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ajout de l'exercice sur les indices
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‎README.md‎

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- Au sein du fichier `fish_mfa.Rmd`, complétez les zones manquantes. Ce fichier se trouve dans le dossier `analysis`.
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- au sein du fichier `....Rmd`, complétez les zones manquantes. Ce fichier se trouve dans le dossier `analysis` et s'intéresse aux indices de biodiversité.
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- au sein du fichier `fish_diversity.Rmd`, complétez les zones manquantes. Ce fichier se trouve dans le dossier `analysis` et s'intéresse aux indices de biodiversité.
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- Au sein du fichier `open_data.Rmd`, Complétez ce document. Ce fichier se trouve dans le dossier `analysis`.

‎analysis/bibliography/biblio.bib‎

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@misc{johannesen_2017, title={Barents Sea fish abundances}, url={https://dryad.figshare.com/articles/Barents_Sea_fish_abundances/4792690/1}, DOI={10.5061/dryad.6r5j8/1}, abstractNote={Abundance counts of 41 fish species at 158 stations in the Barents Sea. This is a subset of a larger data set that spans more stations and years.}, publisher={Dryad}, author={Johannesen, Edda}, year={2017}, month={Mar} }

‎analysis/fish_diversity.Rmd‎

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---
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title: "Les indices de diversité"
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output: bookdown::html_document2
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bibliography: "bibliography/biblio.bib"
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---
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```{r setup, include=FALSE}
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knitr::opts_chunk$set(echo = TRUE)
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SciViews::R
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```
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# Objectif
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Ce document s'intéresse aux indices de biodiversité.
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# Jeu de données
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Le jeu de données employé est à votre disposition dans le dossier `data`. Il s'intéresse à un dénombrement de poissons en mer de Barents [@johannesen_2017].
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**N'hésitez pas à consulter les informations en lien avec ces données. La license lié à ces données est une licence CC0. La section sur l'Open Data vous en apprendra plus sur les licence.**
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# Analyses
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> Importez les données `fish_2006.csv`
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```{r import}
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```
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> Découvrez vos données. Réalisez un graphique si cela vous semble nécessaire.
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```{r decouverte}
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# il existe de nombreuses fonctions dans R pour découvrir des nouvelles données.
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#names(...)
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#range(...)
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#rowSums(...)
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#colSums(...)
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```
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> Transformez la colonne StationCode en nom des lignes avec la fonction tibble::column_to_rownames()
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```{r rownames}
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```
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> Calculez la richesse spécifique de chaque station. Quelle est la station avec la plus grande richesse spécifique ? Quels sont les avantages et inconvénients d'un tel indice ? Commentez en maximum 4 lignes.
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```{r specnumber}
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```
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> Calculez l'indice de Shannon de chaque station. Quelle est la station avec le plus grand indice de Shannon ? Quels sont les avantages et inconvénients d'un tel indice ? Commentez en maximum 4 lignes.
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```{r shannon}
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```
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> Calculez l'indice d’équitabilité de Piélou de chaque station. Quelle est la station avec le plus grand indice d’équitabilité de Piélou ? Quels sont les avantages et inconvénients d'un tel indice ? Commentez en maximum 4 lignes.
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```{r pielou}
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```
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> Calculez l'indice de Simpson de chaque station. Quelle est la station avec le plus grand indice de Simpson ? Quels sont les avantages et inconvénients d'un tel indice ? Commentez en maximum 4 lignes.
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```{r simpson}
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```
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> Vous venez de calculer plusieurs indices de diversité alpha. Réalisez un tableau comparatif de ces indices.
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> Quel(s) indice(s) utiliseriez vous avec ces données d'abondance de poisson ?
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> Calculez l'indice de Jaccard sur vos stations. Quelles sont les deux stations les plus similaire ? Quels sont les avantages et inconvénients d'un tel indice ? Quelles est la différence entre les indices de diversité alpha et les indices de diversité beta? Commentez en maximum 4 lignes.
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```{r jaccard}
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```
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# Bibliographie {-}

