easyFulcrum: An R package to process and analyze ecological sampling data generated using the Fulcrum mobile application.

Large-scale ecological sampling can be difficult and costly, especially for organisms that are too small to be easily identified in a natural environment by eye. Typically, these microscopic floral and fauna are sampled by collecting substrates from nature and then separating organisms from substrat...

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Autores principales:	Matteo Di Bernardo, Timothy A Crombie, Daniel E Cook, Erik C Andersen
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/faaef8759def4ca9849125d6ae552012
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spelling	oai:doaj.org-article:faaef8759def4ca9849125d6ae5520122021-12-02T20:17:21ZeasyFulcrum: An R package to process and analyze ecological sampling data generated using the Fulcrum mobile application.1932-620310.1371/journal.pone.0254293https://doaj.org/article/faaef8759def4ca9849125d6ae5520122021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0254293https://doaj.org/toc/1932-6203Large-scale ecological sampling can be difficult and costly, especially for organisms that are too small to be easily identified in a natural environment by eye. Typically, these microscopic floral and fauna are sampled by collecting substrates from nature and then separating organisms from substrates in the laboratory. In many cases, diverse organisms can be identified to the species-level using molecular barcodes. To facilitate large-scale ecological sampling of microscopic organisms, we used a geographic data-collection platform for mobile devices called Fulcrum that streamlines the organization of geospatial sampling data, substrate photographs, and environmental data at natural sampling sites. These sampling data are then linked to organism isolation data from the laboratory. Here, we describe the easyFulcrum R package, which can be used to clean, process, and visualize ecological field sampling and isolation data exported from the Fulcrum mobile application. We developed this package for wild nematode sampling, but it can be used with other organisms. The advantages of using Fulcrum combined with easyFulcrum are (1) the elimination of transcription errors by replacing manual data entry and/or spreadsheets with a mobile application, (2) the ability to clean, process, and visualize sampling data using a standardized set of functions in the R software environment, and (3) the ability to join disparate data to each other, including environmental data from the field and the molecularly defined identities of individual specimens isolated from samples.Matteo Di BernardoTimothy A CrombieDaniel E CookErik C AndersenPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 10, p e0254293 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Matteo Di Bernardo Timothy A Crombie Daniel E Cook Erik C Andersen easyFulcrum: An R package to process and analyze ecological sampling data generated using the Fulcrum mobile application.
description	Large-scale ecological sampling can be difficult and costly, especially for organisms that are too small to be easily identified in a natural environment by eye. Typically, these microscopic floral and fauna are sampled by collecting substrates from nature and then separating organisms from substrates in the laboratory. In many cases, diverse organisms can be identified to the species-level using molecular barcodes. To facilitate large-scale ecological sampling of microscopic organisms, we used a geographic data-collection platform for mobile devices called Fulcrum that streamlines the organization of geospatial sampling data, substrate photographs, and environmental data at natural sampling sites. These sampling data are then linked to organism isolation data from the laboratory. Here, we describe the easyFulcrum R package, which can be used to clean, process, and visualize ecological field sampling and isolation data exported from the Fulcrum mobile application. We developed this package for wild nematode sampling, but it can be used with other organisms. The advantages of using Fulcrum combined with easyFulcrum are (1) the elimination of transcription errors by replacing manual data entry and/or spreadsheets with a mobile application, (2) the ability to clean, process, and visualize sampling data using a standardized set of functions in the R software environment, and (3) the ability to join disparate data to each other, including environmental data from the field and the molecularly defined identities of individual specimens isolated from samples.
format	article
author	Matteo Di Bernardo Timothy A Crombie Daniel E Cook Erik C Andersen
author_facet	Matteo Di Bernardo Timothy A Crombie Daniel E Cook Erik C Andersen
author_sort	Matteo Di Bernardo
title	easyFulcrum: An R package to process and analyze ecological sampling data generated using the Fulcrum mobile application.
title_short	easyFulcrum: An R package to process and analyze ecological sampling data generated using the Fulcrum mobile application.
title_full	easyFulcrum: An R package to process and analyze ecological sampling data generated using the Fulcrum mobile application.
title_fullStr	easyFulcrum: An R package to process and analyze ecological sampling data generated using the Fulcrum mobile application.
title_full_unstemmed	easyFulcrum: An R package to process and analyze ecological sampling data generated using the Fulcrum mobile application.
title_sort	easyfulcrum: an r package to process and analyze ecological sampling data generated using the fulcrum mobile application.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/faaef8759def4ca9849125d6ae552012
work_keys_str_mv	AT matteodibernardo easyfulcrumanrpackagetoprocessandanalyzeecologicalsamplingdatageneratedusingthefulcrummobileapplication AT timothyacrombie easyfulcrumanrpackagetoprocessandanalyzeecologicalsamplingdatageneratedusingthefulcrummobileapplication AT danielecook easyfulcrumanrpackagetoprocessandanalyzeecologicalsamplingdatageneratedusingthefulcrummobileapplication AT erikcandersen easyfulcrumanrpackagetoprocessandanalyzeecologicalsamplingdatageneratedusingthefulcrummobileapplication
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easyFulcrum: An R package to process and analyze ecological sampling data generated using the Fulcrum mobile application.

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