Mercurial > repos > ecology > cb_div
annotate div_index.r @ 1:eabd2cf09cf0 draft default tip
planemo upload for repository https://github.com/Marie59/champ_blocs commit 075fd90d1a39ae7912b48549e5537971635b9620
author | ecology |
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date | Sat, 18 Mar 2023 16:49:02 +0000 |
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a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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1 # author: "Jonathan Richir" |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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2 # date: "01 October 2022" |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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3 |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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4 |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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5 #Rscript |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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6 |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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7 ############################### |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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8 ## ## |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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9 ############################### |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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10 |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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11 #####Packages : dplyr |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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12 # tidyr |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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13 #####Load arguments |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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14 |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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15 args <- commandArgs(trailingOnly = TRUE) |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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16 |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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17 #####Import data |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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18 |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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19 if (length(args) < 1) { |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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20 stop("This tool needs at least 1 argument") |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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21 }else { |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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22 qecnato0 <- args[1] |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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23 |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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24 } |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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25 |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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26 qecnato0 <- readRDS(qecnato0) |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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27 |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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28 |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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29 # first, create vector (4) for qecb and fishing by region (same as above) |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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30 |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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31 bret_egmp_basq_qecb <- c( |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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32 "X..algues.brunes", |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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33 "X..algues.rouges", |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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34 "X..algues.vertes", |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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35 "X..Cladophora", |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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36 "X..Lithophyllum", |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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37 "Nb.Littorina.obtusata", |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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38 "Nb.Gibbula.cineraria", |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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39 "Nb.Gibbula.pennanti", |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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40 "Nb.Gibbula.umbilicalis", |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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41 "Nb.Phallusia.mamillata", |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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42 "Nb.Tethya.aurantium", |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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43 "Nb.Spirobranchus.lamarckii.total", |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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44 "Nb.spirorbis.total", |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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45 "X..Eponges", |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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46 "X..Ascidies.Coloniales", |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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47 "X..Ascidies.Solitaires", |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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48 "X..Bryozoaires.Dresses", |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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49 "X..Balanes.Vivantes" |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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50 #, "X..Recouvrement.Sediment" |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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51 #, "X..Roche.Nue" |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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52 #, "X..Surface.Accolement" |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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53 ) |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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54 |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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55 egmp_basq_qecb <- c("Nb.Crassostrea.gigas", "Nb.Ostrea.edulis", "X..Mytilus.sp.", "X..Hermelles", "X..Hydraires") |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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56 |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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57 bret_egmp_basq_fishing <- c("Nb.Cancer.pagurus..Tourteau.", |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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58 "Nb.Necora.puber..Etrille.", |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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59 "Nb.Carcinus.maenas..Crabe.vert.", |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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60 "Nb.Nucella.lapilus..Pourpre.", |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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61 "Nb.Galathea..Galathées.", |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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62 "Nb.Lophozozymus.incisus..ancien.Xantho.incisus.", |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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63 "Nb.Palaemon.sp..Crevette.bouquet.ou.crevette.rose.", |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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64 "Nb.Haliotis.tuberculata..Ormeau.", |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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65 "Nb.Littorina.littorea..Bigorneau.", |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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66 "Nb.Xantho.pilipes..Xanthe.poilu.", |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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67 "Nb.Mimachlamys.varia..Pétoncle.noir.") |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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68 |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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69 egmp_basq_fishing <- c("Nb.Eriphia.verrucosa..Crabe.verruqueux.", "Nb.Octopus.vulgaris..Poulpe.", "Nb.Paracentrotus.lividus..Oursin.", "Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.") |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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70 |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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71 # here I can choose to either replace spirorbis and/or spirobranchus by their log10 transformation in bret_egmp_basq_qecb vector |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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72 bret_egmp_basq_qecb <- replace(bret_egmp_basq_qecb, bret_egmp_basq_qecb == "Nb.spirorbis.total", "log10.Nb.spirorbis.total") |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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73 |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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74 ## Diversity index |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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75 |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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76 |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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77 # adiv contains two main functions for species diversity indices: speciesdiv, which includes widely used indices such as species richness and the Shannon index, and divparam, which includes indices that have a parameter to control the importance given to rare versus abundant species in diversity measurements (Pavoine (2020) - adiv: An r package to analyse biodiversity in ecology). |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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78 |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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79 # NB: just like for dissimilarity distance matrices, no sense to use the "fishing" variable lists, because either they are present for the bloc mobile and not for the bloc fixe (therefore false higher diversity for bloc mobile), either they are repeated between face supérieure and face inférieure of bloc mobile. |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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80 |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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81 # function in a loop |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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82 |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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83 row.names(qecnato0) <- c(paste0(qecnato0$region.site_year_month_day, "_", qecnato0$Quadrat.bis, "_", qecnato0$Type.Bloc, "_", qecnato0$Numéro.Bloc.échantillon, "_", qecnato0$Face)) |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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84 |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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85 # later on I can copy-paste above code to recreate variable names vector |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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86 #bret_egmp_basq_qecb |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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87 #egmp_basq_qecb |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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88 #Bret_EGMP.BASQ_fishing |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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89 #EGMP.BASQ_fishing |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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90 |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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91 # remove boulder variables |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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92 bret_egmp_basq_qecb <- bret_egmp_basq_qecb[! bret_egmp_basq_qecb %in% c("X..Recouvrement.Sediment", "X..Roche.Nue", "X..Surface.Accolement")] |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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93 |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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94 qecnato0$period <- as.character(qecnato0$period) |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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95 qecnato0$Face <- as.character(qecnato0$Face) |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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96 |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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97 div_list <- vector("list", length(unique(qecnato0$site_year_month_day))) |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 075fd90d1a39ae7912b48549e5537971635b9620
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98 library(dplyr) |
0
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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99 for (i in c(1:nrow(qecnato0))) { |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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100 div_i <- dplyr::filter(qecnato0, site_year_month_day == qecnato0$site_year_month_day[i]) |
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101 |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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102 ifelse(unique(div_i$region) == "Bretagne", var. <- c(bret_egmp_basq_qecb), var. <- c(bret_egmp_basq_qecb, egmp_basq_qecb)) # Qu. : Why can't R's ifelse statements return vectors? => you can circumvent the problem if you assign the result inside the ifelse. |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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103 |
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104 #8 remove empty row cfr: In speciesdiv(div_i[, var.]) & divparam(div_i[, var.]) : empty communities should be discarded |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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105 div_i <- dplyr::filter(div_i, rowSums(div_i[, var.]) > 0) |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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106 |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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107 div_i_speciesdiv <- adiv::speciesdiv(div_i[, var.]) |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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108 adiv_i_df <- data.frame(div_i_speciesdiv) |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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109 |
