annotate div_index.r @ 0:a8924f69348d draft

planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
author ecology
date Wed, 04 Jan 2023 13:21:04 +0000
parents
children eabd2cf09cf0
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1 # author: "Jonathan Richir"
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
2 # date: "01 October 2022"
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
3
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
4
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
5 #Rscript
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
6
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
7 ###############################
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
8 ## ##
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
9 ###############################
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
10
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
11 #####Packages : dplyr
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
12 # tidyr
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
13 # readr
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
14 # writexl
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
15 # stringr
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
16 # readxl
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
17 # tibble
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
18 # lubridate
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
19 # cowplot
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
20 # magrittr
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
21 # rmarkdown
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
22 library(magrittr)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
23 library(dplyr)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
24 #####Load arguments
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
25
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
26 args <- commandArgs(trailingOnly = TRUE)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
27
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
28 #####Import data
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
29
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
30 if (length(args) < 1) {
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
31 stop("This tool needs at least 1 argument")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
32 }else {
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
33 qecnato0 <- args[1]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
34
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
35 }
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
36
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
37 qecnato0 <- readRDS(qecnato0)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
38
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
39
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
40 # 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
parents:
diff changeset
41
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
42 bret_egmp_basq_qecb <- c(
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
43 "X..algues.brunes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
44 "X..algues.rouges",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
45 "X..algues.vertes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
46 "X..Cladophora",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
47 "X..Lithophyllum",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
48 "Nb.Littorina.obtusata",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
49 "Nb.Gibbula.cineraria",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
50 "Nb.Gibbula.pennanti",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
51 "Nb.Gibbula.umbilicalis",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
52 "Nb.Phallusia.mamillata",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
53 "Nb.Tethya.aurantium",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
54 "Nb.Spirobranchus.lamarckii.total",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
55 "Nb.spirorbis.total",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
56 "X..Eponges",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
57 "X..Ascidies.Coloniales",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
58 "X..Ascidies.Solitaires",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
59 "X..Bryozoaires.Dresses",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
60 "X..Balanes.Vivantes"
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
61 #, "X..Recouvrement.Sediment"
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
62 #, "X..Roche.Nue"
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
63 #, "X..Surface.Accolement"
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
64 )
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
65
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
66 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
ecology
parents:
diff changeset
67
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
68 bret_egmp_basq_fishing <- c("Nb.Cancer.pagurus..Tourteau.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
69 "Nb.Necora.puber..Etrille.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
70 "Nb.Carcinus.maenas..Crabe.vert.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
71 "Nb.Nucella.lapilus..Pourpre.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
72 "Nb.Galathea..Galathées.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
73 "Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
74 "Nb.Palaemon.sp..Crevette.bouquet.ou.crevette.rose.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
75 "Nb.Haliotis.tuberculata..Ormeau.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
76 "Nb.Littorina.littorea..Bigorneau.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
77 "Nb.Xantho.pilipes..Xanthe.poilu.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
78 "Nb.Mimachlamys.varia..Pétoncle.noir.")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
79
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
80 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
ecology
parents:
diff changeset
81
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
82 # 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
ecology
parents:
diff changeset
83 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
ecology
parents:
diff changeset
84
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
85 ## Diversity index
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
86
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
87
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
88 # 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
ecology
parents:
diff changeset
89
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
90 # 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
ecology
parents:
diff changeset
91
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
92 # function in a loop
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
93
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
94 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
ecology
parents:
diff changeset
95
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
96 # 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
ecology
parents:
diff changeset
97 #bret_egmp_basq_qecb
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
98 #egmp_basq_qecb
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
99 #Bret_EGMP.BASQ_fishing
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
100 #EGMP.BASQ_fishing
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
101
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
102 # remove boulder variables
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
103 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
ecology
parents:
diff changeset
104
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
105 qecnato0$period <- as.character(qecnato0$period)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
106 qecnato0$Face <- as.character(qecnato0$Face)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
107
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
108 div_list <- vector("list", length(unique(qecnato0$site_year_month_day)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
109
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
110 for (i in c(1:nrow(qecnato0))) {
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
111 div_i <- dplyr::filter(qecnato0, site_year_month_day == qecnato0$site_year_month_day[i])
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
112
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
113 ifelse(unique(div_i$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.
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
114
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
115 #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
ecology
parents:
diff changeset
116 div_i <- dplyr::filter(div_i, rowSums(div_i[, var.]) > 0)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
117
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
118 div_i_speciesdiv <- adiv::speciesdiv(div_i[, var.])
