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A Primer in Biological Data Analysis and Visualization Using R

Author: Gregg Hartvigsen

    "Taught at a workshop on network analysis using R at the national Institute for mathematical and Biological Synthesis at the University of Tennessee, Knoxville."

Published: February 18, 2014 by Columbia University Press

Summary: This book guides readers through the processes of entering data into R, working with data in R, and using R to visualize data using histograms, boxplots, barplots, scatterplots, and other common graph types.  Hartvigsen covers testing data for normality, defining and identifying outliers, and working with non-normal data.  Students are introduced to common one- and two-sample tests as well as one- and two-analysis of variance (ANOVA), correlation, and linear and non-linear regression analyses. Also included is a secion on advanced procedures and a chapter inroducing algorithms and the art of programming using R.

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Getting Started with R: An Introduction for Biologists

Author: Andrew P. Beckerman, Owen L. Petchey

    "Evolutionary Ecologists with over 20 years of combined experience using R for data analysis and visualization"

Published: July 22, 2012 by Oxford University Press

This book provides a fundamental introduction for biologists new to R.  While teaching how to import, explore, graph and analyze data, it keeps readers focussed on their ultimate goals-communicating their data in oral presentations, posters, papers, and reports.  It also provides a consistent workflow for using R that is simple, efficient, reliable, accurate, and reproducible.  The material in the book reproduces the engaging and sometimes humorous nature of the three-day course on which it is based.

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The New Statistics with R: An Introduction for Biologist

Author: Andy Hector

    " He currently convenes and teaches statistics on the Quantitative Methods for Biologsits course for undergraduates at the Universtiy of Oxford.  He has contributed to several publications on eccologal analysis."

Published: March 15, 2015 by Oxford University Press

Summary: This book provides a contemporary introduction to the classical techniques and modern ectensions of linear model analysis.  It emphasizes on estimation-based approach that accounts for recent criticisms of over-use of probability values and introduces the alternative approach using information criteria.  It is based on the use of the open-source R programming language for statistics and graphics that is rapidly becoming the lingua franca in many areas of science.  Statistics is introduced through worked analyses preformed in R using interesting data sets from ecology, evoluntionary biology, and environmental science.  Data sets and R scripts are available as supporting material.

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Northwest BioSciences Consortium

QUBES site for the NWBC group. To learn more about NWBC.

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Slides from SABER West 2019 workshop

Powerpoint slides used during the SABER West 2019 "Scaffolding Core Competency Learning Outcomes across the Undergraduate Biology Curriculum" workshop.

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Core competency reference sheet

Reference sheet from the workshop. Adapted from 2011 Vision and Change report by Stasinos Stavrianeas.

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Process of Science

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Modeling & Simulation

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Communication & Collaboration

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Quantitative Reasoning

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Interdisciplinary Nature of Science

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Science & Society

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Impact of faculty mind set on student success

 

Canning, E.A., Muenks, K., Green, D.J., Murphy, M. 2019. STEM faculty who believe ability is fixed have larger racial achievement gaps and inspire less student motivation in their classes Science Advances  15 Feb 2019: Vol. 5, no. 2, eaau4734 DOI: 10.1126/sciadv.aau4734

"Results from a longitudinal university-wide sample (150 STEM professors and more than 15,000 students) revealed that the racial achievement gaps in courses taught by more fixed mindset faculty were twice as large as the achievement gaps in courses taught by more growth mindset faculty. Course evaluations revealed that students were demotivated and had more negative experiences in classes taught by fixed (versus growth) mindset faculty. Faculty mindset beliefs predicted student achievement and motivation above and beyond any other faculty characteristic, including their gender, race/ethnicity, age, teaching experience, or tenure status. "

 

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David Leaf onto Inclusion

R Markdown Reference Guide

Quick guide to syntax and functions in R Markdown.

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R Markdown Help Articles

A collection of articles to help in the use of R Markdown.

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R Markdown Cheat Sheet

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RStudio Data Transformation Cheat Sheet

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RAY Conservation Diversity Fellowship

About the RAY Fellowship

Inspired by efforts to increase racial diversity in conservation, the Roger Arliner Young (RAY) Conservation Diversity Fellowship aims to increase and facilitate conservation-related career pathways for emerging leaders of color. The RAY Fellowship is a paid fellowship designed to equip recent college graduates with the tools, experiences, support, and community they need to become leaders in the conservation sector—one that, in our visions of the future, fully represents, includes, and is lead by the diverse communities, perspectives, and experiences of the United States.

