Ggmap: Spatial Visualization with Ggplot2 by David Kahle and Hadley Wickham
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Realistic Modeling and Rendering of Plant Ecosystems
Realistic modeling and rendering of plant ecosystems Oliver Deussen1 Pat Hanrahan2 Bernd Lintermann3 RadomÂõr MechÏ 4 Matt Pharr2 Przemyslaw Prusinkiewicz4 1 Otto-von-Guericke University of Magdeburg 2 Stanford University 3 The ZKM Center for Art and Media Karlsruhe 4 The University of Calgary Abstract grasslands, human-made environments, for instance parks and gar- dens, and intermediate environments, such as lands recolonized by Modeling and rendering of natural scenes with thousands of plants vegetation after forest ®res or logging. Models of these ecosystems poses a number of problems. The terrain must be modeled and plants have a wide range of existing and potential applications, including must be distributed throughout it in a realistic manner, re¯ecting the computer-assisted landscape and garden design, prediction and vi- interactions of plants with each other and with their environment. sualization of the effects of logging on the landscape, visualization Geometric models of individual plants, consistent with their po- of models of ecosystems for research and educational purposes, sitions within the ecosystem, must be synthesized to populate the and synthesis of scenes for computer animations, drive and ¯ight scene. The scene, which may consist of billions of primitives, must simulators, games, and computer art. be rendered ef®ciently while incorporating the subtleties of lighting Beautiful images of forests and meadows were created as early in a natural environment. as 1985 by Reeves and Blau [50] and featured in the computer We have developed a system built around a pipeline of tools that animation The Adventures of Andre and Wally B. [34]. Reeves and address these tasks. -
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). -
Supplementary Materials
Tomic et al, SIMON, an automated machine learning system reveals immune signatures of influenza vaccine responses 1 Supplementary Materials: 2 3 Figure S1. Staining profiles and gating scheme of immune cell subsets analyzed using mass 4 cytometry. Representative gating strategy for phenotype analysis of different blood- 5 derived immune cell subsets analyzed using mass cytometry in the sample from one donor 6 acquired before vaccination. In total PBMC from healthy 187 donors were analyzed using 7 same gating scheme. Text above plots indicates parent population, while arrows show 8 gating strategy defining major immune cell subsets (CD4+ T cells, CD8+ T cells, B cells, 9 NK cells, Tregs, NKT cells, etc.). 10 2 11 12 Figure S2. Distribution of high and low responders included in the initial dataset. Distribution 13 of individuals in groups of high (red, n=64) and low (grey, n=123) responders regarding the 14 (A) CMV status, gender and study year. (B) Age distribution between high and low 15 responders. Age is indicated in years. 16 3 17 18 Figure S3. Assays performed across different clinical studies and study years. Data from 5 19 different clinical studies (Study 15, 17, 18, 21 and 29) were included in the analysis. Flow 20 cytometry was performed only in year 2009, in other years phenotype of immune cells was 21 determined by mass cytometry. Luminex (either 51/63-plex) was performed from 2008 to 22 2014. Finally, signaling capacity of immune cells was analyzed by phosphorylation 23 cytometry (PhosphoFlow) on mass cytometer in 2013 and flow cytometer in all other years. -
Identifying Locations of Social Significance: Aggregating Social Media Content to Create a New Trust Model for Exploring Crowd Sourced Data and Information
Identifying Locations of Social Significance: Aggregating Social Media Content to Create a New Trust Model for Exploring Crowd Sourced Data and Information Al Di Leonardo, Scott Fairgrieve Adam Gribble, Frank Prats, Wyatt Smith, Tracy Sweat, Abe Usher, Derek Woodley, and Jeffrey B. Cozzens The HumanGeo Group, LLC Arlington, Virginia, United States {al,scott,adam,frank,wyatt,tracy,abe,derek}@thehumangeo.com Abstract. Most Internet content is no longer produced directly by corporate organizations or governments. Instead, individuals produce voluminous amounts of informal content in the form of social media updates (micro blogs, Facebook, Twitter, etc.) and other artifacts of community communication on the Web. This grassroots production of information has led to an environment where the quantity of low-quality, non-vetted information dwarfs the amount of professionally produced content. This is especially true in the geospatial domain, where this information onslaught challenges Local and National Governments and Non- Governmental Organizations seeking to make sense of what is happening on the ground. This paper proposes a new model of trust for interpreting locational data without a clear pedigree or lineage. By applying principles of aggregation and inference, it is possible to identify locations of social significance and discover “facts” that are being asserted by crowd sourced information. Keywords: geospatial, social media, aggregation, trust, location. 1 Introduction Gathering geographical data on populations has always constituted an essential element of census taking, political campaigning, assisting in humanitarian disasters/relief, law enforcement, and even in post-conflict areas where grand strategy looks beyond the combat to managing future peace. Warrior philosophers have over the millennia praised indirect approaches to warfare as the most effective means of combat—where influence and information about enemies and their supporters trumps reliance on kinetic operations to achieve military objectives. -
