elter-so-costs-web-application

This is a repository that hosts the tool to calculate the costs of standard observations to upgrade and operate eLTER sites.

https://github.com/allantsouza/elter-so-costs-web-application

Keywords

Repository

This is a repository that hosts the tool to calculate the costs of standard observations to upgrade and operate eLTER sites.

README.html

eLTER SO Costs web application



Quick Links

Authors
CRediT
author statement
Access policy
Context and aims
Input data
Structure of
files
Development
Reproducibility
Citation
Acknowledgements
Related resources



Authors :busts_in_silhouette:

Name: Allan T. Souza

Affiliation: Institute for Atmospheric and Earth System
Research (INAR), Forest Sciences, Faculty of Agriculture and Forestry,
University of Helsinki, P.O. Box 27, 00014 Helsinki, Finland
:finland:
 Institution ROR: https://ror.org/040af2s02
E-mail: allan.souza@helsinki.fi / allantsouza@gmail.com
ORCID: 0000-0002-1851-681X

Name: Syed Ashraful Alam

Affiliation: Institute for Atmospheric and Earth System
Research (INAR), Forest Sciences, Faculty of Agriculture and Forestry,
University of Helsinki, P.O. Box 27, 00014 Helsinki, Finland
:finland:
 Institution ROR: https://ror.org/040af2s02
E-mail: ashraful.alam@helsinki.fi
ORCID: 0000-0001-9870-1494

Name: Terhi Rasilo

Affiliation: Institute for Atmospheric and Earth System
Research (INAR), Forest Sciences, Faculty of Agriculture and Forestry,
University of Helsinki, P.O. Box 27, 00014 Helsinki, Finland
:finland:
 Institution ROR: https://ror.org/040af2s02
E-mail: terhi.rasilo@helsinki.fi
ORCID: 0000-0002-3502-4040

Name: Steffen Zacharias

Affiliation: Department for Monitoring and Exploration
Technologies, UFZ—Helmholtz Centre for Environmental Research GmbH,
Leipzig, Germany :de:
 Institution ROR: https://ror.org/000h6jb29
E-mail: steffen.zacharias@ufz.de
ORCID: 0000-0002-7825-0072

Name: Jaana Bäck

Affiliation: Institute for Atmospheric and Earth System
Research (INAR), Forest Sciences, Faculty of Agriculture and Forestry,
University of Helsinki, P.O. Box 27, 00014 Helsinki, Finland
:finland:
 Institution ROR: https://ror.org/040af2s02
E-mail: jaana.back@helsinki.fi
ORCID: 0000-0002-6107-667X




CRediT
author statement :man_scientist: :woman_scientist:







Contributor
Contributions




Allan T. Souza
Conceptualization, Data Curation, Formal analysis, Methodology,
Software, Validation, Visualization, Writing - Original Draft.


Syed Ashraful Alam
Conceptualization, Validation, Visualization, Writing - Review &
Editing.


Terhi Rasilo
Conceptualization, Project Administration, Validation, Writing -
Review & Editing.


Steffen Zacharias
Conceptualization, Data Curation, Investigation, Supervision,
Validation, Writing - Review & Editing.


Jaana Bäck
Conceptualization, Data Curation, Funding Acquisition,
Investigation, Project Administration, Resources, Supervision,
Validation, Writing - Review & Editing.





Access policy :balance_scale:

This project is open and freely available for use under the terms of
the CC0
1.0. For more information about the access rights and usage
policies, please refer to the license file.



Context and aims :book: :dart:
This repository hosts the information used to build the eLTER SO Costs web application. This
tool is a specialized resource designed to assist the eLTER (European
Long-Term Ecosystem Research) community in estimating the costs
associated with upgrading and operating standard
observations across various eLTER sites.
The essence of this tool lies in its ability to adapt calculations
based on unique site-specific criteria, ensuring tailored cost
estimations. Key factors taken into consideration include the site
category, the habitats, the focus spheres, and the potential co-location
with other Research Infrastructures, which cover the costs of specific
standard observations.
The goal of this tool is to provide a user-friendly, efficient, and
reliable means for the eLTER community to plan and allocate resources
effectively.


Input data :floppy_disk:
The input data was built based on the agreement of the eLTER
community regarding the standard observations. The data is located at
the data folder and contains consensus information on the
target sampling protocols, equipment, as well as estimations on the
costs associated to upgrade and operate the standard observations.


Structure of files :open_file_folder:
├── .github # Folder containing information how to interact with the repository on GitHub
│ ├── bug_report.md # Instructions to bug reporting
│ ├── feature_request.md # Instructions to fearure requesting
│ ├── CODE_OF_CONDUCT.md # Information on the code of conduct of the repository
│ └── CONTRIBUTING.md # Instructions to contribute to this repository
├── data # Folder for input data used by the app
│ ├── eLTER-SO-costs_list-of-standard-observations.xlsx # Data file in xlsx format
│ └── eLTER-SO-costs_standard-observations-detailed-costs_V18.csv # Data file in csv format
├── www # Folder containing web assets
│ ├── eLTER-SO-costs_landing-page-picture.jpg # Picture for the web application landing page
│ ├── eLTER-SO-costs_elter-logo.png # eLTER simplified logo in png format
│ ├── eLTER-SO-costs_application-logo.jpg # SO Costs logo in jpg format
│ └── eLTER-SO-Costs_app-webinar-20240328_v1.0.0.pdf # slide presentation introducing the application
├── app.R # The main application script for the Shiny web app
├── .Rprofile # R project-specific configuration file
├── eLTER-SO-costs-App.Rproj # RStudio project file
├── .gitignore # Lists files to be ignored by version control system
├── LICENSE # The full text of the license for the project
├── README.html # Compiled HTML from README.md for detailed project information
├── README.md # Markdown text providing an overview of the project
├── CITATION.cff # Information on how to cite the repository
├── renv # R environment setup with reproducibility in mind
│ └── ... # folders and files by renv to compile the needed information for reproducibility   
└── renv.lock # Lock file to capture the state of the R environment


Development :man_technologist:

The web application is coded entirely in the R programming language, with a
user interface developed using R Shiny. R
Shiny is a powerful framework for building interactive web
applications directly from R scripts, making it an ideal choice for
creating accessible and user-friendly tools.

