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MCR LTER: Coral Reef: Material legacy disturbance type model; data for Kopecky et al., 2023 Ecology

General Information
Data Package:
Local Identifier:knb-lter-mcr.2011.1
Title:MCR LTER: Coral Reef: Material legacy disturbance type model; data for Kopecky et al., 2023 Ecology
Alternate Identifier:DOI PLACE HOLDER
Abstract:

This data package contains the code necessary to create a theoretical model of coral reef recovery dynamics following different types and intensities of disturbances that either remove dead coral skeletons (e.g., tropical storms) or leave standing dead skeletons (e.g., coral bleaching) and run associated analyses. We explored the sensitivity of the model to variation in key parameters, such as the strength of herbivory, and the degree to which dead skeletons protect algae from herbivory. Further, we assessed disturbance intensities and values of these parameters that lead to shifts between coral and macroalgae-dominated reefs.

These data were published in Ecology and were a part of the thesis of K. Kopecky (2023). Analyses and full methods descriptions of this model can be found in the manuscript “Material legacies can degrade resilience: Structure-retaining disturbances promote regime shifts on coral reefs” (DOI: https://doi.org/10.1002/ecy.4006). No novel data were used or generated in this study.

This manuscript uses data collected by the U.S. National Science Foundation's (NSF) Moorea Coral Reef Long Term Ecological Research (MCR LTER) site under Grant No. OCE 2224354 (and earlier awards). Additional financial support to the MCR LTER site was provided through a generous gift from the Gordon and Betty Moore Foundation. Research was completed under permits issued by the French Polynesian Government (Délégation à la Recherche) and the Haut-commissariat de la République en Polynésie Francaise (DTRT) (Protocole d'Accueil 2005-2023).

Publication Date:2023-08-27
For more information:
Visit: DOI PLACE HOLDER

Time Period
Begin:
2020
End:
2023

People and Organizations
Contact:Information Manager (Moorea Coral Reef LTER) [  email ]
Organization:Moorea Coral Reef LTER
Creator:Kopecky, Kai (Moorea Coral Reef LTER, Graduate Student)
Creator:Stier, Adrian (Moorea Coral Reef LTER, Investigator)
Creator:Schmitt, Russell (Moorea Coral Reef LTER, Principle Investigator)
Creator:Holbrook, Sally (Moorea Coral Reef LTER, Principle Investigator)
Creator:Moeller, Holly (Moorea Coral Reef LTER, Investigator)

Data Entities
Other Name:
Material Legaceis Model
Description:
All R code used to construct the model and create figures 1, 2, 4, and 5 of the manuscript "Material legacies can degrade resilience: Structure-retaining disturbances promote regime shifts on coral reefs".
Other Name:
CodeMeta file for Material_Legaceis_Model_July 2022.Rmd
Description:
CodeMeta file for annotated RMarkdown script to construct the model and create figures 1, 2, 4, and 5 of the manuscript.
Other Name:
Fig. 3 - Analytical Solution
Description:
This code shows how you can use a semi-analytical approach in which you ask MATLAB to generate the numerical values of the equilibria for a set of parameter values.
Other Name:
CodeMeta file for Fig3_AnalyticalSolution.m.
Description:
CodeMeta file for annotated RMarkdown script to show how you can use a semi-analytical approach in which you ask MATLAB to generate the numerical values of the equilibria for a set of parameter values.
Detailed Metadata

Data Entities

Non-Categorized Data Resource

Name:Material Legaceis Model
Entity Type:Rmd
Description:All R code used to construct the model and create figures 1, 2, 4, and 5 of the manuscript "Material legacies can degrade resilience: Structure-retaining disturbances promote regime shifts on coral reefs".
Physical Structure Description:
Object Name:Material_Legaceis_Model_July 2022.Rmd
Size:43832 byte
Authentication:0cde59fc3d51bce82ab37e1aff6fbabb Calculated By MD5
Externally Defined Format:
Format Name:Rmd
Data:https://pasta-s.lternet.edu/package/data/eml/knb-lter-mcr/2011/1/b0d1c07d9f4673aa95247c43eeb72e24