Visualization in Multiobjective Optimization
Final version Visualization in Multiobjective Optimization Bogdan Filipič Tea Tušar Tutorial slides are available at CEC Tutorial, Donostia - San Sebastián, June 5, 2017 http://dis.ijs.si/tea/research.htm Computational Intelligence Group Department of Intelligent Systems Jožef Stefan Institute Ljubljana, Slovenia 2 Contents Introduction A taxonomy of visualization methods Visualizing single approximation sets Introduction Visualizing repeated approximation sets Summary References 3 Introduction Introduction Multiobjective optimization problem Visualization in multiobjective optimization Minimize Useful for different purposes [14] f: X ! F • Analysis of solutions and solution sets f:(x ;:::; x ) 7! (f (x ;:::; x );:::; f (x ;:::; x )) 1 n 1 1 n m 1 n • Decision support in interactive optimization • Analysis of algorithm performance • X is an n-dimensional decision space ⊆ Rm ≥ • F is an m-dimensional objective space (m 2) Visualizing solution sets in the decision space • Problem-specific ! Conflicting objectives a set of optimal solutions • If X ⊆ Rm, any method for visualizing multidimensional • Pareto set in the decision space solutions can be used • Pareto front in the objective space • Not the focus of this tutorial 4 5 Introduction Introduction Visualization can be hard even in 2-D Stochastic optimization algorithms Visualizing solution sets in the objective space • Single run ! single approximation set • Interested in sets of mutually nondominated solutions called ! approximation sets • Multiple runs multiple approximation sets • Different -
The Rockerverse: Packages and Applications for Containerisation
PREPRINT 1 The Rockerverse: Packages and Applications for Containerisation with R by Daniel Nüst, Dirk Eddelbuettel, Dom Bennett, Robrecht Cannoodt, Dav Clark, Gergely Daróczi, Mark Edmondson, Colin Fay, Ellis Hughes, Lars Kjeldgaard, Sean Lopp, Ben Marwick, Heather Nolis, Jacqueline Nolis, Hong Ooi, Karthik Ram, Noam Ross, Lori Shepherd, Péter Sólymos, Tyson Lee Swetnam, Nitesh Turaga, Charlotte Van Petegem, Jason Williams, Craig Willis, Nan Xiao Abstract The Rocker Project provides widely used Docker images for R across different application scenarios. This article surveys downstream projects that build upon the Rocker Project images and presents the current state of R packages for managing Docker images and controlling containers. These use cases cover diverse topics such as package development, reproducible research, collaborative work, cloud-based data processing, and production deployment of services. The variety of applications demonstrates the power of the Rocker Project specifically and containerisation in general. Across the diverse ways to use containers, we identified common themes: reproducible environments, scalability and efficiency, and portability across clouds. We conclude that the current growth and diversification of use cases is likely to continue its positive impact, but see the need for consolidating the Rockerverse ecosystem of packages, developing common practices for applications, and exploring alternative containerisation software. Introduction The R community continues to grow. This can be seen in the number of new packages on CRAN, which is still on growing exponentially (Hornik et al., 2019), but also in the numbers of conferences, open educational resources, meetups, unconferences, and companies that are adopting R, as exemplified by the useR! conference series1, the global growth of the R and R-Ladies user groups2, or the foundation and impact of the R Consortium3. -
Inviwo — a Visualization System with Usage Abstraction Levels
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS, VOL X, NO. Y, MAY 2019 1 Inviwo — A Visualization System with Usage Abstraction Levels Daniel Jonsson,¨ Peter Steneteg, Erik Sunden,´ Rickard Englund, Sathish Kottravel, Martin Falk, Member, IEEE, Anders Ynnerman, Ingrid Hotz, and Timo Ropinski Member, IEEE, Abstract—The complexity of today’s visualization applications demands specific visualization systems tailored for the development of these applications. Frequently, such systems utilize levels of abstraction to improve the application development process, for instance by providing a data flow network editor. Unfortunately, these abstractions result in several issues, which need to be circumvented through an abstraction-centered system design. Often, a