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National Park Service Inventory and Monitoring Program Analyses and Reporting for Long-term Kelp Forest Monitoring at Channel Islands National Park David.

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Presentation on theme: "National Park Service Inventory and Monitoring Program Analyses and Reporting for Long-term Kelp Forest Monitoring at Channel Islands National Park David."— Presentation transcript:

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 6 th 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” –

9 Mediterranean Coast I&M Network How to Present Overviews at Multiple Scales? Tiling to present 1 figure per island, plus 6 th 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 Length in cm

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 Size in mm S F 00 F 90 S 01 S 91 F 01 F 91 S 02 S 92 F 02 F 92 S 03 S 93 F 03 F 93 S 04 S 94 F 04 F 94 S 05 S 95 F 05 F 95 S 06 F 96 F 06 S 97S 07 F 97F 07 S 98S 08 F 98F 08 S 99S 09 F 99F S 00S 10 CAB1CAB2CAB3

15 Mediterranean Coast Inventory and Monitoring Network Quantile Regression Sp 1990Sp 1995Sp 2000Sp2005F Year Size in mm Median 25 th 10 th 75 th 90 th Lottia Sizes in CABR Tidepools Quantiles

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


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