Rekyt

#' Extinction probablity based on IUCN status
#' 
#' This function returns an extinction probability based on a IUCN Red List
#' status. The extinction probability it returns is based on the EDGE2 metric as
#' defined by Gumbs et al. (2023) <doi:10.1371/journal.pbio.3001991>.
#' In particular, it returns the Global Endangerment 2 score (GE2).
#' See their Figure 1, Supplementary Info S1 for more information and the
#' underlying data with data sheet S4.
#' 
#' The idea is that each IUCN status is associated with a median extinction risk

Rekyt

list(traits = structure(c(0.0672472331207246, 0.795684163691476, 
0.997313872678205, 0.542126356624067, 0.266995168523863, 0.954949954524636, 
0.108523507369682, 0.249139602528885, 0.588747339788824, 0.900564769050106, 
0.0302994444500655, 0.407474847277626, 0.1075431893114, 0.733778670197353, 
0.133502611424774, 0.103931269142777, 0.238055266439915, 0.819211864378303, 
0.349372869357467, 0.661441418575123, 0.415594322374091, 0.894165905192494, 
0.59261961793527, 0.74796782550402, 0.319392101606354, 0.40641696867533, 
0.817589435493574, 0.207942749606445, 0.0987115791067481, 0.443528626346961, 
0.24516011425294, 0.174178527202457, 0.439530419418588, 0.36717617767863, 
0.570931863738224, 0.38591324724257, 0.89054117561318, 0.821960192639381, 

Rekyt

{
  "idiv-computer": {
    "auto_append_newline": true,
    "default_encoding": "UTF-8",
    "doc_outline_show": "sections_and_chunks",
    "document_author": "Matthias Grenié and Hugo Gruson",
    "editor_theme": "Monokai",
    "font_size_points": 12,
    "graphics_antialiasing": "subpixel",
    "highlight_r_function_calls": true,

Rekyt

# remotes::install_github("ropensci/solrium")
library(solrium)
(cli <- SolrClient$new(host = "api.archives-ouvertes.fr", path = "search",
                       port = NULL))

# Get all fields back
cli$search(params = list(q = "tomate", wt = "xml", fl="*"))

Rekyt

---
title             : "How to use papaja: An Example Manuscript Including Basic Instructions"
shorttitle        : "How to use papaja"

author:
  - name          : "Frederik Aust"
    affiliation   : "1"
    corresponding : yes    # Define only one corresponding author
    address       : "Department Psychology, University of Cologne, Herbert-Lewin-Str. 2, 50931 Köln, Germany"
    email         : "[email protected]"

Rekyt

#' Plot network of package dependencies
#'
#' @param pkg package description, can be path or package name.
#' See \code{\link[devtools]{as.package}} for more information.
#' @param type which packages should be included in the network
#'
#' @details The resulting plot visualizes the network of package dependencies.
#'    If you are trying to cut down on package dependencies look for big red
#'    dots that represent a lot of upstream but few downstream  dependencies.
#' @import ggplot2

Rekyt

---
title: "Phylogeny with traits in branches and clade labels"
author: "Matthias Grenié"
date: /today
output: pdf_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

Rekyt

---
title: "Prettier SFÉcologie 2018 Program"
author: "Matthias Grenié"
date: "17 octobre 2018"
header-includes:
    - \usepackage{booktabs}
    - \usepackage{longtable}
    - \usepackage{array}
    - \usepackage{multirow}
    - \usepackage[table]{xcolor}

Rekyt

---
title: "Adding arrows to PCoA"
author: "Matthias Grenié"
date: "26 septembre 2018"
output: pdf_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

Rekyt

# Function to add number ontop of geom_boxplot
library(ggplot2)
library(dplyr)

# /!\ Need to manually change the "groups" if ks_test included
add_groups_and_number = function(given_plot, ks_tests) {
    y_range = ggplot_build(given_plot)$layout$panel_params[[1]]$y.range
    
    y_upper = max(y_range)