corvus

Measurement stations managing R shiny application

https://github.com/gehco-univ-tours/corvus

Science Score: 52.0%

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CITATION.cff file
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Organization gehco-univ-tours has institutional domain (geosciences.univ-tours.fr)
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Low similarity (15.3%) to scientific vocabulary

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Repository

Measurement stations managing R shiny application

Basic Info

Host: GitHub
Owner: gehco-univ-tours
License: gpl-3.0
Language: R
Default Branch: main
Homepage:
Size: 336 KB

Statistics

Stars: 0
Watchers: 1
Forks: 0
Open Issues: 0
Releases: 0

Created about 2 years ago · Last pushed about 1 year ago

Metadata Files

Readme License Citation

README.Rmd

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# corvus 




corvus is a measurement stations managing application. The app is built with the {shiny} package and uses a PostgreSQL database with the TimescaleDB extension. The app is designed to manage measurement stations and their time series data. The app allows to insert, update and delete data. The app also allows to visualize the data with different plots, make correction and validation.

## Installation

### Install package from GitHub

``` {r, eval=FALSE}
remotes::install_github("https://github.com/gehco-univ-tours/corvus.git")
```

### Install PostgreSQL timescaleDB database

- Install PostreSQL lastest version compatible with TimescaleDB extension. See the version compatibility in [TimescaleDB install documentation](https://docs.timescale.com/self-hosted/latest/install/) for your operating system. The PostgreSQL version for each operating system are [here](https://www.postgresql.org/download/).
- Install TimescaleDB extension following the [installation documentation](https://docs.timescale.com/self-hosted/latest/install/).
- With Docker you can follow this [guide](https://docs.timescale.com/self-hosted/latest/install/installation-docker/).
  - The app has been tested with the latest-pg16 version of the [TimescaleDB Docker timescale/timescaledb-ha image](https://hub.docker.com/r/timescale/timescaledb-ha).
  - docker-compose.yml example :

```{yml, eval=FALSE}
timescaledb:
    image: timescale/timescaledb-ha:pg16
    container_name: timescaledb
    ports:
      - "5434:5432"
    volumes:
      - ./timescaledb_data:/var/lib/postgresql/data
    environment:
      - POSTGRES_PASSWORD=my_password
      - POSTGRES_DB=my_first_db
      - POSTGRES_USER=my_user
```

### Create database

- Create an empty database with TimescaleDB extension.
- The database structure : 
![](inst/sql/db_model_pg_timescale.png)
- Create database infrastructure with the SQL script in the `inst/sql` folder or in the package with the following command:
```{r, eval=FALSE}
library(corvus)
system.file("sql", "db_model_pg_timescale.sql", package = "corvus") # file to create an empty database
system.file("sql", "db_data_example.sql", package = "corvus") # file to add example data
```
## Run app

```{r, eval=FALSE}
corvus::run_app()
```

## Insert data


## How to cite

Manière, L. (2024). corvus (Version 0.0.0.9000) [Computer software]. https://github.com/gehco-univ-tours/corvus

## Licence

This program is released under the GNU Public License v3.

Owner

Name: GéoHydrosytèmes COntinentaux (GeHCO) - Université de Tours
Login: gehco-univ-tours
Kind: organization
Location: France

Website: https://geosciences.univ-tours.fr/
Repositories: 1
Profile: https://github.com/gehco-univ-tours

E.A 6293 GéoHydrosytèmes COntinentaux (GeHCO) laboratory repositories

Citation (CITATION.cff)

# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------

cff-version: 1.2.0
message: 'To cite package "corvus" in publications use:'
type: software
license: GPL-3.0-or-later
title: 'corvus: corvus'
version: 0.0.0.9000
abstract: Measurement stations managing R shiny application.
authors:
- family-names: Manière
  given-names: Louis
  email: louis.maniere@univ-tours.fr
contact:
- family-names: Manière
  given-names: Louis
  email: louis.maniere@univ-tours.fr
references:
- type: software
  title: bslib
  abstract: 'bslib: Custom ''Bootstrap'' ''Sass'' Themes for ''shiny'' and ''rmarkdown'''
  notes: Imports
  url: https://rstudio.github.io/bslib/
  repository: https://CRAN.R-project.org/package=bslib
  authors:
  - family-names: Sievert
    given-names: Carson
    email: carson@posit.co
    orcid: https://orcid.org/0000-0002-4958-2844
  - family-names: Cheng
    given-names: Joe
    email: joe@posit.co
  - family-names: Aden-Buie
    given-names: Garrick
    email: garrick@posit.co
    orcid: https://orcid.org/0000-0002-7111-0077
  year: '2024'
- type: software
  title: config
  abstract: 'config: Manage Environment Specific Configuration Values'
  notes: Imports
  url: https://rstudio.github.io/config/
  repository: https://CRAN.R-project.org/package=config
  authors:
  - family-names: Allaire
    given-names: JJ
    email: jj@rstudio.com
  year: '2024'
  version: '>= 0.3.2'
- type: software
  title: golem
  abstract: 'golem: A Framework for Robust Shiny Applications'
  notes: Imports
  url: https://github.com/ThinkR-open/golem
  repository: https://CRAN.R-project.org/package=golem
  authors:
  - family-names: Fay
    given-names: Colin
    email: contact@colinfay.me
    orcid: https://orcid.org/0000-0001-7343-1846
  - family-names: Guyader
    given-names: Vincent
    email: vincent@thinkr.fr
    orcid: https://orcid.org/0000-0003-0671-9270
  - family-names: Rochette
    given-names: Sébastien
    email: sebastien@thinkr.fr
    orcid: https://orcid.org/0000-0002-1565-9313
  - family-names: Girard
    given-names: Cervan
    email: cervan@thinkr.fr
    orcid: https://orcid.org/0000-0002-4816-4624
  year: '2024'
  version: '>= 0.4.1'
- type: software
  title: plotly
  abstract: 'plotly: Create Interactive Web Graphics via ''plotly.js'''
  notes: Imports
  url: https://plotly-r.com
  repository: https://CRAN.R-project.org/package=plotly
  authors:
  - family-names: Sievert
    given-names: Carson
    email: cpsievert1@gmail.com
    orcid: https://orcid.org/0000-0002-4958-2844
  - family-names: Parmer
    given-names: Chris
    email: chris@plot.ly
  - family-names: Hocking
    given-names: Toby
    email: tdhock5@gmail.com
  - family-names: Chamberlain
    given-names: Scott
    email: myrmecocystus@gmail.com
  - family-names: Ram
    given-names: Karthik
    email: karthik.ram@gmail.com
  - family-names: Corvellec
    given-names: Marianne
    email: marianne.corvellec@igdore.org
    orcid: https://orcid.org/0000-0002-1994-3581
  - family-names: Despouy
    given-names: Pedro
    email: pedro@plot.ly
  year: '2024'
- type: software
  title: shiny
  abstract: 'shiny: Web Application Framework for R'
  notes: Imports
  url: https://shiny.posit.co/
  repository: https://CRAN.R-project.org/package=shiny
  authors:
  - family-names: Chang
    given-names: Winston
    email: winston@posit.co
    orcid: https://orcid.org/0000-0002-1576-2126
  - family-names: Cheng
    given-names: Joe
    email: joe@posit.co
  - family-names: Allaire
    given-names: JJ
    email: jj@posit.co
  - family-names: Sievert
    given-names: Carson
    email: carson@posit.co
    orcid: https://orcid.org/0000-0002-4958-2844
  - family-names: Schloerke
    given-names: Barret
    email: barret@posit.co
    orcid: https://orcid.org/0000-0001-9986-114X
  - family-names: Xie
    given-names: Yihui
    email: yihui@posit.co
  - family-names: Allen
    given-names: Jeff
  - family-names: McPherson
    given-names: Jonathan
    email: jonathan@posit.co
  - family-names: Dipert
    given-names: Alan
  - family-names: Borges
    given-names: Barbara
  year: '2024'
  version: '>= 1.8.1'
- type: software
  title: spelling
  abstract: 'spelling: Tools for Spell Checking in R'
  notes: Suggests
  url: https://ropensci.r-universe.dev/spelling
  repository: https://CRAN.R-project.org/package=spelling
  authors:
  - family-names: Ooms
    given-names: Jeroen
    email: jeroen@berkeley.edu
    orcid: https://orcid.org/0000-0002-4035-0289
  - family-names: Hester
    given-names: Jim
    email: james.hester@rstudio.com
  year: '2024'
- type: software
  title: testthat
  abstract: 'testthat: Unit Testing for R'
  notes: Suggests
  url: https://testthat.r-lib.org
  repository: https://CRAN.R-project.org/package=testthat
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2024'
  version: '>= 3.0.0'

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Dependencies

DESCRIPTION cran

DBI * imports
RPostgres * imports
bslib * imports
config >= 0.3.2 imports
dplyr * imports
glue * imports
golem >= 0.4.1 imports
magrittr * imports
plotly * imports
rlang * imports
shiny >= 1.8.1 imports
utils * imports
spelling * suggests
testthat >= 3.0.0 suggests

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science