Table of Contents

Welcome

Welcome to the MERMAID Documentation. Here we will walk you through how to use MERMAID.

MERMAID is an open-source application that collects and manages real-time coral reef health data, developed in partnership between the WCS, WWF, and Sparkgeo.

With MERMAID, scientists input their observations straight into the platform using the Web app. MERMAID does the job of tagging and sorting data, avoiding duplicates, standardizing scientific names and summarizing critical indicators.

We save you time so you can save coral reefs!

MERMAID joins you in the field with its off-line capabilities, but it stands apart from Excel or personal database apps like Access because it requires virtually zero post-entry data clean up! 

Users can select reef fish and coral names from a standard list of taxa with only a few keystrokes; MERMAID will autocomplete the rest. Selecting names means saving time typing in species names or cleaning up typos of misspelled species names.

MERMAID also allows you to calculate reef fish biomass while you type, or see your total coral cover as soon as you have finished entering a transect. When you have finished collecting data, it can be exported to standard field reports (Excel) and used to create graphs or other reports. You can also analyze your data by accessing it directly from MERMAID using the mermaidr package.

The MERMAID workflow

The MERMAID workflow:

  1. Sign up and set up a project

    1. Sign up for an account

    2. Set up a project and add users

    3. Prepare for off-line use

  2. Collect data

    1. Select a transect type

    2. Enter site information

    3. Enter management regime

    4. Include benthic attributes and fish species

    5. Complete and save the transect

  3. Review and submit 

    1. Validate data

    2. Address errors and warnings

    3. Submit data

  4. Export and analyze data

    1. Export to .XLSX for further analysis

    2. Analyze directly using mermaidr

Questions? You can reach out to us when online via the Contact link at the bottom of the app. An off-line (pdf) version of this documentation is available through the "Download" button at the left menu bar.

A Deep Dive into MERMAID V2

MERMAID has a fresh design and smarter performance. Dive into everything you need to know about the new MERMAID!
Take a tour of MERMAID version 2 in our latest webinar

The Projects Page

The Projects Page provides a complete summary of what is happening in each project: the number of submitted and unsubmitted sample units, the total number of sites with data, the number of users added to the project, and how the per-protocol data sharing policies have been set. Click on each to go directly to the specific project page; for example, you can access a project's Submitted data page by clicking Submitted. MERMAID Version 2 also added an all-new notification area in the menu (the "bell") that informs you of the latest updates from MERMAID and your projects. Close to the notification button, you can find the Reference button which you can access from any page. Now, you can download References in XLSX format and have all the benthic and fish data in one document. Each project also includes the Copy project and Off-line Ready buttons from MERMAID Version 1.

The Overview Page

As a data manager, you might want to see at a glance all the data that has been submitted as well as who to chase for unsubmitted data. MERMAID Version 2 understands you. It now has Overview pages that allow you to inspect the number of submitted sample units per method for each site as well as who has not yet submitted which sample units, and make sure that sites are associated with the right management regimes. Clicking on any sample unit number provides you with direct access to that sample unit. To make changes, the sample unit must be moved from the Submitted to the Collecting page. Re-validation is required before submitting the updated sample unit. This means no more unexpected site changes or other unintended errors.

The Overview Page showing submitted and unsubmitted data

The Collecting Page

The new Collecting Page is designed to allow users to handle warnings and errors more easily. It also shows a reminder of why a sample unit cannot be submitted, to help you address problems more quickly. Messages are easier to read and appear next to the field where the problem is. MERMAID Version 2 also deals with site and management regime duplications in a smarter way; Version 1 would check for duplication every time a site or management regime was saved, whereas in Version 2, duplication is checked only with sample unit validation, and only against submitted sample units -- a more efficient and more relevant process. The photo transect method is now available in MERMAID Version 2 to store your photo classification results. On the Submitted page, the Export to XSLX button now produces a single file with data aggregated to sample unit and sample event levels as well as raw observations.

The Users Page

The new Users page provides more detailed information on users in the project, for teams of any size. MERMAID Version 2 supports filtering users by name or email address. Admins can also change roles, add and remove users without going to another page, and access the user's email addresses for easy contact.

See our MERMAID Version 2 announcement. If you have any questions or want to learn more about MERMAID Version 2, contact us.

Getting started

Signing up

To use MERMAID,  you need to sign up at https://app.datamermaid.org.

You can 'sign up with Google' to use an existing Gmail account and associated password, or enter a different email and create a password specific to MERMAID. Your account will be linked to your email.

Only users who have a MERMAID account can collect data on MERMAID. Emails not associated with MERMAID accounts can be specified by other users as Sample Unit observers; but without an account you cannot interact with the data.

MERMAID is only officially supported on Google Chrome, Firefox, and Edge browsers, and may not fully work with other browsers, like Explorer or Safari.

After signing up you will receive a confirmation email to verify your new account. You can access your profile information by clicking on the avatar in the upper right corner of any page. Here you can view your email and name, and change your MERMAID account name.

If you forget your unique password for MERMAID, click 'Don’t remember your password?' on the login page to receive an email with a link to reset your password.

If you signed up for MERMAID using Google and forget your Gmail password, you must reset your password through Google.

Setting up a new project

A project consists of a set of observations collected in sample units (transect/quadrat/etc.) surveyed at particular sites, on particular dates, associated with management regimes. All data, data sharing, and user access in MERMAID is organized by project. It is up to you to decide how to organize your observations; many users define a project as containing the data from a single expedition.

A new project can only be created while online. To create, click the red ‘New Project’ button, enter a project name, then click “Create Project” to complete your new MERMAID project. A name is required for every new project. All other information can be added using "Project Info" in the lefthand menu.

After a project is created, add users, sites, management regimes, and organization, and set data sharing policies while online.

Creating a new project.

1. Add Users:

Enter the email addresses for users involved in the project and select their roles. Users should be signed up for a MERMAID account before they can be added to a project. You can add an email that has not yet been associated with an account, but that project user's name will appear as '(pending user)' and they will not be able to access MERMAID until they associate that email with an account.

Adding user(s) to the project.

The project creator is automatically the administrator (‘admin’) of the project. Other users will default to the collector role when added and can be changed to admin or read-only by selecting the appropriate role from the available options. Additional users can be added or deleted by the administrator after a project is created.

The scope of each role is as follows:

  • Read-Only: user can only view, export, and analyze data in the analysis tools, but cannot collect new observations.

    • i.e. a project manager who is in charge of writing reports or analyses but is not collecting data in the field

  • Collector: user can view, export, and analyze data, and collect new observations. Once a transect is submitted, the user can no longer edit or delete observations.

    • i.e. a member of the project team who is tasked with collecting data

  • Admin: user has all Collector privileges, and can additionally change project information and data sharing, add and remove project users, transfer unsubmitted sample units between project users, and un-submit sample units for further editing.

    • i.e. typically one person designated as the lead of the project

If a user must leave a project or reaches the end of their position, their data can be transferred to other users within a project. This can be done within a project through the "Users" tab. Simply select ‘Transfer’ for the user that will be removed from the project, then indicate the user from the project to whom you would like to transfer the unsubmitted sample units. Users can also be removed from a project on this page. If a user still has unsubmitted sample units on their “collecting” page, be sure to transfer records prior to removing them from the project.

Transfer unsubmitted sample unit(s) to another user.

2. Add Sites:

Adding sites to a project is done after the project has been created, by selecting the "Sites" item under "METADATA" in the lefthand menu within a project. Once on the sites page, there are two ways to add a site to a project:

  1. Create a new site using the "+ New site" button at the top right of the page, fill in the details and click the 'Save' button on the top right of the page.

  2. Choose from sites that are already in the MERMAID system using the "Copy sites from other projects" button next to the create new site button. These may be sites that you or your organization are monitoring and have used before in previous surveys. The search bar allows you to filter the list by site name, project name, or country. Click the check box next to any site you would like to add to your project, then click the “Copy selected sites to project” button at the bottom of the dialog. A map at the bottom of the dialog also displays where the site is located with a red dot.

Adding site(s) by selecting from existing sites in MERMAID.

3. Add Management Regime:

A management regime categorizes the regulations and restrictions placed on an area in which a survey site is located, on the date of the survey. These may be management regimes for sites that you or your organization are monitoring or have used in previous surveys. To add management regimes, navigate to "Management Regimes" in the lefthand menu within a project. 

If you are surveying sites with a new management regime, or if your site’s management regime has changed, it must be added after creating your new project. 

There are two ways to add management regimes to a project:

  1. Create a new management regimes using the "+ New MR" button at the top right of the page, fill in all the details, and then click 'Save' on the top right of the page.

  2. Choose from existing management regimes in the MERMAID system using "Copy MRs from other projects". You can save time by selecting and adding previous management regimes to your project here. The ‘Filter’ bar allows you to search the list by management name, project name, or year. Click the check box next to any management type you would like to add to your project, then click the “Copy selected MRs to project” button at the bottom of the dialog.

Adding management regime(s) by selecting from existing management regimes in MERMAID.

4. Add organization

Add your organization to the project. By adding your organization, it will help you monitor your surveys easily by using the filter function on the MERMAID dashboard. To add your organization, use the "Project Info" item under "Admin" in the lefthand menu within a project. As soon as you type, MERMAID will show you a dropdown options of the available organizations for you to select. You can add more than one organization in a project. Once you're done adding organizations, click the "Save" button on the upper right to record your changes.

