and evaluation phases may also serve as a vehicle for these institutions to familiarize themselves with the utilization and exploitation of patent information and related issues of patent protection. WIPO welcomes proposals for collaboration. • Each report also serves as an illustrative example for retrieving patent in- formation in the respective field and how search strategies may be tailored accordingly. It therefore includes detailed explanations of the particular search methodology, the databases used and well documented search queries that should ideally enable the reader to conduct a similar search. Each report of this project is contracted out to an external firm selected in a tendering procedure. The tender is open to a limited number of bidders that were pre-selected based on their submission of an Expression of Interest (EOI). -
Tools for Reproducible Research Organizing Projects; Exploratory Data Analysis
Tools for Reproducible Research Organizing projects; exploratory data analysis Karl Broman Biostatistics & Medical Informatics, UW–Madison kbroman.org github.com/kbroman @kwbroman Course web: kbroman.org/Tools4RR I’m trying to cover two things here: how to organize data analysis projects, so in the end the results will be reproducible and clear, and how to capture the results of exploratory data analysis. The hardest part, regarding organizing projects, concerns how to coordinate collaborative projects: to keep data, code, and results synchronized among collaborators. Regarding exploratory data analysis, we want to capture the whole process: what you’re trying to do, what you’re thinking about, what you’re seeing, and what you’re concluding and why. And we want to do so without getting in the way of the creative process. I’ll sketch what I try to do, and the difficulties I’ve had. But I don’t have all of the answers. File organization and naming are powerful weapons against chaos. – Jenny Bryan 2 You don’t need to be organized, but it sure will help others (or yourself, later), when you try to figure out what it was that you did. Segregate all the materials for a project in one directory/folder on your harddrive. I prefer to separate raw data from processed data, and I put code in a separate directory. Write ReadMe files to explain what’s what. Organizing your stuff Code/d3examples/ /Others/ /PyBroman/ /Rbroman/ /Rqtl/ /Rqtlcharts/ Docs/Talks/ /Meetings/ /Others/ /Papers/ /Resume/ /Reviews/ /Travel/ Play/ Projects/AlanAttie/ /BruceTempel/ /Hassold_QTL/ /Hassold_Age/ /Payseur_Gough/ /PhyloQTL/ /Tar/ 3 This is basically how I organize my hard drive. -
A Guide to Teaching Data Science
A Guide to Teaching Data Science 1,2 1,2 Stephanie C. Hicks , Rafael A. Irizarry 1 Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 2 Department of Biostatistics, Harvard School of Public Health, Boston, MA Emails: Stephanie C. Hicks, [email protected] Rafael A. Irizarry, [email protected] Abstract Demand for data science education is surging and traditional courses offered by statistics departments are not meeting the needs of those seeking this training. This has led to a number of opinion pieces advocating for an update to the Statistics curriculum. The unifying recommendation is that computing should play a more prominent role. We strongly agree with this recommendation, but advocate that the main priority is to bring applications to the forefront as proposed by Nolan and Speed (1999). We also argue that the individuals tasked with developing data science courses should not only have statistical training, but also have experience analyzing data with the main objective of solving real-world problems. Here, we share a set of general principles and offer a detailed guide derived from our successful experience developing and teaching data science courses centered entirely on case studies. We argue for the importance of statistical thinking, as defined by Wild and Pfannkuck (1999) and describe how our approach teaches students three key skills needed to succeed in data science, which we refer to as creating, connecting, and computing. This guide can also be used for statisticians wanting to gain more practical knowledge about data science before embarking on teaching a course. -
Advanced Environmental Data Analysis Bren School of Environmental Science & Management
