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PPLANE is a tool for Phase Plane Analysis of a System of Differential Equations of the form: x’ = dx/dt = f(x,y), y’ = dy/dt = g(x,y).

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Jeff Denny onto Software

{xhub:include type=“stylesheet” filename=”/site/media/css/nocontentpaneopen.css”} {xhub:include type=“stylesheet” filename=”/templates/qubes/html/system/css/introduction.css”} {xhub:include type=“stylesheet” filename=”/site/media/css/searchandbrowse.css”} Resources: Software Submit a resource…

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Jeff Denny onto Software

Amazing Sheep Cyclone Caught On Camera - Must Watch

Anyone want to try their hand at modeling this behavior?

Thanks, Amy Hurford!

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Drew LaMar onto Agent-based modeling

R Cheat Sheet

By Nicolás E. Campione

Modified from: P. Dalgaard (2002). Introductory Statistics with R. Springer, New York. 

Download

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Drew LaMar onto Learning and Using R

by Tom Short, EPRI PEAC, tshort@epri-peac.com 2004-11-07

Granted to the public domain. See www.Rpad.org for the source and latest version. Includes material from R for Beginners by Emmanuel Paradis (with permission).

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Drew LaMar onto Learning and Using R

Get R (and RStudio)

Just getting started as an R user?  You can first try running R on QUBES Hub here, without installing anything.  Eventually, though you will want to install it on your own computer by downloading it here.  RStudio provides a friendlier interface for using R, and can be downloaded here.  Rstudio requires R to be installed, so start by downloading R.

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Drew LaMar onto Learning and Using R

Here is an interesting blog post from John Bohannon, who made news in 2013 with his article in Science exposing the seedy underbelly of the open-access pay-as-you-publish journals.  This…

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Drew LaMar onto Statistics and Data Analysis

intRo

IntRo is a shiny app similar to Radiant, designed for teaching intro stats.  It also provides a tutorial and help files.  Drew is planning to add some of the intRo functionality into future versions of BioRadiant.

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Drew LaMar onto Statistics and Data Analysis

Link to data sets used in The Analysis of Biological Data .  All data are in CSV format.

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Drew LaMar onto Statistics and Data Analysis

Quick R

This is a great source for basic R functionality like importing and manipulating data.  It also has very helpful information on making graphs (see this page).  

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Drew LaMar onto Learning and Using R

Try R Code School

A free online tutorial for learning basic R commands.  It runs through your browser and does not require you to install R.

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Drew LaMar onto Learning and Using R

Making beautiful plots

Trying to customize plots in R?  This page from the Quick R site provides a great deal of information on customizing plot options, in a much more visual (and less terrifying) format than "?par"

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Drew LaMar onto Learning and Using R

Making beautiful plots

Trying to customize plots in R?  This page from the Quick R site provides a great deal of information on customizing plot options, in a much more visual (and less terrifying) format than "?par"

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Drew LaMar onto Data Visualization

A nice introduction to building apps with R Shiny. Written by the folks at NEON (National Ecological Observatory Network).

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Drew LaMar onto Learning and Using R

Cheatsheets are quickstart guides to using some of the most popular packages and features of Rstudio. This link will direct you to the following cheatsheets: Shiny cheatsheet Data visualization cheatsheet Package development cheatsheet Data wrangling cheatsheet R markdown cheatsheet R markdown reference guide

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Drew LaMar onto Learning and Using R

Diversity of ageing across the tree of life

I stumbled across this paper when looking for survivorship information on different species and it has be a great teaching resource. Mostly I use the subplots of Figure 1 (partially reproduced here) which has a whole bunch of graphs of relative mortality and fertility as a function of age for a wide range of taxa. 

Full Citation: Jones, O. R., Scheuerlein, A., Salguero-Gómez, R., Camarda, C. G., Schaible, R., Casper, B. B., ... & Vaupel, J. W. (2014). Diversity of ageing across the tree of life. Nature, 505(7482), 169-173.

When you go to the Nature site for this paper be sure to check out the "related audio" which has a nice discussion with the authors about the paper. 

Alternative Link: http://izt.ciens.ucv.ve/ecologia/Archivos/ECO_POB%202014/ECOPO2_2014/Jones%20et%20al%202014.pdf

 

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Cheatsheets are quickstart guides to using some of the most popular packages and features of Rstudio. This link will direct you to the following cheatsheets: Shiny cheatsheet Data visualization cheatsheet Package development cheatsheet Data wrangling cheatsheet R markdown cheatsheet R markdown reference guide

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Arietta Fleming-Davies onto Shiny

A nice introduction to building apps with R Shiny. Written by the folks at NEON (National Ecological Observatory Network).

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Arietta Fleming-Davies onto Shiny

"Essay to students about the fallacy of fixed math ability"

test of tracking a comment.

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Sam S Donovan onto sam test

A Survivorship Recitation Activity

This is an activity that is based on the data available from the "Survivorship in the Natural World" module. Joshua Adelman, who was a post-doc in the Department of Biological Sciences at the University of Pittsburgh at the time, was the lead developer of this activity. 

 

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Example of using the ODD protocol to describe land-use change models

Polhill, J. Gary, Parker, Dawn, Brown, Daniel and Grimm, Volker (2008). 'Using the ODD Protocol for Describing Three Agent-Based Social Simulation Models of Land-Use Change'. Journal of Artificial Societies and Social Simulation 11(2)3 <http://jasss.soc.surrey.ac.uk/11/2/3.html>.

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The original ODD protocol paper

Grimm V, Berger U, Bastiansen F, Eliassen S, Ginot V, Giske J, Goss-Custard J, Grand T, Heinz S, Huse G, Huth A, Jepsen JU, Jørgensen C, Mooij WM, Müller B, Pe’er G, Piou C, Railsback SF, Robbins AM, Robbins MM, Rossmanith E, Rüger N, Strand E, Souissi S, Stillman RA, Vabø R, Visser U, DeAngelis DL. 2006. A standard protocol for describing individual-based and agent-based modelsEcological Modelling 198:115-126.

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The ODD protocol: A review and first update

This is a collection of links to the paper, a pre-publication version (in case you can't get past the pay wall), the electronic supplements, and a bonus item. 

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