Rekyt

---
title: "Workflow for Reproductible Analysis"
author: "Matthias Grenié"
date: "8 mars 2017"
output: word_document
---

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

Rekyt

library(ggtree)

set.seed(2017-05-19)

my_tree = rtree(50)

clade_df = data.frame(node = c(52, 71, 80, 94),
                          clade = paste0("clade_", 1:4),
                          color = rep(c("#000000", "#AAAAAA"), size = 4))

Rekyt

library(ade4)
library(dplyr)

n_species = 7000

trait_df = data.frame(
    c_tr1 = rnorm(n_species),
    c_tr2 = rnorm(n_species),
    c_tr3 = rnorm(n_species),
    c_tr4 = rnorm(n_species),

Rekyt

# Text analysis of Proust

library(proustr)
library(tidytext)
library(dplyr)
library(stringr)

proust_words = proust_books() %>%
    group_by(book) %>%
    mutate(linenumber = row_number(),

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)
    

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

---
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: "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

#' 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             : "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         : "frederik.aust@uni-koeln.de"