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Usage

Minka is a citizen science platform created by the research group EMBIMOS of the Institut de Cienciès del Mar (ICM-CSIC). The platform is open for all users to create their projects, collaborate on others, help the community with identifications or simply upload observations that will be validated with the help of the community and that can be used, in the future, to contribute openly to science and the improvement of the environment.
The link to access Minka’s website is https://minka-sdg.org/

The goals of the rminka package are:

  1. Directly access the data stored in the Minka platform to be able to process them with R through the API.

  2. Treat the data to be able to use them directly with other packages such as vegan, dismo, labdsv or others.

Overview

rminka is a toolkit for interacting with the Minka API, providing a consistent set of functions to help you query and retrieve biodiversity data. The package’s functions are grouped by the type of data they return:

a) Project Queries: A set of complementary functions to find projects and their associated observations.

  • mnk_proj_byname(): Finds a project’s ID using an approximate project name.
  • mnk_proj_info(): Retrieves detailed project information using its known ID.
  • mnk_proj_obs(): Fetches all observations for a specific year within that project.

b) User Queries: Functions to find users and their contributed observations.

  • mnk_user_byname(): Finds a user’s ID from their approximate login name.
  • mnk_user_proj(): Find the projects to which a user has explicitly subscribed based on their user_ID.
  • mnk_user_obs(): Retrieves all observations contributed by that user for a given year ( all the year or only a specific month) from their id_user.

c) Place Queries: Functions to find places and retrieve their spatial data.

  • mnk_places_byname(): Finds the ID for a location using an approximate place name.
  • mnk_place_sf(): Returns the sf geometry for a place, ready for plotting with packages like ggplot2 or leaflet.
  • mnk_place_obs(): Retrieves all observations for a place for a given year ( all the year or only a specific month) from their id_user.

d) Observation Queries: A variety of functions to fetch observation data based on different parameters.

  • mnk_obs_id(): Retrieves a single observation’s complete data using its unique ID.
  • mnk_obs(): Fetches observations based on various parameters for a full year, a specific month, or a single day.
  • mnk_obs_bydays(): Retrieves all observations within a date range in the same year.

e) Auxiliary functions: a set of functions with different utilities that complement Minka’s observational data and help in processing them when used in other R packages (vegan, dismo, labdsv or others).

  • get_wrm_tax(): Retrieves the complete taxonomy and additional data (e.g., marine or terrestrial ) from WoRMS for a given scientific name.
  • shrt_name(): Returns the CEP name (abbreviated scientific name) with separation point, given a scientific name.

These functions are designed to be used together. For queries that span multiple years, you can easily loop through the years of interest, run the appropriate function, and then combine the resulting tibbles with dplyr::bind_rows().

Installation

You can install the development version of rminka from GitHub with:

# install.packages("pak")
pak::pak("Raiservi/rminka")

Using rminka

If you are new to rminka you are better off starting with a starting web page of rminka in the github page of the project.

  1. The main page directions is rminka website

  2. The starting web page is rminka starting

Getting help

There are two main places to get help with rminka:

  1. The RStudio community is a friendly place to ask any questions about R.

  2. Stack Overflow is a great source of answers to common R questions. It is also a great place to get help, once you have created a reproducible example that illustrates your problem.

If you encounter a clear bug, please file an issue with a minimal reproducible example on GitHub.

Code of conduct

Please note that this project is released following a Code of Conduct. By participating in this project you agree to abide by its terms.