AkadoR package

AkadoR: data quality analysis for fisheries

Overview

The AkadoR package is a Shiny application designed to facilitate data validation and correction in the field of fishing and marine science. It conducts a series of automated tests to assess data consistency. The main objective is to determine the quality of the data according to specific business rules defined by experts. AkadoR is designed to be connected to an Observe database, but its core control functions are also accessible independently through the Codama package (https://github.com/OB7-IRD/codama). This allows users to perform data checks without requiring a connection to an Observe database.

Installation

You can install the AkadoR package directly from GitHub using the devtools package:

devtools::install_github("https://github.com/OB7-IRD/akado-shiny-apps",
                         INSTALL_opts=c("--no-multiarch"))

Development version

To access bug fixes or new features from the development version, you can install it directly from GitHub.

devtools::install_github("https://github.com/OB7-IRD/akado-shiny-apps",
                         ref = "development",
                         INSTALL_opts=c("--no-multiarch"))

Start Application

When launching the application for the first time, you may need to install additional packages. A second launch may be necessary, after all, packages are installed.

AkadoR::run_app()

To connect to your database, you need to provide the configuration_file.yml file in the Setting tab.
You can use the furdeb package function to help you create the file.

furdeb::configuration_file()

Otherwise, the structure must be as follows:

You can connect one or more databases with logbook data.

databases_configuration:
  your_database_name_1:
    login: your_username_1
    password: your_password_1
    dbname: your_database_name_1
    host: your_host_1
    port: your_port_1
  your_database_name_2:
    login: your_username_2
    password: your_password_2
    dbname: your_database_name_2
    host: your_host_2
    port: your_port_2

The structure used for adding a VMS base remains the same.

vms_databases_configuration:
  vms:
    login: your_username
    password: your_password
    dbname: your_database_name
    host: your_host
    port: your_port

Several optional elements are available to configure the application in the configuration_file.yml file.
Numerical value of the difference deemed acceptable between two numbers

epsilon : 0.01

String vector allowing the selection of logbook programs

logbook_program : ["your_first_programs", "your_second_program", ...]

String vector allowing the selection of species used to calculate weights captured in RF1

species_RF1 : ["your_first_species", "your_second_species", ...]

String vector allowing the selection of reference list of species used for well distribution control

reference_list_species_well_distribution_control : ["your_first_reference_list", "your_second_reference_list", ...]

Configuring the secure connection to AkadoR.
A default database is created when the secure connection is activated for the first time. The database includes a user shiny with the password azerty, check user types logbook (access to logbook check only) and an administrator shinymanager with the password 12345, check user types logbook;vms_logbook (access to logbook and vms logbook check) . These credentials must be changed immediately ! Which can be done directly within the application by logging in as the administrator. The administrator must also specify which databases each user is authorized to access (list the database names defined in the configuration file at step databases_configuration, databases must be separated by ; for example “your_database_name_1;your_database_name_2” in the column database_user_types of the database).

start_AkadoR_configuration :
  # If you wish to enable secure connection to the application, set TRUE, otherwise set FALSE
  secure_connection : FALSE
  # Session expiry time (in minutes) before disconnection in standby mode if secure connection is enabled
  set_timeout : 120.0
  # Path to file containing data base connection
  path_database : your_path

Getting help

If you encounter a clear bug, please file an issue with a minimal reproducible example on GitHub issues page. This link is also available if you have any questions and improvement propositions.