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

National Park ServiceInventory 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, CATom Philippi, Quantitative Ecologist, NPS IMD,

Cabrillo NM

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


Unindicted Co-conspirators


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.

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?



• Consistency in layouts and legends– Consistent with maps if applicable

• Aligned scales across panels• Data Visualization

– Cleveland, Friendly, etc.– Spend time on this!


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!)


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



• 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)


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


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 2007Sebastes caurinus

Count

(0,5](5,10]

(10,15](15,20](20,25](25,30](30,35](35,40](40,45](45,50](50,75]

All Islands Combined

0 2 4 6 8

Anacapa

(0,5](5,10]

(10,15](15,20](20,25](25,30](30,35](35,40](40,45](45,50](50,75]

San Miguel Santa Barbara

(0,5](5,10]

(10,15](15,20](20,25](25,30](30,35](35,40](40,45](45,50](50,75]

0 2 4 6 8

Santa Cruz Santa Rosa

Leng

th in

cm


Fish Size Histograms• Changes across years


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


Pooled Size DistributionsLottia Sizes in CABR Tidepools 1990-2010

Size in mm

S 9

0

20 40 60 80

F 00

F 90

S 0

1

S 9

1

F 01

F 91

S 0

2

S 9

2

F 02

F 92

S 0

3

S 9

3

F 03

F 93

S 0

4

S 9

4

F 04

F 94

S 0

5

S 9

5

F 05

F 95

S 0

6

F 96

F 06

S 9

7

S 0

7

F 97

F 07

S 9

8

S 0

8

F 98

F 08

S 9

9

S 0

9

F 99

F 09

20 40 60 80

S 0

0

S 1

0

CAB1 CAB2 CAB3


Quantile Regression

Sp 1990 Sp 1995 Sp 2000 Sp2005 F 2010

0

20

40

60

80

Year

Siz

e in

mm

Median

25th

10th

75th

90th

Lottia Sizes in CABR Tidepools 1990-2010

Quantiles


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

Quadrat Counts Macrocystis pyrifera Juvenile (<1m)

Cou

nt p

er 1

m^2

Qua

drat

0

5

10

AR BSBR CC EFC KH LC LH

Anacapa

HR MM WL

San Miguel

0

5

10

AP CAT GC SER SESL WA

Santa Barbara

CVP DPM FH GI LS PB PP PRF SA YB

Santa Cruz

0

5

10

CP CSAW JLNO JLSO RR SP TC

Santa Rosa

Quadrat Counts Parastichopus parvimensis

Cou

nt p

er 1

m^2

Qua

drat

0.5

1.0

1.5

2.0

2.5

3.0

AR BSBR CC EFC KH LC LH

Anacapa

HR MM WL

San Miguel

0.5

1.0

1.5

2.0

2.5

3.0

AP CAT GC SER SESL WA

Santa Barbara

CVP DPM FH GI LS PB PP PRF SA YB

Santa Cruz

0.5

1.0

1.5

2.0

2.5

3.0

CP CSAW JLNO JLSO RR SP TC

Santa Rosa


Quadrat Counts


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


SWord


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.



• 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


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


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


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

http://science.nature.nps.gov/im/monitor/stats/R

• 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

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

Documents

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