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marinebon / info-beachcombers

Beach COMBERS dataset extraction for infographics
https://marinebon.github.io/info-beachcombers
MIT License
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create initial plots of BeachCOMBERS data #1

Open bbest opened 4 years ago

bbest commented 4 years ago

BeachCombers (who's best? Erica Donnelly-Greenan / James Harvey /Andrew DeVogelaere) will get draft viz from downloaded BeachCombers - Google Drive

From Jenn Brown:

the latest products and thinking regarding BeachCOMBERS is compiled in this set of slides

BeachCOMBERS program data is now publically discoverable in ERDDAP (thanks to Lynn deWitt): BeachCOMBERS Effort-Based Marine Mammal and Seabird Beach Cast Survey

BeachCOMBERS data: probably best to start working with Patrick Daniel at CeNCOOS and he helped get the data into the MBON portal once Lynn got it onto ERDDAP. Note that there are two versions of the Beached animals data in ERDDAP. 1 version includes the BeachCOMBERS, Beach Watch and HSU data - this ERDDAP is password protected. The other version is just BeachCOMBERS and it has the cause of death info which we need for entanglement, oiling, etc. This version is not password protect. USE THIS ONE to allow reproduce some of the outputs we have included in past condition reports including entanglements and oiling.

Eyes on the Ocean™ - IOOS Bi-weekly - 2 October 2019:

  • New BeachCOMBERS Data Portal and Products: On Monday, September 23, Patrick Daniel (CeNCOOS), Jennifer Brown (ECOS Consulting with Monterey Bay National Marine Sanctuary and MBON), Andrew DeVogelaere and Erica Burton (MBNMS) presented the new Data Portal and data products for the BeachCOMBERS Coastal Ocean Mammal and Bird Education and Research Surveys to the Office of National Marine Sanctuary West Coast Regional office and MBNMS leadership team. MBON has been working to establish a protocol for on-going monitoring information to dynamically update sanctuary status and trends reports. This effort to build out interactive infographics for various habitats in sanctuaries, led by Jennifer Brown and Ben Best (EcoQuants) with support from MBON, US IOOS and others, has been using Multi-Agency Rocky Intertidal Network (MARINe) monitoring data for rocky reef habitats in Monterey Bay and Channel Islands National Marine Sanctuaries and is expanding to incorporate other data types and other sanctuaries. The presentation was very well-received; pursuant discussion included a number of other data types and management issues for which the teams would like to have data available in this way to help with sanctuary management. To learn more, please contact Gabrielle Canonico.
bbest commented 4 years ago

Hi @jenn-brown,

Ok, I integrated:

here for just MBNMS:

Plots

See plots:

eg bird carcasses : static

image

Note: goes up to 2019.

eg mammal carcasses : interactive

image

Note: goes up to only 2016. Shows species information on hover.

Questions

I still have some open questions though:

Q1. Just MBNMS?

Since this data is only on the mainland, does it belong in CINMS or just MBNMS? Check out the section spatial : intersect sanctuary with segments for an interactive map: image

Q2. Other plots?

Where can I get more information about these plots in slide 14 of Beached birds and mammals info summaries - Google Slides? image I can't find this in CCIEA 2019 ESR 508.pdf, only this in Appendix J.2: image

Q3. Which infographic elements?

And where shall these go? Here are some options:

jenn-brown commented 4 years ago

Hi Ben, I focused only on seabirds for now since you have the most recent data from BeachCOMBERS only for seabirds. We can add mammals after we work through the seabirds stuff listed below.

Here are my responses to your questions:

Q1. Just MBNMS?

Since this data is only on the mainland, does it belong in CINMS or just MBNMS?

Correct we do not have beached carcass data from beach segments in CINMS and we likely never will be cause the remote island location makes it too difficult for regular volunteer access. So we will use the mainland beaches south of Point Conception as our best proxy for gauging mortality rates for the region around CINMS.

As for MBNMS we want to include all beach segments covered by BeachCOMBERS are overlap with the spatial extent of MBNMS. Not sure why some beaches (e.g., north of Santa Cruz) are red instead of green in your map.

Q2. Other plots?

Where can I get more information about these plots in slide 14 of Beached birds and mammals info summaries - Google Slides https://docs.google.com/presentation/d/18Ez8lMeKDbJvDNagOeNHU9GT7qLf_BZcTh4nwtwNcb8/edit#slide=id.g5ddce32724_2_144?