Web application workflow :gear:

Initial setup and library loading

The app begins by installing necessary R packages and loading them
into the session. This ensures that all required functions and UI
elements are available for use.

Data preparation

Reads and processes two datasets

one detailing the costs associated with Standard Observations (SOs)
and another providing metadata on SOs. The app performs cleaning,
filtering, and merging operations to prepare the data for analysis.


User Interface (UI) construction

Constructs a web interface with multiple tabs and input options.
Users can navigate through these tabs to input specific parameters
related to their site, such as category, habitat, and focus spheres, and
to manage the list of SOs relevant to their needs.

Dynamic parameter selection and SO filtering

Based on user inputs regarding site characteristics, the app filters
the list of SOs to only include those relevant to the user’s specific
conditions. Users can further refine this list by deselecting any SOs
already covered or not needed.

Cost calculation and data aggregation

For the selected SOs, the app calculates various costs (e.g.,
purchase, maintenance, sampling, lab analysis) and aggregates this data
to provide a comprehensive view of the financial requirements for
implementing and maintaining the SOs at the user’s site.

Visualization and insights

Generates visualizations that offer insights into the cost
distribution by type and sphere, as well as the total number of SOs
required. These visualizations help users understand the financial and
operational implications of their selections.

Downloading results

Provides options for users to download detailed cost breakdowns and
visualizations. This feature allows for easy sharing and reporting of
the findings generated by the app.

User guidance

Includes mechanisms for user guidance (e.g., tooltips) to ensure a
smooth user experience and to provide assistance as needed.




Deployed version of the web application :globe_with_meridians:
You can access the current version of the Shiny app here.


Future hosting on eLTER service portal :motorway:
Upon completion and thorough testing, this tool will be hosted as
part of the eLTER service
portal. This integration aims to provide seamless access and utility
for the eLTER community. Until then, this repository serves as the
primary hub for development, where updates, enhancements, and bug fixes
will be continuously pushed.



Reproducibility :repeat:
This repository utilizes the renv package to
manage R dependencies, ensuring that everyone working on the project has
access to the same package versions. By locking the project to specific
versions of R packages, renv ensures that the project can
be run consistently across different setups and over time.

Getting started :beginner:
When you clone or fork this repository for the first time, follow
these steps to set up renv:

Install renv (if you haven’t already)

You can install renv globally in your R setup
using:


install.packages("renv")

Clone the repository

Clone this repository to your local machine.

Launch R

Open an R session and set the working directory to the root of the
cloned repository.

Restore the environment

Install all the necessary packages, as specified in the
renv.lock file, into a project-local library by running the
following command in your R console:


renv::restore()

Start working

After the restoration process is complete, you can start working on
the project. The renv environment will automatically be
activated when you open the project in the future.





Citation :memo:
Souza, A. T., Ashraful Alam, S., Rasilo, T., Zacharias, S., &
Bäck, J. (2024). eLTER SO Costs web application (Version 0.1.0)
[Computer software]. https://doi.org/10.5281/zenodo.10948558


Acknowledgements :bank: :eu:
This work has been supported by the European Union’s H2020 (grant
agreement No 871128 - eLTER PLUS).


Related resources :paperclips:

Zacharias,
S. et al. (2021). Discussion paper on eLTER Standard Observations
(eLTER SOs). Deliverable D3.1 EU Horizon 2020 eLTER PLUS Project, Grant
agreement No. 871128.

Owner

Citation (CITATION.cff)

cff-version: 1.2.0
title: eLTER SO Costs web application
message: If you use this software in your work, please cite it using the following metadata
type: software
authors:
  - family-names: Souza
    given-names: Allan T
    orcid: 'https://orcid.org/0000-0002-1851-681X'
    affiliation: Institute for Atmospheric and Earth System Research (INAR), Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, P.O. Box 27, 00014 Helsinki, Finland
  - family-names: Ashraful Alam
    given-names: Syed
    orcid: 'https://orcid.org/0000-0001-9870-1494'
    affiliation: Institute for Atmospheric and Earth System Research (INAR), Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, P.O. Box 27, 00014 Helsinki, Finland
  - family-names: Rasilo
    given-names: Terhi
    orcid: 'https://orcid.org/0000-0002-3502-4040'
    affiliation: Institute for Atmospheric and Earth System Research (INAR), Forest Sciences, Faculty of  Agriculture and Forestry, University of Helsinki, P.O. Box 27, 00014 Helsinki, Finland
  - family-names: Zacharias
    given-names: Steffen
    orcid: 'https://orcid.org/0000-0002-7825-0072'
    affiliation: Department for Monitoring and Exploration Technologies, UFZ—Helmholtz Centre for Environmental Research GmbH, Leipzig, Germany
  - family-names: Bäck
    given-names: Jaana
    orcid: 'https://orcid.org/0000-0002-6107-667X'
    affiliation: Institute for Atmospheric and Earth System Research (INAR), Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, P.O. Box 27, 00014 Helsinki, Finland
version: 0.1.0
repository-code: "https://github.com/allantsouza/eLTER-SO-Costs-web-application"
license: CC0 1.0
year: 2024

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