Non-Categorized Data Resource

Name:CodeMeta file for Material_Legaceis_Model_July 2022.Rmd
Entity Type:json
Description:CodeMeta file for annotated RMarkdown script to construct the model and create figures 1, 2, 4, and 5 of the manuscript.
Physical Structure Description:
Object Name:codemeta_Material_Legacies_script.json
Size:1081 byte
Authentication:5b7a517f9330e307c33b7b26beca7f56 Calculated By MD5
Externally Defined Format:
Format Name:json
Data:https://pasta-s.lternet.edu/package/data/eml/knb-lter-mcr/2011/1/3d619c33d6d6e59b4e70b2344b90b636

Non-Categorized Data Resource

Name:Fig. 3 - Analytical Solution
Entity Type:m
Description:This code shows how you can use a semi-analytical approach in which you ask MATLAB to generate the numerical values of the equilibria for a set of parameter values.
Physical Structure Description:
Object Name:Fig3_AnalyticalSolution.m
Size:19930 byte
Authentication:671389efda38881b923a7ea931affd80 Calculated By MD5
Externally Defined Format:
Format Name:m
Data:https://pasta-s.lternet.edu/package/data/eml/knb-lter-mcr/2011/1/9e363d0ef989e9de11722524a6fd7d3d

Non-Categorized Data Resource

Name:CodeMeta file for Fig3_AnalyticalSolution.m.
Entity Type:json
Description:CodeMeta file for annotated RMarkdown script to show how you can use a semi-analytical approach in which you ask MATLAB to generate the numerical values of the equilibria for a set of parameter values.
Physical Structure Description:
Object Name:codemeta_figure_3_Analytical_Solution.json
Size:1070 byte
Authentication:6101d0bf08e3a6dd59c043652b63cfca Calculated By MD5
Externally Defined Format:
Format Name:json
Data:https://pasta-s.lternet.edu/package/data/eml/knb-lter-mcr/2011/1/d1673ecd6e7f00f0174f8ee6d2e12c7b

Data Package Usage Rights

This data package is released under the Creative Commons license Attribution 4.0

International (CC BY 4.0 , see

The Data User has an ethical obligation to cite the data source appropriately in any

publication or product that results from its use, and notify the data contact or creator.

Communication, collaboration, or co-authorship (as appropriate) with the creators of this

data package is encouraged to prevent duplicate research or publication. The Data User is

urged to contact the authors of these data if any questions about methodology or results

occur. The Data User should realize that these data may be actively used by others for

ongoing research and that coordination may be necessary to prevent duplication or

inappropriate use. The Data User should realize that misinterpretation may occur if data are

used outside of the context of the original study. The Data User should be aware that data

are updated periodically and it is the responsibility of the Data User to check for new

versions of the data.

While substantial efforts are made to ensure the accuracy of data and associated

documentation, complete accuracy of data sets cannot be guaranteed. This data package (with

its components) is made available "as is" and with no warranty of accuracy or fitness for

use. The creators of this data package and the repository where these data were obtained

shall not be liable for any damages resulting from misinterpretation, use or misuse of the

data package or its components.