‎analysis/fish_diversity.html‎

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‎data/fish_2006.csv‎

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StationCode,Ambl_ra,Ammo_,Anar_de,Anar_lu,Anar_mi,Arct_ri,Arge_si,Arte_at,Bore_sa,Bros_br,Capr_sp,Clup_ha,Cott_mi,Ente_ae,Eumi_sp,Gadi_ar,Gadu_mo,Hipp_pl,Icel_sp,Lept_de,Lept_ma,Lump_la,Lyco_es,Lyco_eu,Lyco_gr,Lyco_pa,Lyco_re,Lyco_ro,Mall_vi,Mela_ae,Micr_po,Micr_ki,Poll_vi,Raje_fy,Rein_hi,Seba_ma,Seba_me,Seba_vi,Trig_mu,Trig_pi,Tris_es
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2006-NF108,3,0,0,1,2,0,0,35,0,0,0,0,0,0,0,0,254,312,1,40,1,5,0,0,0,0,0,11,1,95,0,0,0,0,7,0,0,0,3,0,5
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2006-NF112,2,0,0,0,0,0,0,87,1,0,0,0,0,0,0,0,598,653,0,53,9,14,0,0,0,0,0,3,3,29,0,0,0,0,18,0,1,0,0,0,1
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2006-NF46,2,0,1,0,0,0,0,4,0,0,6,0,3,0,0,0,8,23,0,0,0,0,0,0,1,0,0,2,0,11,23,0,0,0,0,0,27,0,0,0,0
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2006-NF49,14,0,2,0,0,0,0,2,3,0,0,0,0,1,0,0,8,157,0,0,0,5,0,0,4,5,0,0,1,17,17,0,0,0,32,0,22,0,0,0,0
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2006-NF52,2,0,1,5,0,0,0,32,0,0,0,0,0,0,0,0,28,212,0,0,0,16,0,0,34,0,0,0,0,6,4,0,0,0,0,0,14,0,0,0,0
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2006-NF55,8,0,0,3,0,0,0,5,0,0,0,0,0,0,0,0,179,1672,0,1,9,9,0,0,0,0,0,0,0,23,0,0,0,0,0,0,0,0,0,0,0
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2006-NF56,8,0,0,3,0,0,0,0,359,0,0,0,0,0,0,0,99,221,0,0,2,0,0,0,0,0,0,0,0,67,0,0,0,0,0,0,0,0,0,0,0
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2006-NF59,7,0,1,0,0,0,0,0,0,0,0,0,0,1,0,0,61,269,0,1,0,0,0,2,0,0,0,0,0,22,141,0,0,0,8,0,105,0,0,0,0
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2006-NF60,2,0,0,5,7,0,0,22,0,0,0,0,0,0,0,0,178,545,0,4,2,49,0,0,0,0,0,0,3,217,0,0,0,0,0,0,0,0,24,0,0
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2006-NF63,0,0,0,0,0,0,0,5,0,0,0,0,0,0,11,0,112,21,0,0,0,0,0,0,0,0,0,0,0,29,0,0,0,0,0,0,0,0,0,0,0
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2006-NF64,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,79,0,0,0,0,0,0,0,0,0,0,0,0,424,0,0,0,0,0,0,0,0,0,0,0
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2006-NF67,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,94,2,1,0,0,0,0,0,0,0,0,0,0,28,0,0,0,0,0,0,0,0,2,0,0
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2006-NF68,1,0,0,0,6,0,0,0,4,0,0,0,0,0,10,0,22,274,12,6,58,6,0,0,0,0,2,0,360,1,0,0,0,0,0,0,0,0,608,0,0
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2006-NF72,0,0,0,1,12,0,0,10,0,0,0,0,0,0,0,0,399,175,0,4,2,38,0,0,0,0,0,0,76,328,0,0,0,0,0,0,0,0,7,0,0
67+
2006-NF73,1,0,1,0,11,1,0,91,1,0,0,0,1,0,0,0,62,93,1,5,1,1,1,0,6,0,0,1,7,7,82,0,0,0,3,9,0,1,14,0,1
68+
2006-NF76,2,0,0,0,2,0,0,55,0,0,1,0,0,0,0,0,53,101,0,3,2,0,0,0,3,0,0,9,10,69,3,0,0,0,5,5,215,0,1,0,2
69+
2006-NF77,2,0,0,1,0,0,0,6,1,0,6,0,5,0,0,0,18,28,0,2,0,0,0,0,10,0,0,4,6,25,14,0,0,0,3,0,25,0,0,0,0
70+
2006-NF80,1,0,0,0,0,6,0,6,0,0,4,0,2,0,0,0,13,22,0,2,1,0,0,0,16,0,0,1,3,7,46,0,0,0,4,2,5,0,0,0,0
71+
2006-NF81,0,0,0,0,0,1,0,11,0,0,4,0,1,0,0,0,18,29,0,3,0,0,0,1,2,0,0,2,13,7,44,0,0,0,19,0,7,0,0,0,0
72+
2006-NF82,6,0,0,0,0,4,0,7,1,0,5,0,3,0,0,0,14,153,0,1,0,0,0,1,9,0,0,1,6,8,71,0,0,0,6,0,9,0,0,0,0
73+
2006-NF98,3,0,1,0,0,2,0,3,0,0,1,0,0,0,0,0,26,72,0,0,1,0,0,0,0,0,0,3,19,5,7,0,0,0,18,0,3,0,0,0,0
74+
2006-NF99,1,0,0,0,0,0,0,15,0,0,0,0,2,0,0,0,33,58,0,1,0,0,0,0,0,1,0,9,8,6,0,0,0,0,4,0,77,0,0,0,0
75+
2006-UFJJ99,0,0,0,0,0,0,0,35,0,0,0,0,0,0,0,0,26,140,0,3,38,1,0,0,1,0,0,0,1,3,0,0,0,0,0,0,3,0,13,0,0

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