Adding organization to a project.
Adding organization to a project.

If you can't find your organization under the available options, you can suggest a new organization. To do this, type your organization name in the "Organizations" field and select "Suggest a new organization to MERMAID" option. Type again your organization name in the "New Organization Name" field and click "Send to MERMAID for review". Once your organization is accepted, it will be available in the dropdown list.

Suggesting a new organization.
Suggesting a new organization.

5. Data Sharing:

MERMAID is committed to working collectively as a community of researchers and reef managers to use the power of data to make faster, better decisions. Coral reef monitoring data is collected with the intent of advancing coral reef science and improving management. We recognize the large effort to collect data and your sense of ownership. While not required, we hope you choose to make your data available to fuel new discoveries and inform conservation solutions.

Choosing a data policy for your project determines how much of your project’s data can be shared with other users to facilitate global collaboration and understanding of coral reef health via future global dashboard features in MERMAID. It can be chosen independently for different survey methods, so that fish and benthic data can have different levels of sharing. Your data policy level can be changed at any time after creating a project.

The three policy levels are:

  • Public summary – Collected observations are private, but site-level summary statistics are public, along with metadata for the project, protocol, and site. This option is the default.

  • Public – All collected observations are public.

  • Private – Collected observations and site-level summary statistics are private, but metadata for project, protocol, and site, including site location and type and count of sample unit at each site, are public.

Detailed information on what data are shared in each data sharing policy option.

If you are creating a project to practice using MERMAID or train others, you can indicate this with the 'This is a test project' checkbox at the bottom of the page. Data added for a test project will be omitted from all public reporting.

Set your data sharing options or assign a project as a test project on the Data Sharing Page.

Now your project is ready to be used!

The Projects page

The Projects Page lists all the MERMAID projects of which you are a part, in any role (admin, collector, or read-only). The Projects Page provides a complete summary of what is happening in each project: the number of submitted and unsubmitted sample units, the total number of sites with data, the number of users added to the project, and how the pre-protocol data sharing policies have been set. If you are an admin of a project, there will be an Administrator Tag appear next to the project name.

Click the top-left “MERMAID” icon or “Projects” in the top navigation bar of any page to go to your main Projects page.

Project details can only be edited while online.

Access the Collecting Page, Submitted Page, Sites Page, and Data Sharing Page directly from the Project Page.

You can access common project pages directly by clicking each item under each project. For example, if you click COLLECTING, you will be directed to that project's Collecting page. In this way, the Projects page provides easy access to directly start entering data, review submitted sample units, manage your sites, remove or add additional users, and change your data sharing settings for each project.

If you're doing a repeat survey and would like to create a new project for it, you can use the Copy button on the project you want to copy. This will create a new project and copy the sites, management regimes, data sharing policies, and users and their roles.

Use the filter bar to search the projects by name or country. You can also download a Reference xlsx file containing the fish and benthic attributes used in MERMAID, go to the Global Dashboard, view the What's New page, and check updates using the notification (bell) icon.

Preparing for offline use

Before heading to the field, there are a few steps that must be followed to ensure you are able to enter data offline.

Be sure to follow each step carefully prior to your expedition while connected to the internet:

  1. All project members create accounts

  2. A project admin creates the project

  3. The project admin must add all other users to the project. Optionally, copy or add sites and management regimes before going to the field.

  4. Ensure that the 'Offline Ready' button to the right of each project in the project list that you will use offline has a checked sign. If it is not checked, click the 'Offline Ready' button to make sure data is available offline. 

  5. Test offline access by clicking the 'You're ONLINE' toggle on the bottom left of all pages so that it reads 'You're OFFLINE', turning off your Wi-Fi, restarting Chrome, and entering test data into your project.

  6. Ensure that you and all other project members are logged in to MERMAID and can access the project with all the latest sites and management regimes, then toggle the 'You're ONLINE' button to 'You're OFFLINE'. Do not sign out of your MERMAID account. Now your project is ready to be used offline and it is safe to turn off your computer.

Click the 'Offline Ready' button and toggle the 'You're ONLINE' button to prepare for offline use.

Delete Projects

Unused or multiple test projects can submerge users in unnecessary data, clogging up projects. You can delete dormant projects using the 'Delete Project' button on the Project Info Page. Rest assured, the process involves multiple steps to prevent accidental deletion and safeguard essential data.

Steps to delete a project is as follow:

  1. Ensure that you have the admin rights to the relevant project. Only an admin can delete a project.
  2. Remove all users.
  3. Remove all submitted and unsubmitted sample units.
  4. Head to the Project Info Page and click the 'Delete Project' button.
Steps to delete a project.

Fish and benthic taxonomies

Click on 'Reference' in the main toolbar (upper right of the MERMAID Collect app) to download an xlsx file of all benthic attributes and fish species / genera / families that are used in MERMAID. This works offline as well as online.

Unduh Referensi xlsx dari toolbar MERMAID pada menu Collect (daring atau luring).

In the xlsx file, you will find five sheets: Fish Families, Fish Genera, Fish Species, Fish Groupings, and Benthic. Each sheet provides information for that taxonomic level. Using filters, you can search and sort for the specific information you are looking for.

Referensi lembar kerja mermaid_attributes.xlsx mencakup lembar kerja yang berbeda untuk atribut ikan dan bentik yang tersedia untuk digunakan di MERMAID.

Fish and benthic attributes in MERMAID are standardized, and aligned with accepted names in the World Register of Marine Species (WORMS), eliminating discrepancies between different users' data. However, if you want to record an observation of something you think is missing, you can propose to add it in the app, and it will be reviewed by the MERMAID team. Before adding a new fish or benthic species, please make sure that you are using the accepted scientific name by WORMS.

Once you propose a new fish species or benthic attribute, you can directly use it while entering data. The MERMAID team will either accept your proposal, making it available for all other MERMAID users, or work with you to normalize the proposed species or attribute with an existing one; either way, we will let you know by email.

Propose new fish species

  1. In any fish belt transect, scroll down to the Observations table.
  2. Type the fish species that you want to add. When what you have typed does not match any fish species in MERMAID, the option to propose a new species will appear.
  3. Click the “Propose New Species” option.
  4. Type the genus name in the Genus field. If the genus you are looking for is not there ("No results found"), send us an email by clicking “Contact” button in the bottom right of the app.
  5. Type the species name in the Species field and click "Next".
  6. Click "Send to MERMAID for review" to complete your proposal.
Mengusulkan spesies ikan baru di MERMAID.

Propose a new benthic attribute

  1. In any benthic transect, scroll down to the Observations table
  2. Type the benthic attribute that you want to add. When what you have typed does not match any benthic attribute in our database, the option to propose a new benthic attribute will appear.
  3. Click the “Propose New Benthic Attribute” option.
  4. Type the parent name in the Parent field. Typically, "Parent" will be a coral genus or family, but can be a non-trophic attribute. For example, to add a new Acropora species named Acropora test, type/select Acropora in the Parent field, then type Acropora test in the Name field, and click “Next”.
  5. Click "Send to MERMAID for review" to complete your proposal.
Mengusulkan atribut bentik baru.

Standard taxonomic hierarchies

MERMAID has developed a single set of standard taxonomic hierarchies for reef fish and benthic observations that are shared across the MERMAID Collect, Dashboard and R Package apps. This eliminates lengthy data cleaning, simplifies analysis, and makes it easy to create reproducible charts and reports from your data. 

Reef fish observations aggregate from species to genus to family to trophic group (e.g. herbivore, planktivore, etc). 

Benthic observations aggregate from species to genera to family to a benthic top-level category (e.g. hard coral, soft coral, macroalgae).

Reef fish (left) and benthic (right) taxonomic hierarchies in MERMAID.

Reef fish observations 

For reef fish observations, the biomass constants, maximum length, trophic level, fishing vulnerability, climate score, and geographic distribution are drawn from FishBase

  • Since reference values of biomass constants and trophic level are provided by species in FishBase, when using a genus- or family-level fish observation in Collect, MERMAID automatically averages species-level values. For example, typing "Acanth'' allows you to record an observation for the "Acanthuridae" family, the "Acanthurus" genus, or the "Acanthurus achilles" species; if you chooose "Acanthurus" biomass constants will be the averages of all species in the "Acanthurus" genus.

Benthic observations 

MERMAID uses a hierarchical taxonomy of benthic attributes. This means that every attribute can be ‘rolled up’ into one of 12 top-level benthic categories which are available in xlsx data downloads from MERMAID and shown in the MERMAID dashboard.

The 12 top-level categories are:

  • Bare substrate (e.g., rock)
  • Crustose coralline algae
  • Cyanobacteria
  • Hard coral
  • Macroalgae
  • Other (e.g., trash, plastic, etc)
  • Other invertebrates
  • Rubble
  • Sand (including silt)
  • Seagrass
  • Soft coral
  • Turf algae (including dead coral or dead coral with algae)

For example, ‘Acropora palmata’ rolls up to ‘Acropora’ then ‘Acroporidae’ then the final top-level category of ‘Hard coral’. Top-level category classifications are provided as a separate column in xlsx downloads from your submitted MERMAID data. 

  • Custom analyses, such as calculating percentages for benthic attributes that are not top-level categories, can be done using observation-level data by exporting submitted data from a project or accessing directly using the mermaidr package.

Using a ‘blank’ filter in the Parent column of the Reference xlsx file will provide you with a list of the 12 top-level categories.