The report to the PFMC which you reference only contains a subset of the full indicator portfolio. The tech report is the complete source document: Harvey, C., et al. 2019. Ecosystem Status Report of the California Current for 2019: A Summary of Ecosystem Indicators Compiled by the California Current Integrated Ecosystem Assessment Team (CCEIA). U.S. Department of Commerce, NOAA Technical Memorandum NMFS-NWFSC-149 https://www.nwfsc.noaa.gov/assets/25/9707_11192019_113138_TechMemo149.pdf See pages 53-56 for seabird mortality info.

Information also available on CCIEA Indicator website https://www.integratedecosystemassessment.noaa.gov/regions/california-current/cc-indicator-status-trends under focal component ’Seabirds’ https://www.integratedecosystemassessment.noaa.gov/regions/california-current/cc-indicator-seabirds

Q3. Which infographic elements?

And where shall these go? Here are some options:

MBNMS Overview https://marinebon.org/mbnms > Key human activities and impacts > Human Impacts > Seabird disturbance, Marine mammal disturbance similar to CINMS Overview https://marinebon.org/cinms/index.html > Key human activities and impacts https://marinebon.org/cinms/modals/key-human-activities.html > Human Impacts > Seabird disturbance Feature also in specific habitats for MBNMS? Pelagic https://marinebon.org/mbnms/pelagic.html Sandy Beach https://marinebon.org/mbnms/sandy-beach.htmlHere is what I am thinking:

CINMS& MBNMS Pelagic habitat > flying seabird element: This element will include data products of two types:

1) Seabird mortality estimates using beach cast seabird carcass data from BeachCOMBERS. The data products here would include i) Encounter rate (birds/km) of all seabirds combined ii) Encounter rate (bird/km) for the most commonly encountered species: Common Murre, Cassin’s Auklet, Northern Fulmar, Sooty Shearwater, Rhinoceros Auklet, Brown Pelican, Gulls, Grebes [let’s start with these] I periodically update information on that data here https://docs.google.com/document/d/1900J3xMq-LVF9KictzmAtT0Tqve2UVeZL3KvLDKLrNU/edit#heading=h.8mhfnqfkihyn in my Data Sources and Data Products https://docs.google.com/document/d/1900J3xMq-LVF9KictzmAtT0Tqve2UVeZL3KvLDKLrNU/edit?usp=sharing tracking document.

2) at-sea seabird density observations that I am currently in communication about with Bill Sydeman (Farallon Institute), Clarissa Anderson (SCCOOS), and Lynn Dewitt (SWFSC). This are getting incorporated into ERDDAP and will be available in the near future (exact time frame TBD). More information about this is summarized here https://docs.google.com/document/d/1900J3xMq-LVF9KictzmAtT0Tqve2UVeZL3KvLDKLrNU/edit#heading=h.8mhfnqfkihyn in my Data Sources and Data Products https://docs.google.com/document/d/1900J3xMq-LVF9KictzmAtT0Tqve2UVeZL3KvLDKLrNU/edit?usp=sharing tracking document.

CINMS & MBNMS Overview > Key human activities and impacts > Human Impacts > Seabird oiling *BeachCOMBERS Cause_of_death_code 5 = oil 1) MBNMS: Seabird deposition & percent oiled (as shown on slide 4 in Beached birds and mammals info summaries). Note significant oiling events occurred when the percent oiled birds exceeded 2% mortality for MBNMS [somehow we want to highlight when this threshold has been exceeded] 2) CINMS: Seabird deposition & percent oiled (as shown on slide 5 in Beached birds and mammals info summaries). Note significant oiling events occurred when the percent oiled birds exceeded 9% mortality for southern region [want to highlight when this threshold has been exceeded]

CINMS & MBNMS Overview > Key human activities and impacts > Human Impacts > Seabird entanglement *BEachCOMBERS Cause_of_death_code 2 = tangled in fishing net/line; Cause_of_death_code 3 = tangled in plastic 1) MBNMS: Annual number of seabird carcasses reported as entangled in a) fishing gear or b) plastic [similar to stacked bar graph shown on slide 6] 2) CINMS: Annual number of seabird carcasses reported as entangled in a) fishing gear or b) plastic [similar to stacked bar graph shown on slide 6]

