diff --git a/Rcodes/real_data/application_dore.Rmd b/Rcodes/real_data/application_dore.Rmd new file mode 100644 index 0000000..919e7c5 --- /dev/null +++ b/Rcodes/real_data/application_dore.Rmd @@ -0,0 +1,157 @@ +# Application to \cite{doreRelativeEffectsAnthropogenic2021} data +\label{sec:application-to-dorerelativeeffectsanthropogenic2021-data} + +```{r, setup, include=FALSE, warning=FALSE} +knitr::opts_chunk$set(echo = FALSE, dpi = 300) +``` + +```{r} +# import fix +if (getwd() == "/home/polarolouis/Nextcloud/Documents/APT/CEI/Stage Recherche Mathématiques/Depuis PC Portable/Stage MIA 2023/rapport-MIA-2023") { + path_to_add <- "Rcodes/real_data/" +} else { + path_to_add <- "" +} +``` + +```{r require_lib, echo = FALSE, include=FALSE, warning=FALSE} +require("tidyverse") +require("knitr") +require("colSBM") +require("ggplot2") +require("patchwork") +source(paste0(path_to_add, "temporary_plot.R")) +``` + +```{r better_collection_extraction, echo = FALSE, warning=FALSE} +extract_unlist_reorder <- function(clustering_data_path) { + clustering <- readRDS(clustering_data_path) + if (!is.list(clustering)) { + clustering <- list(clustering) + } + best_partition <- extract_best_bipartite_partition(clustering) + best_partition_unlist <- unlist(best_partition) + if (!is.list(best_partition_unlist)) { + best_partition_unlist <- list(best_partition_unlist) + } + size <- length(best_partition_unlist) + return(setNames(lapply(best_partition_unlist, function(collection) { + reorder_parameters(collection) + }), paste(rep("Collection", size), seq_len(size)))) +} +``` + +```{r load data, echo = FALSE, include = FALSE, warning=FALSE} +# All results +iid_unlist <- extract_unlist_reorder(paste0(path_to_add, "data/dore_collection_clustering_nb_run1_iid_123networks_24-05-23-21:40:42.Rds")) +``` + +Here we apply the network clustering procedure (we refer to it as *netclustering*) +to the data from \cite{doreRelativeEffectsAnthropogenic2021}. These data are +plant-pollinator bipartite networks from differents areas and times. + +In a second part we will use additional information for the networks to +try to identify the impact and correlations with the observed structures. + +## Netclustering with the $iid\text{-}colBiSBM$ model +We obtained the more interpretable results with $iid\text{-}colBiSBM$ model. +This resulted in `r length(iid_unlist)` collections to partition the $M = 123$ +networks. + +```{r meso-plots, echo = FALSE, results='asis'} +#| fig.cap=sapply(seq_along(iid_unlist), function(idx) paste0("Collection N°", idx)), +##| fig.cap = "Structure of the collections in the partition and respective proportions of blocks", +##| fig.subcap = sapply(seq_along(iid_unlist), function(idx) paste0("Collection N°", idx)), +#| fig.asp = 0.5 + + +meso_print <- function(unlisted_partition) { + for (idx in seq_along(unlisted_partition)) { + print(plot(unlisted_partition[[idx]], type = "meso", mixture = TRUE) + ggtitle(paste("Collection ", idx))) + cat("\\newline") + } +} +meso_print(iid_unlist) + +``` + +In all the obtained collections the structure is the classical nested structure. +As this is a well-known structure for plant-pollinator data this tends to +indicate that we are not going in a wrong direction. + +The \nth{3} collection consists of only one network, indicating that for this +model, the small76 network was really different of all the others. +One reason might be that it's the oldest network and maybe the data collection +protocol is different. + +## Comparison with additional information + +```{r supinfo, echo = FALSE} +supinfo <- readxl::read_xlsx(paste0(path_to_add, "data/supinfo.xlsx"), sheet = 2) +interaction_data <- read.table(file = paste0(path_to_add, "data/interaction-data.txt"), sep = "\t", header = TRUE) + +seq_ids_network_aggreg <- unique(interaction_data$id_network_aggreg) +incidence_matrices <- readRDS(file = paste0(path_to_add, "data/dore-matrices.Rds")) +names_aggreg_networks <- names(incidence_matrices) +vectorClusteringNet <- numeric(nrow(supinfo)) +for (k in 1:length(iid_unlist)) { + idclust <- match(iid_unlist[[k]]$net_id, names_aggreg_networks) + supinfoclust <- match(seq_ids_network_aggreg[idclust], supinfo$Idweb) + vectorClusteringNet[supinfoclust] <- k +} +``` + +Using supplementary information we obtain the following boxplots. + +A + +```{r boxplot-function, echo = FALSE} +supinfo_boxplot <- function(parameter, pretty_name) { + return(ggplot(supinfo) + + aes( + x = vectorClusteringNet, y = parameter, + fill = as.factor(vectorClusteringNet), group = as.factor(vectorClusteringNet) + ) + + geom_boxplot() + + labs( + x = "Collection number", y = pretty_name, + fill = "Collection number" + )) +} +``` + +```{r boxplots_annual_timespan, echo = FALSE} +#| fig.cap = "\\label{fig:boxplot-annual-time-span}Boxplot of annual time span in function of the collection number" +ggplot(supinfo) + + aes(x = vectorClusteringNet, y = Annual_time_span, + fill = as.factor(vectorClusteringNet), group = as.factor(vectorClusteringNet)) + + geom_boxplot() + + labs( + x = "Collection number", y = "Annual time span", + fill = "Collection number" + ) +``` + +The annual time span is the number of days the sampling period lasted. So we can +thus see in figure \ref{fig:boxplot-annual-time-span} that collections 1 and 4 were +sampled for a larger period of time than collections 2 and 5. +This could explain observed differences in the structure detected : the +"checkerboard" appearance of the alpha matrices representations may represent +interactions that only occurs at a given period of time. +Thus the shorter time period doesn't capture such interactions. + +```{r boxplot_rainfall, echo = FALSE} +#| fig.cap = "\\label{fig:boxplot-total-rainfall}Boxplot of total rainfall in function of the collection number" +supinfo_boxplot(supinfo$Tot_Rainfall_IPCC, "Total rainfall") +``` + +There seems to be the same trend for the total rainfall. + +```{r boxplot_sampling_effort, echo = FALSE} +#| fig.cap = "\\label{fig:boxplot-sampling-effort}Boxplot of the sampling effort in function of the collection number" +supinfo_boxplot(supinfo$Sampling_effort, "Sampling effort") +``` + +The sampling effort seems to be quite higher for collection 5 and a little +higher for collection 2. And collection 1 and 4 have the inverse trend. The +dichotomy between collections 1,4 and 2,5 seems to still hold. \ No newline at end of file diff --git a/Rcodes/real_data/application_dore.tex b/Rcodes/real_data/application_dore.tex new file mode 100644 index 0000000..30181e3 --- /dev/null +++ b/Rcodes/real_data/application_dore.tex @@ -0,0 +1,80 @@ +\hypertarget{application-to-data}{% +\section{\texorpdfstring{Application to +\cite{doreRelativeEffectsAnthropogenic2021} +data}{Application to data}}\label{application-to-data}} + +\label{sec:application-to-dorerelativeeffectsanthropogenic2021-data} + +Here we apply the network clustering procedure (we refer to it as +\emph{netclustering}) to the data from +\cite{doreRelativeEffectsAnthropogenic2021}. These data are +plant-pollinator bipartite networks from differents areas and times. + +In a second part we will use additional information for the networks to +try to identify the impact and correlations with the observed +structures. + +\hypertarget{netclustering-with-the-iidtext-colbisbm-model}{% +\subsection{\texorpdfstring{Netclustering with the +\(iid\text{-}colBiSBM\) +model}{Netclustering with the iid\textbackslash text\{-\}colBiSBM model}}\label{netclustering-with-the-iidtext-colbisbm-model}} + +We obtained the more interpretable results with \(iid\text{-}colBiSBM\) +model. This resulted in 5 collections to partition the \(M = 123\) +networks. + +\includegraphics{./img/22d3409f045c956ffc0773e508871c61db4ad1e9.png}\newline\includegraphics{./img/2859d1c94af6539cced6aee6ee6bf6d49498518d.png}\newline\includegraphics{./img/037bcbcbc85f8a9562f98706ad7766c4099516ef.png}\newline\includegraphics{./img/f730f05cb60a7cdc837102601660f03edd767a60.png}\newline\includegraphics{./img/90d21c2459f68c2a6bc6cce93f9f1e10c3f0fef5.png}\newline + +In all the obtained collections the structure is the classical nested +structure. As this is a well-known structure for plant-pollinator data +this tends to indicate that we are not going in a wrong direction. + +The \nth{3} collection consists of only one network, indicating that for +this model, the small76 network was really different of all the others. +One reason might be that it's the oldest network and maybe the data +collection protocol is different. + +\hypertarget{comparison-with-additional-information}{% +\subsection{Comparison with additional +information}\label{comparison-with-additional-information}} + +Using supplementary information we obtain the following boxplots. + +A + +\begin{figure} +\centering +\includegraphics{./img/de77b630fb66744d3a3ed68e45be765532d1eb0f.png} +\caption{\label{fig:boxplot-annual-time-span}Boxplot of annual time span +in function of the collection number} +\end{figure} + +The annual time span is the number of days the sampling period lasted. +So we can thus see in figure \ref{fig:boxplot-annual-time-span} that +collections 1 and 4 were sampled for a larger period of time than +collections 2 and 5. This could explain observed differences in the +structure detected : the ``checkerboard'' appearance of the alpha +matrices representations may represent interactions that only occurs at +a given period of time. Thus the shorter time period doesn't capture +such interactions. + +\begin{figure} +\centering +\includegraphics{./img/5bbc4b4b07c0e990a3ae2755165958ffbf517902.png} +\caption{\label{fig:boxplot-total-rainfall}Boxplot of total rainfall in +function of the collection number} +\end{figure} + +There seems to be the same trend for the total rainfall. + +\begin{figure} +\centering +\includegraphics{./img/c75a33aa046b6f1bbcff45268346c4ec39067917.png} +\caption{\label{fig:boxplot-sampling-effort}Boxplot of the sampling +effort in function of the collection number} +\end{figure} + +The sampling effort seems to be quite higher for collection 5 and a +little higher for collection 2. And collection 1 and 4 have the inverse +trend. The dichotomy between collections 1,4 and 2,5 seems to still +hold. diff --git a/Rcodes/real_data/application_dore_data.Rmd b/Rcodes/real_data/application_dore_data.Rmd deleted file mode 100644 index 4651b8b..0000000 --- a/Rcodes/real_data/application_dore_data.Rmd +++ /dev/null @@ -1,2 +0,0 @@ -# Application to \cite{doreRelativeEffectsAnthropogenic2021} data -\label{sec:application-to-dorerelativeeffectsanthropogenic2021-data} \ No newline at end of file diff --git a/Rcodes/real_data/application_dore_data.tex b/Rcodes/real_data/application_dore_data.tex deleted file mode 100644 index 95dbc95..0000000 --- a/Rcodes/real_data/application_dore_data.tex +++ /dev/null @@ -1,6 +0,0 @@ -\hypertarget{application-to-data}{% -\section{\texorpdfstring{Application to -\cite{doreRelativeEffectsAnthropogenic2021} -data}{Application to data}}\label{application-to-data}} - -\label{sec:application-to-dorerelativeeffectsanthropogenic2021-data} diff --git a/Rcodes/real_data/presentation_dore.Rmd b/Rcodes/real_data/presentation_dore.Rmd index 7647c25..56d589c 100644 --- a/Rcodes/real_data/presentation_dore.Rmd +++ b/Rcodes/real_data/presentation_dore.Rmd @@ -1,18 +1,5 @@ ---- -title: "Présentation de l'application de colSBM sur Doré et al. 2020" -output: - html_document: - toc: true - theme: united - pdf_document: - keep_tex: true ---- - ```{r, setup, include=FALSE, warning=FALSE} knitr::opts_chunk$set(echo = FALSE) -options(knitr.table.format = function() { - if (knitr::is_latex_output()) "latex" else "pandoc" -}) ``` ```{r require_lib, echo = FALSE, include=FALSE, warning=FALSE} @@ -47,13 +34,13 @@ knit_print.latex <- function(x, ...) { # Now, define a method as_latex for matrix as_latex.matrix <- function(x, ...) { as_latex(c( - "\\begin{bmatrix}", + "\\begin{pmatrix}", paste( t(x), rep(c(rep("&", nrow(x) - 1), "\\\\"), ncol(x)), collapse = "" ), - "\\end{bmatrix}" + "\\end{pmatrix}" )) } @@ -82,10 +69,17 @@ extract_unlist_reorder <- function(clustering_data_path) { meso_print <- function(unlisted_partition) { for (idx in seq_along(unlisted_partition)) { - cat(paste("\n\n\n\nPour la collection", idx, "\n\n")) + cat(paste("\\subsubsection{Pour la