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Application Catalogue
7 RShiny apps , 1 RMarkdown
  1. Marine Aggregates Application Baseline
    Author(s): Cooper,K. ; Martinez,R. (2017)
    Category: R Shiny App
    Acronym: (MAAB)
    Keywords:

    MAAB provides a range of benthic related tools to assist with marine licence application and compliance monitoring. Baseline tool Explore the faunal cluster identity of ‘baseline’ sampling stations. For details of the different cluster groups see table S2 on the following page.

  2. Marine Aggregates Application Mahalanobis
    Author: Cooper,K. ; Martinez,R. (2017)
    Category: R Shiny App
    Acronym: (MAMT)
    Keywords:

    M-test tool The Mahalanobis or M-test tool assesses whether sediments at baseline stations remain suitable for (re)colonization by the original faunal assemblage. The tool uses input data from the RSMP sediment workbook template, and outputs a ‘traffic light’ style map and table. Where samples fail the M-test, this will require further investigation outside the tool.

  3. OneBenthic Non-Native Species Tool
    Author: Cooper, K; Martinez, R
    Category: R Shiny App
    Acronym: (OBNNST)
    Keywords: benthic, non-native, species, OneBenthic

    This tool provides distribution records for benthic non-native species. The tool also shows the species distribution range (min and max latitude and longitude) by year, providing an indication of possible spread.

  4. Phytoplankton observations, products and services
    Author: Collingridge, K. (2018)
    Category: R Shiny App
    Acronym: (PHYTOOPS)
    Keywords:

    PHYTO-OPS (phytoplankton observations, products and services), is an R shiny application designed to make biological data collected during regular surveys on board the RV Cefas Endeavour around the UK more accessible, by visualising the data and improving their interoperability to inform experts in phytoplankton ecology such as remote sensing scientists, modellers, data managers and monitoring agencies. Users can view quality control information, explore the data through maps and plots, and download data.

  5. Faunal Cluster ID Tool
    Author: Cooper,K. (2019)
    Category: R Shiny App
    Acronym: (FACID)
    Keywords:

    This tool matches new macrofaunal data to the existing faunal cluster groups identified in Cooper and Barry (2017, http://rdcu.be/wi6C ). The tool request the data to OneBEtnhic database and provides functionalities to query, visualize and download the selected datasets.

  6. Parafish Economic Tool
    Author: Mcpherson,N. (2019)
    Category: R Shiny App
    Acronym: (PARAFISH)
    Keywords:

    The Parafish Economic Tool has been developed as part of the Parafish project. It has been designed to improve awareness of how farm characteristics and management impact parasite presence and severity in net pen ongrowing sites. The information presented has been gathered through an expert consultation, and an epidemiological study of 39 farms, both carried out as part of the Parafish project. You can find out more about these studies, and view the data which drives the model, on the Cefas Data Hub.

  7. Monitoring added value
    Author: R. Martinez (2020)
    Category: R Markdown
    Acronym: (PARAFISH)
    Keywords:

    RMarkdown document to explore and analyse the correlation between POC, depth and fishing benthic impact indicator swept area ratio (SAR) . The interactive document provide user interface widgets to filter these parameters and observe changes based on user selection . In addition , the document provide access to the soruce and filtered datasets.

  8. OneBenthic Survey Array Tool
    Author: Cooper,K.(2020)
    Category: R Shiny App
    Acronym: (OBSAT)
    Keywords:

    This app allows users to visualize individual survey arrays for a variety of different sectoral monitoring programmes. The tool is primarily intended for use by surveyors, providing station array positions, protocols for sample collection and processing, survey timetables and details of previously collected samples. However, it is also provides a means for identifying potential synergies between disperate survey programmes, and thus opportunities for future collaboration (for further details see Barrio Frojan, Cooper and Bolam, 2018).

  9. OneBenthic Dashboard
    Author: Cooper,K.(2020)
    Category: R Shiny App
    Acronym: (OBDASH)
    Keywords:benthic, OneBenthic, dashboard

    This tool is a dashboard for the OneBenthic initiative. It includes stats on the number of database records, an interactive map showing sample locations, summary plots, links to associated apps, papers and latest news. The dashboard also includes a mission statement and further info (pdf download).

  10. OneBenthic Data Extraction Tool (Grab/Core)
    Author: Cooper,K.(2020)
    Category: R Shiny App
    Acronym: (OBDASH)
    Keywords:benthic, OneBenthic, data, extraciton, abundance , sediment particle size

    This app allows users to explore and download macrofaunal and sediment particle size data (grabs/cores) from the OneBenthic database. Select by ‘survey’ (drop-down list), or ‘sample’ (map drawing tool). Selected samples are shown in a table (see appropriate tab), with data available for csv download.