On Feb 10, 2020, at 11:00 AM, Ben Best notifications@github.com wrote:

Hi @jenn-brown https://github.com/jenn-brown,

Ok, I integrated:

the newer Axiom file BeachCOMBERS_formatted_2019.csv https://researchworkspace.com/file/5851070/BeachCOMBERS_formatted_2019.csv, which is birds only up to 2019; with the existing ERDDAP - oceanview.../EB_MM_BC https://oceanview.pfeg.noaa.gov/erddap/tabledap/EB_MM_BC.html, which is birds and mammals up to 2016 here for just MBNMS:

marinebon.org/info-beachcombers https://marinebon.org/info-beachcombers Plots

See plots:

bird carcasses static interactive, color by species on hover mammal carcasses static interactive, color by species on hover eg bird carcasses : static

https://user-images.githubusercontent.com/2837257/74180337-30242500-4bf4-11ea-9a20-c3975325e09f.png Note: goes up to 2019.

eg mammal carcasses : interactive

https://user-images.githubusercontent.com/2837257/74180410-4c27c680-4bf4-11ea-8049-f8f4102eb78d.png Note: goes up to only 2016. Shows species information on hover.

Questions

I still have some open questions though:

Q1. Just MBNMS?

Since this data is only on the mainland, does it belong in CINMS or just MBNMS? Check out the section spatial : intersect sanctuary with segments for an interactive map: https://user-images.githubusercontent.com/2837257/74174852-8b044f00-4be9-11ea-9bf6-9c46bc18f4c0.png Q2. Other plots?

Where can I get more information about these plots in slide 14 of Beached birds and mammals info summaries - Google Slides https://docs.google.com/presentation/d/18Ez8lMeKDbJvDNagOeNHU9GT7qLf_BZcTh4nwtwNcb8/edit#slide=id.g5ddce32724_2_144? https://user-images.githubusercontent.com/2837257/74175101-fe0dc580-4be9-11ea-903c-2f18530dea65.png I can't find this in CCIEA 2019 ESR 508.pdf https://www.integratedecosystemassessment.noaa.gov/sites/default/files/2019-04/CCIEA%202019%20ESR%20508.pdf, only this in Appendix J.2: https://user-images.githubusercontent.com/2837257/74175352-84c2a280-4bea-11ea-9e6e-177a6cbcbf44.png Q3. Which infographic elements?

And where shall these go? Here are some options:

MBNMS Overview https://marinebon.org/mbnms > Key human activities and impacts > Human Impacts > Seabird disturbance, Marine mammal disturbance similar to CINMS Overview https://marinebon.org/cinms/index.html > Key human activities and impacts https://marinebon.org/cinms/modals/key-human-activities.html > Human Impacts > Seabird disturbance Feature also in specific habitats for MBNMS? Pelagic https://marinebon.org/mbnms/pelagic.html Sandy Beach https://marinebon.org/mbnms/sandy-beach.html — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/marinebon/info-beachcombers/issues/1?email_source=notifications&email_token=AOL4TB7PTOHALVJKF2U2MPTRCGP57A5CNFSM4KJNPNUKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOELJ2OQA#issuecomment-584296256, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOL4TB6TLYY6YW6APIUBZJ3RCGP57ANCNFSM4KJNPNUA.

bbest commented 4 years ago

Hey @jenn-brown, testing your email

jenn-brown commented 4 years ago

Got it - thanks

Jennifer Brown, Ph.D. Principal, ECOS Consulting, LLC

Contractor: SIMoN Ecosystem Scientist | Monterey Bay National Marine Sanctuary Project Scientist | Channel Islands National Marine Sanctuary

jennifer.brown@noaa.gov | 415-310-6764

On Tue, Feb 11, 2020 at 10:34 AM Ben Best notifications@github.com wrote:

Hey @jenn-brown https://github.com/jenn-brown, testing your email

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/marinebon/info-beachcombers/issues/1?email_source=notifications&email_token=AOL4TB4W7MTGLPNVAOHZFTTRCLVRZA5CNFSM4KJNPNUKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOELNRY4I#issuecomment-584785009, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOL4TB2G7VZFIAK6TVMDHW3RCLVRZANCNFSM4KJNPNUA .

bbest commented 4 years ago

@mspector13, can you please let me know where these should go in the MBNMS website?