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Software Tools

Software Tools. Statistics. Good Texts: Zar, Biostatistical Analysis Legendre and Legendre, Numerical Ecology. Major Statistical Packages. SAS, Systat, Stata, SPSS, etc. Large number of capabilities – do just about all general statistics Have graphing components, programming capability

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Software Tools

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  1. Software Tools

  2. Statistics Good Texts: Zar, Biostatistical Analysis Legendre and Legendre, Numerical Ecology

  3. Major Statistical Packages • SAS, Systat, Stata, SPSS, etc. • Large number of capabilities – do just about all general statistics • Have graphing components, programming capability • Might take longer to learn (but maybe not…) others exist, these are just some big ones I know are used in our discipline. SPlus, Statistica, Statistix, Statgraphics, etc.

  4. Comparisons SAS/STAT: http://www.sas.com/ • Win, Mac, Unix. • UCSD special price: $125/150, but is lease • SAS/GRAPH is separate package Stata: http://www.stata.com/ • Win, Mac, Unix • $380-895 Systat: http://www.systat.com/products/Systat/ • Just Windows • $499 • Free 30-day trial SPSS: http://www.spss.com/ • Windows & Mac • $499-$599 • free 14-day trial • used less now? Most do most stats…look at detailed list for what you are interested in.

  5. Lets have a look… Statistix, Systat, SPSS

  6. Test Data Sets • College GPA, High School GPA, SATs, quality of letter of recommendation • Descriptive stats (means, standard dev.) • Scatterplot, Paired t-test of College GPA and HS GPA • Linear regression of all factors • Normal probability plot • Seamount by species presence/absence matrix for Hawaiian seamounts • Cluster seamounts

  7. Easier to Learnbut fewer capabilities Excel with Analyse-it: http://www.analyse-it.com/ • Windows only (?). • $149. Free trial download What you are missing • Fewer capabilities, including ordination/clustering routines • programming

  8. Another Optionif you’re willing to learn a new system Matlab • http://www.mathworks.com/products/matlab/index.html • originally a matrix manipulation environment • now does statistics and graphing • programmable • highly used in the oceanographic community – lots of tailored routines. Good for interacting with environmental data (moored and shipboard instruments, satellite data, model output, 3-d visualization) • SIO has group license – ask Jerry Wanetick

  9. For Those on a Budget Websites listing free tools • http://freestatistics.altervista.org/stat.php • comparison chart: http://freestatistics.altervista.org/comp.php • http://members.aol.com/johnp71/javasta2.html • links to reviews • http://www.statistics.com/content/javastat.html • web tools, by category • A lot of tools exist – some are very specific R: http://www.r-project.org/ (relative of SPlus) • w/ADE 4 (windows and mac) • Free! Windows, Mac, Unix • Originally, more of a programming language than a statistical toolkit, not has a base set of operations • lots of online routines • But hard to learn: good for the programmers…only

  10. Ecology-Specific The major packages will do generic ordinations, but not specific similarity measures, diversity metrics, rarefaction, etc. Some are free, some are very “home grown” For links and summary of capabilities: • http://ordination.okstate.edu/software.htm

  11. A look at Primer • http://www.primer-e.com/ • Windows only • Price: ???? = Multivariate statistics for ecology • Clustering and ordination • Anosim (Anova-like) • BioEnv

  12. BioEnv

  13. Relate environmental factors to community ordination

  14. EstimateS – Freehttp://viceroy.eeb.uconn.edu/EstimateS Rarefaction and species accumulation curves Species richness estimators and diversity indices • Computes non-parametric species richness estimators for abundance-based data (Chao 1 and ACE) and for sample-based data (Chao2, ICE, first and second order Jackknives, and Bootstrap). • For Chao1 and Chao 2, computes log-linear confidence intervals. • Computes a species richness estimator based on fitting an asymptotic function (the Michaelis-Menten equation) to the sample-based rarefaction curve. • Computes Shannon, Simpson, and Fisher's alpha diversity indices. Shared species estimation and biotic similarity indices, with estimators • Computes Chao's estimator of total shared species (including observed and unseen shared species) for sample pairs. • Computes classic Sørensen and Jaccard similarity indices for sample pairs based on incidence (presence-absence) or abundance data sets • Computes Chao's abundance-based Sørensen and Jaccard similarity indices, with statisically rigorous estimators and their standard errors, for sample pairs based on abundance or on replicated incidence (presence-absence) data sets. • Computes Morisita-Horn and Bray-Curtis (= "Sørensen quantitative") similarity indices for sample pairs based on abundance data sets. Has some format input issues; user guide is “hidden” in About EstimateS, not under Help.

  15. Stella - Modeling To create dynamic computer models of biological system with a simple, graphic interface Steps: build the model, add parameters, then run it. Used for: population/community/food webs, nutrient cycles.

  16. 4 Components Stocks (containers): e.g. an animal population Flows: changes in stocks over time. E.g. births Converters: modify flows. E.g. make birth rate dependent upon number of adults of that species and of a competitor Connectors: connect pieces needed by a converter to that converter.

  17. Build Model • Build model with symbols • Then parameterize (set the stock sizes, flow rates, etc.) • Then run and see how stocks and flows change over time (lots of output).

  18. Output

  19. Example

  20. GIS/Visualization Tools

  21. ESRI GIS • The leader in the field. Complex to learn, but very powerful • UCSD Price: $500 full, $250 lesser version (but then much less expensive for second license per lab)

  22. Core Products • ArcReader: Free. Lets you look at other peoples maps (like Adobe PDF) • ArcGIS (components can also stand alone) • Arc Explorer • Free. Very limited import, zoom, query functionality • ArcView • Basic functionality • ArcEditor • Adds editing features for shapefiles and geodatabases • ArcInfo • The works • GIS server options – if you are setting up a website

  23. Extensions 3-D Analyst, including ArcGlobe • work on spherical earth • 3-d visualization (sort of...) • better zooming in and out • export as videos

  24. Extensions, Cont • Geostatistical Analyst • Network Analyst • Schematics • Spatial Analyst • Distances, interpolation, contour, slope, hillshade, conversions • Survey Analyst • Tracking Analyst

  25. Google Earth • Basic program is free • Google Earth Plus is $20 – lets you add points, vectors, polygon data of your own • Pro for $$. For features see http://earth.google.com/product_comparison.html

  26. Ocean Data View • Free, all platforms • For oceanographic data, particularly 3-dimensional • Connected to some major data sources (WOCE, WOA)

  27. Try it yourself Ecological • EstimateS: Free download. Mac and Windows. 4.9 MB • Karen has on stick • Try user guide and test data • Primer: windows only. • Karen has CD • has tutorial in book General Statistics • Analyze-it, SPSS, or Systat - downloads Stella • windows or mac • trial download, but need to register • tutorial comes with software. You won’t be able to print, but you can alt-printscreen, then paste the image in a word document to refer to. Google Earth

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