Pilih filter "(Blanks)" pada kolom "Parent" untuk menampilkan daftar 12 kategori bentik tingkat teratas.

Filtering for a specific benthic attribute in the "Parent" column will show all benthic attributes that belong to it.

Pilih filter atribut bentik tertentu pada kolom "Parent" untuk menampilkan semua atribut bentik yang menjadi miliknya.

Collect data

Process and definitions

The data collection process

All information entered in MERMAID goes through validation before becoming live, scientifically valid data. When entering information from your dive sheets, whether online or offline, you work with transects and quadrats that are only visible to you, in the "Collecting" area of a project.

When you are online and ready to commit your observations, you validate each sample unit individually, and once all warnings and errors are addressed, submit it. Only then does the sample unit become visible to all project members in the "Submitted" area of the project. It is also part of all exported xlsx files, and available via authenticated mermaidr access. If the project's data sharing policy for that sample unit is not "private", the sample unit will also be available to non-project members, accessible via the MERMAID dashboard.

Definitions

  • Site: A place, defined per-project as a unique set of latitude and longitude coordinates with a name and other attributes, where data is collected
  • Management Regime: A set of rules in effect at the time of data collection governing coral reef resources, with a name and other optional attributes.
  • Sample event: An episode of data collection occurring at a Site on a date, with a Management Regime in place. The unique combination of Site, date, and Management Regime defines a Sample Event, which is used for the aggregated calculation of sample unit-level survey results.
  • Sample unit: A group of observations collected as part of a particular survey protocol, at a given place on a given date (sample event). Because many survey protocols define a transect, "sample unit" is often used interchangably with "transect" but is more general, including, for example, collections of bleaching quadrats.
  • Observation: an individual measurement of an observable phenomenon collected as part of a sample unit, for example a benthic attribute at a point along a benthic Point Intercept Transect.
  • Validation: The MERMAID online process all sample units must undergo before becoming scientifically valid data.
  • Error: a validation issue prohibiting submission because it violates fundamental survey protocol definitions; for example, a transect cannot be submitted without a defined length.
  • Warning: a validation issue that flags an unusual value, such as a fish size greater than previously recorded. Warnings can be addressed by changing the relevant value or by indicating that the warning should be ignored.

The Collecting page

The ‘Collecting’ page is where you can add new sample unit observations and view other observations that you have already collected and saved but not yet submitted. 

Select a project from your list to enter the project’s "Collecting” page, or directly click the "COLLECTING" tab on the Project Page.

The red number next to the “Collecting” tab in the lefthand menu indicates the number of records you have collected and saved but not yet submitted. The search bar allows you to filter the records by site name, management regime, or observer name. Use the "Filter Method" button to filter based on the method. It allows users to filter in multiple ways and show the total sample unit(s) using the chosen method(s) next to the filter button. Click on the "x" symbol to remove all filters applied. Click on the table headers to sort based on your preference.

Filter data based on the method using the "Filter Method" button and sort data by clicking the header(s).

Only users with ‘Collector’ or ‘Administrator’ roles can collect and submit new observations; ‘Read-only’ users cannot collect sample units.

A sample unit requires validation prior to submission. Validation will ensure that all data in a sample unit are correct. If not, an error or warning will appear on top of the page and next to the issue that need to be resolved.

Observations can be added both online and offline, but they can only be validated and submitted when connected to the internet.

MERMAID Version 2 also provides an improved experience to record data using a mobile phone.

Adding new sites and management regimes

In the lefthand menu you can find "Sites" and "Management Regimes". Here admins and collectors can add a new site or management regime to a project. A site is a unique latitude and longitude, with accompanying attributes; a management regime is the area (including MPAs, OECMs, or open access zones) defined by a set of rules in effect at the time of data collection.

Adding a new site

Navigate to the “Sites” tab and select “+ New site” 

A new site requires a name, country, coordinates, and details on the exposure, reef type, and reef zone. The name can be the site’s common name or unique ID. A point symbol will appear on the map below it to show the site location based on the coordinates. The point can be move around to adjust to the right location and the coordinates will follow. When all details have been added the "Save" button will turned on to allow saving the site.

In the “Sites” tab you can choose “Copy sites from other projects” to add existing sites and their metadata from other MERMAID projects.

Adding new site to the project.

A new site created by one user is shared across the project with all other users and available for them to use in observations. Best practice is to plan the sampling sites for your project in advance and add them before going to the field.

If multiple new sites have identical coordinates, they will be flagged as duplicate sites if used in submitted sample units. In other words, MERMAID will detect duplicate sites only if used in a project. If this happens, for example because multiple team members add the same site while offline, you will see a warning after you hit the "Validate" button next to the "Site" field within a sample unit  that says “Site: Similar records detected”. Click “Resolve” to decide whether to merge the duplicate sites or keep them separate.

Resolve duplicate sites in a project.

A dialog box will show you which sites are considered duplicates. Here you can decide whether to keep one site and merge it with the duplicate sites, or to edit a site and change the metadata to indicate that they actually are separate, unique sites. Unique sites must have different coordinates.

 

If you choose to keep a site, the site that will be merged with the site you chose to keep will be highlighted in yellow. Select “Merge” to confirm.

Merge duplicate sites.

When sites have been merged, the sites will be updated with the single merged site, and this merged site will automatically be assigned to all sample units that were using the duplicate sites. All observation data will be preserved.

Adding a new management regime

Navigate to the “Management Regimes” tab and select “+ New MR”

Create new management regime in a project.

A new management regime requires a name and at least one rule; all other details are optional. "Open Access" is the default for the "Rules". When you are finished, save the management regime. You can also delete using the “Delete Management Regime” button at the bottom of the page. Only saved management regime can be deleted.

 

On the “Management Regimes” page you can also choose “Copy MRs from other projects” to add existing management regimes and their metadata from other MERMAID projects. 

A new management regime created by one user is shared across the project with all other users and is available for them to use in observations. Best practice is to know the management regimes within your project in advance and add them while online, before going to the field. Management regime details can be edited after creation if needed.

Multiple management regimes with identical names will be flagged as duplicate management regimes. If this happens, you will see a warning next to the "Management" filed that says “Another Management Regime is similar to this one”.

These management regimes can be merged or kept separate. Click “Resolve” button to decide whether to merge the duplicate management regimes or keep them separate.

A dialog box will show you which management regimes are considered duplicates. Here you can decide whether to keep just one management regime or to edit a management regime and change the metadata to indicate that they actually are separate, unique management regimes. Unique management regimes must have different names.

If you want to keep just one management regime, select the “Keep MR” button. The duplicate management regime(s) that will be merged with the management regime you choose to keep will be highlighted in yellow. This merged management regime will now be assigned to all sample units that had been associated with the duplicate management regime. All observation data will be preserved. If you want to keep both management regimes, select “Keep both”.

Entering a transect

When you’re ready to enter new data for a project, click “+ Add Sample Unit” at the top right of the Collecting page and select a method.

There are six methods available in MERMAID: fish belt transect, benthic point intercept (PIT) transect, benthic line intercept (LIT) transect, benthic photo quadrat transect, bleaching quadrat collections, and habitat complexity transect. These transects are similar to methods described in the Coral Reef Monitoring Protocol for Assessing Marine Protected Areas (Ahmadia et. al 2013) (Appendix 2). The benthic photo quadrat transect currently stores your photo identification results only. 

There are six methods available in MERMAID.

After selecting a method, you must fill in all required fields, marked with a red asterisk. Sites and Management Regimes that you added previously will appear in the dropdowns. A helper text is also availaible to all input fields. You can view this feature by clicking the info icon next to any relevant field. Each will have its own explanation, including text-filling examples.

Use the show and hide feature for the helper text. This approach applies to all methods in MERMAID.

Optional transect information includes label, sample time, reef slope, visibility, current, relative depth, tide, and any notes.

When filling in any sample unit, all necessary information (shown with an asterisk symbol) cannot be empty.

Each transect requires at least one ‘observer’, defined as a person who collected transect observations. This is a required field, and you can choose from the available list of users associated with your project. To remove an observer, uncheck the box next to the observer's name.

Choose an observer by clicking the checkbox next to the observer's name.

You can save a transect any time, online or offline. A disabled Save button indicates that no data have changed since the last time you saved the transect.

When online, you can validate and submit the transect. Offline, only the ‘Save’ button will appear.

Deleting a Transect

If you wish to delete a transect, click the "Delete Record" button at the bottom of any unsubmitted Sample Unit in Collecting. This will permanently remove the record and its observations from MERMAID, so be sure that you want to remove it before confirming.

Sample unit types

Fish Belt Transect

Assess reef fish populations by recording the size and abundance of fish along a 'belt' transect of a specific width and length.

In MERMAID, fish belt transects require users to specify the length of the surveyed transect (meters), and the total width of the surveyed transect (meters). MERMAID users can choose their values to estimate the total transect area surveyed for their biomass calculations. E.g., a transect of 50 m length x 5 m total width = 250 m^2 area, or 0.025 ha. 

Metode transek sabuk.

MERMAID also requires users to enter a transect number (e.g., 1, 2, etc.) to keep track of replicate transects. Users can add more text information to the optional 'label' field if necessary, e.g., 'long swim transect'. In addition, MERMAID users can select how fish sizes are estimated underwater. Typically, scientists use  1cm, 5cm, or 10cm size bins. This provides information on whether a fish was observed as: 

  • 26 cm (1 cm bin)

  • 25-30 cm (5 cm bin)

  • 20-30 cm  (10 cm bin)

For all fish larger than 50+ cm, select the '50+cm' bin and enter in the exact size estimate in cm. 