Keywords

By Thesaurus:
(No thesaurus)MCR, LTER, Moorea Coral Reef
Institute, Organization, or Funding AgencyCalifornia State University Northridge, Gordon and Betty Moore Foundation, NSF, Richard B. Gump South Pacific Research Station, University of California Santa Barbara
LTER Controlled Vocabularycorals, modeling, disturbance, herbivory, macroalgae, coral reefs

Methods and Protocols

These methods, instrumentation and/or protocols apply to all data in this dataset:

Methods and protocols used in the collection of this data package
Description:

Using a system of differential equations, we simulated the fraction of reef space occupied by 2 substrate types (primary reef and dead coral skeleton) and 4 coral reef benthic space holders (live coral on primary substrate, live coral on dead coral, macroalgae on primary reef, and macroalgae on dead coral). We assessed the changes in stable equilibrium values of both classes of coral and macroalgae cover across ranges in two key parameters: the rate of herbivory and the degree to which algae are protected from herbivory by dead skeletons. We modeled recovery rates and trajectories after varying intensities of disturbances that either remove dead coral skeletons (e.g., tropical storms) or leave dead skeletons in place (e.g., coral bleaching). Further, we identified the intensities of each disturbance type that were required to cause transitions from coral to algae-dominated reefs, and from algae to coral-dominated reefs, for a range in the strength of algal protection.

Data Source
Material Legacy Disturbance Type Model - GitHub

People and Organizations

Publishers:
Organization:Environmental Data Initiative
Email Address:
info@edirepository.org
Web Address:
https://edirepository.org
Id:https://ror.org/0330j0z60
Creators:
Organization:Moorea Coral Reef LTER
Address:
Marine Science Institute,
University of California,
Santa Barbara, CA 93106-6150 USA
Web Address:
http://mcr.lternet.edu/
Individual: Kai Kopecky
Organization:Moorea Coral Reef LTER
Position:Graduate Student
Address:
UC Santa Barbara, Marine Science Institute, Building 520,
Santa Barbara, CA 93106-6150 United States
Email Address:
kaikopecky@ucsb.edu
Id:https://orcid.org/0000-0002-0021-3087
Individual: Adrian Stier
Organization:Moorea Coral Reef LTER
Position:Investigator
Address:
UC Santa Barbara, Department of Ecology, Evolution and Maine Biology ,
Santa Barbara, CA 93106-9620 United States
Email Address:
astier@ucsb.edu
Id:https://orcid.org/0000-0002-4704-4145
Individual: Russell Schmitt
Organization:Moorea Coral Reef LTER
Position:Principle Investigator
Address:
Marine Science Institute, University of California,,
Santa Barbara, CA 93106-6150 United States
Email Address:
schmitt@lifesci.ucsb.edu
Id:https://orcid.org/0000-0002-9674-4244
Individual: Sally Holbrook
Organization:Moorea Coral Reef LTER
Position:Principle Investigator
Address:
Marine Science Institute, University of California,,
Santa Barbara, CA 93106-6150 United States
Email Address:
holbrook@lifesci.ucsb.edu
Id:https://orcid.org/0000-0002-3015-3484
Individual: Holly Moeller
Organization:Moorea Coral Reef LTER
Position:Investigator
Address:
UC Santa Barbara Department of Ecology, Evolution and Maine Biology,
Santa Barbara, CA 93106-9620 United States
Email Address:
holly.moeller@lifesci.ucsb.edu
Id:https://orcid.org/0000-0002-9335-0039
Contacts:
Organization:Moorea Coral Reef LTER
Position:Information Manager
Address:
Marine Science Institute,
University of California,
Santa Barbara, CA 93106-6150 USA
Phone:
805.893.2071 (voice)
Email Address:
mcrlter@msi.ucsb.edu
Web Address:
http://mcr.lternet.edu/
Metadata Providers:
Individual: Information Manager
Organization:Moorea Coral Reef LTER
Address:
Marine Science Institute, University of California,,
Santa Barbara, CA 93106-6150 United States
Email Address:
mcrlter@msi.ucsb.edu

Temporal, Geographic and Taxonomic Coverage

Temporal, Geographic and/or Taxonomic information that applies to all data in this dataset:

Time Period
Begin:
2020
End:
2023
Geographic Region:
Description:Moorea, French Polynesia
Bounding Coordinates:
Northern:  -17.45Southern:  -17.62
Western:  -150.0Eastern:  -149.67
Altitude Minimum:-20.0Altitude Maximum:0.0