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110 div_i_divparam <- adiv::divparam(div_i[, var.], q = c(0, 0.25, 0.5, 1, 2, 4, 8)) # When q increases, abundant species are overweighted compared to rare species, we thus expect that the evenness in species weights decreases. |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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111 |
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112 |
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113 par(mfrow = c (1, 1)) |
a8924f69348d
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114 plot(adiv::divparam(div_i[, var.], q = 0), main = unique(div_i$site_year_month_day)) |
a8924f69348d
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115 plot(adiv::divparam(div_i[, var.], q = 0:10), legend = FALSE, main = unique(div_i$site_year_month_day)) |
a8924f69348d
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116 |
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117 adiv_i_df$x <- div_i_divparam$div$`1` |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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118 colnames(adiv_i_df)[which(colnames(adiv_i_df) == "x")] <- paste0("Para. ISD, q = ", div_i_divparam$q[1], " (equi. richness)") |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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119 adiv_i_df$x <- div_i_divparam$div$`2` |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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120 colnames(adiv_i_df)[which(colnames(adiv_i_df) == "x")] <- paste0("Para. ISD, q = ", div_i_divparam$q[2]) |
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121 adiv_i_df$x <- div_i_divparam$div$`3` |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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122 colnames(adiv_i_df)[which(colnames(adiv_i_df) == "x")] <- paste0("Para. ISD, q = ", div_i_divparam$q[3]) |
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123 adiv_i_df$x <- div_i_divparam$div$`4` |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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124 colnames(adiv_i_df)[which(colnames(adiv_i_df) == "x")] <- paste0("Para. ISD, q = ", div_i_divparam$q[4]) |
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125 adiv_i_df$x <- div_i_divparam$div$`5` |
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126 colnames(adiv_i_df)[which(colnames(adiv_i_df) == "x")] <- paste0("Para. ISD, q = ", div_i_divparam$q[5], " (equi. Simpson)") |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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127 adiv_i_df$x <- div_i_divparam$div$`6` |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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128 colnames(adiv_i_df)[which(colnames(adiv_i_df) == "x")] <- paste0("Para. ISD, q = ", div_i_divparam$q[6]) |
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129 adiv_i_df$x <- div_i_divparam$div$`7` |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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130 colnames(adiv_i_df)[which(colnames(adiv_i_df) == "x")] <- paste0("Para. ISD, q = ", div_i_divparam$q[7]) |
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131 |
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132 # plot |
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133 par(mfrow = c(3, 2)) |
a8924f69348d
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134 sapply(names(adiv_i_df[, c(1, 8, 2, 3, 12, 4:7, 9:11, 13:ncol(adiv_i_df))]), |
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135 function(cname) { |
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136 png(paste0(cname, "_histo.png")) |
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137 hist(adiv_i_df[, c(1, 8, 2, 3, 12, 4:7, 9:11, 13:ncol(adiv_i_df))][[cname]], main = "", xlab = cname, breaks = length(unique(adiv_i_df[, c(1, 8, 2, 3, 12, 4:7, 9:11, 13:ncol(adiv_i_df))][[cname]]))) |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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138 dev.off() |
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139 } |
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140 |
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141 ) |
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142 par(mfrow = c(1,1)) |
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143 |
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144 div_list[[i]] <- adiv_i_df |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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145 |
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146 rm(div_i, adiv_i_df, div_i_speciesdiv, div_i_divparam) |
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147 |
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148 } |
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149 |
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150 # for the error message due to richness NA data => 35 observations in 21 surveys; no reason to remove these data "...remo", was checked in the complete script. |
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151 |
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152 |
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153 div_df <- do.call("rbind", div_list) |
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154 |
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155 |
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156 # There is an issue with region.terri that are merged with no "_" ... |
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157 |
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158 div_df <- tibble::add_column(div_df, rownames. = rownames(div_df), .before = "richness") |
a8924f69348d
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159 div_df <- tidyr::separate(div_df, rownames., into = c("region.terri.", "site_year_month_day", "Quadrat.bis", "Type.Bloc", "Numéro.Bloc.échantillon", "Face"), sep = "_") |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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160 |
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161 # I therefore add these lines to solve that issue |
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162 |
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163 div_df <- tibble::add_column(div_df, terri. = substring(div_df$region.terri., nchar(div_df$region.terri.)-3), .after = "region.terri.") |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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164 |
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165 div_df$region.terri. <- substring(div_df$region.terri., 1, nchar(div_df$region.terri)-4) |
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166 div_df <- dplyr::rename(div_df, region = region.terri.) |
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167 |
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168 div_df$site_year_month_day <- paste0(div_df$terri., "_", div_df$site_year_month_day) |
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169 div_df <- subset(div_df, select = -c(terri.)) |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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170 |
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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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171 div_df$Type.Bloc <- as.factor(div_df$Type.Bloc) |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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172 div_df$Face <- as.factor(div_df$Face) |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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173 div_df$Numéro.Bloc.échantillon <- as.integer(div_df$Numéro.Bloc.échantillon) |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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174 |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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175 saveRDS(div_df, "div_df.RDS") |
a8924f69348d
planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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176 write.table(div_df, "Valeurs_stat.tabular", row.names = FALSE, quote = FALSE, sep = "\t", dec = ".", fileEncoding = "UTF-8") |