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Data Handling & Analysis BD7054 2012-2013

Data Handling & Analysis BD7054 2012-2013. Andrew Jackson Zoology, School of Natural Sciences a.jackson@tcd.ie. Statistics in science. Analysis of data is central to science Metaphorically Literally (Introduction -> methods -> results -> discussion) Underpins one’s own research

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Data Handling & Analysis BD7054 2012-2013

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  1. Data Handling & AnalysisBD70542012-2013 Andrew Jackson Zoology, School of Natural Sciences a.jackson@tcd.ie

  2. Statistics in science • Analysis of data is central to science • Metaphorically • Literally(Introduction -> methods -> results -> discussion) • Underpins one’s own research • Your own research project • Essential in understanding others’ research • To question what they did • To incorporate their ideas in your own research

  3. The scientific method • Ask a question about the world around you • Why are vultures the only obligate scavengers among the extant terrestrial vertebrates?

  4. The scientific method • Decide what measurable outcome you will use to test a specific hypothesis • Physiology of vultures favours this mode of life • Compare metabolic costs of flight across vertebrate taxa • Design an experiment or field study to test this idea • Use statistics to determine whether your predictions hold • Frame your findings within the broader background of the precedent science –introduction and discussion

  5. Course Outline • 8th Oct – 12th Oct • Introduction to R and statistics • 21st Jan – 25th Jan • General Linear Models • 29th April – 3rd May • Generalised Linear Models • Multivariate methods

  6. Assessment • On the Friday ending each week, you will be asked to submit either • an assessment, or • complete an online exam assessing your proficiency in data analysis using R

  7. Learning outcomes • NB slightly different from course handbooks • summarise and communicate quantitative results graphically and textually to scientific standards. • apply appropriate statistical analyses of commonly encountered data types. • discuss the context of the analyses within a hypothesis driven framework of scientific logic. • use the R statistical computing language for data analysis.

  8. Course structure • Series of Lecture / tutorials and computer practicals • Lectures will be as interactive as possible • Computer practicals • Use R to analyse data • Follow video podcasts for instruction • Demonstrators present to help

  9. Week 1 • Lectures / Tutorials • Monday to Thursday 10-12 • GGSR-A • Computer sessions • Monday to Thursday 14-16 • Botany Hut computer rooms

  10. Summary of statistics covered • Linear regression • General linear models • As a way to ask increasingly complex questions of our data using a common framework (ANCOVA / multiple regression) • Generalised linear models • Extending these concepts to deal with non-normal data types (binary / surivival / count data)

  11. Statistical software - R • R is a command line interfaced software • Scary the first few times • Incredibly powerful and adaptable • Free • Open development • Time-tabled computer sessions • Complete video-podcast and examples in your own time • When Googling for R related topics add “cran” to your search terms

  12. Delivery of course content • Attendance at lectures/tutorials is mandatory • Moodle website associated with course • Lectures will be posted • Web-based discussions • Links to video-podcasts • Statistics, An introduction using R. Michael J Crawley. Wiley. ISBN 0-470-02298-1

  13. Basic Experimental Design For more details see Experimental Design for the Life Sciences by Ruxton and Colegrave

  14. Relationship between hormone levels in male chimpanzees and #females • Measure hormone levels of male chimps and then count how many females are they foraging with. • Higher hormone levels are expected when there are more females to mate with. • However, hormone levels are influenced by age, diet, time of day etc.

  15. Male hormones and #females Hormone level difference could be due to age, diet, time of day OR #females

  16. Relationship between hormone levels in male chimpanzees and #females All chimps are the same age, diet, and time of day so hormone level difference ~ #females

  17. Class Exercise Come up with a scientific question and plot your predictions

  18. Computer Session 8th October • Work through 3 podcasts on my website • http://www.tcd.ie/Zoology/research/research/theoretical/Rpodcasts.php • Opening R for the first time • Working with script files • Importing data into R

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