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
119 adiv_i_df <- data.frame(div_i_speciesdiv)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
120
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
121 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.
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
122
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
123
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
124 par(mfrow = c (1, 1))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
125 plot(adiv::divparam(div_i[, var.], q = 0), main = unique(div_i$site_year_month_day))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
126 plot(adiv::divparam(div_i[, var.], q = 0:10), legend = FALSE, main = unique(div_i$site_year_month_day))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
127
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
128 adiv_i_df$x <- div_i_divparam$div$`1`
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
129 colnames(adiv_i_df)[which(colnames(adiv_i_df) == "x")] <- paste0("Para. ISD, q = ", div_i_divparam$q[1], " (equi. richness)")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
130 adiv_i_df$x <- div_i_divparam$div$`2`
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
131 colnames(adiv_i_df)[which(colnames(adiv_i_df) == "x")] <- paste0("Para. ISD, q = ", div_i_divparam$q[2])
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
132 adiv_i_df$x <- div_i_divparam$div$`3`
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
133 colnames(adiv_i_df)[which(colnames(adiv_i_df) == "x")] <- paste0("Para. ISD, q = ", div_i_divparam$q[3])
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
134 adiv_i_df$x <- div_i_divparam$div$`4`
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
135 colnames(adiv_i_df)[which(colnames(adiv_i_df) == "x")] <- paste0("Para. ISD, q = ", div_i_divparam$q[4])
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
136 adiv_i_df$x <- div_i_divparam$div$`5`
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
137 colnames(adiv_i_df)[which(colnames(adiv_i_df) == "x")] <- paste0("Para. ISD, q = ", div_i_divparam$q[5], " (equi. Simpson)")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
138 adiv_i_df$x <- div_i_divparam$div$`6`
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
139 colnames(adiv_i_df)[which(colnames(adiv_i_df) == "x")] <- paste0("Para. ISD, q = ", div_i_divparam$q[6])
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
140 adiv_i_df$x <- div_i_divparam$div$`7`
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
141 colnames(adiv_i_df)[which(colnames(adiv_i_df) == "x")] <- paste0("Para. ISD, q = ", div_i_divparam$q[7])
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
142
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
143 # plot
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
144 par(mfrow = c(3, 2))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
145 sapply(names(adiv_i_df[, c(1, 8, 2, 3, 12, 4:7, 9:11, 13:ncol(adiv_i_df))]),
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
146 function(cname) {
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
147 png(paste0(cname, "_histo.png"))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
148 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
ecology
parents:
diff changeset
149 dev.off()
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
150 }
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
151
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
152 )
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
153 par(mfrow = c(1,1))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
154
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
155 div_list[[i]] <- adiv_i_df
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
156
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
157 rm(div_i, adiv_i_df, div_i_speciesdiv, div_i_divparam)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
158
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
159 }
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
160
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
161 # 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.
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
162
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
163
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
164 div_df <- do.call("rbind", div_list)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
165
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
166
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
167 # There is an issue with region.terri that are merged with no "_" ...
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
168
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
169 div_df <- tibble::add_column(div_df, rownames. = rownames(div_df), .before = "richness")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
170 div_df <- tidyr::separate(div_df, rownames., into = c("region.terri.", "site_year_month_day", "Quadrat.bis", "Type.Bloc", "Numéro.Bloc.échantillon", "Face"), sep = "_")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
171
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
172 # I therefore add these lines to solve that issue
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
173
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
174 div_df <- tibble::add_column(div_df, terri. = substring(div_df$region.terri., nchar(div_df$region.terri.)-3), .after = "region.terri.")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
175
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
176 div_df$region.terri. <- substring(div_df$region.terri., 1, nchar(div_df$region.terri)-4)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
177 div_df <- dplyr::rename(div_df, region = region.terri.)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
178
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
179 div_df$site_year_month_day <- paste0(div_df$terri., "_", div_df$site_year_month_day)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
180 div_df <- subset(div_df, select = -c(terri.))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
181
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
182 div_df$Type.Bloc <- as.factor(div_df$Type.Bloc)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
183 div_df$Face <- as.factor(div_df$Face)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
184 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
ecology
parents:
diff changeset
185
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
186 saveRDS(div_df, "div_df.RDS")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
187 write.table(div_df, "Valeurs_stat.tabular", row.names = FALSE, quote = FALSE, sep = "\t", dec = ".", fileEncoding = "UTF-8")