 

The RAY Fellowship provides first-time career access opportunities for recent college graduates who do not have previous professional experience or a graduate degree. RAY Fellows are placed within one of our Member Organizations for a year-long paid fellowship position, with the resources and support to develop experiences that will launch them onto a path of career growth in conservation. Fellows work with mentors, grow their networks, and forge lasting relationships with their cohort of Fellows. RAY Fellowship positions are full-time paid positions with competitive entry-level salaries plus benefits. Fellows will also receive a stipend of $1,000 to go towards professional development opportunities, in addition to coordinated professional development through RAY Member Organizations and the Environmental Leadership Program.

 

Eligibility & How to Apply

Eligible applicants will:

  • Come from a racial / ethnic background underrepresented in conservation and demonstrate a commitment to the values of diversity, equity, and inclusion
  • Be less than 2 years out of college and have a Bachelor's Degree by July 2019 (we are not considering individuals with graduate degrees at this time) 
  • Have not had a full-time job in conservation 
  • Have the ability to work in the United States and commit to the entire fellowship

Applications for the 2019 cycle are open and descriptions of Fellowship positions will be added on a rolling basis. Completed applications should include a CV or resume, a letter of support, two essays, and a short answer response. Visit our website at http://www.rayconservationfellows.org for application instructions and deadlines.

 

Informational Webinars

Applicants may join one of our upcoming informational webinar series to ask questions, learn more about the application process, and hear from a current RAY Fellow. Registration links, webinar dates and times, and featured Fellows can be found here on our website: https://rayconservationfellows.org/informational-webinars-applicants

 

For more information please contact Jordan Williams, Program Manager, RAY Conservation Diversity Fellowship at jordan@elpnet.org / (617) 942-0585.

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Kimberly Diep onto Opportunities in the Field

RStudio Data Transformation Cheat Sheet

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Drew LaMar onto Data Life Cycle: Wrangle

RStudio Data Import Cheat Sheet

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Impact of faculty mind set on student success

 

Canning, E.A., Muenks, K., Green, D.J., Murphy, M. 2019. STEM faculty who believe ability is fixed have larger racial achievement gaps and inspire less student motivation in their classes Science Advances  15 Feb 2019: Vol. 5, no. 2, eaau4734 DOI: 10.1126/sciadv.aau4734

"Results from a longitudinal university-wide sample (150 STEM professors and more than 15,000 students) revealed that the racial achievement gaps in courses taught by more fixed mindset faculty were twice as large as the achievement gaps in courses taught by more growth mindset faculty. Course evaluations revealed that students were demotivated and had more negative experiences in classes taught by fixed (versus growth) mindset faculty. Faculty mindset beliefs predicted student achievement and motivation above and beyond any other faculty characteristic, including their gender, race/ethnicity, age, teaching experience, or tenure status. "

 

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Kristin Jenkins onto Inclusive Teaching Practices

Data for Black Lives Operations Manager

Data for Black Lives is seeking an enthusiastic, independent and dynamic professional to serve as our Operations Manager. The ideal candidate will have experience creating and maintaining systems, will be organized and detail oriented, and have a shared commitment to our mission. The Operations Manager will be an integral part of the team providing short and long-term strategic vision that supports our maximum effectiveness, efficiency, financial and organizational sustainability.

For more information, or to apply, submit a short statement of interest and a resume that highlights your experiences most relevant to the role: info@d4bl.org with subject “Operations Manager.”
 

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FactoMineR: Multivariate Exploratory Data Analysis and Data Mining

Exploratory data analysis methods to summarize, visualize and describe datasets. The main principal component methods are available, those with the largest potential in terms of applications: principal component analysis (PCA) when variables are quantitative, correspondence analysis (CA) and multiple correspondence analysis (MCA) when variables are categorical, Multiple Factor Analysis when variables are structured in groups, etc. and hierarchical cluster analysis. F. Husson, S. Le and J. Pages (2017) <doi:10.1201/b10345-2>.

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psych: Procedures for Psychological, Psychometric, and Personality Research

A general purpose toolbox for personality, psychometric theory and experimental psychology. Functions are primarily for multivariate analysis and scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis, although others provide basic descriptive statistics. Item Response Theory is done using factor analysis of tetrachoric and polychoric correlations. Functions for analyzing data at multiple levels include within and between group statistics, including correlations and factor analysis. Functions for simulating and testing particular item and test structures are included. Several functions serve as a useful front end for structural equation modeling. Graphical displays of path diagrams, factor analysis and structural equation models are created using basic graphics. Some of the functions are written to support a book on psychometric theory as well as publications in personality research.

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