Project

Parent Project Information:

Title:The Moorea Coral Reef (MCR) LTER
Personnel:
Individual: Russell Schmitt
Organization:Moorea Coral Reef LTER
Position:Lead Principal Investigator
Address:
Marine Science Institute,
University of California,
Santa Barbara, CA 93106-6150 USA
Phone:
805.893.3777 (facsimile)
Email Address:
schmitt@lifesci.ucsb.edu
Web Address:
http://mcr.lternet.edu/
Id:https://orcid.org/0000-0002-9674-4244
Role:Principal Investigator
Individual: Sally Holbrook
Organization:Moorea Coral Reef LTER
Position:Principal Investigator
Address:
Marine Science Institute,
University of California,
Santa Barbara, CA 93106-6150 USA
Phone:
805.893.3777 (facsimile)
Email Address:
holbrook@lifesci.ucsb.edu
Web Address:
http://mcr.lternet.edu/
Id:https://orcid.org/0000-0002-3015-3484
Role:Principal Investigator
Individual: Peter Edmunds
Organization:Moorea Coral Reef LTER
Position:Principal Investigator
Address:
Department of Biological Sciences, California State University,
18111 Nordhoff Street,
Northridge, CA 91330-8303 USA
Phone:
818.677.2502 (voice)
Email Address:
peter.edmunds@csun.edu
Web Address:
http://mcr.lternet.edu/
Id:https://orcid.org/0000-0002-9039-9347
Role:Principal Investigator
Individual: Robert Carpenter
Organization:Moorea Coral Reef LTER
Position:Principal Investigator
Address:
Department of Biological Sciences, California State University,
18111 Nordhoff Street,
Northridge, CA 91330-8303 USA
Phone:
818-677-3256 (voice)
Phone:
818-677-2034 (facsimile)
Email Address:
robert.carpenter@csun.edu
Web Address:
http://mcr.lternet.edu/
Id:https://orcid.org/0000-0003-4232-1868
Role:Principal Investigator
Funding:

NSF (LTER) MCR I #OCE-0417412, MCR II #OCE-1026851, MCR IIb #OCE-1236905, MCR III #OCE-1637396, and MCR IV #OCE-2224354

Additional Award Information:
Funder:National Science Foundation
Funder ID:http://dx.doi.org/10.13039/100000001
Number:0417412
Title:LTER: Long-Term Dynamics of a Coral Reef Ecosystem
URL:https://www.nsf.gov/awardsearch/showAward?AWD_ID=0417412
Additional Award Information:
Funder:National Science Foundation
Funder ID:http://dx.doi.org/10.13039/100000001
Number:1026851
Title:LTER: MCR II - Long-Term Dynamics of a Coral Reef Ecosystem
URL:https://www.nsf.gov/awardsearch/showAward?AWD_ID=1026851
Additional Award Information:
Funder:National Science Foundation
Funder ID:http://dx.doi.org/10.13039/100000001
Number:1236905
Title:LTER: MCR IIB: Long-Term Dynamics of a Coral Reef Ecosystem
URL:https://www.nsf.gov/awardsearch/showAward?AWD_ID=1236905
Additional Award Information:
Funder:National Science Foundation
Number:1637396
Title:LTER: MCR III: Long-Term Dynamics of a Coral Reef Ecosystem
URL:https://www.nsf.gov/awardsearch/showAward?AWD_ID=1637396&HistoricalAwards=false
Additional Award Information:
Funder:National Science Foundation
Number:2224354
Title:LTER: MCR IV: Long-Term Dynamics of a Coral Reef Ecosystem
URL:https://www.nsf.gov/awardsearch/showAward?AWD_ID=2224354&HistoricalAwards=false

Maintenance

Maintenance:
Description:

These data are from a short-term study, not planned as a time series.

Frequency:notPlanned
Other Metadata

Additional Metadata

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