Additionally, there are other size bin groupings that can be selected: 

  • AGRRA: 0-5cm, 6-10cm, 11-20cm, 21-30cm, 31-40cm, 40-50cm, 50+cm

  • WCS India: 0-5cm, 5-10cm, 10-20cm, 20-30cm, 30-50cm, 50+cm

Entering transect and observations information.

After entering information about the transect and observers, you can enter in your reef fish observations. Note: Once you have selected a fish 'size bin' and entered data, you are not able to change the size bin without deleting your observations. 

Entering observation data to the Observation Table. Use the predictive feature to type faster.

To enter a reef fish name, simply type any three letters of an observed fish family, genus, or species, MERMAID will provide a predictive dropdown with names. This ensures all spelling is correct and consistent. Select the fish family, genus, or species to use for an observation by using the ‘up’ or ‘down’ arrow keys or entering more letters so that there is only one choice and press the Enter or Return key to select a name.

MERMAID's fish names use the World Register of Marine Species (WORMS) taxonomy standard. Before proposing new fish species to the MERMAID team, check the species is an accepted standard on WORMS. Biomass coefficients are linked in from FishBase Bayesian length-weight coefficients in order to calculate biomass 'on the fly' as you enter each observations. Not seeing your biomass estimates? Double check that you have entered a transect length and width (so MERMAID knows the transect size that you are estimating biomass). 

To avoid common errors, MERMAID will flag the following warnings and errors:

  • Warning: Total biomass less than 100 kg/ha or greater than 2,000 kg/ha

  • Warning: Total fish count less than 10

  • Warning: Total observations less than 5

  • Errors: Missing metadata information (e.g., depth, transect length or width, observers, etc.)

Be a sailfish: enter your data at top speeds! 

Did you know that the Indo-Pacific Sailfish (Istiophorus platypterus) is the fastest fish in the world with swimming speeds at >110 km/hour? MERMAID helps you be a sailfish too and enter your data at top speeds! 

How? Use the ‘tab’ and 'return' keys and your 'up' and 'down' arrows on your keyboard to quickly enter your observations.  After typing a few letters and selecting your observed fish with the 'up' or 'down' arrow keys on your keyboard, use the 'tab' key to move across to the size and count columns, then type or select your entry (still on your keyboard). At the end of a row, press 'tab' at the end of a row to duplicate the fish species. This is helpful if you are entering on row of Acanthuridae 5-10cm bin observations, then press 'tab' to enter Acanthuridae 10-15cm observations, for example. Or maybe then you see a sailfish! Press 'return' to type in 'Istpl' and use the down arrow key to select Istiophorus platypterus.

Benthic Point Intercept Transect (PIT)

The benthic point intercept transect (PIT) records observations of benthic cover at regular intervals along a transect.

Each transect requires a transect number, depth, the surveyed transect length (m), the interval between point observations (m), and the interval point where you start to record your data (m). For example, points counted every 50 cm can be entered as 0.5m in the “Interval size” field.

Image: Komaruddin/WCS Indonesia
Entering the transect and observations information.

Enter the benthic attribute observed at each point at the bottom of the page.

Entering observation data to the Observation Table. Use the predictive feature to type faster.

After typing any three letters of an observed benthic attribute, MERMAID will provide a predictive dropdown with names. This ensures that all spelling is correct and consistent. Select the benthic attribute by using the ‘up’ or ‘down’ arrow keys on your keyboard or with your mouse, or entering more letters so that there is only one choice, and then pressing the 'Enter'/'Return' or 'Tab' key to select a name. Growth forms can be selected from the dropdown list or predicted by typing.

Available benthic attributes can be found using the “Reference” icon at the header of any page. New benthic attributes can be proposed to the MERMAID science team for approval and addition.

The number of rows should equal the total number of expected points based on your transect length and interval size. You will receive a warning if the number of entered rows does not match this.

The percent cover of each benthic category along the transect will automatically be calculated and displayed at the bottom of the rows. All benthic attributes belong hierarchically to a small number of top-level benthic categories commonly used for analysis, such as "hard coral".

NAVIGATION TIP

Use the ‘Tab’ key to move across to the attribute and growth form columns. At the end of the row, press 'Enter'/'Return' to create a blank row and add a new benthic attribute observation. Press the 'Tab' key at the end of the row to duplicate the benthic attribute in the next row.

Benthic Line Intercept Transect (LIT)

The benthic line intercept transect (LIT) records observations of benthic cover length along a transect.

Each transect requires a transect number, depth (m), and the surveyed transect length (m).

Entering transect and observations information.

Enter the benthic observations from the transect at the bottom of the form.

Entering observation data to the Observation Table. Use the predictive feature to type faster.

After typing any three letters of an observed benthic attribute, MERMAID will provide a predictive dropdown with names. This ensures that all spelling is correct and consistent. Select the benthic attribute by using the ‘up’ or ‘down’ arrow keys on your keyboard or with your mouse, or entering more letters so that there is only one choice, and then pressing the 'Enter'/'Return' or 'Tab' key to select a name. Growth forms can be selected from the dropdown list or predicted by typing.

Available benthic attributes can be found using the “Reference” icon at the header of any page. New benthic attributes can be proposed to the MERMAID science team for approval and addition.

The sum of the observation lengths entered should equal the total transect length. You will receive a warning if not.

The percent cover of each benthic category along the transect will automatically be calculated and displayed at the bottom of the rows. All benthic attributes belong hierarchically to a small number of top-level benthic categories commonly used for analysis, such as "hard coral".

 

NAVIGATION TIP

Use the ‘Tab’ key to move across to the attribute, growth form, and length columns. At the end of the row, press 'Enter'/'Return' to create a blank row and add a new benthic attribute observation. If the same attribute is observed but with a different length, press the ‘Tab’ key at the end of the row to duplicate the benthic attribute in the next row.

Benthic Photo Quadrat

This sample unit records the results of classified photo quadrat images.

Each transect requires a transect number, depth (m), surveyed transect length (m), the starting quadrat number, the quadrat size (m2), the number of quadrats, and the number of points per quadrat.

Entering transect and observations information.

Enter the photo identification results from the photo quadrat observations at the bottom of the form.

Entering observation data to the Observation Table. Use the predictive feature to type faster.

Each observation must record the total number of points identified as a particular benthic attribute in a particular photo quadrat.

After typing any three letters of an observed benthic attribute, MERMAID will provide a predictive dropdown with names. This ensures that all spelling is correct and consistent. Select the benthic attribute by using the ‘up’ or ‘down’ arrow keys on your keyboard or with your mouse, or entering more letters so that there is only one choice, and then pressing the 'Enter'/'Return' or 'Tab' key to select a name. Growth forms can be selected from the dropdown list or predicted by typing.

Available benthic attributes can be found using the “Reference” icon at the header of any page. New benthic attributes can be proposed to the MERMAID science team for approval and addition.

The sum of the points in the observations entered for that quadrat must equal the total number of points entered at the transect level above.

The percent cover of each benthic category along the transect will automatically be calculated and displayed at the bottom of the rows. All benthic attributes belong hierarchically to a small number of top-level benthic categories commonly used for analysis, such as "hard coral".

NAVIGATION TIP

Use the ‘Tab’ key to move across to the attribute, growth form, and number of points columns. At the end of the row, press 'Enter'/'Return' to create a blank row and add a new benthic attribute observation. Press the 'Tab' key at the end of the row to duplicate the benthic attribute in the next row.

Bleaching

This rapid assessment field method can be used to quantify coral bleaching for different genera of hard corals.

In this rapid assessment field method, the sample unit is a collection of quadrats observed for coral bleaching on a single dive/snorkel. The method is described in detail here.

Watch our step-by-step guide to perform rapid bleaching survey and how to input it into MERMAID.

First, observers choose a consistent quadrat size (typically 1 to 2 m2) to use on the survey. During a survey, an observer records information from a set of quadrats, typically ~15-20 quadrats. Within a quadrat, an observer first counts the number of coral colonies for each hard coral genus and classifies each colony within 7 categories of bleaching severity: normal, pale, 0-20% bleached, 20-50% bleached, 50-80% bleached, 80-100% , and recently dead. After recording the coral colonies, the observer then visually estimates the cover of three main benthic groups within the quadrat: hard coral, macroalgae, and soft coral. Then, the observer swims a set distance (e.g., 10 fin kicks) to begin the next quadrat. 

Entering transect and observations information.

In MERMAID, observations from the surveys are recorded in 2 sections. The 'Colonies Bleached' section records the total number of colonies in each bleaching category for each genus. The 'Percent Cover' section records the % cover of hard coral, macroalgae, and soft coral for each quadrat. 

Entering observation data to the Observation Table. Use the predictive feature to type faster. The bleaching observation is divided into two sections, i.e. 'Colonies Bleached' section and 'Percent Cover' section.

NAVIGATION TIP

Use the 'Tab' key to move across the colonies bleached and percent cover columns. At the end of the row, press 'Enter'/'Return' key to create a blank row to add the next complexity observation. If the same bleaching or percent cover is observed at the next interval, press the 'Tab' key at the end of the row to duplicate.

