Horizon / Plein textes La base de ressources documentaires de l'IRD

IRD

Publications des scientifiques de l'IRD

Sirot C., Ferraton F., Panfili Jacques, Childs A. R., Guilhaumon François, Darnaude A. M. (2017). ELEMENTR : An R package for reducing elemental data from LA-ICPMS analysis of biological calcified structures. Methods in Ecology and Evolution, 8 (12), 1659-1667. ISSN 2041-210X

Accès réservé (Intranet IRD) Document en accès réservé (Intranet IRD)

Lien direct chez l'éditeur doi:10.1111/2041-210x.12822

Titre
ELEMENTR : An R package for reducing elemental data from LA-ICPMS analysis of biological calcified structures
Année de publication2017
Type de documentArticle référencé dans le Web of Science WOS:000417239200002
AuteursSirot C., Ferraton F., Panfili Jacques, Childs A. R., Guilhaumon François, Darnaude A. M.
SourceMethods in Ecology and Evolution, 2017, 8 (12), p. 1659-1667. ISSN 2041-210X
Résumé1. Elemental analysis of biological calcified structures (e.g. fish otoliths, mollusc shelves, coral skeletons or fish and shark bones) provides invaluable information regarding ecological processes for many aquatic species. Despite this importance, the reduction of the raw data obtained through Laser-ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICPMS) (i.e. the conversion of the machine raw signal into elemental concentrations) remains a challenge as the tools developed so far for carrying out this task have important limitations for aquatic ecologists. 2. Here, we introduce the elementr R-package which provides a handy, reliable and transparent way to reduce elemental data acquired from spot or transect LA-ICPMS analysis of biological calcified structures. This free and open-source software, implemented based on state-of-the-art literature, handles data from both standards and samples, allowing fast and simultaneous calculations of concentration for any chemical element, correction for potential machine drift, and realignment and averaging for sample replicates when needed. 3. The major attributes of elementr are: (i) its user-friendly graphical interface which provides widgets to set all the reduction settings (i.e. no programming skills are required to run it), (ii) its reactivity whereby the software continuously observes any setting change made by the user, re-calculates and displays all updated results, allowing therefore users to visually check the validity of their settings and to tune them if needed and (iii) an object oriented underlying that facilitates subsequent handling of LA-ICPMS data in R. 4. Despite the elementr design being most suited to the needs of aquatic ecologists, its use could be broadened to other research fields (i.e. geology, material engineering) due to its flexibility. Moreover, the open-source approach used for programming this software allows its expansion in order to refine calculation procedures or to add new functionalities.
Plan de classementInformatique [122] ; Ecologie, systèmes aquatiques [036] ; Sciences fondamentales / Techniques d'analyse et de recherche [020]
LocalisationFonds IRD [F B010071871]
Identifiant IRDfdi:010071871
Lien permanenthttp://www.documentation.ird.fr/hor/fdi:010071871

Export des données

Disponibilité des documents

Télechargment fichier PDF téléchargeable

Lien sur le Web lien chez l'éditeur

Accès réservé en accès réservé

HAL en libre accès sur HAL


Accès aux documents originaux :

Le FDI est labellisé CollEx

Accès direct

Bureau du chercheur

Site de la documentation

Espace intranet IST (accès réservé)

Suivi des publications IRD (accès réservé)

Mentions légales

Services Horizon

Poser une question

Consulter l'aide en ligne

Déposer une publication (accès réservé)

S'abonner au flux RSS

Voir les tableaux chronologiques et thématiques

Centres de documentation

Bondy

Montpellier (centre IRD)

Montpellier (MSE)

Cayenne

Nouméa

Papeete

Abidjan

Dakar

Niamey

Ouagadougou

Tunis

La Paz

Quito