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Analyses and Reporting for Long-term Kelp Forest Monitoring at Channel Islands National Park

National Park Service Inventory and Monitoring Program. Analyses and Reporting for Long-term Kelp Forest Monitoring at Channel Islands National Park. David Kushner , Marine Biologist, Channel Islands National Park, Ventura, CA

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Analyses and Reporting for Long-term Kelp Forest Monitoring at Channel Islands National Park

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  1. National Park Service Inventory and Monitoring Program Analyses and Reporting for Long-term Kelp Forest Monitoring at Channel Islands National Park David Kushner, Marine Biologist, Channel Islands National Park, Ventura, CA Stacey Ostermann-Kelm, Program Manager, NPS IMD Mediterranean Coast Network, Thousand Oaks, CA Tom Philippi, Quantitative Ecologist, NPS IMD, Cabrillo NM

  2. Mediterranean Coast Inventory and Monitoring Network The Issues • CHIS Prototype Park with >20 years of monitoring data • State of the Art & Pride of NPS when started • Aging data management • Substantial time requirement for annual reporting • Role for MEDN when most biologists base funded in 2 big units • Database support & modernizing • Improved reporting • Science Communication • Analysis & reporting issues looming for all I&M networks • CHIS extant data for developing analytical approaches & tools for trends • Ballpark 7 units per network and 7 vital signs per unit

  3. Mediterranean Coast Inventory and Monitoring Network Unindicted Co-conspirators

  4. Mediterranean Coast Inventory and Monitoring Network CHIS Kelp Forest Monitoring • 5 Islands; 33 Sites • Some sites in marine preserves • Many taxa (varying abundances) • 16 species of fish • 37 invertebrate taxa • 14 algal taxa • Multiple protocol components: • Quadrats, band transects, point contact, fish counts, etc. • Complex data: • Counts, but also size distributions, point cover, etc.

  5. Mediterranean Coast I&M Network How to Present Overviews at Multiple Scales? • Tiling to present 1 figure per island, plus 6th figure of all islands combined • If individual sites within islands, must be colors or columns within island panels, not 33 figures • Trend lines & simple control charts for quantities • Histograms, tables, & densityplots (probability distributions) for size distributions • Quantile regressions for trends over time? • Trends in species composition?

  6. Mediterranean Coast I&M Network How to Present Overviews at Multiple Scales? • Consistency in layouts and legends • Consistent with maps if applicable • Aligned scales across panels • Data Visualization • Cleveland, Friendly, etc. • Spend time on this!

  7. Mediterranean Coast Inventory and Monitoring Network Tools • R for analyses & graphing (& tables) • Scripting for repeating each year • SWord plugin for embedding live R objects in MS word .doc documents • Menu item to insert objects or regenerate objects Annual report template with headings, boilerplate, tables, figures, everything but the discussion / interpretation (your knowledge cannot be replaced!)

  8. Mediterranean Coast Inventory and Monitoring Network Alternatives • MS Office • Embed Access queries, Excel charts, etc. in Word document • Chrystal Reports • Embedded or pasted into Word or InDesign document • R2wd • R-side build more appropriate for starting 200 NPScape .doc files • Sweave, LaTEX, ODF (OpenOffice) full “Reproducible Research” • www.reproducibleresearch.org

  9. Mediterranean Coast I&M Network How to Present Overviews at Multiple Scales? • Tiling to present 1 figure per island, plus 6th figure of all islands combined • If individual sites, must be colors or columns within island panels • Emphasize patterns consistent across islands v island-specific responses • Patterns consistent across sites v site to site variability (including protected / unprotected)

  10. Mediterranean Coast Inventory and Monitoring Network Fish Size Histograms • Species-specific size ranges, so species-specific cutpoints for binning • Some species rare enough that size distributions not meaningful at individual sites or islands • Comparisons between size distributions inside v. outside of reserves informative

  11. Mediterranean Coast Inventory and Monitoring Network Fish Size Histograms • Lattice graphics • Panel or condition by island • Dataframe for graphics duplicated with “All Islands” pooled numbers • Boxplot() not histogram() to get horizontal bars • Species-specific cutpoints Copper rockfish 2007 Sebastescaurinus 0 2 4 6 8 All Islands Combined Anacapa (50,75] (45,50] (40,45] (35,40] (30,35] (25,30] (20,25] (15,20] (10,15] (5,10] (0,5] San Miguel Santa Barbara Length in cm (50,75] (45,50] (40,45] (35,40] (30,35] (25,30] (20,25] (15,20] (10,15] (5,10] (0,5] Santa Rosa Santa Cruz (50,75] (45,50] (40,45] (35,40] (30,35] (25,30] (20,25] (15,20] (10,15] (5,10] (0,5] 0 2 4 6 8 Count