Habitat Complexity

This transect records observations of benthic habitat complexity on a scale of 0 to 5, based on the methodology proposed in Wilson et al. (2007) and described in Darling et al. (2017) and Gurney and Darling (2017) (Appendix 2).

To enter a habitat complexity transect, you will need to provide a transect number, depth (m), the surveyed transect length (m), and the interval between complexity observations (m). For example, assessing complexity every 5 m can be entered at ‘5 m’ in the “Interval size” box.

Entering transect and observations information.

Enter the habitat complexity score at each interval at the bottom of the page. You must have as many rows of observations as you do intervals in the transect length.

Entering observation data to the Observation Table.

NAVIGATION TIP 

Use the 'Tab' key to move across the interval and habitat complexity score columns. At the end of the row, press 'Enter'/'Return' key to create a blank row and add the next complexity observation. If the same habitat complexity is observed at the next interval, press the 'Tab' key at the end of the row to duplicate the previous row.

Saving a transect

Once you enter any new information into a transect, you can save it using the button in the upper right corner of the page. 

The save button is bright red when there is new information to be saved. If the button is gray and says “Saved”, you have already saved the transect and there is no new information to be saved.

Click the red 'Save' button to save a sample unit. Once saved, the button will greyed out and read 'Saved'.

After saving, you can always return to the transect to add or change data and information and resave.

If you try to navigate away from a page with unsaved information, you will see a warning on the screen that you have unsaved data – choose “Cancel” to stay on the transect and save; choose “Ok” to leave the transect unsaved.

Once you validate and successfully submit your transect, you can no longer edit it. If you need to edit a submitted transect, a project admin must un-submit it; if you are not the project admin, they will then need to transfer it to you for editing.

All sample units are always saved on your computer. Any time you are online, MERMAID also saves to a backed-up database in the Cloud.

Validate and submit data

After your data has been saved, it can be validated. Validation is the “proofreading” of the sample unit information and observations. This is where mistakes and outliers are caught and brought to your attention to correct. Site and management regime validations are checked only against submitted sample units. A reminder of why a sample unit cannot be submitted is shown under the Submit button to help you address problems more quickly.

Validation can only be done online.

After saving a transect, click the activated red “Validate” button to validate your transect.

Validating a sample unit can only be done when connected to the internet.

After successfully validating a transect and resolving any errors or warnings, the Validate button will be grayed out and the Submit button will be activated in red.

After validating, you will receive one of the following results:

A. Success!

Nice work, your sample unit was validated successfully! There are no errors with the data and it is ready to submit.

B. Warnings

Warning messages can be either ignored or solved by correcting the data in the field.

A yellow warning will appear at the top of the page or by and individual form field if MERMAID identifies a potential issue in your transect information. Warnings are validations that identify entered data that are possible, but unusual.

You can decide whether each warning can safely be ignored for your data. If the issue resulted from a data entry mistake, you can correct the data in the field, or in some cases by clicking a “Resolve” button to open a dialog where you can add or change the information. Click “update” to incorporate your changes into the transect. You can also navigate to fields with issues by clicking 'Scroll to observations' next to the warning.

After addressing warnings, resave the transect and validate again. Repeat the process for any additional warnings that are identified. If you don’t believe a warning is accurate for your transect, you can disregard it by clicking the 'Ignore warning' checkbox next to the warning.

C. Errors

Errors can not be ignored and must be resolved before a sample unit can be submitted.

A red warning message will appear if MERMAID identifies an error in a sample unit’s information or observations. Errors must be resolved before a transect can be submitted; they cannot be ignored. To address each error, scroll down to the field that has the 'ERROR' notice and directly change the information.

After resolving all errors, resave the transect and validate again. Repeat the process for any additional errors that are identified, until all 'ERROR' notices have disappeared.

D. Submit data

When you are finished entering data for a sample unit and have resolved all Errors and Warnings, you can Submit the sample unit.

After submitting data, admin users can still edit the transect or return a transect to the observer, so as a collector, make sure your data are finalized and clean before submitting! Submitting data can only be done when online.

To submit data, select the red button in a validated transect that says “Submit”.

Submit a sample unit by clicking the 'Submit' button after all errors and warnings addressed.

Submitting data moves it from the "Collecting" page to the "Submitted" page. This shares your observations with the other users in the project (and depending on Data Sharing settings, potentially with the world). Within the “Submitted” page, admins can edit or delete transects or return them to their original observers for further editing.

If you are a read-only member on a project you can see data once it has been submitted and you can export it, but you cannot edit this data while it is in MERMAID.

You can also view your submitted data per project in the MERMAID Dashboard directly from the Collect app. Simply click on the icon 'View on Dashboard' next to the project name to navigate to the dashboard.

Manage your data

The OVERVIEW area provides project-level views of how a project is progressing and easy ways to find out who to chase for missing data. It is also enchanced with filtering by method feature through a butten next to the search bar. This feature allows users to filter in multiple ways. The total sample unit using the chosen method(s) will appear next to the filter button.

The 'Observers and Transects' page summarizes the number of submitted and unsubmitted transect(s) per site and method. Hover over each transect number to see detailed information including who was the last person editing the transect, who were the observer(s) collecting the transect, site name, management regime, and collecting date. You can also head to the submitted transect by clicking the 'View Submitted Sample Unit'.

The Observers and Transects page helps you to easily identify who to chase for unsubmitted sampe unit(s).

The 'Management Regimes Overview' summarizes the number of submitted (not unsubmitted) sample units per management regime. Management regimes that have no submitted transects will not appear in the 'Management Regimes Overview' table. You can click on the transect number to jump to the submitted sample unit information.

The Management Regimes Overview table helps you to make sure that all sites have the correct management regimes.

Upload spreadsheets

Good news! You can now upload your existing data or 'legacy data' directly to MERMAID using our R package mermaidr.
Watch our step-by-step guide in uploading spreadsheest using the historical fishbelt data as an example.

If you are new to MERMAID and have existing data from past surveys in other formats that you would like to add to MERMAID, you can use our R package mermaidr to upload this old data into MERMAID. 

The workflow for uploading data should only be used for existing 'legacy' data. For an ongoing project, it is easier and better to enter your underwater observations directly in the app.

The ingestion workflow.

Steps for ingestion using the mermaidr package:

  1. Create a project in MERMAID with sites, management regimes, and users added.

  2. Adjust your data format to the MERMAID template. You can download the template for each method using the mermaid_import_get_template_and_options function from the MERMAID R package mermaidr. More information on how to use it can be seen here.

  3. Ensure the mandatory fields are filled. Mandatory fields include an asterisk (*) sign in the column name. Download our example of PIT data using the MERMAID template here.

  4. Check each field to make sure it matches allowed field options for importing data for a given method. To check each field, use the mermaid_import_check_options function from the MERMAID R package mermaidr. More information and example on how to use it can be seen here. A field that matches will produce a green check sign.

  5. After all fields have passed the checking process, you can import your data using the mermaid_import_project_data function from the MERMAID R package mermaidr. Detailed information and an example can be seen here.

All ingested data will appear on the Collecting page. These data will need to go through the regular validation and submission process. For an example how to ingest your legacy data using the MERMAID R package mermaidr, head to the ingesting fishbelt data example.

Unsubmitted ingested transects appear on the Collecting page of the user who did the ingesting. To transfer unsubmitted sample units to another user, a project admin can use the project's Users page.

Ingested data will appear in your collecting page and will be shown on the Project Page under the COLLECTING tab. The number in the red circle shows the number of sample units in your collecting page, while the number without the red circle show the total unsubmitted sample units in a project.

Read and download here the step-by-step guide on how to upload your existing data into MERMAID using the mermaidr package in R.

Upload your CoralNet data with Easy PQT

You can now upload your CoralNet data using our Easy PQT app.

Try Easy PQT

Photo benthic quadrat data that are annotated using CoralNet can be imported to MERMAID in two ways, i.e., the MERMAID R package mermaidr and Easy PQT. Using the MERMAID R package mermaidr to upload your photo benthic quadrat data to MERMAID requires a good knowledge of R. If you are familiar with R, you can follow the steps in the Upload spreadsheets documentation, which has all the information you need, including the tutorial video and examples.

Another way to upload your photo benthic quadrat data is using the Easy PQT app. Easy PQT is a shiny app that supports MERMAID users, especially users unfamiliar with R, who want to upload their CoralNet exported data to MERMAID. It’s straightforward and user-friendly. Similar to using the MERMAID R package mermaidr, your data will appear on your Collecting Page after you upload it using Easy PQT. However, you will need to fill in some of the mandatory fields on MERMAID before validating and submitting your data. See the Easy PQT workflow below:

Easy PQT workflow
Easy PQT workflow

Only an admin of a project can upload data using Easy PQT and make sure that your project is not a test project. A test project will not appear on the Easy PQT list of projects.

Steps to upload your CoralNet exported data using Easy PQT:

  • Prepare a project in MERMAID with sites, management regimes, organizations, and users added, and data sharing policies set up.

  • Export your photo benthic quadrat data from CoralNet, including the auxiliary fields. You will need to set up your auxiliary fields to contain Sites and Management Regimes that correspond to what you have added on MERMAID, as well as Transect numbers. You are also free to rename your auxiliary fields. To download your data with its auxiliary fields, navigate to “Images” in a CoralNet project. Under the “Image Actions”, select “Export Annotations, CSV”, and select the optional columns “Image metadata - date and auxiliary fields”, as shown below:

Export your CoralNet data with additional columns in CoralNet.
Export your CoralNet data with additional columns in CoralNet.
  • Open Easy PQT and follow the instructions. Once you open the Easy PQT, it will automatically ask you to authenticate yourself. This way, Easy PQT can provide a list of your projects. Only project(s) that are not a test project will be shown on the list.