high level of abstraction hides low level details, which makes it difficult to directly access the underlying computing platform, which would be important to achieve an optimal performance. Therefore, we propose a layer structure developed for modern and sustainable visualization systems allowing developers to interact with all contained abstraction levels. We refer to this interaction capabilities as usage abstraction levels, since we target application developers with various levels of experience. We formulate the requirements for such a system, derive the desired architecture, and present how the concepts have been exemplary realized within the Inviwo visualization system. Furthermore, we address several specific challenges that arise during the realization of such a layered architecture, such as communication between different computing platforms, performance centered encapsulation, as well as layer-independent development by supporting cross layer documentation and debugging capabilities. Index Terms—Visualization systems, data visualization, visual analytics, data analysis, computer graphics, image processing. F 1 INTRODUCTION The field of visualization is maturing, and a shift can be employing different layers of abstraction. -
A Very Simple Approach for 3-D to 2-D Mapping
Image Processing & Communications, vol. 11, no. 2, pp. 75-82 75 A VERY SIMPLE APPROACH FOR 3-D TO 2-D MAPPING SANDIPAN DEY (1), AJITH ABRAHAM (2),SUGATA SANYAL (3) (1) Anshin Soft ware Pvt. Ltd. INFINITY, Tower - II, 10th Floor, Plot No.- 43. Block - GP, Salt Lake Electronics Complex, Sector - V, Kolkata - 700091 email: [email protected] (2) IITA Professorship Program, School of Computer Science, Yonsei University, 134 Shinchon-dong, Sudaemoon-ku, Seoul 120-749, Republic of Korea email: [email protected] (3) School of Technology & Computer Science Tata Institute of Fundamental Research Homi Bhabha Road, Mumbai - 400005, INDIA email: [email protected] Abstract. libraries with any kind of system is often a tough trial. This article presents a very simple method of Many times we need to plot 3-D functions e.g., in mapping from 3-D to 2-D, that is free from any com- many scientific experiments. To plot this 3-D func- plex pre-operation, also it will work with any graph- tions on 2-D screen it requires some kind of map- ics system where we have some primitive 2-D graph- ping. Though OpenGL, DirectX etc 3-D rendering ics function. Also we discuss the inverse transform libraries have made this job very simple, still these and how to do basic computer graphics transforma- libraries come with many complex pre-operations tions using our coordinate mapping system. that are simply not intended, also to integrate these 76 S. Dey, A. Abraham, S. Sanyal 1 Introduction 2 Proposed approach We have a pictorial representation (Fig.1) of our 3-D to 2-D mapping system: We have a function f : R2 → R, and our intention is to draw the function in 2-D plane. -
The New Plot to Hijack GIS and Mapping
The New Plot to Hijack GIS and Mapping A bill recently introduced in the U.S. Senate could effectively exclude everyone but licensed architects, engineers, and surveyors from federal government contracts for GIS and mapping services of all kinds – not just those services traditionally provided by surveyors. The Geospatial Data Act (GDA) of 2017 (S.1253) would set up a system of exclusionary procurement that would prevent most companies and organizations in the dynamic and rapidly growing GIS and mapping sector from receiving federal contracts for a very-wide range of activities, including GPS field data collection, GIS, internet mapping, geospatial analysis, location based services, remote sensing, academic research involving maps, and digital or manual map making or cartography of almost any type. Not only would this bill limit competition, innovation and free-market approaches for a crucial high-growth information technology (IT) sector of the U.S. economy, it also would cripple the current vibrant GIS industry and damage U.S. geographic information science, research capacity, and competitiveness. The proposed bill would also shackle government agencies, all of which depend upon the productivity, talent, scientific and technical skills, and the creativity and innovation that characterize the vast majority of the existing GIS and mapping workforce. The GDA bill focuses on a 1972 federal procurement law called the Brooks Act that reasonably limits federal contracts for specific, traditional architectural and engineering services to licensed A&E firms. We have no problem with that. However, if S.1253 were enacted, the purpose of the Brooks Act would be radically altered and its scope dramatically expanded by also including all mapping and GIS services as “A&E services” which would henceforth would be required to be procured under the exclusionary Brooks Act (accessible only to A&E firms) to the great detriment of the huge existing GIS IT sector and all other related companies and organizations which have long been engaged in cutting-edge GIS and mapping. -