collection", idx, "}")) print(plot(unlisted_partition[[idx]], type = "meso", mixture = TRUE)) - cat("\n\n") - print(knitr::kable(unlisted_partition[[idx]]$net_id, col.names = "Networks")) + cat("\\newline \\tiny") + print(knitr::kable(unlisted_partition[[idx]]$net_id, + col.names = "Networks", + format = "latex", + position = "!h", + booktabs = TRUE + )) + cat("\\normalsize\\newline") + cat(knitr::knit_print(unlisted_partition[[idx]]$alpha)) } } @@ -251,12 +245,17 @@ pi_unlist <- extract_unlist_reorder("data/dore_collection_clustering_nb_run1_pi_ pirho_unlist <- extract_unlist_reorder("data/dore_collection_clustering_nb_run1_pirho_123networks_26-05-23-19:22:55.Rds") ``` +# Application to \cite{doreRelativeEffectsAnthropogenic2021} data +\label{sec:application-to-dorerelativeeffectsanthropogenic2021-data} -## Clustering avec le modèle iid -Avec le modèle *iid* nous obtenons les `r length(iid_unlist)` collections et -les structures suivantes: +## Clustering with model iid +With the *iid-colBiSBM* we obtain `r length(iid_unlist)` collections with the +following structures: -```{r iid_meso_plot, echo = FALSE, message=FALSE, results="asis", fig.cap=paste(names(iid_unlist), rep("- iid",length(iid_unlist))), warning=FALSE} +```{r iid_meso_plot, echo = FALSE, message=FALSE, results="asis", warning=FALSE} +#| fig.cap=paste(names(iid_unlist), rep("- iid",length(iid_unlist))), +#| fig.asp = 0.5, +#| dpi = 300 meso_print(iid_unlist) ``` @@ -352,7 +351,7 @@ iid_taxonomy_long %>% ``` -## Clustering avec le modèle pi +## Clustering with model pi Avec le modèle *pi* nous obtenons les `r length(pi_unlist)` collections et les structures suivantes: @@ -410,7 +409,7 @@ taxonomy_plot( ) ``` -## Clustering avec le modèle rho +## Clustering with model rho Avec le modèle *rho* nous obtenons les `r length(rho_unlist)` collections et les structures suivantes: @@ -468,7 +467,7 @@ taxonomy_plot( ) ``` -## Clustering avec le modèle pirho +## Clustering with model pirho Avec le modèle *pirho* nous obtenons les `r length(pirho_unlist)` collections et les structures suivantes: diff --git a/Rcodes/real_data/presentation_dore.tex b/Rcodes/real_data/presentation_dore.tex index 2637ebd..f947ad3 100644 --- a/Rcodes/real_data/presentation_dore.tex +++ b/Rcodes/real_data/presentation_dore.tex @@ -1,232 +1,243 @@ -\hypertarget{clustering-avec-le-moduxe8le-iid}{% -\subsection{Clustering avec le modèle -iid}\label{clustering-avec-le-moduxe8le-iid}} +\hypertarget{application-to-data}{% +\section{\texorpdfstring{Application to +\cite{doreRelativeEffectsAnthropogenic2021} +data}{Application to data}}\label{application-to-data}} -Avec le modèle \emph{iid} nous obtenons les 5 collections et les -structures suivantes: +\label{sec:application-to-dorerelativeeffectsanthropogenic2021-data} -Pour la collection 1 +\hypertarget{clustering-with-model-iid}{% +\subsection{Clustering with model iid}\label{clustering-with-model-iid}} -\begin{figure} -\centering -\includegraphics{figure/iid_meso_plot-1.png} -\caption{Collection 1 - iid} -\end{figure} +With the \emph{iid-colBiSBM} we obtain 5 collections with the following +structures: -\begin{longtable}[]{@{}l@{}} +\subsubsection{Pour la collection 1 } + +\includegraphics{./img/4c7e9819bb707372d35035947dfe7848b594b688.png}\newline \tiny + +\begin{tabular}{l} \toprule -Networks\tabularnewline +Networks\\ \midrule -\endhead -arroyo1982\_1+arroyo1982\_2+arroyo3\tabularnewline -eberling1999\tabularnewline -kato1990\tabularnewline -petanidou1991\tabularnewline -Junker2013\tabularnewline -bartomeus2008\tabularnewline -Benadi2013\_1(950m)+Benadi2013\_2(1170m)+Benadi2013\_6(2020m)\tabularnewline -Benadi2013\_4(1700m)+Benadi2013\_5(1800m)\tabularnewline -Struck1994\tabularnewline -Kato2000\tabularnewline -Albrecht2010\_49yr+Albrecht2010\_63yr+Albrecht2010\_84yr+Albrecht2010\_109yr+Albrecht2010\_130yr\tabularnewline -Baldock2011\_TB+Baldock2011\_JN\tabularnewline -Dattilo2016\tabularnewline -Devoto2005\_PP+Devoto2005\_AP\tabularnewline -Devoto2005\_VT\tabularnewline -Devoto2005\_LL+Devoto2005\_CT\tabularnewline -Freitas2006\tabularnewline -Gibson2006\_TA2\tabularnewline -Jedrzejewska2013\_Ochata+Jedrzejewska2013\_Kabaty\tabularnewline -MonteroCastano2017\_Albufera+MonteroCastano2017\_Llimpa+MonteroCastano2017\_Tirant\tabularnewline -Kehinde2014\_Joostenberg\_Conv+Kehinde2014\_Joostenberg\_Org+Kehinde2014\_Joostenberg\_Nat+Kehinde2014\_Laibach\_Conv+Kehinde2014\_Laibach\_Org+Kehinde2014\_Laibach\_Nat+Kehinde2014\_Spier\_Conv+Kehinde2014\_Spier\_Nat\tabularnewline -Pinheiro2008\tabularnewline -Watts2016\_Chicon+Watts2016\_Mantanay+Watts2016\_Choquebamba+Watts2016\_Huaran+Watts2016\_Piscacucho+Watts2016\_Poques+Watts2016\_Pumamarca+Watts2016\_Tiaparo+Watts2016\_Yanacocha\tabularnewline -Kato1993\tabularnewline -KatoMiura1996\tabularnewline -Kakutani1990\tabularnewline -Inoue1990\tabularnewline -Fragoso\_RA2+Fragoso\_RA3+Fragoso\_RD1+Fragoso\_RD3\tabularnewline -Souza\_cerrado\tabularnewline -Souza\_chaco\tabularnewline -Souza\_pantanal\tabularnewline -Souza\_vereda\tabularnewline -Adedoja2019\tabularnewline -Oleques2019\tabularnewline -Baldock2019\_Bristol\tabularnewline -Baldock2019\_Edinburgh\tabularnewline -Baldock2019\_Leeds\tabularnewline -Baldock2019\_Reading\tabularnewline +arroyo1982\_1+arroyo1982\_2+arroyo3\\ +eberling1999\\ +kato1990\\ +petanidou1991\\ +Junker2013\\ +\addlinespace +bartomeus2008\\ +Benadi2013\_1(950m)+Benadi2013\_2(1170m)+Benadi2013\_6(2020m)\\ +Benadi2013\_4(1700m)+Benadi2013\_5(1800m)\\ +Struck1994\\ +Kato2000\\ +\addlinespace +Albrecht2010\_49yr+Albrecht2010\_63yr+Albrecht2010\_84yr+Albrecht2010\_109yr+Albrecht2010\_130yr\\ +Baldock2011\_TB+Baldock2011\_JN\\ +Dattilo2016\\ +Devoto2005\_PP+Devoto2005\_AP\\ +Devoto2005\_VT\\ +\addlinespace +Devoto2005\_LL+Devoto2005\_CT\\ +Freitas2006\\ +Gibson2006\_TA2\\ +Jedrzejewska2013\_Ochata+Jedrzejewska2013\_Kabaty\\ +MonteroCastano2017\_Albufera+MonteroCastano2017\_Llimpa+MonteroCastano2017\_Tirant\\ +\addlinespace +Kehinde2014\_Joostenberg\_Conv+Kehinde2014\_Joostenberg\_Org+Kehinde2014\_Joostenberg\_Nat+Kehinde2014\_Laibach\_Conv+Kehinde2014\_Laibach\_Org+Kehinde2014\_Laibach\_Nat+Kehinde2014\_Spier\_Conv+Kehinde2014\_Spier\_Nat\\ +Pinheiro2008\\ +Watts2016\_Chicon+Watts2016\_Mantanay+Watts2016\_Choquebamba+Watts2016\_Huaran+Watts2016\_Piscacucho+Watts2016\_Poques+Watts2016\_Pumamarca+Watts2016\_Tiaparo+Watts2016\_Yanacocha\\ +Kato1993\\ +KatoMiura1996\\ +\addlinespace +Kakutani1990\\ +Inoue1990\\ +Fragoso\_RA2+Fragoso\_RA3+Fragoso\_RD1+Fragoso\_RD3\\ +Souza\_cerrado\\ +Souza\_chaco\\ +\addlinespace +Souza\_pantanal\\ +Souza\_vereda\\ +Adedoja2019\\ +Oleques2019\\ +Baldock2019\_Bristol\\ +\addlinespace +Baldock2019\_Edinburgh\\ +Baldock2019\_Leeds\\ +Baldock2019\_Reading\\ \bottomrule -\end{longtable} +\end{tabular} -Pour la collection 2 +\normalsize\newline\[\begin{pmatrix} 1 &0.83 &0.43 &0.73 &0.2 &0.5 &0.05 &0.18 \\1 &0.67 &0.36 &0.51 &0.22 &0.3 &0.05 &0.07 \\1 &0.53 &1 &0.01 &0.02 &0.89 &0 &0 \\0.97 &0.45 &0.62 &0.18 &0.47 &0.06 &0.2 &0.03 \\0.76 &0.46 &0.1 &0.27 &0.1 &0.14 &0.02 &0.03 \\0.96 &0.2 &0.37 &0.03 &0.24 &0.01 &0.09 &0.01 \\0.54 &0.28 &0.04 &0.12 &0.03 &0.05 &0.01 &0.01 \\0.69 &0.1 &0.3 &0.02 &0.06 &0.01 &0.03 &0 \\ \end{pmatrix}\] -\begin{figure} -\centering -\includegraphics{figure/iid_meso_plot-2.png} -\caption{Collection 2 - iid} -\end{figure} +\subsubsection{Pour la collection 2 } -\begin{longtable}[]{@{}l@{}} +\includegraphics{./img/2e1295ef8143b9413e953a4c0c2da20d962158f6.png}\newline \tiny + +\begin{tabular}{l} \toprule -Networks\tabularnewline +Networks\\ \midrule -\endhead -dupont2003\tabularnewline -herrera1988\tabularnewline -inouye1988\tabularnewline -medan2002ld\tabularnewline -medan2002rb\tabularnewline -ramirez1992\tabularnewline -ramirez1989\tabularnewline -Burkle2013\tabularnewline -Olito-Fox2014\tabularnewline -Benadi2013\_3(1340m)\tabularnewline -Aizen2008\_Challhuaco\_U+Aizen2008\_Challhuaco\_D\tabularnewline -Aizen2008\_Cerro Otto\_U+Aizen2008\_Cerro Otto\_D\tabularnewline -Aizen2008\_Llao-llao\_U+Aizen2008\_Llao-llao\_D\tabularnewline -Chamberlain\_cr1+Chamberlain\_cr2+Chamberlain\_fs1+Chamberlain\_fs2+Chamberlain\_go1+Chamberlain\_go2+Chamberlain\_mm1+Chamberlain\_mm2+Chamberlain\_mz1+Chamberlain\_mz2+Chamberlain\_sm1+Chamberlain\_sm2\tabularnewline -Chamberlain\_HLU+Chamberlain\_HLG+Chamberlain\_OKU+Chamberlain\_OKG+Chamberlain\_WLU+Chamberlain\_WLG+Chamberlain\_SOU+Chamberlain\_SOG\tabularnewline -Devoto2005\_LQ\tabularnewline -Devoto2005\_LT+Devoto2005\_LH\tabularnewline -LemusJimenez2003\tabularnewline -Lundgren2005\tabularnewline -Marrero2013\tabularnewline -Trojelsgaard2015\_La Gomera\tabularnewline -Trojelsgaard2015\_Gran Canaria\tabularnewline -Zackenberg\tabularnewline -Yoshihara2008\tabularnewline -Fragoso\_RA1+Fragoso\_RD2\tabularnewline -PopicThesis\tabularnewline -Pornon2017\tabularnewline -Orford\_B1+Orford\_B2+Orford\_B3+Orford\_B4+Orford\_B5+Orford\_B10\tabularnewline -Orford\_B6+Orford\_B7+Orford\_B8+Orford\_B9\tabularnewline -Blumel2016\tabularnewline -Kantsa2018\tabularnewline -Bennett2018\tabularnewline -Adedoja2018b\_baseZone+Adedoja2018b\_MidZone+Adedoja2018b\_HighZone+Adedoja2018b\_PeakZone\tabularnewline -CordenizPicanco2018\_NatVeg\tabularnewline -CordenizPicanco2018\_ExoFor\tabularnewline -Benadi2018\tabularnewline -Hackett2019\_NZ\_salt\_marsh+Hackett2019\_NZ\_sand\_dune+Hackett2019\_NZ\_scrub\_coprosma\tabularnewline -Jolls2019\tabularnewline -Traveset2013\_Fernandina\tabularnewline -Traveset2013\_Pinta\tabularnewline -Traveset2013\_Santiago\tabularnewline -Traveset2013\_SantaCruz\tabularnewline -Traveset2013\_SanCristobal\tabularnewline -Simanonok2014\tabularnewline -Son2019\_a1+Son2019\_a2+Son2019\_a3+Son2019\_a4+Son2019\_a5+Son2019\_a6+Son2019\_a7+Son2019\_a8+Son2019\_F1+Son2019\_F2+Son2019\_F3+Son2019\_F4+Son2019\_F5+Son2019\_F6+Son2019\_F7+Son2019\_F8\tabularnewline +dupont2003\\ +herrera1988\\ +inouye1988\\ +medan2002ld\\ +medan2002rb\\ +\addlinespace +ramirez1992\\ +ramirez1989\\ +Burkle2013\\ +Olito-Fox2014\\ +Benadi2013\_3(1340m)\\ +\addlinespace +Aizen2008\_Challhuaco\_U+Aizen2008\_Challhuaco\_D\\ +Aizen2008\_Cerro Otto\_U+Aizen2008\_Cerro Otto\_D\\ +Aizen2008\_Llao-llao\_U+Aizen2008\_Llao-llao\_D\\ +Chamberlain\_cr1+Chamberlain\_cr2+Chamberlain\_fs1+Chamberlain\_fs2+Chamberlain\_go1+Chamberlain\_go2+Chamberlain\_mm1+Chamberlain\_mm2+Chamberlain\_mz1+Chamberlain\_mz2+Chamberlain\_sm1+Chamberlain\_sm2\\ +Chamberlain\_HLU+Chamberlain\_HLG+Chamberlain\_OKU+Chamberlain\_OKG+Chamberlain\_WLU+Chamberlain\_WLG+Chamberlain\_SOU+Chamberlain\_SOG\\ +\addlinespace +Devoto2005\_LQ\\ +Devoto2005\_LT+Devoto2005\_LH\\ +LemusJimenez2003\\ +Lundgren2005\\ +Marrero2013\\ +\addlinespace +Trojelsgaard2015\_La Gomera\\ +Trojelsgaard2015\_Gran Canaria\\ +Zackenberg\\ +Yoshihara2008\\ +Fragoso\_RA1+Fragoso\_RD2\\ +\addlinespace +PopicThesis\\ +Pornon2017\\ +Orford\_B1+Orford\_B2+Orford\_B3+Orford\_B4+Orford\_B5+Orford\_B10\\ +Orford\_B6+Orford\_B7+Orford\_B8+Orford\_B9\\ +Blumel2016\\ +\addlinespace +Kantsa2018\\ +Bennett2018\\ +Adedoja2018b\_baseZone+Adedoja2018b\_MidZone+Adedoja2018b\_HighZone+Adedoja2018b\_PeakZone\\ +CordenizPicanco2018\_NatVeg\\ +CordenizPicanco2018\_ExoFor\\ +\addlinespace +Benadi2018\\ +Hackett2019\_NZ\_salt\_marsh+Hackett2019\_NZ\_sand\_dune+Hackett2019\_NZ\_scrub\_coprosma\\ +Jolls2019\\ +Traveset2013\_Fernandina\\ +Traveset2013\_Pinta\\ +\addlinespace +Traveset2013\_Santiago\\ +Traveset2013\_SantaCruz\\ +Traveset2013\_SanCristobal\\ +Simanonok2014\\ +Son2019\_a1+Son2019\_a2+Son2019\_a3+Son2019\_a4+Son2019\_a5+Son2019\_a6+Son2019\_a7+Son2019\_a8+Son2019\_F1+Son2019\_F2+Son2019\_F3+Son2019\_F4+Son2019\_F5+Son2019\_F6+Son2019\_F7+Son2019\_F8\\ \bottomrule -\end{longtable} +\end{tabular} -Pour la collection 3 +\normalsize\newline\[\begin{pmatrix} 0.84 &0.69 &0.13 &0.32 \\0.71 &0.49 &0.11 &0.14 \\0.54 &0.26 &0.14 &0.05 \\0.26 &0.07 &0.14 &0.01 \\ \end{pmatrix}\] -\begin{figure} -\centering -\includegraphics{figure/iid_meso_plot-3.png} -\caption{Collection 3 - iid} -\end{figure} +\subsubsection{Pour la collection 3 } -\begin{longtable}[]{@{}l@{}} +\includegraphics{./img/e69b18419936d1e08301cce4cb1c78acba2044c4.png}\newline \tiny + +\begin{tabular}{l} \toprule -Networks\tabularnewline +Networks\\ \midrule -\endhead -small1976\tabularnewline +small1976\\ \bottomrule -\end{longtable} +\end{tabular} -Pour la collection 4 +\normalsize\newline\[\begin{pmatrix} 0.87 &0.33 \\0.11 &0.09 \\ \end{pmatrix}\] -\begin{figure} -\centering -\includegraphics{figure/iid_meso_plot-4.png} -\caption{Collection 4 - iid} -\end{figure} +\subsubsection{Pour la collection 4 } -\begin{longtable}[]{@{}l@{}} +\includegraphics{./img/c1e07feffa95efd0355d15ccfec6dff687c1ef88.png}\newline \tiny + +\begin{tabular}{l} \toprule -Networks\tabularnewline +Networks\\ \midrule -\endhead -smith-ramirez2005\tabularnewline -Weiner2011\tabularnewline -Kaiser\_control+Kaiser\_restored\tabularnewline -Gilarranz2014\_amarante+Gilarranz2014\_barrosa+Gilarranz2014\_cincocerros+Gilarranz2014\_difuntito+Gilarranz2014\_difuntos+Gilarranz2014\_elmorro+Gilarranz2014\_labrava+Gilarranz2014\_lachata+Gilarranz2014\_lapaja+Gilarranz2014\_piedraalta+Gilarranz2014\_vigilancia+Gilarranz2014\_volcan\tabularnewline -Kaiser-Bunbury2017\_Bernica+Kaiser-Bunbury2017\_Casse-dent+Kaiser-Bunbury2017\_Copolia+Kaiser-Bunbury2017\_La-Reserve+Kaiser-Bunbury2017\_Rosebelle+Kaiser-Bunbury2017\_Salazie+Kaiser-Bunbury2017\_Tea-Plantation+Kaiser-Bunbury2017\_Trois-Freres\tabularnewline -Fang2012\tabularnewline -Aizen2008\_Puerto Blest\_U+Aizen2008\_Puerto Blest\_D\tabularnewline -Chamberlain\_Site1+Chamberlain\_Site2+Chamberlain\_Site3+Chamberlain\_Site4+Chamberlain\_Site5+Chamberlain\_Site6\tabularnewline -Dupont2009\_IsenBjerg+Dupont2009\_Other\tabularnewline -Gibson2006\_GA1\tabularnewline -Gibson2006\_TA1\tabularnewline -LaraRomero2016\_pe?alara\_EP+LaraRomero2016\_pe?alara\_PA+LaraRomero2016\_nevero\_EP+LaraRomero2016\_nevero\_PA\tabularnewline -Trojelsgaard2015\_Tenerife Teno Bajo+Trojelsgaard2015\_Tenerife -Fasnia\tabularnewline -Vanbergen2013\_balfarm+Vanbergen2013\_bridgend+Vanbergen2013\_dalhaikie+Vanbergen2013\_netherton+Vanbergen2013\_backhill+Vanbergen2013\_corntulloch+Vanbergen2013\_allancreich\tabularnewline -Pfeiffer\_CNE+Pfeiffer\_CNM+Pfeiffer\_CNT+Pfeiffer\_CPB+Pfeiffer\_CPM+Pfeiffer\_CPR+Pfeiffer\_CPS+Pfeiffer\_M2+Pfeiffer\_RP1+Pfeiffer\_RP2+Pfeiffer\_LM+Pfeiffer\_LO+Pfeiffer\_BD+Pfeiffer\_BH+Pfeiffer\_BS\tabularnewline -Carstensen\_Gigante+Carstensen\_Paulino+Carstensen\_Tinkerbell+Carstensen\_Midway+Carstensen\_Cedro+Carstensen\_Elefante+Carstensen\_Soizig\tabularnewline -Welti\_ID+Welti\_K1B+Welti\_K4A+Welti\_4B+Welti\_20B+Welti\_20C+Welti\_N1A+Welti\_N1B+Welti\_N4A+Welti\_N4B+Welti\_N20A+Welti\_N20B\tabularnewline -Grass2013\_1+Grass2013\_2+Grass2013\_3+Grass2013\_4+Grass2013\_5+Grass2013\_6+Grass2013\_7+Grass2013\_8+Grass2013\_9+Grass2013\_10+Grass2013\_11+Grass2013\_12+Grass2013\_13+Grass2013\_14+Grass2013\_15+Grass2013\_16+Grass2013\_17\tabularnewline -Hackett2019\_UK\_sand\_dune+Hackett2019\_UK\_grassland+Hackett2019\_UK\_heathland+Hackett2019\_UK\_woodland+Hackett2019\_UK\_salt\_marsh+Hackett2019\_UK\_scrub\tabularnewline -Neli2014\tabularnewline +smith-ramirez2005\\ +Weiner2011\\ +Kaiser\_control+Kaiser\_restored\\ +Gilarranz2014\_amarante+Gilarranz2014\_barrosa+Gilarranz2014\_cincocerros+Gilarranz2014\_difuntito+Gilarranz2014\_difuntos+Gilarranz2014\_elmorro+Gilarranz2014\_labrava+Gilarranz2014\_lachata+Gilarranz2014\_lapaja+Gilarranz2014\_piedraalta+Gilarranz2014\_vigilancia+Gilarranz2014\_volcan\\ +Kaiser-Bunbury2017\_Bernica+Kaiser-Bunbury2017\_Casse-dent+Kaiser-Bunbury2017\_Copolia+Kaiser-Bunbury2017\_La-Reserve+Kaiser-Bunbury2017\_Rosebelle+Kaiser-Bunbury2017\_Salazie+Kaiser-Bunbury2017\_Tea-Plantation+Kaiser-Bunbury2017\_Trois-Freres\\ +\addlinespace +Fang2012\\ +Aizen2008\_Puerto Blest\_U+Aizen2008\_Puerto Blest\_D\\ +Chamberlain\_Site1+Chamberlain\_Site2+Chamberlain\_Site3+Chamberlain\_Site4+Chamberlain\_Site5+Chamberlain\_Site6\\ +Dupont2009\_IsenBjerg+Dupont2009\_Other\\ +Gibson2006\_GA1\\ +\addlinespace +Gibson2006\_TA1\\ +LaraRomero2016\_pe?alara\_EP+LaraRomero2016\_pe?alara\_PA+LaraRomero2016\_nevero\_EP+LaraRomero2016\_nevero\_PA\\ +Trojelsgaard2015\_Tenerife Teno Bajo+Trojelsgaard2015\_Tenerife Fasnia\\ +Vanbergen2013\_balfarm+Vanbergen2013\_bridgend+Vanbergen2013\_dalhaikie+Vanbergen2013\_netherton+Vanbergen2013\_backhill+Vanbergen2013\_corntulloch+Vanbergen2013\_allancreich\\ +Pfeiffer\_CNE+Pfeiffer\_CNM+Pfeiffer\_CNT+Pfeiffer\_CPB+Pfeiffer\_CPM+Pfeiffer\_CPR+Pfeiffer\_CPS+Pfeiffer\_M2+Pfeiffer\_RP1+Pfeiffer\_RP2+Pfeiffer\_LM+Pfeiffer\_LO+Pfeiffer\_BD+Pfeiffer\_BH+Pfeiffer\_BS\\ +\addlinespace +Carstensen\_Gigante+Carstensen\_Paulino+Carstensen\_Tinkerbell+Carstensen\_Midway+Carstensen\_Cedro+Carstensen\_Elefante+Carstensen\_Soizig\\ +Welti\_ID+Welti\_K1B+Welti\_K4A+Welti\_4B+Welti\_20B+Welti\_20C+Welti\_N1A+Welti\_N1B+Welti\_N4A+Welti\_N4B+Welti\_N20A+Welti\_N20B\\ +Grass2013\_1+Grass2013\_2+Grass2013\_3+Grass2013\_4+Grass2013\_5+Grass2013\_6+Grass2013\_7+Grass2013\_8+Grass2013\_9+Grass2013\_10+Grass2013\_11+Grass2013\_12+Grass2013\_13+Grass2013\_14+Grass2013\_15+Grass2013\_16+Grass2013\_17\\ +Hackett2019\_UK\_sand\_dune+Hackett2019\_UK\_grassland+Hackett2019\_UK\_heathland+Hackett2019\_UK\_woodland+Hackett2019\_UK\_salt\_marsh+Hackett2019\_UK\_scrub\\ +Neli2014\\ \bottomrule -\end{longtable} +\end{tabular} -Pour la collection 5 +\normalsize\newline\[\begin{pmatrix} 0.96 &0.83 &0.96 &0.39 &0.8 &0.16 &0.66 \\0.98 &0.86 &0.83 &0.51 &0.56 &0.19 &0.09 \\0.8 &0.46 &0.74 &0.12 &0.4 &0.05 &0.13 \\0.89 &0.69 &0.44 &0.35 &0.15 &0.07 &0.01 \\0.7 &0.29 &0.35 &0.03 &0.15 &0.01 &0.03 \\0.66 &0.43 &0.1 &0.17 &0.03 &0.02 &0 \\0.32 &0.12 &0.02 &0.04 &0 &0 &0 \\ \end{pmatrix}\] -\begin{figure} -\centering -\includegraphics{figure/iid_meso_plot-5.png} -\caption{Collection 5 - iid} -\end{figure} +\subsubsection{Pour la collection 5 } -\begin{longtable}[]{@{}l@{}} +\includegraphics{./img/be6eb1cef4cfa33f60e7f12e0d81b62fb4805328.png}\newline \tiny + +\begin{tabular}{l} \toprule -Networks\tabularnewline +Networks\\ \midrule -\endhead -olensen2002aig\tabularnewline -olensen2002flo\tabularnewline -vazquez2002\tabularnewline -Shay2016\tabularnewline -Gibson2006\_GA2\tabularnewline -Gibson2006\_SG\tabularnewline -Trojelsgaard2015\_El Hierro\tabularnewline -Trojelsgaard2015\_Fuerteventura\tabularnewline -Trojelsgaard2015\_Western Sahara\tabularnewline -Robinson2018\tabularnewline -CordenizPicanco2018\_NatFor\tabularnewline -CordenizPicanco2018\_SemiPast\tabularnewline -CordenizPicanco2018\_IntPast\tabularnewline -Biella2019\tabularnewline -Nel2017\tabularnewline -Villalobos2019\tabularnewline -LaraRomero2019\_blanca+LaraRomero2019\_rajada+LaraRomero2019\_refugio+LaraRomero2019\_torre\tabularnewline -Ferrero2013\tabularnewline -Sritongchuay2019\_near+Sritongchuay2019\_far\tabularnewline +olensen2002aig\\ +olensen2002flo\\ +vazquez2002\\ +Shay2016\\ +Gibson2006\_GA2\\ +\addlinespace +Gibson2006\_SG\\ +Trojelsgaard2015\_El Hierro\\ +Trojelsgaard2015\_Fuerteventura\\ +Trojelsgaard2015\_Western Sahara\\ +Robinson2018\\ +\addlinespace +CordenizPicanco2018\_NatFor\\ +CordenizPicanco2018\_SemiPast\\ +CordenizPicanco2018\_IntPast\\ +Biella2019\\ +Nel2017\\ +\addlinespace +Villalobos2019\\ +LaraRomero2019\_blanca+LaraRomero2019\_rajada+LaraRomero2019\_refugio+LaraRomero2019\_torre\\ +Ferrero2013\\ +Sritongchuay2019\_near+Sritongchuay2019\_far\\ \bottomrule -\end{longtable} +\end{tabular} + +\normalsize\newline\[\begin{pmatrix} 0.71 &0.9 &0.57 &0.83 \\0.74 &0.22 &0.7 &0.33 \\0.09 &0.44 &0.07 &0.02 \\ \end{pmatrix}\] Et voici donc les valeurs numériques pour les \(\alpha\) (paramètres de connectivité). Pour la collection 1 : -\[\begin{bmatrix} 1 &0.83 &0.43 &0.73 &0.2 &0.5 &0.05 &0.18 \\1 &0.67 &0.36 &0.51 &0.22 &0.3 &0.05 &0.07 \\1 &0.53 &1 &0.01 &0.02 &0.89 &0 &0 \\0.97 &0.45 &0.62 &0.18 &0.47 &0.06 &0.2 &0.03 \\0.76 &0.46 &0.1 &0.27 &0.1 &0.14 &0.02 &0.03 \\0.96 &0.2 &0.37 &0.03 &0.24 &0.01 &0.09 &0.01 \\0.54 &0.28 &0.04 &0.12 &0.03 &0.05 &0.01 &0.01 \\0.69 &0.1 &0.3 &0.02 &0.06 &0.01 &0.03 &0 \\ \end{bmatrix}\] +\[\begin{pmatrix} 1 &0.83 &0.43 &0.73 &0.2 &0.5 &0.05 &0.18 \\1 &0.67 &0.36 &0.51 &0.22 &0.3 &0.05 &0.07 \\1 &0.53 &1 &0.01 &0.02 &0.89 &0 &0 \\0.97 &0.45 &0.62 &0.18 &0.47 &0.06 &0.2 &0.03 \\0.76 &0.46 &0.1 &0.27 &0.1 &0.14 &0.02 &0.03 \\0.96 &0.2 &0.37 &0.03 &0.24 &0.01 &0.09 &0.01 \\0.54 &0.28 &0.04 &0.12 &0.03 &0.05 &0.01 &0.01 \\0.69 &0.1 &0.3 &0.02 &0.06 &0.01 &0.03 &0 \\ \end{pmatrix}\] Pour la collection 2 : -\[\begin{bmatrix} 0.84 &0.69 &0.13 &0.32 \\0.71 &0.49 &0.11 &0.14 \\0.54 &0.26 &0.14 &0.05 \\0.26 &0.07 &0.14 &0.01 \\ \end{bmatrix}\] +\[\begin{pmatrix} 0.84 &0.69 &0.13 &0.32 \\0.71 &0.49 &0.11 &0.14 \\0.54 &0.26 &0.14 &0.05 \\0.26 &0.07 &0.14 &0.01 \\ \end{pmatrix}\] Pour la collection 3 : -\[\begin{bmatrix} 0.87 &0.33 \\0.11 &0.09 \\ \end{bmatrix}\] Pour la +\[\begin{pmatrix} 0.87 &0.33 \\0.11 &0.09 \\ \end{pmatrix}\] Pour la collection 4 : -\[\begin{bmatrix} 0.96 &0.83 &0.96 &0.39 &0.8 &0.16 &0.66 \\0.98 &0.86 &0.83 &0.51 &0.56 &0.19 &0.09 \\0.8 &0.46 &0.74 &0.12 &0.4 &0.05 &0.13 \\0.89 &0.69 &0.44 &0.35 &0.15 &0.07 &0.01 \\0.7 &0.29 &0.35 &0.03 &0.15 &0.01 &0.03 \\0.66 &0.43 &0.1 &0.17 &0.03 &0.02 &0 \\0.32 &0.12 &0.02 &0.04 &0 &0 &0 \\ \end{bmatrix}\] +\[\begin{pmatrix} 0.96 &0.83 &0.96 &0.39 &0.8 &0.16 &0.66 \\0.98 &0.86 &0.83 &0.51 &0.56 &0.19 &0.09 \\0.8 &0.46 &0.74 &0.12 &0.4 &0.05 &0.13 \\0.89 &0.69 &0.44 &0.35 &0.15 &0.07 &0.01 \\0.7 &0.29 &0.35 &0.03 &0.15 &0.01 &0.03 \\0.66 &0.43 &0.1 &0.17 &0.03 &0.02 &0 \\0.32 &0.12 &0.02 &0.04 &0 &0 &0 \\ \end{pmatrix}\] Pour la collection 5 : -\[\begin{bmatrix} 0.71 &0.9 &0.57 &0.83 \\0.74 &0.22 &0.7 &0.33 \\0.09 &0.44 &0.07 &0.02 \\ \end{bmatrix}\] +\[\begin{pmatrix} 0.71 &0.9 &0.57 &0.83 \\0.74 &0.22 &0.7 &0.33 \\0.09 &0.44 &0.07 &0.02 \\ \end{pmatrix}\] \#\#\# Comparaison avec des infos supplémentaires \begin{figure} \centering -\includegraphics{figure/Annual_timespan_plot-1.png} +\includegraphics{./img/85d1f067903ecf46ea5379990605207eea6dfa23.png} \caption{plot of chunk Annual\_timespan\_plot} \end{figure} @@ -234,9 +245,9 @@ Pour la collection 5 : \subsubsection{Répartition dans les clusters selon la taxonomie}\label{ruxe9partition-dans-les-clusters-selon-la-taxonomie}} -\includegraphics{figure/iid_plot_taxonomy_pollinators-1.png}\includegraphics{figure/iid_plot_taxonomy_pollinators-2.png} +\includegraphics{./img/0bd4d6aa00bf51bbf8e966b7664bea52ace7bede.png}\includegraphics{./img/ba57007c0b13d1fdaa06e6b689f6aaa356359870.png} -\includegraphics{figure/iid_plot_taxonomy_plants-1.png}\includegraphics{figure/iid_plot_taxonomy_plants-2.png} +\includegraphics{./img/482a3d80d6f3afab8ca8818d634d42ce2fc8e6d0.png}\includegraphics{./img/05f987b57c85b14df8f5e89bf0e380ecc9721edc.png} \hypertarget{tables}{% \paragraph{Tables}\label{tables}} @@ -263,753 +274,758 @@ taxonomie}\label{ruxe9partition-dans-les-clusters-selon-la-taxonomie}} ## # Collection_4_Bloc_2 , Collection_4_Bloc_3 , … \end{verbatim} -\hypertarget{clustering-avec-le-moduxe8le-pi}{% -\subsection{Clustering avec le modèle -pi}\label{clustering-avec-le-moduxe8le-pi}} +\hypertarget{clustering-with-model-pi}{% +\subsection{Clustering with model pi}\label{clustering-with-model-pi}} Avec le modèle \emph{pi} nous obtenons les 2 collections et les structures suivantes: -Pour la collection 1 +\subsubsection{Pour la collection 1 } -\begin{figure} -\centering -\includegraphics{figure/pi_meso_plot-1.png} -\caption{Collection 1 - pi} -\end{figure} +\includegraphics{./img/c8d33c523cb7b1b863840ffe9f838cc1a4dafff2.png}\newline \tiny -\begin{longtable}[]{@{}l@{}} +\begin{tabular}{l} \toprule -Networks\tabularnewline +Networks\\ \midrule -\endhead -arroyo1982\_1+arroyo1982\_2+arroyo3\tabularnewline -eberling1999\tabularnewline -inouye1988\tabularnewline -kato1990\tabularnewline -ramirez1992\tabularnewline -petanidou1991\tabularnewline -ramirez1989\tabularnewline -smith-ramirez2005\tabularnewline -Junker2013\tabularnewline -Kaiser\_control+Kaiser\_restored\tabularnewline -bartomeus2008\tabularnewline -Olito-Fox2014\tabularnewline -Benadi2013\_1(950m)+Benadi2013\_2(1170m)+Benadi2013\_6(2020m)\tabularnewline -Benadi2013\_3(1340m)\tabularnewline -Benadi2013\_4(1700m)+Benadi2013\_5(1800m)\tabularnewline -Kaiser-Bunbury2017\_Bernica+Kaiser-Bunbury2017\_Casse-dent+Kaiser-Bunbury2017\_Copolia+Kaiser-Bunbury2017\_La-Reserve+Kaiser-Bunbury2017\_Rosebelle+Kaiser-Bunbury2017\_Salazie+Kaiser-Bunbury2017\_Tea-Plantation+Kaiser-Bunbury2017\_Trois-Freres\tabularnewline -Fang2012\tabularnewline -Shay2016\tabularnewline -Struck1994\tabularnewline -Kato2000\tabularnewline -Aizen2008\_Cerro Otto\_U+Aizen2008\_Cerro Otto\_D\tabularnewline -Aizen2008\_Llao-llao\_U+Aizen2008\_Llao-llao\_D\tabularnewline -Aizen2008\_Puerto Blest\_U+Aizen2008\_Puerto Blest\_D\tabularnewline -Albrecht2010\_49yr+Albrecht2010\_63yr+Albrecht2010\_84yr+Albrecht2010\_109yr+Albrecht2010\_130yr\tabularnewline -Baldock2011\_TB+Baldock2011\_JN\tabularnewline -Chamberlain\_cr1+Chamberlain\_cr2+Chamberlain\_fs1+Chamberlain\_fs2+Chamberlain\_go1+Chamberlain\_go2+Chamberlain\_mm1+Chamberlain\_mm2+Chamberlain\_mz1+Chamberlain\_mz2+Chamberlain\_sm1+Chamberlain\_sm2\tabularnewline -Chamberlain\_HLU+Chamberlain\_HLG+Chamberlain\_OKU+Chamberlain\_OKG+Chamberlain\_WLU+Chamberlain\_WLG+Chamberlain\_SOU+Chamberlain\_SOG\tabularnewline -Chamberlain\_Site1+Chamberlain\_Site2+Chamberlain\_Site3+Chamberlain\_Site4+Chamberlain\_Site5+Chamberlain\_Site6\tabularnewline -Dattilo2016\tabularnewline -Devoto2005\_PP+Devoto2005\_AP\tabularnewline -Devoto2005\_VT\tabularnewline -Devoto2005\_LL+Devoto2005\_CT\tabularnewline -Dupont2009\_IsenBjerg+Dupont2009\_Other\tabularnewline -Freitas2006\tabularnewline -Gibson2006\_TA1\tabularnewline -Gibson2006\_TA2\tabularnewline -Jedrzejewska2013\_Ochata+Jedrzejewska2013\_Kabaty\tabularnewline -LaraRomero2016\_pe?alara\_EP+LaraRomero2016\_pe?alara\_PA+LaraRomero2016\_nevero\_EP+LaraRomero2016\_nevero\_PA\tabularnewline -LemusJimenez2003\tabularnewline -Marrero2013\tabularnewline -MonteroCastano2017\_Albufera+MonteroCastano2017\_Llimpa+MonteroCastano2017\_Tirant\tabularnewline -Kehinde2014\_Joostenberg\_Conv+Kehinde2014\_Joostenberg\_Org+Kehinde2014\_Joostenberg\_Nat+Kehinde2014\_Laibach\_Conv+Kehinde2014\_Laibach\_Org+Kehinde2014\_Laibach\_Nat+Kehinde2014\_Spier\_Conv+Kehinde2014\_Spier\_Nat\tabularnewline -Pinheiro2008\tabularnewline -Trojelsgaard2015\_La Gomera\tabularnewline -Trojelsgaard2015\_Tenerife Teno Bajo+Trojelsgaard2015\_Tenerife -Fasnia\tabularnewline -Vanbergen2013\_balfarm+Vanbergen2013\_bridgend+Vanbergen2013\_dalhaikie+Vanbergen2013\_netherton+Vanbergen2013\_backhill+Vanbergen2013\_corntulloch+Vanbergen2013\_allancreich\tabularnewline -Zackenberg\tabularnewline -Yoshihara2008\tabularnewline -Watts2016\_Chicon+Watts2016\_Mantanay+Watts2016\_Choquebamba+Watts2016\_Huaran+Watts2016\_Piscacucho+Watts2016\_Poques+Watts2016\_Pumamarca+Watts2016\_Tiaparo+Watts2016\_Yanacocha\tabularnewline -Kato1993\tabularnewline -KatoMiura1996\tabularnewline -Kakutani1990\tabularnewline -Inoue1990\tabularnewline -Fragoso\_RA2+Fragoso\_RA3+Fragoso\_RD1+Fragoso\_RD3\tabularnewline -PopicThesis\tabularnewline -Pfeiffer\_CNE+Pfeiffer\_CNM+Pfeiffer\_CNT+Pfeiffer\_CPB+Pfeiffer\_CPM+Pfeiffer\_CPR+Pfeiffer\_CPS+Pfeiffer\_M2+Pfeiffer\_RP1+Pfeiffer\_RP2+Pfeiffer\_LM+Pfeiffer\_LO+Pfeiffer\_BD+Pfeiffer\_BH+Pfeiffer\_BS\tabularnewline -Carstensen\_Gigante+Carstensen\_Paulino+Carstensen\_Tinkerbell+Carstensen\_Midway+Carstensen\_Cedro+Carstensen\_Elefante+Carstensen\_Soizig\tabularnewline -Orford\_B1+Orford\_B2+Orford\_B3+Orford\_B4+Orford\_B5+Orford\_B10\tabularnewline -Orford\_B6+Orford\_B7+Orford\_B8+Orford\_B9\tabularnewline -Blumel2016\tabularnewline -Welti\_ID+Welti\_K1B+Welti\_K4A+Welti\_4B+Welti\_20B+Welti\_20C+Welti\_N1A+Welti\_N1B+Welti\_N4A+Welti\_N4B+Welti\_N20A+Welti\_N20B\tabularnewline -Souza\_cerrado\tabularnewline -Souza\_chaco\tabularnewline -Souza\_pantanal\tabularnewline -Souza\_vereda\tabularnewline -Grass2013\_1+Grass2013\_2+Grass2013\_3+Grass2013\_4+Grass2013\_5+Grass2013\_6+Grass2013\_7+Grass2013\_8+Grass2013\_9+Grass2013\_10+Grass2013\_11+Grass2013\_12+Grass2013\_13+Grass2013\_14+Grass2013\_15+Grass2013\_16+Grass2013\_17\tabularnewline -Bennett2018\tabularnewline -Adedoja2018b\_baseZone+Adedoja2018b\_MidZone+Adedoja2018b\_HighZone+Adedoja2018b\_PeakZone\tabularnewline -Adedoja2019\tabularnewline -CordenizPicanco2018\_NatVeg\tabularnewline -Benadi2018\tabularnewline -Hackett2019\_NZ\_salt\_marsh+Hackett2019\_NZ\_sand\_dune+Hackett2019\_NZ\_scrub\_coprosma\tabularnewline -Oleques2019\tabularnewline -Jolls2019\tabularnewline -Traveset2013\_Fernandina\tabularnewline -Traveset2013\_Santiago\tabularnewline -Traveset2013\_SantaCruz\tabularnewline -Traveset2013\_SanCristobal\tabularnewline -Simanonok2014\tabularnewline -Son2019\_a1+Son2019\_a2+Son2019\_a3+Son2019\_a4+Son2019\_a5+Son2019\_a6+Son2019\_a7+Son2019\_a8+Son2019\_F1+Son2019\_F2+Son2019\_F3+Son2019\_F4+Son2019\_F5+Son2019\_F6+Son2019\_F7+Son2019\_F8\tabularnewline -Baldock2019\_Bristol\tabularnewline -Baldock2019\_Edinburgh\tabularnewline -Baldock2019\_Leeds\tabularnewline -Baldock2019\_Reading\tabularnewline +arroyo1982\_1+arroyo1982\_2+arroyo3\\ +eberling1999\\ +inouye1988\\ +kato1990\\ +ramirez1992\\ +\addlinespace +petanidou1991\\ +ramirez1989\\ +smith-ramirez2005\\ +Junker2013\\ +Kaiser\_control+Kaiser\_restored\\ +\addlinespace +bartomeus2008\\ +Olito-Fox2014\\ +Benadi2013\_1(950m)+Benadi2013\_2(1170m)+Benadi2013\_6(2020m)\\ +Benadi2013\_3(1340m)\\ +Benadi2013\_4(1700m)+Benadi2013\_5(1800m)\\ +\addlinespace +Kaiser-Bunbury2017\_Bernica+Kaiser-Bunbury2017\_Casse-dent+Kaiser-Bunbury2017\_Copolia+Kaiser-Bunbury2017\_La-Reserve+Kaiser-Bunbury2017\_Rosebelle+Kaiser-Bunbury2017\_Salazie+Kaiser-Bunbury2017\_Tea-Plantation+Kaiser-Bunbury2017\_Trois-Freres\\ +Fang2012\\ +Shay2016\\ +Struck1994\\ +Kato2000\\ +\addlinespace +Aizen2008\_Cerro Otto\_U+Aizen2008\_Cerro Otto\_D\\ +Aizen2008\_Llao-llao\_U+Aizen2008\_Llao-llao\_D\\ +Aizen2008\_Puerto Blest\_U+Aizen2008\_Puerto Blest\_D\\ +Albrecht2010\_49yr+Albrecht2010\_63yr+Albrecht2010\_84yr+Albrecht2010\_109yr+Albrecht2010\_130yr\\ +Baldock2011\_TB+Baldock2011\_JN\\ +\addlinespace +Chamberlain\_cr1+Chamberlain\_cr2+Chamberlain\_fs1+Chamberlain\_fs2+Chamberlain\_go1+Chamberlain\_go2+Chamberlain\_mm1+Chamberlain\_mm2+Chamberlain\_mz1+Chamberlain\_mz2+Chamberlain\_sm1+Chamberlain\_sm2\\ +Chamberlain\_HLU+Chamberlain\_HLG+Chamberlain\_OKU+Chamberlain\_OKG+Chamberlain\_WLU+Chamberlain\_WLG+Chamberlain\_SOU+Chamberlain\_SOG\\ +Chamberlain\_Site1+Chamberlain\_Site2+Chamberlain\_Site3+Chamberlain\_Site4+Chamberlain\_Site5+Chamberlain\_Site6\\ +Dattilo2016\\ +Devoto2005\_PP+Devoto2005\_AP\\ +\addlinespace +Devoto2005\_VT\\ +Devoto2005\_LL+Devoto2005\_CT\\ +Dupont2009\_IsenBjerg+Dupont2009\_Other\\ +Freitas2006\\ +Gibson2006\_TA1\\ +\addlinespace +Gibson2006\_TA2\\ +Jedrzejewska2013\_Ochata+Jedrzejewska2013\_Kabaty\\ +LaraRomero2016\_pe?alara\_EP+LaraRomero2016\_pe?alara\_PA+LaraRomero2016\_nevero\_EP+LaraRomero2016\_nevero\_PA\\ +LemusJimenez2003\\ +Marrero2013\\ +\addlinespace +MonteroCastano2017\_Albufera+MonteroCastano2017\_Llimpa+MonteroCastano2017\_Tirant\\ +Kehinde2014\_Joostenberg\_Conv+Kehinde2014\_Joostenberg\_Org+Kehinde2014\_Joostenberg\_Nat+Kehinde2014\_Laibach\_Conv+Kehinde2014\_Laibach\_Org+Kehinde2014\_Laibach\_Nat+Kehinde2014\_Spier\_Conv+Kehinde2014\_Spier\_Nat\\ +Pinheiro2008\\ +Trojelsgaard2015\_La Gomera\\ +Trojelsgaard2015\_Tenerife Teno Bajo+Trojelsgaard2015\_Tenerife Fasnia\\ +\addlinespace +Vanbergen2013\_balfarm+Vanbergen2013\_bridgend+Vanbergen2013\_dalhaikie+Vanbergen2013\_netherton+Vanbergen2013\_backhill+Vanbergen2013\_corntulloch+Vanbergen2013\_allancreich\\ +Zackenberg\\ +Yoshihara2008\\ +Watts2016\_Chicon+Watts2016\_Mantanay+Watts2016\_Choquebamba+Watts2016\_Huaran+Watts2016\_Piscacucho+Watts2016\_Poques+Watts2016\_Pumamarca+Watts2016\_Tiaparo+Watts2016\_Yanacocha\\ +Kato1993\\ +\addlinespace +KatoMiura1996\\ +Kakutani1990\\ +Inoue1990\\ +Fragoso\_RA2+Fragoso\_RA3+Fragoso\_RD1+Fragoso\_RD3\\ +PopicThesis\\ +\addlinespace +Pfeiffer\_CNE+Pfeiffer\_CNM+Pfeiffer\_CNT+Pfeiffer\_CPB+Pfeiffer\_CPM+Pfeiffer\_CPR+Pfeiffer\_CPS+Pfeiffer\_M2+Pfeiffer\_RP1+Pfeiffer\_RP2+Pfeiffer\_LM+Pfeiffer\_LO+Pfeiffer\_BD+Pfeiffer\_BH+Pfeiffer\_BS\\ +Carstensen\_Gigante+Carstensen\_Paulino+Carstensen\_Tinkerbell+Carstensen\_Midway+Carstensen\_Cedro+Carstensen\_Elefante+Carstensen\_Soizig\\ +Orford\_B1+Orford\_B2+Orford\_B3+Orford\_B4+Orford\_B5+Orford\_B10\\ +Orford\_B6+Orford\_B7+Orford\_B8+Orford\_B9\\ +Blumel2016\\ +\addlinespace +Welti\_ID+Welti\_K1B+Welti\_K4A+Welti\_4B+Welti\_20B+Welti\_20C+Welti\_N1A+Welti\_N1B+Welti\_N4A+Welti\_N4B+Welti\_N20A+Welti\_N20B\\ +Souza\_cerrado\\ +Souza\_chaco\\ +Souza\_pantanal\\ +Souza\_vereda\\ +\addlinespace +Grass2013\_1+Grass2013\_2+Grass2013\_3+Grass2013\_4+Grass2013\_5+Grass2013\_6+Grass2013\_7+Grass2013\_8+Grass2013\_9+Grass2013\_10+Grass2013\_11+Grass2013\_12+Grass2013\_13+Grass2013\_14+Grass2013\_15+Grass2013\_16+Grass2013\_17\\ +Bennett2018\\ +Adedoja2018b\_baseZone+Adedoja2018b\_MidZone+Adedoja2018b\_HighZone+Adedoja2018b\_PeakZone\\ +Adedoja2019\\ +CordenizPicanco2018\_NatVeg\\ +\addlinespace +Benadi2018\\ +Hackett2019\_NZ\_salt\_marsh+Hackett2019\_NZ\_sand\_dune+Hackett2019\_NZ\_scrub\_coprosma\\ +Oleques2019\\ +Jolls2019\\ +Traveset2013\_Fernandina\\ +\addlinespace +Traveset2013\_Santiago\\ +Traveset2013\_SantaCruz\\ +Traveset2013\_SanCristobal\\ +Simanonok2014\\ +Son2019\_a1+Son2019\_a2+Son2019\_a3+Son2019\_a4+Son2019\_a5+Son2019\_a6+Son2019\_a7+Son2019\_a8+Son2019\_F1+Son2019\_F2+Son2019\_F3+Son2019\_F4+Son2019\_F5+Son2019\_F6+Son2019\_F7+Son2019\_F8\\ +\addlinespace +Baldock2019\_Bristol\\ +Baldock2019\_Edinburgh\\ +Baldock2019\_Leeds\\ +Baldock2019\_Reading\\ \bottomrule -\end{longtable} +\end{tabular} -Pour la collection 2 +\normalsize\newline\[\begin{pmatrix} 1 &0.9 &0.92 &0.55 &0.75 &0.57 &0.17 \\0.1 &0.21 &0.81 &0.86 &0.7 &0.4 &0.54 \\0.38 &0.12 &0.03 &0.09 &0.92 &0.65 &0.17 \\0.76 &0.5 &0.1 &0.33 &0.17 &0.04 &0.65 \\0.71 &0.5 &0.18 &0.28 &0.19 &0.04 &0.01 \\0.03 &0.89 &0.4 &0.05 &0.53 &0.2 &0.03 \\0.22 &0.07 &0.01 &0.22 &0.35 &0.21 &0.06 \\0.11 &0.07 &0.01 &0.01 &0.01 &0.6 &0.15 \\0.02 &0.21 &0.06 &0.01 &0.06 &0.01 &0 \\ \end{pmatrix}\] -\begin{figure} -\centering -\includegraphics{figure/pi_meso_plot-2.png} -\caption{Collection 2 - pi} -\end{figure} +\subsubsection{Pour la collection 2 } -\begin{longtable}[]{@{}l@{}} +\includegraphics{./img/66882e0b770527a45b5ba01441cbb86ed71491bd.png}\newline \tiny + +\begin{tabular}{l} \toprule -Networks\tabularnewline +Networks\\ \midrule -\endhead -dupont2003\tabularnewline -herrera1988\tabularnewline -medan2002ld\tabularnewline -medan2002rb\tabularnewline -olensen2002aig\tabularnewline -olensen2002flo\tabularnewline -small1976\tabularnewline -vazquez2002\tabularnewline -Burkle2013\tabularnewline -Weiner2011\tabularnewline -Gilarranz2014\_amarante+Gilarranz2014\_barrosa+Gilarranz2014\_cincocerros+Gilarranz2014\_difuntito+Gilarranz2014\_difuntos+Gilarranz2014\_elmorro+Gilarranz2014\_labrava+Gilarranz2014\_lachata+Gilarranz2014\_lapaja+Gilarranz2014\_piedraalta+Gilarranz2014\_vigilancia+Gilarranz2014\_volcan\tabularnewline -Aizen2008\_Challhuaco\_U+Aizen2008\_Challhuaco\_D\tabularnewline -Devoto2005\_LQ\tabularnewline -Devoto2005\_LT+Devoto2005\_LH\tabularnewline -Gibson2006\_GA1\tabularnewline -Gibson2006\_GA2\tabularnewline -Gibson2006\_SG\tabularnewline -Lundgren2005\tabularnewline -Trojelsgaard2015\_El Hierro\tabularnewline -Trojelsgaard2015\_Gran Canaria\tabularnewline -Trojelsgaard2015\_Fuerteventura\tabularnewline -Trojelsgaard2015\_Western Sahara\tabularnewline -Fragoso\_RA1+Fragoso\_RD2\tabularnewline -Pornon2017\tabularnewline -Kantsa2018\tabularnewline -Robinson2018\tabularnewline -CordenizPicanco2018\_NatFor\tabularnewline -CordenizPicanco2018\_ExoFor\tabularnewline -CordenizPicanco2018\_SemiPast\tabularnewline -CordenizPicanco2018\_IntPast\tabularnewline -Hackett2019\_UK\_sand\_dune+Hackett2019\_UK\_grassland+Hackett2019\_UK\_heathland+Hackett2019\_UK\_woodland+Hackett2019\_UK\_salt\_marsh+Hackett2019\_UK\_scrub\tabularnewline -Biella2019\tabularnewline -Nel2017\tabularnewline -Villalobos2019\tabularnewline -LaraRomero2019\_blanca+LaraRomero2019\_rajada+LaraRomero2019\_refugio+LaraRomero2019\_torre\tabularnewline -Traveset2013\_Pinta\tabularnewline -Ferrero2013\tabularnewline -Neli2014\tabularnewline -Sritongchuay2019\_near+Sritongchuay2019\_far\tabularnewline +dupont2003\\ +herrera1988\\ +medan2002ld\\ +medan2002rb\\ +olensen2002aig\\ +\addlinespace +olensen2002flo\\ +small1976\\ +vazquez2002\\ +Burkle2013\\ +Weiner2011\\ +\addlinespace +Gilarranz2014\_amarante+Gilarranz2014\_barrosa+Gilarranz2014\_cincocerros+Gilarranz2014\_difuntito+Gilarranz2014\_difuntos+Gilarranz2014\_elmorro+Gilarranz2014\_labrava+Gilarranz2014\_lachata+Gilarranz2014\_lapaja+Gilarranz2014\_piedraalta+Gilarranz2014\_vigilancia+Gilarranz2014\_volcan\\ +Aizen2008\_Challhuaco\_U+Aizen2008\_Challhuaco\_D\\ +Devoto2005\_LQ\\ +Devoto2005\_LT+Devoto2005\_LH\\ +Gibson2006\_GA1\\ +\addlinespace +Gibson2006\_GA2\\ +Gibson2006\_SG\\ +Lundgren2005\\ +Trojelsgaard2015\_El Hierro\\ +Trojelsgaard2015\_Gran Canaria\\ +\addlinespace +Trojelsgaard2015\_Fuerteventura\\ +Trojelsgaard2015\_Western Sahara\\ +Fragoso\_RA1+Fragoso\_RD2\\ +Pornon2017\\ +Kantsa2018\\ +\addlinespace +Robinson2018\\ +CordenizPicanco2018\_NatFor\\ +CordenizPicanco2018\_ExoFor\\ +CordenizPicanco2018\_SemiPast\\ +CordenizPicanco2018\_IntPast\\ +\addlinespace +Hackett2019\_UK\_sand\_dune+Hackett2019\_UK\_grassland+Hackett2019\_UK\_heathland+Hackett2019\_UK\_woodland+Hackett2019\_UK\_salt\_marsh+Hackett2019\_UK\_scrub\\ +Biella2019\\ +Nel2017\\ +Villalobos2019\\ +LaraRomero2019\_blanca+LaraRomero2019\_rajada+LaraRomero2019\_refugio+LaraRomero2019\_torre\\ +\addlinespace +Traveset2013\_Pinta\\ +Ferrero2013\\ +Neli2014\\ +Sritongchuay2019\_near+Sritongchuay2019\_far\\ \bottomrule -\end{longtable} +\end{tabular} + +\normalsize\newline\[\begin{pmatrix} 0.84 &0.99 &0.66 &0.99 &0.38 &0.79 \\0.79 &0.5 &0.01 &0.19 &0.46 &0.51 \\0.15 &0.02 &0.08 &0.83 &0.22 &0.44 \\0 &0.05 &0.49 &0.07 &0.15 &0 \\0.01 &0.16 &0 &0.04 &0 &0 \\ \end{pmatrix}\] Et voici donc les valeurs numériques pour les \(\alpha\) (paramètres de connectivité). Pour la collection 1 : -\[\begin{bmatrix} 1 &0.9 &0.92 &0.55 &0.75 &0.57 &0.17 \\0.1 &0.21 &0.81 &0.86 &0.7 &0.4 &0.54 \\0.38 &0.12 &0.03 &0.09 &0.92 &0.65 &0.17 \\0.76 &0.5 &0.1 &0.33 &0.17 &0.04 &0.65 \\0.71 &0.5 &0.18 &0.28 &0.19 &0.04 &0.01 \\0.03 &0.89 &0.4 &0.05 &0.53 &0.2 &0.03 \\0.22 &0.07 &0.01 &0.22 &0.35 &0.21 &0.06 \\0.11 &0.07 &0.01 &0.01 &0.01 &0.6 &0.15 \\0.02 &0.21 &0.06 &0.01 &0.06 &0.01 &0 \\ \end{bmatrix}\] +\[\begin{pmatrix} 1 &0.9 &0.92 &0.55 &0.75 &0.57 &0.17 \\0.1 &0.21 &0.81 &0.86 &0.7 &0.4 &0.54 \\0.38 &0.12 &0.03 &0.09 &0.92 &0.65 &0.17 \\0.76 &0.5 &0.1 &0.33 &0.17 &0.04 &0.65 \\0.71 &0.5 &0.18 &0.28 &0.19 &0.04 &0.01 \\0.03 &0.89 &0.4 &0.05 &0.53 &0.2 &0.03 \\0.22 &0.07 &0.01 &0.22 &0.35 &0.21 &0.06 \\0.11 &0.07 &0.01 &0.01 &0.01 &0.6 &0.15 \\0.02 &0.21 &0.06 &0.01 &0.06 &0.01 &0 \\ \end{pmatrix}\] Pour la collection 2 : -\[\begin{bmatrix} 0.84 &0.99 &0.66 &0.99 &0.38 &0.79 \\0.79 &0.5 &0.01 &0.19 &0.46 &0.51 \\0.15 &0.02 &0.08 &0.83 &0.22 &0.44 \\0 &0.05 &0.49 &0.07 &0.15 &0 \\0.01 &0.16 &0 &0.04 &0 &0 \\ \end{bmatrix}\] +\[\begin{pmatrix} 0.84 &0.99 &0.66 &0.99 &0.38 &0.79 \\0.79 &0.5 &0.01 &0.19 &0.46 &0.51 \\0.15 &0.02 &0.08 &0.83 &0.22 &0.44 \\0 &0.05 &0.49 &0.07 &0.15 &0 \\0.01 &0.16 &0 &0.04 &0 &0 \\ \end{pmatrix}\] \hypertarget{ruxe9partition-dans-les-clusters-selon-la-taxonomie-1}{% \subsubsection{Répartition dans les clusters selon la taxonomie}\label{ruxe9partition-dans-les-clusters-selon-la-taxonomie-1}} -\includegraphics{figure/pi_plot_taxonomy_pollinators-1.png}\includegraphics{figure/pi_plot_taxonomy_pollinators-2.png} +\includegraphics{./img/ff78b3a602b38666524674a6e38d94ee26963376.png}\includegraphics{./img/57ebffb0873b5079093d6f7d474c00142ee5e2ab.png} -\includegraphics{figure/pi_plot_taxonomy_plants-1.png}\includegraphics{figure/pi_plot_taxonomy_plants-2.png} +\includegraphics{./img/1616c974be02698dd5c80725494a650ced9db214.png}\includegraphics{./img/b7dacdc5d5ad116b7b9b2c16dcd4084230bcf8cf.png} -\hypertarget{clustering-avec-le-moduxe8le-rho}{% -\subsection{Clustering avec le modèle -rho}\label{clustering-avec-le-moduxe8le-rho}} +\hypertarget{clustering-with-model-rho}{% +\subsection{Clustering with model rho}\label{clustering-with-model-rho}} Avec le modèle \emph{rho} nous obtenons les 1 collections et les structures suivantes: -Pour la collection 1 +\subsubsection{Pour la collection 1 } -\begin{figure} -\centering -\includegraphics{figure/rho_meso_plot-1.png} -\caption{Collection 1 - rho} -\end{figure} +\includegraphics{./img/ddafd83b5651fceb6261e4b7a7637e13859cac33.png}\newline \tiny -\begin{longtable}[]{@{}l@{}} +\begin{tabular}{l} \toprule -Networks\tabularnewline +Networks\\ \midrule -\endhead -arroyo1982\_1+arroyo1982\_2+arroyo3\tabularnewline -dupont2003\tabularnewline -eberling1999\tabularnewline -herrera1988\tabularnewline -inouye1988\tabularnewline -kato1990\tabularnewline -medan2002ld\tabularnewline -medan2002rb\tabularnewline -olensen2002aig\tabularnewline -olensen2002flo\tabularnewline -ramirez1992\tabularnewline -small1976\tabularnewline -vazquez2002\tabularnewline -petanidou1991\tabularnewline -ramirez1989\tabularnewline -smith-ramirez2005\tabularnewline -Burkle2013\tabularnewline -Junker2013\tabularnewline -Weiner2011\tabularnewline -Kaiser\_control+Kaiser\_restored\tabularnewline -bartomeus2008\tabularnewline -Olito-Fox2014\tabularnewline -Gilarranz2014\_amarante+Gilarranz2014\_barrosa+Gilarranz2014\_cincocerros+Gilarranz2014\_difuntito+Gilarranz2014\_difuntos+Gilarranz2014\_elmorro+Gilarranz2014\_labrava+Gilarranz2014\_lachata+Gilarranz2014\_lapaja+Gilarranz2014\_piedraalta+Gilarranz2014\_vigilancia+Gilarranz2014\_volcan\tabularnewline -Benadi2013\_1(950m)+Benadi2013\_2(1170m)+Benadi2013\_6(2020m)\tabularnewline -Benadi2013\_3(1340m)\tabularnewline -Benadi2013\_4(1700m)+Benadi2013\_5(1800m)\tabularnewline -Kaiser-Bunbury2017\_Bernica+Kaiser-Bunbury2017\_Casse-dent+Kaiser-Bunbury2017\_Copolia+Kaiser-Bunbury2017\_La-Reserve+Kaiser-Bunbury2017\_Rosebelle+Kaiser-Bunbury2017\_Salazie+Kaiser-Bunbury2017\_Tea-Plantation+Kaiser-Bunbury2017\_Trois-Freres\tabularnewline -Fang2012\tabularnewline -Shay2016\tabularnewline -Struck1994\tabularnewline -Kato2000\tabularnewline -Aizen2008\_Challhuaco\_U+Aizen2008\_Challhuaco\_D\tabularnewline -Aizen2008\_Cerro Otto\_U+Aizen2008\_Cerro Otto\_D\tabularnewline -Aizen2008\_Llao-llao\_U+Aizen2008\_Llao-llao\_D\tabularnewline -Aizen2008\_Puerto Blest\_U+Aizen2008\_Puerto Blest\_D\tabularnewline -Albrecht2010\_49yr+Albrecht2010\_63yr+Albrecht2010\_84yr+Albrecht2010\_109yr+Albrecht2010\_130yr\tabularnewline -Baldock2011\_TB+Baldock2011\_JN\tabularnewline -Chamberlain\_cr1+Chamberlain\_cr2+Chamberlain\_fs1+Chamberlain\_fs2+Chamberlain\_go1+Chamberlain\_go2+Chamberlain\_mm1+Chamberlain\_mm2+Chamberlain\_mz1+Chamberlain\_mz2+Chamberlain\_sm1+Chamberlain\_sm2\tabularnewline -Chamberlain\_HLU+Chamberlain\_HLG+Chamberlain\_OKU+Chamberlain\_OKG+Chamberlain\_WLU+Chamberlain\_WLG+Chamberlain\_SOU+Chamberlain\_SOG\tabularnewline -Chamberlain\_Site1+Chamberlain\_Site2+Chamberlain\_Site3+Chamberlain\_Site4+Chamberlain\_Site5+Chamberlain\_Site6\tabularnewline -Dattilo2016\tabularnewline -Devoto2005\_LQ\tabularnewline -Devoto2005\_PP+Devoto2005\_AP\tabularnewline -Devoto2005\_LT+Devoto2005\_LH\tabularnewline -Devoto2005\_VT\tabularnewline -Devoto2005\_LL+Devoto2005\_CT\tabularnewline -Dupont2009\_IsenBjerg+Dupont2009\_Other\tabularnewline -Freitas2006\tabularnewline -Gibson2006\_GA1\tabularnewline -Gibson2006\_GA2\tabularnewline -Gibson2006\_SG\tabularnewline -Gibson2006\_TA1\tabularnewline -Gibson2006\_TA2\tabularnewline -Jedrzejewska2013\_Ochata+Jedrzejewska2013\_Kabaty\tabularnewline -LaraRomero2016\_pe?alara\_EP+LaraRomero2016\_pe?alara\_PA+LaraRomero2016\_nevero\_EP+LaraRomero2016\_nevero\_PA\tabularnewline -LemusJimenez2003\tabularnewline -Lundgren2005\tabularnewline -Marrero2013\tabularnewline -MonteroCastano2017\_Albufera+MonteroCastano2017\_Llimpa+MonteroCastano2017\_Tirant\tabularnewline -Kehinde2014\_Joostenberg\_Conv+Kehinde2014\_Joostenberg\_Org+Kehinde2014\_Joostenberg\_Nat+Kehinde2014\_Laibach\_Conv+Kehinde2014\_Laibach\_Org+Kehinde2014\_Laibach\_Nat+Kehinde2014\_Spier\_Conv+Kehinde2014\_Spier\_Nat\tabularnewline -Pinheiro2008\tabularnewline -Trojelsgaard2015\_El Hierro\tabularnewline -Trojelsgaard2015\_La Gomera\tabularnewline -Trojelsgaard2015\_Gran Canaria\tabularnewline -Trojelsgaard2015\_Fuerteventura\tabularnewline -Trojelsgaard2015\_Tenerife Teno Bajo+Trojelsgaard2015\_Tenerife -Fasnia\tabularnewline -Trojelsgaard2015\_Western Sahara\tabularnewline -Vanbergen2013\_balfarm+Vanbergen2013\_bridgend+Vanbergen2013\_dalhaikie+Vanbergen2013\_netherton+Vanbergen2013\_backhill+Vanbergen2013\_corntulloch+Vanbergen2013\_allancreich\tabularnewline -Zackenberg\tabularnewline -Yoshihara2008\tabularnewline -Watts2016\_Chicon+Watts2016\_Mantanay+Watts2016\_Choquebamba+Watts2016\_Huaran+Watts2016\_Piscacucho+Watts2016\_Poques+Watts2016\_Pumamarca+Watts2016\_Tiaparo+Watts2016\_Yanacocha\tabularnewline -Kato1993\tabularnewline -KatoMiura1996\tabularnewline -Kakutani1990\tabularnewline -Inoue1990\tabularnewline -Fragoso\_RA1+Fragoso\_RD2\tabularnewline -Fragoso\_RA2+Fragoso\_RA3+Fragoso\_RD1+Fragoso\_RD3\tabularnewline -PopicThesis\tabularnewline -Pfeiffer\_CNE+Pfeiffer\_CNM+Pfeiffer\_CNT+Pfeiffer\_CPB+Pfeiffer\_CPM+Pfeiffer\_CPR+Pfeiffer\_CPS+Pfeiffer\_M2+Pfeiffer\_RP1+Pfeiffer\_RP2+Pfeiffer\_LM+Pfeiffer\_LO+Pfeiffer\_BD+Pfeiffer\_BH+Pfeiffer\_BS\tabularnewline -Carstensen\_Gigante+Carstensen\_Paulino+Carstensen\_Tinkerbell+Carstensen\_Midway+Carstensen\_Cedro+Carstensen\_Elefante+Carstensen\_Soizig\tabularnewline -Pornon2017\tabularnewline -Orford\_B1+Orford\_B2+Orford\_B3+Orford\_B4+Orford\_B5+Orford\_B10\tabularnewline -Orford\_B6+Orford\_B7+Orford\_B8+Orford\_B9\tabularnewline -Blumel2016\tabularnewline -Welti\_ID+Welti\_K1B+Welti\_K4A+Welti\_4B+Welti\_20B+Welti\_20C+Welti\_N1A+Welti\_N1B+Welti\_N4A+Welti\_N4B+Welti\_N20A+Welti\_N20B\tabularnewline -Kantsa2018\tabularnewline -Souza\_cerrado\tabularnewline -Souza\_chaco\tabularnewline -Souza\_pantanal\tabularnewline -Souza\_vereda\tabularnewline -Grass2013\_1+Grass2013\_2+Grass2013\_3+Grass2013\_4+Grass2013\_5+Grass2013\_6+Grass2013\_7+Grass2013\_8+Grass2013\_9+Grass2013\_10+Grass2013\_11+Grass2013\_12+Grass2013\_13+Grass2013\_14+Grass2013\_15+Grass2013\_16+Grass2013\_17\tabularnewline -Robinson2018\tabularnewline -Bennett2018\tabularnewline -Adedoja2018b\_baseZone+Adedoja2018b\_MidZone+Adedoja2018b\_HighZone+Adedoja2018b\_PeakZone\tabularnewline -Adedoja2019\tabularnewline -CordenizPicanco2018\_NatFor\tabularnewline -CordenizPicanco2018\_NatVeg\tabularnewline -CordenizPicanco2018\_ExoFor\tabularnewline -CordenizPicanco2018\_SemiPast\tabularnewline -CordenizPicanco2018\_IntPast\tabularnewline -Benadi2018\tabularnewline -Hackett2019\_NZ\_salt\_marsh+Hackett2019\_NZ\_sand\_dune+Hackett2019\_NZ\_scrub\_coprosma\tabularnewline -Hackett2019\_UK\_sand\_dune+Hackett2019\_UK\_grassland+Hackett2019\_UK\_heathland+Hackett2019\_UK\_woodland+Hackett2019\_UK\_salt\_marsh+Hackett2019\_UK\_scrub\tabularnewline -Oleques2019\tabularnewline -Biella2019\tabularnewline -Jolls2019\tabularnewline -Nel2017\tabularnewline -Villalobos2019\tabularnewline -LaraRomero2019\_blanca+LaraRomero2019\_rajada+LaraRomero2019\_refugio+LaraRomero2019\_torre\tabularnewline -Traveset2013\_Fernandina\tabularnewline -Traveset2013\_Pinta\tabularnewline -Traveset2013\_Santiago\tabularnewline -Traveset2013\_SantaCruz\tabularnewline -Traveset2013\_SanCristobal\tabularnewline -Ferrero2013\tabularnewline -Simanonok2014\tabularnewline -Son2019\_a1+Son2019\_a2+Son2019\_a3+Son2019\_a4+Son2019\_a5+Son2019\_a6+Son2019\_a7+Son2019\_a8+Son2019\_F1+Son2019\_F2+Son2019\_F3+Son2019\_F4+Son2019\_F5+Son2019\_F6+Son2019\_F7+Son2019\_F8\tabularnewline -Neli2014\tabularnewline -Sritongchuay2019\_near+Sritongchuay2019\_far\tabularnewline -Baldock2019\_Bristol\tabularnewline -Baldock2019\_Edinburgh\tabularnewline -Baldock2019\_Leeds\tabularnewline -Baldock2019\_Reading\tabularnewline +arroyo1982\_1+arroyo1982\_2+arroyo3\\ +dupont2003\\ +eberling1999\\ +herrera1988\\ +inouye1988\\ +\addlinespace +kato1990\\ +medan2002ld\\ +medan2002rb\\ +olensen2002aig\\ +olensen2002flo\\ +\addlinespace +ramirez1992\\ +small1976\\ +vazquez2002\\ +petanidou1991\\ +ramirez1989\\ +\addlinespace +smith-ramirez2005\\ +Burkle2013\\ +Junker2013\\ +Weiner2011\\ +Kaiser\_control+Kaiser\_restored\\ +\addlinespace +bartomeus2008\\ +Olito-Fox2014\\ +Gilarranz2014\_amarante+Gilarranz2014\_barrosa+Gilarranz2014\_cincocerros+Gilarranz2014\_difuntito+Gilarranz2014\_difuntos+Gilarranz2014\_elmorro+Gilarranz2014\_labrava+Gilarranz2014\_lachata+Gilarranz2014\_lapaja+Gilarranz2014\_piedraalta+Gilarranz2014\_vigilancia+Gilarranz2014\_volcan\\ +Benadi2013\_1(950m)+Benadi2013\_2(1170m)+Benadi2013\_6(2020m)\\ +Benadi2013\_3(1340m)\\ +\addlinespace +Benadi2013\_4(1700m)+Benadi2013\_5(1800m)\\ +Kaiser-Bunbury2017\_Bernica+Kaiser-Bunbury2017\_Casse-dent+Kaiser-Bunbury2017\_Copolia+Kaiser-Bunbury2017\_La-Reserve+Kaiser-Bunbury2017\_Rosebelle+Kaiser-Bunbury2017\_Salazie+Kaiser-Bunbury2017\_Tea-Plantation+Kaiser-Bunbury2017\_Trois-Freres\\ +Fang2012\\ +Shay2016\\ +Struck1994\\ +\addlinespace +Kato2000\\ +Aizen2008\_Challhuaco\_U+Aizen2008\_Challhuaco\_D\\ +Aizen2008\_Cerro Otto\_U+Aizen2008\_Cerro Otto\_D\\ +Aizen2008\_Llao-llao\_U+Aizen2008\_Llao-llao\_D\\ +Aizen2008\_Puerto Blest\_U+Aizen2008\_Puerto Blest\_D\\ +\addlinespace +Albrecht2010\_49yr+Albrecht2010\_63yr+Albrecht2010\_84yr+Albrecht2010\_109yr+Albrecht2010\_130yr\\ +Baldock2011\_TB+Baldock2011\_JN\\ +Chamberlain\_cr1+Chamberlain\_cr2+Chamberlain\_fs1+Chamberlain\_fs2+Chamberlain\_go1+Chamberlain\_go2+Chamberlain\_mm1+Chamberlain\_mm2+Chamberlain\_mz1+Chamberlain\_mz2+Chamberlain\_sm1+Chamberlain\_sm2\\ +Chamberlain\_HLU+Chamberlain\_HLG+Chamberlain\_OKU+Chamberlain\_OKG+Chamberlain\_WLU+Chamberlain\_WLG+Chamberlain\_SOU+Chamberlain\_SOG\\ +Chamberlain\_Site1+Chamberlain\_Site2+Chamberlain\_Site3+Chamberlain\_Site4+Chamberlain\_Site5+Chamberlain\_Site6\\ +\addlinespace +Dattilo2016\\ +Devoto2005\_LQ\\ +Devoto2005\_PP+Devoto2005\_AP\\ +Devoto2005\_LT+Devoto2005\_LH\\ +Devoto2005\_VT\\ +\addlinespace +Devoto2005\_LL+Devoto2005\_CT\\ +Dupont2009\_IsenBjerg+Dupont2009\_Other\\ +Freitas2006\\ +Gibson2006\_GA1\\ +Gibson2006\_GA2\\ +\addlinespace +Gibson2006\_SG\\ +Gibson2006\_TA1\\ +Gibson2006\_TA2\\ +Jedrzejewska2013\_Ochata+Jedrzejewska2013\_Kabaty\\ +LaraRomero2016\_pe?alara\_EP+LaraRomero2016\_pe?alara\_PA+LaraRomero2016\_nevero\_EP+LaraRomero2016\_nevero\_PA\\ +\addlinespace +LemusJimenez2003\\ +Lundgren2005\\ +Marrero2013\\ +MonteroCastano2017\_Albufera+MonteroCastano2017\_Llimpa+MonteroCastano2017\_Tirant\\ +Kehinde2014\_Joostenberg\_Conv+Kehinde2014\_Joostenberg\_Org+Kehinde2014\_Joostenberg\_Nat+Kehinde2014\_Laibach\_Conv+Kehinde2014\_Laibach\_Org+Kehinde2014\_Laibach\_Nat+Kehinde2014\_Spier\_Conv+Kehinde2014\_Spier\_Nat\\ +\addlinespace +Pinheiro2008\\ +Trojelsgaard2015\_El Hierro\\ +Trojelsgaard2015\_La Gomera\\ +Trojelsgaard2015\_Gran Canaria\\ +Trojelsgaard2015\_Fuerteventura\\ +\addlinespace +Trojelsgaard2015\_Tenerife Teno Bajo+Trojelsgaard2015\_Tenerife Fasnia\\ +Trojelsgaard2015\_Western Sahara\\ +Vanbergen2013\_balfarm+Vanbergen2013\_bridgend+Vanbergen2013\_dalhaikie+Vanbergen2013\_netherton+Vanbergen2013\_backhill+Vanbergen2013\_corntulloch+Vanbergen2013\_allancreich\\ +Zackenberg\\ +Yoshihara2008\\ +\addlinespace +Watts2016\_Chicon+Watts2016\_Mantanay+Watts2016\_Choquebamba+Watts2016\_Huaran+Watts2016\_Piscacucho+Watts2016\_Poques+Watts2016\_Pumamarca+Watts2016\_Tiaparo+Watts2016\_Yanacocha\\ +Kato1993\\ +KatoMiura1996\\ +Kakutani1990\\ +Inoue1990\\ +\addlinespace +Fragoso\_RA1+Fragoso\_RD2\\ +Fragoso\_RA2+Fragoso\_RA3+Fragoso\_RD1+Fragoso\_RD3\\ +PopicThesis\\ +Pfeiffer\_CNE+Pfeiffer\_CNM+Pfeiffer\_CNT+Pfeiffer\_CPB+Pfeiffer\_CPM+Pfeiffer\_CPR+Pfeiffer\_CPS+Pfeiffer\_M2+Pfeiffer\_RP1+Pfeiffer\_RP2+Pfeiffer\_LM+Pfeiffer\_LO+Pfeiffer\_BD+Pfeiffer\_BH+Pfeiffer\_BS\\ +Carstensen\_Gigante+Carstensen\_Paulino+Carstensen\_Tinkerbell+Carstensen\_Midway+Carstensen\_Cedro+Carstensen\_Elefante+Carstensen\_Soizig\\ +\addlinespace +Pornon2017\\ +Orford\_B1+Orford\_B2+Orford\_B3+Orford\_B4+Orford\_B5+Orford\_B10\\ +Orford\_B6+Orford\_B7+Orford\_B8+Orford\_B9\\ +Blumel2016\\ +Welti\_ID+Welti\_K1B+Welti\_K4A+Welti\_4B+Welti\_20B+Welti\_20C+Welti\_N1A+Welti\_N1B+Welti\_N4A+Welti\_N4B+Welti\_N20A+Welti\_N20B\\ +\addlinespace +Kantsa2018\\ +Souza\_cerrado\\ +Souza\_chaco\\ +Souza\_pantanal\\ +Souza\_vereda\\ +\addlinespace +Grass2013\_1+Grass2013\_2+Grass2013\_3+Grass2013\_4+Grass2013\_5+Grass2013\_6+Grass2013\_7+Grass2013\_8+Grass2013\_9+Grass2013\_10+Grass2013\_11+Grass2013\_12+Grass2013\_13+Grass2013\_14+Grass2013\_15+Grass2013\_16+Grass2013\_17\\ +Robinson2018\\ +Bennett2018\\ +Adedoja2018b\_baseZone+Adedoja2018b\_MidZone+Adedoja2018b\_HighZone+Adedoja2018b\_PeakZone\\ +Adedoja2019\\ +\addlinespace +CordenizPicanco2018\_NatFor\\ +CordenizPicanco2018\_NatVeg\\ +CordenizPicanco2018\_ExoFor\\ +CordenizPicanco2018\_SemiPast\\ +CordenizPicanco2018\_IntPast\\ +\addlinespace +Benadi2018\\ +Hackett2019\_NZ\_salt\_marsh+Hackett2019\_NZ\_sand\_dune+Hackett2019\_NZ\_scrub\_coprosma\\ +Hackett2019\_UK\_sand\_dune+Hackett2019\_UK\_grassland+Hackett2019\_UK\_heathland+Hackett2019\_UK\_woodland+Hackett2019\_UK\_salt\_marsh+Hackett2019\_UK\_scrub\\ +Oleques2019\\ +Biella2019\\ +\addlinespace +Jolls2019\\ +Nel2017\\ +Villalobos2019\\ +LaraRomero2019\_blanca+LaraRomero2019\_rajada+LaraRomero2019\_refugio+LaraRomero2019\_torre\\ +Traveset2013\_Fernandina\\ +\addlinespace +Traveset2013\_Pinta\\ +Traveset2013\_Santiago\\ +Traveset2013\_SantaCruz\\ +Traveset2013\_SanCristobal\\ +Ferrero2013\\ +\addlinespace +Simanonok2014\\ +Son2019\_a1+Son2019\_a2+Son2019\_a3+Son2019\_a4+Son2019\_a5+Son2019\_a6+Son2019\_a7+Son2019\_a8+Son2019\_F1+Son2019\_F2+Son2019\_F3+Son2019\_F4+Son2019\_F5+Son2019\_F6+Son2019\_F7+Son2019\_F8\\ +Neli2014\\ +Sritongchuay2019\_near+Sritongchuay2019\_far\\ +Baldock2019\_Bristol\\ +\addlinespace +Baldock2019\_Edinburgh\\ +Baldock2019\_Leeds\\ +Baldock2019\_Reading\\ \bottomrule -\end{longtable} +\end{tabular} + +\normalsize\newline\[\begin{pmatrix} 0.77 &0.91 &0.64 &0.73 &0.09 &0.34 &0.98 &0.9 &0.41 \\0.63 &0.09 &0.15 &0.94 &0.56 &0.6 &0.25 &0.24 &0.05 \\0.59 &0.73 &0.19 &0.38 &0.04 &0.09 &0.51 &0.22 &0.46 \\0.07 &0.19 &0.02 &0.73 &0.58 &0.2 &0.22 &0.04 &0.03 \\0.69 &0.13 &0.34 &0.03 &0.1 &0.01 &0.53 &0.33 &0.08 \\0.09 &0.02 &0.01 &0.27 &0.06 &0.12 &0.01 &0.04 &0 \\ \end{pmatrix}\] Et voici donc les valeurs numériques pour les \(\alpha\) (paramètres de connectivité). Pour la collection 1 : -\[\begin{bmatrix} 0.77 &0.91 &0.64 &0.73 &0.09 &0.34 &0.98 &0.9 &0.41 \\0.63 &0.09 &0.15 &0.94 &0.56 &0.6 &0.25 &0.24 &0.05 \\0.59 &0.73 &0.19 &0.38 &0.04 &0.09 &0.51 &0.22 &0.46 \\0.07 &0.19 &0.02 &0.73 &0.58 &0.2 &0.22 &0.04 &0.03 \\0.69 &0.13 &0.34 &0.03 &0.1 &0.01 &0.53 &0.33 &0.08 \\0.09 &0.02 &0.01 &0.27 &0.06 &0.12 &0.01 &0.04 &0 \\ \end{bmatrix}\] +\[\begin{pmatrix} 0.77 &0.91 &0.64 &0.73 &0.09 &0.34 &0.98 &0.9 &0.41 \\0.63 &0.09 &0.15 &0.94 &0.56 &0.6 &0.25 &0.24 &0.05 \\0.59 &0.73 &0.19 &0.38 &0.04 &0.09 &0.51 &0.22 &0.46 \\0.07 &0.19 &0.02 &0.73 &0.58 &0.2 &0.22 &0.04 &0.03 \\0.69 &0.13 &0.34 &0.03 &0.1 &0.01 &0.53 &0.33 &0.08 \\0.09 &0.02 &0.01 &0.27 &0.06 &0.12 &0.01 &0.04 &0 \\ \end{pmatrix}\] \hypertarget{ruxe9partition-dans-les-clusters-selon-la-taxonomie-2}{% \subsubsection{Répartition dans les clusters selon la taxonomie}\label{ruxe9partition-dans-les-clusters-selon-la-taxonomie-2}} -\includegraphics{figure/rho_plot_taxonomy_pollinators-1.png}\includegraphics{figure/rho_plot_taxonomy_pollinators-2.png} +\includegraphics{./img/35ffbce157e0b3bb2a32af4dbc7faa201c946a6b.png}\includegraphics{./img/62d45913b19d56f0ab48a367e53b8ed8fa83c2cc.png} -\includegraphics{figure/rho_plot_taxonomy_plants-1.png}\includegraphics{figure/rho_plot_taxonomy_plants-2.png} +\includegraphics{./img/d1f52d1df28195df25bdfd2bf18f50a176d52c90.png}\includegraphics{./img/ce6571ff09f37636eff0631a2269c77055df1403.png} -\hypertarget{clustering-avec-le-moduxe8le-pirho}{% -\subsection{Clustering avec le modèle -pirho}\label{clustering-avec-le-moduxe8le-pirho}} +\hypertarget{clustering-with-model-pirho}{% +\subsection{Clustering with model +pirho}\label{clustering-with-model-pirho}} Avec le modèle \emph{pirho} nous obtenons les 15 collections et les structures suivantes: -Pour la collection 1 +\subsubsection{Pour la collection 1 } -\begin{figure} -\centering -\includegraphics{figure/pirho_meso_plot-1.png} -\caption{Collection 1 - pirho} -\end{figure} +\includegraphics{./img/1b76f16cf61f19fcd2cd382227f1c1dafbdd86b8.png}\newline \tiny -\begin{longtable}[]{@{}l@{}} +\begin{tabular}{l} \toprule -Networks\tabularnewline +Networks\\ \midrule -\endhead -arroyo1982\_1+arroyo1982\_2+arroyo3\tabularnewline -dupont2003\tabularnewline -petanidou1991\tabularnewline -Aizen2008\_Challhuaco\_U+Aizen2008\_Challhuaco\_D\tabularnewline -Aizen2008\_Llao-llao\_U+Aizen2008\_Llao-llao\_D\tabularnewline -Jedrzejewska2013\_Ochata+Jedrzejewska2013\_Kabaty\tabularnewline -Pinheiro2008\tabularnewline -Souza\_pantanal\tabularnewline -Robinson2018\tabularnewline -Jolls2019\tabularnewline -Traveset2013\_Fernandina\tabularnewline -Baldock2019\_Leeds\tabularnewline -Baldock2019\_Reading\tabularnewline +arroyo1982\_1+arroyo1982\_2+arroyo3\\ +dupont2003\\ +petanidou1991\\ +Aizen2008\_Challhuaco\_U+Aizen2008\_Challhuaco\_D\\ +Aizen2008\_Llao-llao\_U+Aizen2008\_Llao-llao\_D\\ +\addlinespace +Jedrzejewska2013\_Ochata+Jedrzejewska2013\_Kabaty\\ +Pinheiro2008\\ +Souza\_pantanal\\ +Robinson2018\\ +Jolls2019\\ +\addlinespace +Traveset2013\_Fernandina\\ +Baldock2019\_Leeds\\ +Baldock2019\_Reading\\ \bottomrule -\end{longtable} +\end{tabular} -Pour la collection 2 +\normalsize\newline\[\begin{pmatrix} 0.52 &0.6 &0.34 &0.1 &0.15 &0 &0.36 \\0.12 &0.93 &0.01 &0.01 &0 &0.61 &0.16 \\0.05 &0.31 &0.02 &0.08 &0.37 &0.27 &0.12 \\0.04 &0.05 &0.01 &0.38 &0.03 &0.01 &0.17 \\0 &0.03 &0.16 &0.11 &0.04 &0.01 &0.01 \\0.01 &0.22 &0.02 &0.01 &0.05 &0 &0.01 \\ \end{pmatrix}\] -\begin{figure} -\centering -\includegraphics{figure/pirho_meso_plot-2.png} -\caption{Collection 2 - pirho} -\end{figure} +\subsubsection{Pour la collection 2 } -\begin{longtable}[]{@{}l@{}} +\includegraphics{./img/9a6b30dad9046620bd49013adaef8960862792a2.png}\newline \tiny + +\begin{tabular}{l} \toprule -Networks\tabularnewline +Networks\\ \midrule -\endhead -Benadi2013\_3(1340m)\tabularnewline -Trojelsgaard2015\_La Gomera\tabularnewline -CordenizPicanco2018\_SemiPast\tabularnewline +Benadi2013\_3(1340m)\\ +Trojelsgaard2015\_La Gomera\\ +CordenizPicanco2018\_SemiPast\\ \bottomrule -\end{longtable} +\end{tabular} -Pour la collection 3 +\normalsize\newline\[\begin{pmatrix} 0.66 &0.23 \\0.2 &0.05 \\ \end{pmatrix}\] -\begin{figure} -\centering -\includegraphics{figure/pirho_meso_plot-3.png} -\caption{Collection 3 - pirho} -\end{figure} +\subsubsection{Pour la collection 3 } -\begin{longtable}[]{@{}l@{}} +\includegraphics{./img/b8abb8188b0bc33c6f0544fed1eb1ff74aac349a.png}\newline \tiny + +\begin{tabular}{l} \toprule -Networks\tabularnewline +Networks\\ \midrule -\endhead -Kato2000\tabularnewline -Freitas2006\tabularnewline -Inoue1990\tabularnewline -Souza\_cerrado\tabularnewline -Adedoja2019\tabularnewline -Baldock2019\_Bristol\tabularnewline +Kato2000\\ +Freitas2006\\ +Inoue1990\\ +Souza\_cerrado\\ +Adedoja2019\\ +\addlinespace +Baldock2019\_Bristol\\ \bottomrule -\end{longtable} +\end{tabular} -Pour la collection 4 +\normalsize\newline\[\begin{pmatrix} 0.64 &0.32 &0.11 &0.53 &0.19 &0.05 \\0.47 &0.21 &0.02 &0.19 &0.07 &0.03 \\0.16 &0.05 &0.01 &0.07 &0.01 &0 \\ \end{pmatrix}\] -\begin{figure} -\centering -\includegraphics{figure/pirho_meso_plot-4.png} -\caption{Collection 4 - pirho} -\end{figure} +\subsubsection{Pour la collection 4 } -\begin{longtable}[]{@{}l@{}} +\includegraphics{./img/73d8481e68a1a4993a0eda2edcc5b2a65ac241c2.png}\newline \tiny + +\begin{tabular}{l} \toprule -Networks\tabularnewline +Networks\\ \midrule -\endhead -Aizen2008\_Puerto Blest\_U+Aizen2008\_Puerto Blest\_D\tabularnewline -LemusJimenez2003\tabularnewline +Aizen2008\_Puerto Blest\_U+Aizen2008\_Puerto Blest\_D\\ +LemusJimenez2003\\ \bottomrule -\end{longtable} +\end{tabular} -Pour la collection 5 +\normalsize\newline\[\begin{pmatrix} 0.45 &0.07 \\0.22 &0.62 \\0.23 &0.04 \\ \end{pmatrix}\] -\begin{figure} -\centering -\includegraphics{figure/pirho_meso_plot-5.png} -\caption{Collection 5 - pirho} -\end{figure} +\subsubsection{Pour la collection 5 } -\begin{longtable}[]{@{}l@{}} +\includegraphics{./img/f5433f933dadae33c549c51d26316f90eb2bbdcd.png}\newline \tiny + +\begin{tabular}{l} \toprule -Networks\tabularnewline +Networks\\ \midrule -\endhead -inouye1988\tabularnewline -Junker2013\tabularnewline -Kehinde2014\_Joostenberg\_Conv+Kehinde2014\_Joostenberg\_Org+Kehinde2014\_Joostenberg\_Nat+Kehinde2014\_Laibach\_Conv+Kehinde2014\_Laibach\_Org+Kehinde2014\_Laibach\_Nat+Kehinde2014\_Spier\_Conv+Kehinde2014\_Spier\_Nat\tabularnewline -Watts2016\_Chicon+Watts2016\_Mantanay+Watts2016\_Choquebamba+Watts2016\_Huaran+Watts2016\_Piscacucho+Watts2016\_Poques+Watts2016\_Pumamarca+Watts2016\_Tiaparo+Watts2016\_Yanacocha\tabularnewline -Kakutani1990\tabularnewline -Fragoso\_RA1+Fragoso\_RD2\tabularnewline -Souza\_chaco\tabularnewline -Oleques2019\tabularnewline +inouye1988\\ +Junker2013\\ +Kehinde2014\_Joostenberg\_Conv+Kehinde2014\_Joostenberg\_Org+Kehinde2014\_Joostenberg\_Nat+Kehinde2014\_Laibach\_Conv+Kehinde2014\_Laibach\_Org+Kehinde2014\_Laibach\_Nat+Kehinde2014\_Spier\_Conv+Kehinde2014\_Spier\_Nat\\ +Watts2016\_Chicon+Watts2016\_Mantanay+Watts2016\_Choquebamba+Watts2016\_Huaran+Watts2016\_Piscacucho+Watts2016\_Poques+Watts2016\_Pumamarca+Watts2016\_Tiaparo+Watts2016\_Yanacocha\\ +Kakutani1990\\ +\addlinespace +Fragoso\_RA1+Fragoso\_RD2\\ +Souza\_chaco\\ +Oleques2019\\ \bottomrule -\end{longtable} +\end{tabular} -Pour la collection 6 +\normalsize\newline\[\begin{pmatrix} 0.78 &0.43 &0.16 &0.56 \\0.29 &0.04 &0.22 &0.08 \\0.02 &0.12 &0.03 &0 \\ \end{pmatrix}\] -\begin{figure} -\centering -\includegraphics{figure/pirho_meso_plot-6.png} -\caption{Collection 6 - pirho} -\end{figure} +\subsubsection{Pour la collection 6 } -\begin{longtable}[]{@{}l@{}} +\includegraphics{./img/9b8b977552f9856c8f2569fd0a1796c7df59125e.png}\newline \tiny + +\begin{tabular}{l} \toprule -Networks\tabularnewline +Networks\\ \midrule -\endhead -medan2002ld\tabularnewline -small1976\tabularnewline -smith-ramirez2005\tabularnewline -Benadi2013\_1(950m)+Benadi2013\_2(1170m)+Benadi2013\_6(2020m)\tabularnewline -Shay2016\tabularnewline -Aizen2008\_Cerro Otto\_U+Aizen2008\_Cerro Otto\_D\tabularnewline -Lundgren2005\tabularnewline -Zackenberg\tabularnewline -Carstensen\_Gigante+Carstensen\_Paulino+Carstensen\_Tinkerbell+Carstensen\_Midway+Carstensen\_Cedro+Carstensen\_Elefante+Carstensen\_Soizig\tabularnewline -Welti\_ID+Welti\_K1B+Welti\_K4A+Welti\_4B+Welti\_20B+Welti\_20C+Welti\_N1A+Welti\_N1B+Welti\_N4A+Welti\_N4B+Welti\_N20A+Welti\_N20B\tabularnewline -Bennett2018\tabularnewline -CordenizPicanco2018\_NatFor\tabularnewline -CordenizPicanco2018\_ExoFor\tabularnewline -CordenizPicanco2018\_IntPast\tabularnewline -Benadi2018\tabularnewline -Villalobos2019\tabularnewline -Traveset2013\_Santiago\tabularnewline -Traveset2013\_SantaCruz\tabularnewline -Son2019\_a1+Son2019\_a2+Son2019\_a3+Son2019\_a4+Son2019\_a5+Son2019\_a6+Son2019\_a7+Son2019\_a8+Son2019\_F1+Son2019\_F2+Son2019\_F3+Son2019\_F4+Son2019\_F5+Son2019\_F6+Son2019\_F7+Son2019\_F8\tabularnewline -Sritongchuay2019\_near+Sritongchuay2019\_far\tabularnewline +medan2002ld\\ +small1976\\ +smith-ramirez2005\\ +Benadi2013\_1(950m)+Benadi2013\_2(1170m)+Benadi2013\_6(2020m)\\ +Shay2016\\ +\addlinespace +Aizen2008\_Cerro Otto\_U+Aizen2008\_Cerro Otto\_D\\ +Lundgren2005\\ +Zackenberg\\ +Carstensen\_Gigante+Carstensen\_Paulino+Carstensen\_Tinkerbell+Carstensen\_Midway+Carstensen\_Cedro+Carstensen\_Elefante+Carstensen\_Soizig\\ +Welti\_ID+Welti\_K1B+Welti\_K4A+Welti\_4B+Welti\_20B+Welti\_20C+Welti\_N1A+Welti\_N1B+Welti\_N4A+Welti\_N4B+Welti\_N20A+Welti\_N20B\\ +\addlinespace +Bennett2018\\ +CordenizPicanco2018\_NatFor\\ +CordenizPicanco2018\_ExoFor\\ +CordenizPicanco2018\_IntPast\\ +Benadi2018\\ +\addlinespace +Villalobos2019\\ +Traveset2013\_Santiago\\ +Traveset2013\_SantaCruz\\ +Son2019\_a1+Son2019\_a2+Son2019\_a3+Son2019\_a4+Son2019\_a5+Son2019\_a6+Son2019\_a7+Son2019\_a8+Son2019\_F1+Son2019\_F2+Son2019\_F3+Son2019\_F4+Son2019\_F5+Son2019\_F6+Son2019\_F7+Son2019\_F8\\ +Sritongchuay2019\_near+Sritongchuay2019\_far\\ \bottomrule -\end{longtable} +\end{tabular} -Pour la collection 7 +\normalsize\newline\[\begin{pmatrix} 0.82 &0.63 &0.2 &0.74 \\0.34 &0.07 &0.41 &0.13 \\0.02 &0.16 &0.03 &0 \\ \end{pmatrix}\] -\begin{figure} -\centering -\includegraphics{figure/pirho_meso_plot-7.png} -\caption{Collection 7 - pirho} -\end{figure} +\subsubsection{Pour la collection 7 } -\begin{longtable}[]{@{}l@{}} +\includegraphics{./img/2bc2aa5f9522a80d234598c960d2b148c78a0bf0.png}\newline \tiny + +\begin{tabular}{l} \toprule -Networks\tabularnewline +Networks\\ \midrule -\endhead -medan2002rb\tabularnewline -olensen2002flo\tabularnewline -vazquez2002\tabularnewline -Trojelsgaard2015\_Gran Canaria\tabularnewline -Trojelsgaard2015\_Western Sahara\tabularnewline -LaraRomero2019\_blanca+LaraRomero2019\_rajada+LaraRomero2019\_refugio+LaraRomero2019\_torre\tabularnewline +medan2002rb\\ +olensen2002flo\\ +vazquez2002\\ +Trojelsgaard2015\_Gran Canaria\\ +Trojelsgaard2015\_Western Sahara\\ +\addlinespace +LaraRomero2019\_blanca+LaraRomero2019\_rajada+LaraRomero2019\_refugio+LaraRomero2019\_torre\\ \bottomrule -\end{longtable} +\end{tabular} -Pour la collection 8 +\normalsize\newline\[\begin{pmatrix} 0.9 &0.46 &0.72 \\0.17 &0.37 &0.03 \\ \end{pmatrix}\] -\begin{figure} -\centering -\includegraphics{figure/pirho_meso_plot-8.png} -\caption{Collection 8 - pirho} -\end{figure} +\subsubsection{Pour la collection 8 } -\begin{longtable}[]{@{}l@{}} +\includegraphics{./img/2435c20b207156887cade4b89b0572d42c93ab82.png}\newline \tiny + +\begin{tabular}{l} \toprule -Networks\tabularnewline +Networks\\ \midrule -\endhead -Weiner2011\tabularnewline -Kaiser\_control+Kaiser\_restored\tabularnewline -Gilarranz2014\_amarante+Gilarranz2014\_barrosa+Gilarranz2014\_cincocerros+Gilarranz2014\_difuntito+Gilarranz2014\_difuntos+Gilarranz2014\_elmorro+Gilarranz2014\_labrava+Gilarranz2014\_lachata+Gilarranz2014\_lapaja+Gilarranz2014\_piedraalta+Gilarranz2014\_vigilancia+Gilarranz2014\_volcan\tabularnewline -Kaiser-Bunbury2017\_Bernica+Kaiser-Bunbury2017\_Casse-dent+Kaiser-Bunbury2017\_Copolia+Kaiser-Bunbury2017\_La-Reserve+Kaiser-Bunbury2017\_Rosebelle+Kaiser-Bunbury2017\_Salazie+Kaiser-Bunbury2017\_Tea-Plantation+Kaiser-Bunbury2017\_Trois-Freres\tabularnewline -Fang2012\tabularnewline -Gibson2006\_SG\tabularnewline -Gibson2006\_TA1\tabularnewline -Trojelsgaard2015\_Fuerteventura\tabularnewline -Pfeiffer\_CNE+Pfeiffer\_CNM+Pfeiffer\_CNT+Pfeiffer\_CPB+Pfeiffer\_CPM+Pfeiffer\_CPR+Pfeiffer\_CPS+Pfeiffer\_M2+Pfeiffer\_RP1+Pfeiffer\_RP2+Pfeiffer\_LM+Pfeiffer\_LO+Pfeiffer\_BD+Pfeiffer\_BH+Pfeiffer\_BS\tabularnewline -Biella2019\tabularnewline -Nel2017\tabularnewline -Ferrero2013\tabularnewline -Neli2014\tabularnewline +Weiner2011\\ +Kaiser\_control+Kaiser\_restored\\ +Gilarranz2014\_amarante+Gilarranz2014\_barrosa+Gilarranz2014\_cincocerros+Gilarranz2014\_difuntito+Gilarranz2014\_difuntos+Gilarranz2014\_elmorro+Gilarranz2014\_labrava+Gilarranz2014\_lachata+Gilarranz2014\_lapaja+Gilarranz2014\_piedraalta+Gilarranz2014\_vigilancia+Gilarranz2014\_volcan\\ +Kaiser-Bunbury2017\_Bernica+Kaiser-Bunbury2017\_Casse-dent+Kaiser-Bunbury2017\_Copolia+Kaiser-Bunbury2017\_La-Reserve+Kaiser-Bunbury2017\_Rosebelle+Kaiser-Bunbury2017\_Salazie+Kaiser-Bunbury2017\_Tea-Plantation+Kaiser-Bunbury2017\_Trois-Freres\\ +Fang2012\\ +\addlinespace +Gibson2006\_SG\\ +Gibson2006\_TA1\\ +Trojelsgaard2015\_Fuerteventura\\ +Pfeiffer\_CNE+Pfeiffer\_CNM+Pfeiffer\_CNT+Pfeiffer\_CPB+Pfeiffer\_CPM+Pfeiffer\_CPR+Pfeiffer\_CPS+Pfeiffer\_M2+Pfeiffer\_RP1+Pfeiffer\_RP2+Pfeiffer\_LM+Pfeiffer\_LO+Pfeiffer\_BD+Pfeiffer\_BH+Pfeiffer\_BS\\ +Biella2019\\ +\addlinespace +Nel2017\\ +Ferrero2013\\ +Neli2014\\ \bottomrule -\end{longtable} +\end{tabular} -Pour la collection 9 +\normalsize\newline\[\begin{pmatrix} 0.66 &0.97 &0.72 &1 &0.13 &0.71 &0 \\0.99 &0.93 &0.84 &0.64 &0.5 &0.11 &0.17 \\0.71 &0.7 &0.28 &0.32 &0.13 &0.07 &0.05 \\0.96 &0.46 &0.75 &0.14 &0.39 &0.01 &0.07 \\0.62 &0.36 &0.09 &0.11 &0.04 &0.02 &0.01 \\0.62 &0.12 &0.43 &0.02 &0.17 &0 &0.02 \\0.33 &0.03 &0.14 &0 &0.03 &0 &0 \\ \end{pmatrix}\] -\begin{figure} -\centering -\includegraphics{figure/pirho_meso_plot-9.png} -\caption{Collection 9 - pirho} -\end{figure} +\subsubsection{Pour la collection 9 } -\begin{longtable}[]{@{}l@{}} +\includegraphics{./img/01cf8becd8b4fa7e13437d68ce7a48e6365fc5d8.png}\newline \tiny + +\begin{tabular}{l} \toprule -Networks\tabularnewline +Networks\\ \midrule -\endhead -eberling1999\tabularnewline -ramirez1992\tabularnewline -Struck1994\tabularnewline -Albrecht2010\_49yr+Albrecht2010\_63yr+Albrecht2010\_84yr+Albrecht2010\_109yr+Albrecht2010\_130yr\tabularnewline -Devoto2005\_PP+Devoto2005\_AP\tabularnewline -Devoto2005\_VT\tabularnewline -Gibson2006\_TA2\tabularnewline -MonteroCastano2017\_Albufera+MonteroCastano2017\_Llimpa+MonteroCastano2017\_Tirant\tabularnewline -Yoshihara2008\tabularnewline -PopicThesis\tabularnewline -Orford\_B1+Orford\_B2+Orford\_B3+Orford\_B4+Orford\_B5+Orford\_B10\tabularnewline -Souza\_vereda\tabularnewline -Adedoja2018b\_baseZone+Adedoja2018b\_MidZone+Adedoja2018b\_HighZone+Adedoja2018b\_PeakZone\tabularnewline -Hackett2019\_NZ\_salt\_marsh+Hackett2019\_NZ\_sand\_dune+Hackett2019\_NZ\_scrub\_coprosma\tabularnewline +eberling1999\\ +ramirez1992\\ +Struck1994\\ +Albrecht2010\_49yr+Albrecht2010\_63yr+Albrecht2010\_84yr+Albrecht2010\_109yr+Albrecht2010\_130yr\\ +Devoto2005\_PP+Devoto2005\_AP\\ +\addlinespace +Devoto2005\_VT\\ +Gibson2006\_TA2\\ +MonteroCastano2017\_Albufera+MonteroCastano2017\_Llimpa+MonteroCastano2017\_Tirant\\ +Yoshihara2008\\ +PopicThesis\\ +\addlinespace +Orford\_B1+Orford\_B2+Orford\_B3+Orford\_B4+Orford\_B5+Orford\_B10\\ +Souza\_vereda\\ +Adedoja2018b\_baseZone+Adedoja2018b\_MidZone+Adedoja2018b\_HighZone+Adedoja2018b\_PeakZone\\ +Hackett2019\_NZ\_salt\_marsh+Hackett2019\_NZ\_sand\_dune+Hackett2019\_NZ\_scrub\_coprosma\\ \bottomrule -\end{longtable} +\end{tabular} -Pour la collection 10 +\normalsize\newline\[\begin{pmatrix} 0.59 &0.17 &0.32 \\0.06 &0.15 &0.02 \\ \end{pmatrix}\] -\begin{figure} -\centering -\includegraphics{figure/pirho_meso_plot-10.png} -\caption{Collection 10 - pirho} -\end{figure} +\subsubsection{Pour la collection 10 } -\begin{longtable}[]{@{}l@{}} +\includegraphics{./img/f191d6381b05b4f2f4139e717eebf1075211d7ea.png}\newline \tiny + +\begin{tabular}{l} \toprule -Networks\tabularnewline +Networks\\ \midrule -\endhead -herrera1988\tabularnewline -Burkle2013\tabularnewline -bartomeus2008\tabularnewline -Olito-Fox2014\tabularnewline -Benadi2013\_4(1700m)+Benadi2013\_5(1800m)\tabularnewline -Baldock2011\_TB+Baldock2011\_JN\tabularnewline -Chamberlain\_HLU+Chamberlain\_HLG+Chamberlain\_OKU+Chamberlain\_OKG+Chamberlain\_WLU+Chamberlain\_WLG+Chamberlain\_SOU+Chamberlain\_SOG\tabularnewline -Chamberlain\_Site1+Chamberlain\_Site2+Chamberlain\_Site3+Chamberlain\_Site4+Chamberlain\_Site5+Chamberlain\_Site6\tabularnewline -Devoto2005\_LQ\tabularnewline -Devoto2005\_LT+Devoto2005\_LH\tabularnewline -Devoto2005\_LL+Devoto2005\_CT\tabularnewline -Dupont2009\_IsenBjerg+Dupont2009\_Other\tabularnewline -Gibson2006\_GA1\tabularnewline -LaraRomero2016\_pe?alara\_EP+LaraRomero2016\_pe?alara\_PA+LaraRomero2016\_nevero\_EP+LaraRomero2016\_nevero\_PA\tabularnewline -Marrero2013\tabularnewline -Trojelsgaard2015\_Tenerife Teno Bajo+Trojelsgaard2015\_Tenerife -Fasnia\tabularnewline -Vanbergen2013\_balfarm+Vanbergen2013\_bridgend+Vanbergen2013\_dalhaikie+Vanbergen2013\_netherton+Vanbergen2013\_backhill+Vanbergen2013\_corntulloch+Vanbergen2013\_allancreich\tabularnewline -Fragoso\_RA2+Fragoso\_RA3+Fragoso\_RD1+Fragoso\_RD3\tabularnewline -Pornon2017\tabularnewline -Orford\_B6+Orford\_B7+Orford\_B8+Orford\_B9\tabularnewline -Blumel2016\tabularnewline -Kantsa2018\tabularnewline -Grass2013\_1+Grass2013\_2+Grass2013\_3+Grass2013\_4+Grass2013\_5+Grass2013\_6+Grass2013\_7+Grass2013\_8+Grass2013\_9+Grass2013\_10+Grass2013\_11+Grass2013\_12+Grass2013\_13+Grass2013\_14+Grass2013\_15+Grass2013\_16+Grass2013\_17\tabularnewline -CordenizPicanco2018\_NatVeg\tabularnewline -Hackett2019\_UK\_sand\_dune+Hackett2019\_UK\_grassland+Hackett2019\_UK\_heathland+Hackett2019\_UK\_woodland+Hackett2019\_UK\_salt\_marsh+Hackett2019\_UK\_scrub\tabularnewline -Traveset2013\_Pinta\tabularnewline -Traveset2013\_SanCristobal\tabularnewline -Simanonok2014\tabularnewline -Baldock2019\_Edinburgh\tabularnewline +herrera1988\\ +Burkle2013\\ +bartomeus2008\\ +Olito-Fox2014\\ +Benadi2013\_4(1700m)+Benadi2013\_5(1800m)\\ +\addlinespace +Baldock2011\_TB+Baldock2011\_JN\\ +Chamberlain\_HLU+Chamberlain\_HLG+Chamberlain\_OKU+Chamberlain\_OKG+Chamberlain\_WLU+Chamberlain\_WLG+Chamberlain\_SOU+Chamberlain\_SOG\\ +Chamberlain\_Site1+Chamberlain\_Site2+Chamberlain\_Site3+Chamberlain\_Site4+Chamberlain\_Site5+Chamberlain\_Site6\\ +Devoto2005\_LQ\\ +Devoto2005\_LT+Devoto2005\_LH\\ +\addlinespace +Devoto2005\_LL+Devoto2005\_CT\\ +Dupont2009\_IsenBjerg+Dupont2009\_Other\\ +Gibson2006\_GA1\\ +LaraRomero2016\_pe?alara\_EP+LaraRomero2016\_pe?alara\_PA+LaraRomero2016\_nevero\_EP+LaraRomero2016\_nevero\_PA\\ +Marrero2013\\ +\addlinespace +Trojelsgaard2015\_Tenerife Teno Bajo+Trojelsgaard2015\_Tenerife Fasnia\\ +Vanbergen2013\_balfarm+Vanbergen2013\_bridgend+Vanbergen2013\_dalhaikie+Vanbergen2013\_netherton+Vanbergen2013\_backhill+Vanbergen2013\_corntulloch+Vanbergen2013\_allancreich\\ +Fragoso\_RA2+Fragoso\_RA3+Fragoso\_RD1+Fragoso\_RD3\\ +Pornon2017\\ +Orford\_B6+Orford\_B7+Orford\_B8+Orford\_B9\\ +\addlinespace +Blumel2016\\ +Kantsa2018\\ +Grass2013\_1+Grass2013\_2+Grass2013\_3+Grass2013\_4+Grass2013\_5+Grass2013\_6+Grass2013\_7+Grass2013\_8+Grass2013\_9+Grass2013\_10+Grass2013\_11+Grass2013\_12+Grass2013\_13+Grass2013\_14+Grass2013\_15+Grass2013\_16+Grass2013\_17\\ +CordenizPicanco2018\_NatVeg\\ +Hackett2019\_UK\_sand\_dune+Hackett2019\_UK\_grassland+Hackett2019\_UK\_heathland+Hackett2019\_UK\_woodland+Hackett2019\_UK\_salt\_marsh+Hackett2019\_UK\_scrub\\ +\addlinespace +Traveset2013\_Pinta\\ +Traveset2013\_SanCristobal\\ +Simanonok2014\\ +Baldock2019\_Edinburgh\\ \bottomrule -\end{longtable} +\end{tabular} -Pour la collection 11 +\normalsize\newline\[\begin{pmatrix} 0.91 &0.62 &0.3 &0.79 &0.44 \\0.15 &0.7 &0.32 &0.07 &0.36 \\0.15 &0.03 &0.16 &0.05 &0.01 \\ \end{pmatrix}\] -\begin{figure} -\centering -\includegraphics{figure/pirho_meso_plot-11.png} -\caption{Collection 11 - pirho} -\end{figure} +\subsubsection{Pour la collection 11 } -\begin{longtable}[]{@{}l@{}} +\includegraphics{./img/b890876aef1a920f5fdc0fb91d549ad59455c587.png}\newline \tiny + +\begin{tabular}{l} \toprule -Networks\tabularnewline +Networks\\ \midrule -\endhead -kato1990\tabularnewline -ramirez1989\tabularnewline -Kato1993\tabularnewline +kato1990\\ +ramirez1989\\ +Kato1993\\ \bottomrule -\end{longtable} +\end{tabular} -Pour la collection 12 +\normalsize\newline\[\begin{pmatrix} 0.09 &0.36 &1 &0.12 &0.41 \\0.33 &0 &0.07 &0.46 &0.09 \\0 &0.01 &0.07 &0.14 &0 \\0.03 &0.16 &0.02 &0 &0 \\ \end{pmatrix}\] -\begin{figure} -\centering -\includegraphics{figure/pirho_meso_plot-12.png} -\caption{Collection 12 - pirho} -\end{figure} +\subsubsection{Pour la collection 12 } -\begin{longtable}[]{@{}l@{}} +\includegraphics{./img/63fe35c05911cc6ad732c2424d821e1ff6017bcf.png}\newline \tiny + +\begin{tabular}{l} \toprule -Networks\tabularnewline +Networks\\ \midrule -\endhead -Chamberlain\_cr1+Chamberlain\_cr2+Chamberlain\_fs1+Chamberlain\_fs2+Chamberlain\_go1+Chamberlain\_go2+Chamberlain\_mm1+Chamberlain\_mm2+Chamberlain\_mz1+Chamberlain\_mz2+Chamberlain\_sm1+Chamberlain\_sm2\tabularnewline -Dattilo2016\tabularnewline -KatoMiura1996\tabularnewline +Chamberlain\_cr1+Chamberlain\_cr2+Chamberlain\_fs1+Chamberlain\_fs2+Chamberlain\_go1+Chamberlain\_go2+Chamberlain\_mm1+Chamberlain\_mm2+Chamberlain\_mz1+Chamberlain\_mz2+Chamberlain\_sm1+Chamberlain\_sm2\\ +Dattilo2016\\ +KatoMiura1996\\ \bottomrule -\end{longtable} +\end{tabular} -Pour la collection 13 +\normalsize\newline\[\begin{pmatrix} 0.68 &0.37 &0.12 \\0.41 &0.17 &0.04 \\0.19 &0.05 &0.01 \\ \end{pmatrix}\] -\begin{figure} -\centering -\includegraphics{figure/pirho_meso_plot-13.png} -\caption{Collection 13 - pirho} -\end{figure} +\subsubsection{Pour la collection 13 } -\begin{longtable}[]{@{}l@{}} +\includegraphics{./img/3c15b096f5435091aae32ed4477d5df277c2af82.png}\newline \tiny + +\begin{tabular}{l} \toprule -Networks\tabularnewline +Networks\\ \midrule -\endhead -olensen2002aig\tabularnewline +olensen2002aig\\ \bottomrule -\end{longtable} +\end{tabular} -Pour la collection 14 +\normalsize\newline\[\begin{pmatrix} 0.78 \\0.19 \\ \end{pmatrix}\] -\begin{figure} -\centering -\includegraphics{figure/pirho_meso_plot-14.png} -\caption{Collection 14 - pirho} -\end{figure} +\subsubsection{Pour la collection 14 } -\begin{longtable}[]{@{}l@{}} +\includegraphics{./img/888bd40e8c6409a43aae4aa9744e362b2ea7da34.png}\newline \tiny + +\begin{tabular}{l} \toprule -Networks\tabularnewline +Networks\\ \midrule -\endhead -Trojelsgaard2015\_El Hierro\tabularnewline +Trojelsgaard2015\_El Hierro\\ \bottomrule -\end{longtable} +\end{tabular} -Pour la collection 15 +\normalsize\newline\[\begin{pmatrix} 0.44 &0.08 \\ \end{pmatrix}\] -\begin{figure} -\centering -\includegraphics{figure/pirho_meso_plot-15.png} -\caption{Collection 15 - pirho} -\end{figure} +\subsubsection{Pour la collection 15 } -\begin{longtable}[]{@{}l@{}} +\includegraphics{./img/be03e1e125628e702f825f4e55f2a3d50d226045.png}\newline \tiny + +\begin{tabular}{l} \toprule -Networks\tabularnewline +Networks\\ \midrule -\endhead -Gibson2006\_GA2\tabularnewline +Gibson2006\_GA2\\ \bottomrule -\end{longtable} +\end{tabular} + +\normalsize\newline\[\begin{pmatrix} 0.42 &1 \\0.35 &0.01 \\ \end{pmatrix}\] Et voici donc les valeurs numériques pour les \(\alpha\) (paramètres de connectivité). Pour la collection 1 : -\[\begin{bmatrix} 0.52 &0.6 &0.34 &0.1 &0.15 &0 &0.36 \\0.12 &0.93 &0.01 &0.01 &0 &0.61 &0.16 \\0.05 &0.31 &0.02 &0.08 &0.37 &0.27 &0.12 \\0.04 &0.05 &0.01 &0.38 &0.03 &0.01 &0.17 \\0 &0.03 &0.16 &0.11 &0.04 &0.01 &0.01 \\0.01 &0.22 &0.02 &0.01 &0.05 &0 &0.01 \\ \end{bmatrix}\] +\[\begin{pmatrix} 0.52 &0.6 &0.34 &0.1 &0.15 &0 &0.36 \\0.12 &0.93 &0.01 &0.01 &0 &0.61 &0.16 \\0.05 &0.31 &0.02 &0.08 &0.37 &0.27 &0.12 \\0.04 &0.05 &0.01 &0.38 &0.03 &0.01 &0.17 \\0 &0.03 &0.16 &0.11 &0.04 &0.01 &0.01 \\0.01 &0.22 &0.02 &0.01 &0.05 &0 &0.01 \\ \end{pmatrix}\] Pour la collection 2 : -\[\begin{bmatrix} 0.66 &0.23 \\0.2 &0.05 \\ \end{bmatrix}\] Pour la +\[\begin{pmatrix} 0.66 &0.23 \\0.2 &0.05 \\ \end{pmatrix}\] Pour la collection 3 : -\[\begin{bmatrix} 0.64 &0.32 &0.11 &0.53 &0.19 &0.05 \\0.47 &0.21 &0.02 &0.19 &0.07 &0.03 \\0.16 &0.05 &0.01 &0.07 &0.01 &0 \\ \end{bmatrix}\] +\[\begin{pmatrix} 0.64 &0.32 &0.11 &0.53 &0.19 &0.05 \\0.47 &0.21 &0.02 &0.19 &0.07 &0.03 \\0.16 &0.05 &0.01 &0.07 &0.01 &0 \\ \end{pmatrix}\] Pour la collection 4 : -\[\begin{bmatrix} 0.45 &0.07 \\0.22 &0.62 \\0.23 &0.04 \\ \end{bmatrix}\] +\[\begin{pmatrix} 0.45 &0.07 \\0.22 &0.62 \\0.23 &0.04 \\ \end{pmatrix}\] Pour la collection 5 : -\[\begin{bmatrix} 0.78 &0.43 &0.16 &0.56 \\0.29 &0.04 &0.22 &0.08 \\0.02 &0.12 &0.03 &0 \\ \end{bmatrix}\] +\[\begin{pmatrix} 0.78 &0.43 &0.16 &0.56 \\0.29 &0.04 &0.22 &0.08 \\0.02 &0.12 &0.03 &0 \\ \end{pmatrix}\] Pour la collection 6 : -\[\begin{bmatrix} 0.82 &0.63 &0.2 &0.74 \\0.34 &0.07 &0.41 &0.13 \\0.02 &0.16 &0.03 &0 \\ \end{bmatrix}\] +\[\begin{pmatrix} 0.82 &0.63 &0.2 &0.74 \\0.34 &0.07 &0.41 &0.13 \\0.02 &0.16 &0.03 &0 \\ \end{pmatrix}\] Pour la collection 7 : -\[\begin{bmatrix} 0.9 &0.46 &0.72 \\0.17 &0.37 &0.03 \\ \end{bmatrix}\] +\[\begin{pmatrix} 0.9 &0.46 &0.72 \\0.17 &0.37 &0.03 \\ \end{pmatrix}\] Pour la collection 8 : -\[\begin{bmatrix} 0.66 &0.97 &0.72 &1 &0.13 &0.71 &0 \\0.99 &0.93 &0.84 &0.64 &0.5 &0.11 &0.17 \\0.71 &0.7 &0.28 &0.32 &0.13 &0.07 &0.05 \\0.96 &0.46 &0.75 &0.14 &0.39 &0.01 &0.07 \\0.62 &0.36 &0.09 &0.11 &0.04 &0.02 &0.01 \\0.62 &0.12 &0.43 &0.02 &0.17 &0 &0.02 \\0.33 &0.03 &0.14 &0 &0.03 &0 &0 \\ \end{bmatrix}\] +\[\begin{pmatrix} 0.66 &0.97 &0.72 &1 &0.13 &0.71 &0 \\0.99 &0.93 &0.84 &0.64 &0.5 &0.11 &0.17 \\0.71 &0.7 &0.28 &0.32 &0.13 &0.07 &0.05 \\0.96 &0.46 &0.75 &0.14 &0.39 &0.01 &0.07 \\0.62 &0.36 &0.09 &0.11 &0.04 &0.02 &0.01 \\0.62 &0.12 &0.43 &0.02 &0.17 &0 &0.02 \\0.33 &0.03 &0.14 &0 &0.03 &0 &0 \\ \end{pmatrix}\] Pour la collection 9 : -\[\begin{bmatrix} 0.59 &0.17 &0.32 \\0.06 &0.15 &0.02 \\ \end{bmatrix}\] +\[\begin{pmatrix} 0.59 &0.17 &0.32 \\0.06 &0.15 &0.02 \\ \end{pmatrix}\] Pour la collection 10 : -\[\begin{bmatrix} 0.91 &0.62 &0.3 &0.79 &0.44 \\0.15 &0.7 &0.32 &0.07 &0.36 \\0.15 &0.03 &0.16 &0.05 &0.01 \\ \end{bmatrix}\] +\[\begin{pmatrix} 0.91 &0.62 &0.3 &0.79 &0.44 \\0.15 &0.7 &0.32 &0.07 &0.36 \\0.15 &0.03 &0.16 &0.05 &0.01 \\ \end{pmatrix}\] Pour la collection 11 : -\[\begin{bmatrix} 0.09 &0.36 &1 &0.12 &0.41 \\0.33 &0 &0.07 &0.46 &0.09 \\0 &0.01 &0.07 &0.14 &0 \\0.03 &0.16 &0.02 &0 &0 \\ \end{bmatrix}\] +\[\begin{pmatrix} 0.09 &0.36 &1 &0.12 &0.41 \\0.33 &0 &0.07 &0.46 &0.09 \\0 &0.01 &0.07 &0.14 &0 \\0.03 &0.16 &0.02 &0 &0 \\ \end{pmatrix}\] Pour la collection 12 : -\[\begin{bmatrix} 0.68 &0.37 &0.12 \\0.41 &0.17 &0.04 \\0.19 &0.05 &0.01 \\ \end{bmatrix}\] -Pour la collection 13 : \[\begin{bmatrix} 0.78 \\0.19 \\ \end{bmatrix}\] -Pour la collection 14 : \[\begin{bmatrix} 0.44 &0.08 \\ \end{bmatrix}\] +\[\begin{pmatrix} 0.68 &0.37 &0.12 \\0.41 &0.17 &0.04 \\0.19 &0.05 &0.01 \\ \end{pmatrix}\] +Pour la collection 13 : \[\begin{pmatrix} 0.78 \\0.19 \\ \end{pmatrix}\] +Pour la collection 14 : \[\begin{pmatrix} 0.44 &0.08 \\ \end{pmatrix}\] Pour la collection 15 : -\[\begin{bmatrix} 0.42 &1 \\0.35 &0.01 \\ \end{bmatrix}\] +\[\begin{pmatrix} 0.42 &1 \\0.35 &0.01 \\ \end{pmatrix}\] \hypertarget{ruxe9partition-dans-les-clusters-selon-la-taxonomie-3}{% \subsubsection{Répartition dans les clusters selon la taxonomie}\label{ruxe9partition-dans-les-clusters-selon-la-taxonomie-3}} -\includegraphics{figure/pirho_plot_taxonomy_pollinators-1.png}\includegraphics{figure/pirho_plot_taxonomy_pollinators-2.png} +\includegraphics{./img/337973465a11f78731e92a7e62b1f4c2164ab43e.png}\includegraphics{./img/09bed9592345eff7f0e23841c310114fc4b5773d.png} -\includegraphics{figure/pirho_plot_taxonomy_plants-1.png}\includegraphics{figure/pirho_plot_taxonomy_plants-2.png} +\includegraphics{./img/9e913a77139e5e0a619c6c0e9beef79f87c6bb61.png}\includegraphics{./img/c3c10578cbfaf01a313454190bda1efad0227b03.png} diff --git a/figure/boxplot_rainfall-1.png b/figure/boxplot_rainfall-1.png new file mode 100644 index 0000000..367024a Binary files /dev/null and b/figure/boxplot_rainfall-1.png differ diff --git a/figure/boxplot_sampling_effort-1.png b/figure/boxplot_sampling_effort-1.png new file mode 100644 index 0000000..fb4f2bc Binary files /dev/null and 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b/img/ff78b3a602b38666524674a6e38d94ee26963376.png differ diff --git a/rapport.pdf b/rapport.pdf index b772ab3..5fca9f2 100644 Binary files a/rapport.pdf and b/rapport.pdf differ diff --git a/rapport.tex b/rapport.tex index 49cab1e..fcc111b 100644 --- a/rapport.tex +++ b/rapport.tex @@ -15,6 +15,7 @@ \usepackage[citecolor=blueind,urlcolor=blue,bookmarks=false,hypertexnames=true]{hyperref} % pour les hyperliens dans le document \usepackage{tocbibind} % Pour avoir des index pour table des matières, biblio \usepackage{tikz} % For graph plots +\usepackage[super]{nth} \usepackage{caption} % Figures \usepackage{subcaption} % And Subfigures \usepackage{longtable} @@ -1077,10 +1078,8 @@ analysis can be found on the report repository at \include{Rcodes/simulation/netclustering_analyze} \chapter{Applications} -\include{Rcodes/real_data/application_dore_data} -% \include{Rcodes/real_data/presentation_dore} +\include{Rcodes/real_data/application_dore} \subsection{Completing raw data using CoOPLBM \parencite{anakokDisentanglingStructureEcological2022}} - \include{Rcodes/real_data/CoOPLBM_completion_analyze} \printbibliography diff --git a/references.bib b/references.bib index f017e93..9bf5420 100644 --- a/references.bib +++ b/references.bib @@ -261,6 +261,20 @@ keywords = {data,plant-pollinator} } +@book{ottawafield-naturalistsclubCanadianFieldnaturalist1976, + title = {The {{Canadian}} Field-Naturalist}, + author = {Ottawa Field-Naturalists' Club and Club, Ottawa Field-Naturalists'}, + date = {1976}, + volume = {90}, + pages = {1--568}, + publisher = {{Ottawa Field-Naturalists' Club}}, + location = {{Ottawa}}, + issn = {0008-3550}, + url = {https://www.biodiversitylibrary.org/item/89149}, + pagetotal = {568}, + file = {/home/polarolouis/Zotero/storage/DFN9BYBR/28045499.html} +} + @article{pavlopoulosBipartiteGraphsSystems2018, title = {Bipartite Graphs in Systems Biology and Medicine: A Survey of Methods and Applications}, shorttitle = {Bipartite Graphs in Systems Biology and Medicine}, @@ -380,3 +394,14 @@ keywords = {networks,site}, file = {/home/polarolouis/Zotero/storage/9WZE8QLQ/map.html} } + +@online{yumpu.comInsectPollinatorsMer, + title = {Insect Pollinators of the {{Mer Bleue}} Peat Bog of {{Ottawa}} - {{Biodiversity}} ...}, + author = {Yumpu.com}, + url = {https://www.yumpu.com/en/document/view/11762821/insect-pollinators-of-the-mer-bleue-peat-bog-of-ottawa-biodiversity-}, + urldate = {2023-08-06}, + abstract = {Insect pollinators of the Mer Bleue peat bog of Ottawa - Biodiversity ...}, + langid = {english}, + organization = {{yumpu.com}}, + file = {/home/polarolouis/Zotero/storage/DIXT2PYL/insect-pollinators-of-the-mer-bleue-peat-bog-of-ottawa-biodiversity-.html} +}