  • Select the project to which you want to upload your data and upload your CSV data. You can click the “browse” button to find the data you want to upload or drag and drop directly to the upload field.

Seret dan letakkan data Anda yang diekspor dari CoralNet ke Easy PQT.
Seret dan letakkan data Anda yang diekspor dari CoralNet ke Easy PQT.
  • Match your CoralNet auxiliary fields with the MERMAID Site, Management, and Transect number you’ve prepared on the app. Once you’re done matching those three columns, Easy PQT will automatically validate them to see if they match the options in the MERMAID project you’ve prepared. If it does not match, you will receive information on which fields do not match and what the available options are. A button to Restart Easy PQT will also appear for you to click and restart the process after fixing the issue(s).

Cocokkan kolom tambahan Anda untuk Situs, Rezim pengelolaan dan nomor transek.
Cocokkan kolom tambahan Anda untuk Situs, Rezim pengelolaan dan nomor transek.
  • When all your data in the auxiliary fields are validated, Easy PQT will map your CoralNet labels to MERMAID attributes. If it’s not available in Easy PQT, then the MERMAID Benthic attribute field will be left blank and colored in red. You need to select the right benthic attributes by clicking on the field directly and start typing or clicking on the arrow on the right to show the dropdown options. Once you’re done filling in the blank fields, click on the “Confirm” button to continue. Easy PQT will reshape your data to match the MERMAID template.

Pilih atribut bentik MERMAID yang sesuai untuk label yang belum dipetakan dengan mengeklik kolom merah secara langsung dan mulai mengetik atau mengeklik panah di sebelah kanan untuk melihat pilihan tarik-turun.
Pilih atribut bentik MERMAID yang sesuai untuk label yang belum dipetakan dengan mengeklik kolom merah secara langsung dan mulai mengetik atau mengeklik panah di sebelah kanan untuk melihat pilihan tarik-turun.
  • Review your reshaped data, then click the “Continue with ingestion” button to upload your data to MERMAID. If you think the data is incorrect, you can click the “Restart Easy PQT” button to start the process from the beginning or click the “Get help” button to contact us for further assistance. In this section, you can also download the reshaped data in a csv format.

Klik tombol
Klik tombol "Continue with ingestion" setelah meninjau data yang diformat ulang untuk mengunggah data ke proyek Anda di aplikasi MERMAID.
  • Upload your reshaped data to MERMAID by clicking the “Continue with ingestion” button on the Easy PQT app. Your uploaded data will appear on your Collecting Page.

  • Head to your Collecting Page in the MERMAID app to fill in the rest of the mandatory fields. After uploading your data, there are still some mandatory fields that you need to fill in. Those mandatory fields include depth, transect length surveyed, and quadrat size. East PQT will automatically assign you (a user that uploads the data) as the observer. Change the observer to the right data collector if you are not the one who collects the data. Once you’re done filling those information, you can validate and submit your transects.

Buka Halaman Collecting Anda di Aplikasi MERMAID untuk mengisi kolom wajib lainnya dan lanjutkan dengan validasi dan pengiriman.
Buka Halaman Collecting Anda di Aplikasi MERMAID untuk mengisi kolom wajib lainnya dan lanjutkan dengan validasi dan pengiriman.

Unsubmitted uploaded transects will appear on the Collecting Page of the users who uploaded the data using Easy PQT. You can transfer these unsubmitted sample units to another user through the project’s User Page. Only an admin of a project can perform this action.

Use your data

Export to XLSX

Submitted transects can be exported to a tabular format in a .xlsx file for further analysis by clicking the ‘Export To XLSX’ button. Use the 'Filter Method' button next to the search bar to filter the submitted transects based on method. The total transects using the chosen method(s) will appear next to the filter button.

Data can only be exported when online and after transects have been submitted. Data in a test project will not be exported.

Make sure that the project is not a test project. Select which method you would like to download. All records of each sample unit with the same method will be combined into a single spreadsheet. This will begin downloading a .xlsx to your computer. All user levels (admin, observer, and read-only) can export data from a project.

Export submitted sample unit(s) per method by clicking the 'Export To XLSX' button.

To change a project from a "Test Project" to an actual project, click "Data Sharing" in the lefthand menu. Scroll down and uncheck the 'This is a test project' checkbox. Wait approximately 20 minutes for the data to sync with the server, and then you can export your data.

Change a project from a "Test Project" to an actual project by uncheck the 'This is a test project' checkbox.

MERMAID also calculates standard deviations corresponding to estimated sample event (site and date) averages. You can find this information in the exported data, under the Sample Event (SE) tab, or by retrieving sample event data using mermaidr, which gives direct access to MERMAID data through R Studio. 

After exporting your data, you can find the standard deviation values under the Sample Event (SE) tab.

Questions? You can reach out to us when online via the Contact link at the bottom of any page. An offline (pdf) version of this documentation is also available on the left side of the same area.

R Package

MERMAID has a helpful R package for accessing and importing your data.

Although Excel or similar programs work for basic analyses, many scientists use programs like R (often in the RStudio environment) for larger datasets or more sophisticated analyses. The mermaidr is an R package specifically for working with MERMAID data and enables you to access your data from MERMAID, compile datasets from multiple MERMAID projects, and ingest legacy data into MERMAID.

If you would like more information and detailed instructions on usage, you can see the package website. You can also find a helpful list of package functions here. We also prepared an example of using the mermaidr package for analysis, which is demonstrated here. More information on how to ingest legacy data into MERMAID can be found in the Ingesting legacy data using R studio page.

If you are new to the R programming language, our new R users guide is a great place to start! If you find yourself stuck, please don’t hesitate to ask for help.

API

All access to MERMAID data, including that done by mermaidr, the MERMAID web application, and the dashboard, is done through an Application Programming Interface (API). If you need custom access to data, for example because you are creating a map or writing your own tool, you can use API documentation here as a guide. The documentation includes a getting started page on how to use the Insomnia API client file included with the MERMAID API code repository to access all API endpoints.

Global Fund for Coral Reefs

MERMAID has been chosen as the digital tool to facilitate the monitoring and evaluation of the Global Fund for Coral Reefs (GFCR) Programmes.

GFCR Monitoring and Evaluation with MERMAID

MERMAID has been chosen as the digital tool to facilitate the monitoring and evaluation of the Global Fund for Coral Reefs (GFCR) Programmes.

MERMAID supports the Global Fund for Coral Reefs, a blended finance instrument to mobilize action and resources to protect and restore coral reef ecosystems.

The Global Fund for Coral Reefs (GFCR) is a global partnership that aims to mobilize resources to support reef-positive businesses and promote coral reef conservation and restoration around the world (see Theory of Change).

MERMAID is supporting GFCR Programmes to collect baselines for 10 core Fund Indicators (F1 to F10) and 36 sub-indicators, and to monitor progress against targets for these indicators with bi-annual reports and final evaluations (see GFCR Monitoring and Evaluation Toolkit). MERMAID will also be used by the GFCR to obtain summaries of coral reef health indicators.

This is now possible with the new integrated tools for the GFCR M&E Framework in GFCR projects on the MERMAID Collect app.

Creating Fund Indicator targets and reports

As a Convening Agent, you need to first sign up to a MERMAID account, login, then set up a project on MERMAID for your GFCR Programme. You can learn about how to create your MERMAID account and project on Getting Started.

Set up your GFCR project

  1. When creating your project, use the name of your GFCR Programme (e.g., Miamba Yetu Program) for the project name on MERMAID.

  2. Once your GFCR project has been created, open your project and go to 'Project Info' under 'Admin' on the left-hand menu bar.

  3. Add a short description of your GFCR Programme in the 'Notes' field.

  4. Add all organization names (including partner organizations) in the 'Organizations' field. If the organization name is not available in the dropdown options, you can suggest a new organization name to MERMAID. Read more on '4. Add Organizations' in Setting up a new project. Remember to include Global Fund for Coral Reefs in 'Organizations'. This is important for locating the GFCR Programmes portfolio on the MERMAID dashboard.

  5. If you need to add other users that will enter ecological data or sets of Fund Indicators in the GFCR project, or that simply need to visualize data, go to 'Users' under 'Admin' and add users by entering their email address. You may change the role of each user inside this page between Admin, Collector or Read-Only, according to type of permissions they need. Learn more on 1. Add Users in Setting up a new project.

Only Admin users can create or edit GFCR reports and targets. Make sure to check each user's role to confirm they have the right permissions.

Enable the GFCR Indicators

GFCR Fund Indicators can be enabled by a single click inside your GFCR project.

  1. To access the 'GFCR' page and create reports for Fund Indicators, you must first enable the GFCR Indicators by clicking the 'Enable GFCR Indicators for this project' button on the 'Project Info' page under the Admin section.

  2. After you click the button, a 'GFCR' page will appear under the 'Admin' section on the left-hand menu bar.

  3. Access this 'GFCR' page by clicking on the 'Go to GFCR Indicators' button from the 'Project Info' page or directly by clicking on the 'GFCR' page under the 'Admin' section on the lefthand menu bar.

On this page, you can create new sets of Fund Indicators as targets or reports, visualize them, make changes, and download them.