Basic Science: Understanding Numbers
Document name: How to use infogr.am Document date: 2015 Copyright information: Content is made available under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 Licence OpenLearn Study Unit: BASIC SCIENCE: UNDERSTANDING NUMBERS OpenLearn url: http://www.open.edu/openlearn/science-maths-technology/basic-science-understanding-numbers/content-section-overview Basic Science: Understanding Numbers Simon Kelly www.open.edu/openlearn 1 Basic Science: Understanding Numbers A guide to using infogr.am Infographics are friendly looking images and graphs which convey important information. In the past an infographic was the result of a long and painful process between designers and statisticians involving numerous meetings, data management and testing of designs and colour schemes. Nowadays they are much simpler to create. In fact, the company infogr.am has created a website that simplifies this process so that anyone can do it. The guidance below outlines a few simple instructions on how to use infogr.am to create the types of graphs discussed in this course. We will be using the data from the ‘Rainfall data PDF’. You should download the PDF before you start. Remember, you do not need to plot all the graph types or all the data. Simply pick two countries and compare their rainfall. This is a basic guide to Infogr.am; the site can do much more than what we describe below, so have a play and see what you find out! 1. Go to https://infogr.am/. 2. Select ‘Sign up now’ and create a username, enter your email address and choose a password (if you prefer, you can use your Facebook, Twitter or Google+ account to connect and log in). -
What3words Geocoding Extensions and Applications for a University Campus
WHAT3WORDS GEOCODING EXTENSIONS AND APPLICATIONS FOR A UNIVERSITY CAMPUS WEN JIANG August 2018 TECHNICAL REPORT NO. 315 WHAT3WORDS GEOCODING EXTENSIONS AND APPLICATIONS FOR A UNIVERSITY CAMPUS Wen Jiang Department of Geodesy and Geomatics Engineering University of New Brunswick P.O. Box 4400 Fredericton, N.B. Canada E3B 5A3 August 2018 © Wen Jiang, 2018 PREFACE This technical report is a reproduction of a thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in Engineering in the Department of Geodesy and Geomatics Engineering, August 2018. The research was supervised by Dr. Emmanuel Stefanakis, and support was provided by the Natural Sciences and Engineering Research Council of Canada. As with any copyrighted material, permission to reprint or quote extensively from this report must be received from the author. The citation to this work should appear as follows: Jiang, Wen (2018). What3Words Geocoding Extensions and Applications for a University Campus. M.Sc.E. thesis, Department of Geodesy and Geomatics Engineering Technical Report No. 315, University of New Brunswick, Fredericton, New Brunswick, Canada, 116 pp. ABSTRACT Geocoded locations have become necessary in many GIS analysis, cartography and decision-making workflows. A reliable geocoding system that can effectively return any location on earth with sufficient accuracy is desired. This study is motivated by a need for a geocoding system to support university campus applications. To this end, the existing geocoding systems were examined. Address-based geocoding systems use address-matching method to retrieve geographic locations from postal addresses. They present limitations in locality coverage, input address standardization, and address database maintenance. -
A History of R (In 15 Minutes… and Mostly in Pictures)
A history of R (in 15 minutes… and mostly in pictures) JULY 23, 2020 Andrew Zief!ler Lunch & Learn Department of Educational Psychology RMCC University of Minnesota LATIS Who am I and Some Caveats Andy Zie!ler • I teach statistics courses in the Department of Educational Psychology • I have been using R since 2005, when I couldn’t put Me (on the EPSY faculty board) SAS on my computer (it didn’t run natively on a Me Mac), and even if I could have gotten it to run, I (everywhere else) couldn’t afford it. Some caveats • Although I was alive during much of the era I will be talking about, I was not working as a statistician at that time (not even as an elementary student for some of it). • My knowledge is second-hand, from other people and sources. Statistical Computing in the 1970s Bell Labs In 1976, scientists from the Statistics Research Group were actively discussing how to design a language for statistical computing that allowed interactive access to routines in their FORTRAN library. John Chambers John Tukey Home to Statistics Research Group Rick Becker Jean Mc Rae Judy Schilling Doug Dunn Introducing…`S` An Interactive Language for Data Analysis and Graphics Chambers sketch of the interface made on May 5, 1976. The GE-635, a 36-bit system that ran at a 0.5MIPS, starting at $2M in 1964 dollars or leasing at $45K/month. ’S’ was introduced to Bell Labs in November, but at the time it did not actually have a name. The Impact of UNIX on ’S' Tom London Ken Thompson and Dennis Ritchie, creators of John Reiser the UNIX operating system at a PDP-11.