  12. Mediterranean Coast Inventory and Monitoring Network Fish Size Histograms • Changes across years

  13. Mediterranean Coast Inventory and Monitoring Network Benthic Invertebrate Size Distributions • Size Distributions over time • Pool across sites, possibly islands too • Aligned densityplots or histograms • Quantiles of size distribution over time • Observed quantiles each year • fit values from quantile regression

  14. Mediterranean Coast Inventory and Monitoring Network Pooled Size Distributions Lottia Sizes in CABR Tidepools 1990-2010 20 40 60 80 S 90 F 00 F 90 S 01 S 91 F 01 S 02 F 91 F 02 S 92 S 03 F 92 S 93 F 03 F 93 S 04 F 04 S 94 S 05 F 94 F 05 S 95 F 95 S 06 F 06 F 96 S 97 S 07 F 97 F 07 S 98 S 08 F 98 F 08 S 99 S 09 F 09 F 99 S 00 S 10 20 40 60 80 Size in mm CAB1 CAB2 CAB3

  15. Mediterranean Coast Inventory and Monitoring Network Quantile Regression Lottia Sizes in CABR Tidepools 1990-2010 80 Quantiles 90th 60 75th Size in mm 40 Median 25th 10th 20 0 Sp 1990 Sp 1995 Sp 2000 Sp2005 F 2010 Year

  16. Mediterranean Coast Inventory and Monitoring Network Quadrat Counts • This year’s status by site within island • Averaged across quadrats (losing within-site spatial variability) • “Historic Variability” as context for understanding current value • Boxplot of values from period of record, 5 year or 10 year, perhaps corrected means factoring in ENSO or other important covariates

  17. Mediterranean Coast Inventory and Monitoring Network Quadrat Counts

  18. Mediterranean Coast Inventory and Monitoring Network SWord • Free for non-commercial use • http://rcom.univie.ac.at/main.html • Uses statconDCOM, rscproxy (requires admin privileges to install) • Adds “Add-Ins” menu item to Word 2000, 2003, or 2007 (no ETA for 2010) • Menu items: • insert figure, table, code snippet, generate document

  19. Mediterranean Coast Inventory and Monitoring Network SWord

  20. Mediterranean Coast Inventory and Monitoring Network SWord • SWord embeds R code in Word document as fields tagged by {<<xxx>>= } and {@} • In foo.doc, Sword runs foo.R in same directory, then embedded code • Foo.R can create lattice and table or dataframe objects, define functions to generate tweaked graphs • Embedded code then print(object) or plot(object) • Source foo.R as appendix in report • Complete documentation for how missing values handled, graph options, etc.

  21. Mediterranean Coast Inventory and Monitoring Network CHIS Kelp Forest Monitoring • KFMreport.doc • Cover, TOC, headers, footers, boilerplate text • KFMreport.R code • Hits Access tables, cleans, slices, dices, generates lists of objects • Embedded fields • plot() lattice objects • Tables or dataframes to MSword Tables

  22. Mediterranean Coast Inventory and Monitoring Network CHIS Kelp Forest Monitoring

  23. Mediterranean Coast Inventory and Monitoring Network Subsequent Years • Collect Data • Data entry, QA/QC • Copy/rename files KFM_AnnualReport2013.doc KFM_AnnualReport2013.R • Menu: Run SWord then Generate Document • Look at tables & figures • Write interpretation & discussion • Periodically revise boilerplate • Periodic Synthesis Reports

  24. Mediterranean Coast Inventory and Monitoring Network Next Steps • Almost complete collection of possible figures • David & Stacey ideas, tweaks, rejections, requests once they know what is possible • Tom recode against NRDT re-factoring • Possible generation 2011 annual report

  25. Mediterranean Coast Inventory and Monitoring Network Guidance for Networks • Tom will post more detailed instructions and examples on the NPS I&M R website • http://science.nature.nps.gov/im/monitor/stats/R • As Vital Signs monitoring data start rolling in, you can try to spend a great deal of time constructing annual reports for 1 or 2 new Vital Signs each year • Much less effort to maintain & reproduce in subsequent years

  26. National Park Service Inventory and Monitoring Program • Swap Meet • Authors and co-authors scattered around room • Available for specific questions, requests for copies of reports, code, etc.

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