Enable GFCR Indicators in your GFCR project.
Enable GFCR Indicators in your GFCR project.
Go to the GFCR page from the Project Info page in your GFCR project.
Go to the GFCR page from the Project Info page in your GFCR project.

Create your target GFCR Fund Indicators

Each GFCR project should establish three sets of targets for the entire duration of the Programme. As new businesses / financial solutions are added to the Programme, these targets can be adjusted accordingly.

We recommend labelling each set of targets as "Phase 1 Target", "Mid-Term Target" and "Final Target" accordingly.

To create a new set of GFCR Fund Indicators as targets for your GFCR project:

  1. Go to the 'GFCR' page, click on the '+ Create new' button, then select 'Target'.

  2. Fill in the 'Title' and 'Reporting Date', click on the 'Create Indicator Set' button. Reporting date should should correspond to the end date of the reporting period for specific target.

  3. You will visualize all 10 Fund Indicators (F1-F10) on the sidebar. Inside each section, add the values for each sub-indicator, then click on the 'Save' button on the top-right corner. If the value entered does not match the validation criteria (e.g., number is too large, not an integer number), the Fund Indicator will not be saved. You should verify your entry to ensure it is entered and saved correctly.

You can always make changes to your saved target indicators by selecting the set of targets your want to edit from list on the main 'GFCR' page.

Create a new set of GFCR Fund Indicators.
Create a new set of GFCR Fund Indicators.

Create a report of GFCR Fund Indicators

Each GFCR Programme will have a baseline report followed by bi-annual reports to track progress against established targets.

We recommend labelling each report as "Baseline," "Mid-Year Report," or "End-Year Report" accordingly.

The steps are very similar to creating a target for GFCR Fund Indicators:

  1. Go to the 'GFCR' page, click on the '+ Create new' button, then select 'Report'.

  2. Fill in the 'Title' and 'Reporting Date', click on the 'Create Indicator Set' button. The reporting date should correspond to the end date of the reporting period for either the baseline or bi-annual report (e.g., for an End-Year Report, the end date is December 31, so you would enter 31/12 followed by the year).

  3. You will visualize all 10 Fund Indicators (F1-F10) on the sidebar. Inside each section, add the values for each sub-indicator, then click on the 'Save' button on the top-right corner. If the value entered does not match the validation criteria (e.g., number is too large, not an integer number), the Fund Indicator will not be saved. You should verify your entry to ensure it is entered and saved correctly.

Even if your GFCR Programme does not engage in specific activities related to any indicators, you are still required to report on all of them.

If your Programme does not engage in the activity, the default values are set to '0', and you may leave them as is if no related activities are being conducted.

You can always make changes to your saved reported indicators by selecting the report your want to edit from list on the main 'GFCR' page.

Create your GFCR report of Fund Indicators by selecting 'Report' in '+ Create new' on the 'GFCR' page.
Create your GFCR report of Fund Indicators by selecting 'Report' in '+ Create new' on the 'GFCR' page.

For all Fund Indicators, there is a 'Notes' field where you can add additional information to support the analysis and interpretation of your indicators, as well as for your annual narrative report to be submitted to GFCR.

MERMAID provides help text for each of the 36 sub-indicators to assist you with completing them. Simply click on the tool tip 'i' next to the sub-indicator or click on the 'Show Help' on the top right to show all the help texts for all sub-indicators.

View the help text for each component indicator by clicking the 'i' icon next to each component indicator or the
View the help text for each component indicator by clicking the 'i' icon next to each component indicator or the "'Show Help' button on the top right corner to display all help texts.

Enter Fund Indicators F1-F7

For Fund Indicators F1 to F7, each sub-indicator value should represent the total aggregate for your entire Programme, reflecting the combined sum of all businesses or financial solutions included.

F1 Programme area

Click on 'F1 Programme area' on the sidebar and enter the total area of coral reefs (in km²) in the field 'F 1.1 Total area of coral reefs in GFCR Programme'.

Remember to report F 1.1 as cumulative totals across all reporting periods since the start of the GFCR Programme. If sub-indicator has no new value for a given report, simply enter the last reported value.

For example, add the newly included area from the current reporting period to the total reported previously. If 50 km² of coral reef area were recently added to the GFCR Program and 200 km² were reported earlier, you would report a total of 250 km² in the current report.

Enter the value for sub-indicator F 1.1 Total area of coral reefs of GFCR Programme.
Enter the value for sub-indicator F 1.1 Total area of coral reefs of GFCR Programme.

To obtain the reef area, we suggest using Allen Coral Atlas:

  1. On the Atlas, enable the 'Reef Extent' map layer

  2. Zoom into the area of interest

  3. Use to polygon tool to outline your reef area

  4. Once your polygon has been created, hit enter and a 'Stats' modal will pop out with the reef extent area calculated in km².

  5. When logged in, you can name and save your polygon, as well as download data. Ensure to check the 'Reef extent' box before downloading.

Obtain the total area of coral reefs for your GFCR Programme by defining a polygon on the reef extent map layer of Allen Coral Atlas.
Obtain the total area of coral reefs for your GFCR Programme by defining a polygon on the reef extent map layer of Allen Coral Atlas.

F2 Conservation and management

Click on 'F2 Conservation and management' on the sidebar, then input the area sizes (in km²) for F 2.1 to F 2.5. Ensure you enter the correct areas, as there are distinctions between coral reef areas and total areas.

Enter the value for each F2 Conservation and management sub-indicator.
Enter the value for each F2 Conservation and management sub-indicator.

To obtain the reef areas and total areas (in km²), you can use Allen Coral Atlas by following the steps on F1 Project area.

In addition, there are other global platforms and databases to extract data for Marine Protected Areas (MPAs), Other Effective area-based Conservation Measures (OECMS), and Locally-Managed Marine Protected Areas (LMMAs) (e.g., Protected Planet, Marine Protection Atlas, Resources Watch). You can also refer to regional and local databases.

Remember to report F 2.1 to F 2.5 as cumulative totals across all reporting periods since the start of the GFCR Programme. If sub-indicators have no new values for a given report, simply enter the last reported values.

F3 Restoration

Click on 'F3 Restoration' on the sidebar, then input the values and area size (in km²) for F 3.1 to F 3.6.

For 'F 3.1 Area of effective coral reef restoration', to obtain the area of effective coral reef restoration (in km²), you can use Allen Coral Atlas by following the steps on 'F1 Programme area'. This indicator is a subset of F1 and used to measure only the area of coral restoration activities in a GFCR Programme.

For F 3.5, the number of people engaged in coral reef restoration is disaggregated by gender (i.e., men and women), youth (between the ages of 15 and 24 as defined by the United Nations) and Indigenous peoples.

Even if your GFCR Programme does not engage in any restoration activities, you are still required to report this indicator. The default values are set to '0', and you can leave them as they are if no restoration activities are being conducted.

Remember to report F3.1 to F 3.6 as cumulative totals across all reporting periods since the start of the GFCR Programme. If sub-indicators have no new values for a given report, simply enter the last reported values.

Enter the value for each F3 Restoration sub-indicator.
Enter the value for each F3 Restoration sub-indicator.

F4 Coral reef health

MERMAID will automatically add your coral reef health indicators from the ecological data you entered in the same project.

Click on 'F4 Coral reef health' on the sidebar, then input the values for coral reef health indicators F 4.1 to F 4.3.

If you have submitted ecological coral reef data for all your GFCR-associated sites inside this GFCR project, you can use the automated calculation tool for reef health indicators:

  1. Select the start and end date for the 'Reporting date range'. The start date should correspond to the date of the initial reef surveys (baseline), and the end date should be the date of the most recent reef surveys conducted within the reporting period.

  2. Average live hard coral cover, macroalgae cover and reef fish biomass are automatically calculated for all submitted surveys within that period

  3. Fields F 4.1, F 4.2 and F 4.3 are automatically populated with results. This way you do not need to calculate any value manually.

    Another option is to manually input each sub-indicator if your surveys are in other projects on MERMAID or stored in a different database.

Be sure to report F 4.1 to F 4.3 as averages based on the most recent surveys. If there are no new surveys available for this reporting period then enter previously reported averages.

If your GFCR Program includes ecological data from other projects on MERMAID, the automated tool for calculating reef health indicators will not be available. However, you can use the mermaidr package in R to access this data, provided you have authenticated access to all relevant projects. This will allow you to calculate averages for all indicators across GFCR Programme sites for the reporting period. For instructions on using mermaidr, please refer to the documentation.

Alternatively, you may download an individual XLSX file from each project on MERMAID and manually calculate the averages for the reporting date range in any analysis applications.

Where feasible, include the data in the XLSX file used to calculate these reef health indicators as an appendix to your narrative annual reports if they are not accessible in your GFCR project on MERMAID. In the 'Notes' field, add details about how these averages were calculated and how they will be submitted as raw data to the GFCR.

If you want to learn more about submitting ecological data in your GFCR project on MERMAID, please read the sections Getting Started, Collect data, Validate and submit data, and Manage your data, in our documentation.

Enter the reporting date range to automatically calculate the F4 Coral reef health sub-indicators from ecological data submitted in the same GFCR project.
Enter the reporting date range to automatically calculate the F4 Coral reef health sub-indicators from ecological data submitted in the same GFCR project.

F5 Communities

Click on 'F5 Communities' on the sidebar, then input the values for sub-indicators F 5.1 to F 5.6.