  11. Twitter Impact Tool
    Author: R. Martinez (2020)
    Category: R Shiny App
    Acronym: (TIMPT)
    Keywords:

    Social network becomes a important platform for information access and exchange and Twitter is ideal for trend analysis due to the public nature of their publications . TWIT Shiny application was designed to search for key words, tags or user names and obtain the last 7 days tweets , statistics and text mining analysis. In the main page of TWIT the user get access to geographical , publisher users and text mining anlysis of the search result tweets . The second page allows exploring the content of the search result tweets.

OSF Software
  • Data management

  • Analysis

  • Communication & Collaboration


About

An increasingly popular way to make science accessible, reproducible, scalable, and replicable is through Open Science and the development of open-access tools (Lowndes et al., 2017).

The most popular open-access platform for analysis and reporting of data is R (R Development Core Team, 2016). R provides more than 5000 packages for data exploration, visualisation, modelling and statistical analysis. In addition, the R Shiny package allows for the creation of web tools, allowing users to interact with science outputs and methods, without any requirement for software (only web access is required) or a need to understand complex code. Another advantage of R Shiny is that it allows scientists to directly create web tools without any of the disadvantages associated with using 3rd party programmers (e.g. high cost, difficulty communicating ideas or interpreting science).

Within Cefas (Lowestoft and Weymouth), a recent survey suggests at least 12 such tools have been created. These include the Marine Protected Areas Management tool, and the Marine Aggregates App (https://benthosapps.net/ma_tool/), a collection of tools used by the aggregates industry for compliance monitoring. These two examples powerfully demonstrate how stakeholders (industry/regulator/SNCBs) and the public can interact with the Cefas science both for data access/visualisation and innovative analyses/reporting.

Recognising the need to be able to host such tools, Cefas science computing has recently purchased a Shiny R server. To ensure Cefas tools/applications are developed and deployed in a way which satisfies Open Science criteria, we are proposing a framework (Fig. 1). This framework will ensure that tools are based on solid foundations of: i) access to data using Cefas systems, ii) high quality, open access peer review publication, and transparency of methods using code repositories such as gitHub. Developed tools can be brigaded into applications to meet needs of specific groups (e.g. windfarm industry). These applications will ensure Cefas has a leading role in management and science development for particular activities.

Services

The framework workflow is designed to produce four different science outputs during its implementation: i) databases, ii) scientific papers or reports, iii) methods and iv)web applications.

The framework describe the web applications as a collection of multiple methods, the methods as ordered scripts available in R package format used for paper/report writing , the scientific papers as a result of data analysis and the database server as the organized collection of these data used for research.

Service description

The current computer , R and R Shiny details are provided to support application developers. Applications or tools developed with the intention to use the Shiny Server have to compatible with the following system specifications:

Platformm Architecture Operating System
Redhat Linux GNU x86_64 Linux
Language Version Nickname
R R version 3.5.1 (2018-07-02) Feather Spray

Requirements

  1. Data management: The data underlying the web applications on this Open Science Portal source data via links from the Cefas Data Hub , or from external database sources (Terms and Conditions may apply unless those listed under Open Government Licence). Further spatial and non-spatial data needed to run the applications is also made available from Open Source PostgreSQL Database Servers hosted at Cefas. For more information please refer to the Cefas Data Management Policy HERE, or contact via . For more information please refer to the Cefas Data Management Policy here or contact via data.manager@cefas.co.uk.

    We strongly recomend the use of Open Source PostgreSQL/PostGIS . It is a open source database suitable for spatial data management and analysis PostgresSQL site

  2. R Library: In regard to the utilisation of R libraries , they need to be available on CRAN repository for the R version given in service description.

    It will be needed a list of the dependencies libraries of your application , please send with your application description.

  3. Security Assurance: The applications have to go through a proccess of information and security assurance when they are planned to be publicly available. It will depende on the type of content and services taht the application provides. To understand more about htis process or go through it , please contact Richard Page
This list of requirements may change based in the experience we are gaining with the implementation process.

Contact

Projects interested to build a R Shiny application or integrate an existing one into the Cefas Openscience framework, please contact roi.martinez@cefas.co.uk . Further explanation about the openscience framework will be provided soon .

The linux server VM where R Shine Server is hosted have been provided by Cefas Science Office and Cefas IT program. Contact john.bacon@cefas.co.uk

The installation and configuration of the Shiny Server community version and the NGINX server have been done by Roi Martinez.

Each web application have their own development and maintenance responsable. To report any issue related to the applications please refere to the contact person provided with in the applicaiton description