ESM 244: Advanced Environmental Data Analysis Bren School of Environmental Science & Management Live weekly check-in: 30 minutes (time TBD) Live weekly discussions: Each student will attend a 50-minute live discussion weekly (times TBD) Lectures: Pre-recorded (~75 - 90 minutes total each week) Labs: Pre-recorded (~60 minutes each week) Course forum: Slack (you should have received an email invite)) Instructor: Allison Horst ([email protected]) Office Hours: TBD Teaching Assistant: Casey O’Hara ([email protected]) Office Hours: TBD Overview: ESM 244 is a survey course in advanced topics in environmental data analysis, including: logistic regression, bootstrapping, intro to wrangling and analyzing time series data, spatial data visualization and analysis, principal components analysis, hierarchical cluster analysis, and basic text mining. Focus is on building conceptual understanding and applied skills using real-world environmental datasets. Students will also learn modern methods for publication in data science, including by building a website and Shiny app in R. Throughout, we will reinforce skills for data management and organization, reproducible workflows and collaboration in R, RStudio and GitHub. ESM 244 LEARNING OBJECTIVES: ● Building on statistics and regression basics from ESM 206, learn advanced methods for analyzing environmental data including logistic regression, time series data, and spatial analysis ● Grow skills for data wrangling, reshaping, and visualization with functional programming -
User! 2018 Trivia Contest Team Members: Team Name
useR! 2018 Trivia Contest Team members: Team name: 1. (1pt) What is the birth city of R? A. Auckland B. Vienna C. San Francisco D. Boston E. Tokyo F. Brisbane 2. (3pts) Match package maintainer to these hex stickers? Maintainer list: Stefan Milton Bache, Jenny Bryan, Jonathan Carroll, Matteo Fasolo, Saskia Freytag, Jim Hester, Heike Hofmann, Rob Hyndman, Stephanie Kovalchik, Max Kuhn, Thomas Lin Pedersen, Anna Quaglieri, David Robinson, Julia Silge, Adam Sparks, Shian Su, Heather Turner, Earo Wang, Hadley Wickham, Kevin Wright, Yihui Xie, Luke Zappia. 3. (1pt) What year was the S language introduced? 4. (2pts) How many women were in the original team of five that introduced the S language? 5. (2pts) Why was <- and hence also, -> chosen as the assignment operator in favour of = in the original R language? 6. (1pt) What other character was used as an assignment operator historically in the S lan- guage, that has since been abandoned? (Hint: It was a convenient character to type on a TTY37 keyboard.) 7. (3pts) What do each of the following expressions return: NA + 0, NA * 0, NA ^ 0 ? 8. (1pt) What type of object does this code return? df <- data.frame(xyz = "a") df$x 9. (2pts) What is sum(1, 2, 3)? What is mean(1, 2, 3)? 10. (2pts) What do the "ct" and "lt" stand for at the end of the POSIXt time-date classes, POSIXct, POSIXlt? 11. (3pts) Name 3 members of R core. 12. (3pts) How many packages have ever been published on CRAN as of July 10, 2018? (Using the code by daroczig/get-data.R) 13. -
A Complete Bibliography of Publications in R News and the R Journal
A Complete Bibliography of Publications in R News and the R Journal Nelson H. F. Beebe University of Utah Department of Mathematics, 110 LCB 155 S 1400 E RM 233 Salt Lake City, UT 84112-0090 USA Tel: +1 801 581 5254 FAX: +1 801 581 4148 E-mail: [email protected], [email protected], [email protected] (Internet) WWW URL: http://www.math.utah.edu/~beebe/ 21 May 2021 Version 1.02 Title word cross-reference 4 [Ray01]. 4.0 [KMH20]. 5 [SFMR16]. 3 [MSC14]. 4 [MSC14]. g [Pra20]. H 6th [LG13]. [HNL12, Pra20]. K [DDC07, Pra20, WS11]. O(1) [O'N15]. R × C [LMK07]. t Aalen [ABS08, WBS06]. abctools [NP15]. [AHvD09, AH10, Hof13, HBG01, Liu14, Academic [BSZWW14]. Accelerated MUX20, Suc13]. [KF16, SP15]. Acceleration [BK19]. Accelerometer [VP14]. Access -and- [Pra20]. -EGARCH [Suc13]. [Car06, KRJ16, Wal16]. Accessing [Lig06]. -likelihood [HNL12]. -means [WS11]. Accountable [GGHB18]. Achievement -Statistics [Liu14]. -table [DDC07]. [LDM03]. acids [WV06]. across [COGRB16]. ACSNMineR [DBB+16]. 2.0.0 [Rip04]. 2.1.0 [Rip05a, Rip05b]. 2013 Actual [OOFdlFS+16]. actuar [GP08]. [Use13, Ulr13]. 2015 [Tve15]. 2016 Adaptive [AHvD09, Yoo18]. Add [OS18]. [BAB+17, Ric16]. 2017 [BDH17, Ver17]. Add-on [OS18]. added [BGK18]. 2018 [AdSQ18, BKJ+18, Dar18, Ric18]. Addendum [GE14]. addhaz [dLN+18]. 2019 [BPC+20, CvDMvE19]. 22K [Dem16]. 1 2 Additive [BTH+17, SS18]. ade4 [GBB+17]. anomalyDetection [GBB+17]. [CT06, CDT04, DDC07]. adegraphics Anonymization [LOM20]. Antimicrobial [SJLD+17]. Adjusted [BFK+20]. [ORVT15]. apc [Nie15]. apComplex Adjusting [GK17]. AdMit [AHvD09]. [Sch06]. API [GdC11, Win17]. Apple Advanced [B¨ur18, OS18]. AFM [BBTH17]. [AZJH12]. Application [BND11, BS12, afmToolkit [BBTH17].