For F 5.4, the number of local practicioners is disaggregated by gender (i.e., men and women), youth (between the ages of 15 and 24 as defined by the United Nations) and Indigenous peoples.

For F 5.6, you should only report the number of national policies linked to GFCR engagement that have been finalized by the time of reporting. If Programmes are not planning national policy targets, or if a policy is underway but not yet finalized should enter '0'.

Remember to report F 5.1 to F 5.6 as cumulative totals across all reporting periods since the start of the GFCR Programme. If sub-indicators have no new values for a given report, simply enter the last reported values.

Enter the value for each F5 Communities sub-indicator.
Enter the value for each F5 Communities sub-indicator.

F6 People

Click on 'F6 People' on the sidebar, then input the values for sub-indicators F 6.1 to F 6.2.

For F 6.1 and F 6.2, the number of direct jobs created and number of people with increased income and/or nutrition is disaggregated by gender (i.e., men and women), youth (between the ages of 15 and 24 as defined by the United Nations) and Indigenous peoples.

Remember to report F 6.1 and F 6.2 as cumulative totals across all reporting periods since the start of the GFCR Programme. If sub-indicators have no new values for a given report, simply enter the last reported values.

Enter the value for each F6 People sub-indicator.
Enter the value for each F6 People sub-indicator.

F7 Climate Response

Click on 'F7 Climate Response' on the sidebar, then input the values for sub-indicators F 7.1 to F 7.4.

Remember to report F 7.1 to F 7.4 as cumulative totals across all reporting periods since the start of the GFCR Programme. If sub-indicators have no new values for a given report, simply enter the last reported values.

Enter the value for each F7 Climate response sub-indicator.
Enter the value for each F7 Climate response sub-indicator.

Enter Fund Indicators F8-F10

For Fund Indicators F8, F9, F10, data is disaggregated by business or finance solution.

Businesses / Finance solutions

You will enter each business or finance solution from your GFCR Programme separately and disaggregated by sector.

For each business or finance solution:

  1. Go to '+ Add finance solution' to add a new business or finance solution.

  2. Enter name of solution in the 'Finance solution / business name' field.

  3. Select sector type for solution from dropdown options in the 'Sector' field.

  4. In the 'Used an incubator?' field, choose 'Yes: GFCR-funded', 'Yes: non-GFCR-funded' or 'No' to indicate whether an incubator was used for development and identify its funding source.

    If your Programme has developed a GFCR-funded incubator or accelerator, please enter the incubator or accelerator itself as a solution, as well as each business or financial solution it supports individually.

    If your business or finance solution utilized an incubator before the start of the GFCR Programme, you should select 'No' for this field—unless the business or finance solution is also using a GFCR-funded incubator during the Programme period.

    If your GFCR Programme includes a GFCR-funded incubator or accelerator, it should be reported as a separate finance solution. However, when reporting investment and revenue for the incubator or accelerator, do not aggregate the investments and revenues of the businesses or finance solutions it supports. Instead, report only the investments and revenues generated directly by the incubator or accelerator, such as from service provision.

    It is important to ensure that incubators, accelerators, or technical assistance facilities (TAFs) are designed to become financially sustainable by the end of the Programme, with revenue generation as a key objective.

  5. Choose 'Yes' or 'No' to indicate whether the solution is a local enterprise in the 'Local enterprise' field.

  6. Choose 'Yes' or 'No' to indicate whether the solution uses the Gender 2x Criteria in the 'Gender 2x Criteria' field.

    Each business / financial solution should be well-acquainted with the Gender 2X Challenge and its Criteria. An assessment can be conducted to determine whether the solution meet these Criteria thresholds here.

    While GFCR does not mandate a 2X Certification, it expects businesses and financial solutions to strive toward meeting these standards and to evaluate their alignment with the 2X criteria.

  7. Select all sustainable finance mechanisms that apply to the business / finance solution in the 'Sustainable finance mechanisms' field. One solution may have several mechanisms.

  8. Identifying the cycle stage (e.g., launch, growth, maturity) of each business or finance solution is important and can be documented in the 'Notes' field for each entry, as well as in the annual narrative report. This would give more context for determining its success against investments and revenues.

You will have access to a list of all the businesses and financial solutions added on the 'Businesses / Finance Solutions' page. You can make changes to this list at any time.

As new solutions are added to the Programme, include them in your subsequent reports.

Add each business / finance solution in your GFCR Programme disaggregated by sector.
Add each business / finance solution in your GFCR Programme disaggregated by sector.

Investments

The GFCR Programmes categorize investments into three distinct stages: anticipated, committed, and secured.

Secured – investment funds transferred and are with the Convening Agents.

Committed – contract or agreement signed but funds have not yet been transferred. There is a formal obligation to provide funding for a certain period, but the funds have not been deployed yet.

Anticipated – funding expected or planned to occur in the future and discussions are underway, but no formal agreement has been signed.

Convening agents should report only secured or committed funds in MERMAID as data for Fund Indicators F 8.1, F 8.2, F 8.3 or F 9.1 – meaning that there is a signed agreement or the funds have already been received. Anticipated funds can be reported in the annual narrative reports.

You will enter both committed or secured investments for each business / finance solution from your GFCR Programme separately and disaggregated by investment source (i.e., GFCR, philanthropy, private, public) and type.

For each business or finance solution:

  1. Go to '+ Add investment' to add a new investment for a solution.

  2. In 'Business / Finance solution name', choose the solution from the list of businesses and finance solutions previously created. Remember, you will report investments for each solution.

  3. Choose the source from the dropdown options (i.e., GFCR, Philanthropy, Private and Public) in the 'Investment source' field.

    If a solution receives investment from multiple sources (e.g., both GFCR and private), you will need to enter each investment separately for this solution (e.g., once for the GFCR investment and once for the private investment).

  4. Choose the type from the dropdown options in the 'Investment type' field.

    If a solution receives multiple types of investment from a single source (e.g., a grant and technical assistance from GFCR), you will need to enter each type separately under that specific investment source for the solution—for example, once for the grant and once for the technical assistance from GFCR.

  5. Enter the accumulated investment amount in the 'Investment amount' field.

Remember to report committed or secured investments as cumulative totals across all reporting periods since the start of the GFCR Programme. If there are no new investments for a given report, simply enter the last reported investment amounts.

  1. If available, please add cumulative anticipated investment amounts to the "Notes" section and ensure they are included in your annual narrative reports.

You will have access to all the investments listed on the 'Investments' page. You can modify these entries at any time.

Add each investment disaggregated by source and type for individual businesses / finance solutions in your GFCR Programme.
Add each investment disaggregated by source and type for individual businesses / finance solutions in your GFCR Programme.

Revenues

For your GFCR Programme, you will enter the revenues for each business or finance solution separately, disaggregated by revenue type. Revenues for individual businesses or finance solutions should be reported independently and only once to prevent double counting.

For each business or finance solution:

  1. Go to '+ Add revenue' to add a new revenue stream for a solution.

  2. In 'Business / Finance solution name', choose the solution from the list of businesses and finance solutions previously created. Remember, you will report revenues for each solution.

  3. Choose the type from the dropdown options in the 'Revenue type' field.

    If a solution receives revenues from multiple streams (e.g., both biodiversity offsets and blue bonds), you will need to enter each revenue stream separately for this solution (e.g., once for the biodiversity offsets and once for blue bonds).

  4. Choose 'Yes' or 'No' to indicate whether the revenue is sustainable in the 'Sustainable revenue stream' field.

  5. Enter the accumulated revenue amount for the reporting period in the 'Revenue amount' field.

Be sure to report revenues as cumulative totals across all reporting periods since the start of the GFCR Programme. If there are no new revenues for a given report, simply enter the last reported revenue amounts.

You will have access to all the revenues listed on the 'Revenues' page. You can modify these entries at any time.

If your GFCR Programme has a GFCR-funded incubator or accelerator, it is highly recommended to track and report on solutions even after they exit your GFCR-funded incubator or accelerator. Doing so helps demonstrate the long-term impact and return on investment beyond the initial funding period. By monitoring post-incubation success, you can attract further investment opportunities and showcase the added value of the solutions, which is crucial for sustaining growth and scaling beyond 2030.

Add each revenue stream disaggregated by type for individual businesses / finance solutions for your GFCR Programme.
Add each revenue stream disaggregated by type for individual businesses / finance solutions for your GFCR Programme.

Download and visualize your targets and reports

Download your Fund Indicator targets and reports

After creating your targets, baselines, and progress reports, you can download all your reports from the main 'GFCR' page. Simply click on 'Download' to obtain an XLSX file containing all your reports. In the XLSX file, each tab corresponds to a specific Fund Indicator.

Download an XLSX file of all submitted reports from the GFCR page of your project.
Download an XLSX file of all submitted reports from the GFCR page of your project.

View GFCR projects on MERMAID Dashboard

To view all projects tagged with Global Fund for Coral Reefs:

  1. Go to the MERMAID Dashboard

  2. Select the 'Filter' icon on the left-hand toolbar

  3. Filter organizations to 'Global Fund for Coral Reefs' in the 'Organizations' field

Locate GFCR projects on the MERMAID Dashboard.
Locate GFCR projects on the MERMAID Dashboard.

To learn more about the Global Fund for Coral Reefs, visit the GFCR webpage

If you have questions regarding MERMAID or would like to receive further support for using the GFCR M&E tool, contact us when online.