index.Rmd

--- 
title: "User's guide for Ecofog's Ecophysiology Lab"
author: "Marion Boisseaux, Tristan Lafont Rapnouil and hopefully many other people"
date: "`r Sys.Date()`"
url: https://GitHubID.github.io/Repository/
github-repo: GitHubID/Repository
description: ""
cover-image: "images/cover.svg"
# Title page...
maintitlepage:
  epigraph: |
    This document is reproducible thanks to:
    \begin{itemize}
      \item \LaTeX and its class memoir (\url{http://www.ctan.org/pkg/memoir}).
      \item R (\url{http://www.r-project.org/}) and RStudio (\url{http://www.rstudio.com/})
      \item bookdown (\url{http://bookdown.org/}) and memoiR (\url{https://ericmarcon.github.io/memoiR/})
    \end{itemize}
  credits: |
    Name of the owner of the logo
    
    \url{http://www.company.com}
    
    An explanatory sentence.
    Leave an empty line for line breaks.
# ... or a PDF cover
pdftitlepage: images/cover.pdf
# Language
lang: en-US
otherlangs: [fr-FR,it]
# LaTeX
documentclass: memoir
classoption:
  - extrafontsizes
  - onecolumn
  - openright
# Paper, font
papersize: A4
fontsize: 12pt
# Fonts installed by a package. LaTeX tex-gyre package must be installed for:
# mainfont: texgyretermes          # Times New Roman for the text
mainfontoptions:
  - Extension=.otf
  - UprightFont=*-regular
  - BoldFont=*-bold
  - BoldItalicFont=*-bolditalic
# mathfont: texgyretermes-math.otf # Times New Roman for equations
# memoir Style
MemoirChapStyle: daleif1           # or companion with large margins
MemoirPageStyle: Ruled             # or companion with large margins
# Margins
largemargins: false                # or true for large margins
smallmargin: 1.5in                 # outer margin (small).
largemargin: 3in                   # outer margin (large)
marginnote:  1.8in                 # note width in large margin
spinemargin: 1.5in                 # spine margin. Reduce to 1.2 with large margins.
uppermargin: 1.5in                 # upper margin
lowermargin: 1in                   # lower margin
# Table of contents
toc-depth: 2
# Section numbering
secnum-depth: section
# List of tables / Figures
lot: false
lof: true
# Bibliography
bibliography: references.bib
biblatexoptions:
  - backend=biber
  - style=authoryear-ibid  # or verbose-inote with large margins
# - pageref=true           # uncomment for verbose-inotes style
  - isbn=false
  - backref=true
  - giveninits=true
  - uniquename=init
  - maxcitenames=2
  - maxbibnames=150
  - sorting=nyt
  - sortcites=false
# Chapter summary text
chaptersummary: In a Nutshell
# Back Cover
backcover:
  - language: english
    abstract: |
      English abstract, on the last page.
  
      This is the user's guide of EcoFoG's ecophysiology lab
    keywords:
      - Keyword in English
      - As a list
    abstractlabel: Abstract
    keywordlabel: Keywords
backcoverfontsize: normalsize
# Figure cropping may be set to no if ghostscript is not installed
fig_crop: true
# Do not modify
site: bookdown::bookdown_site
always_allow_html: true
graphics: true
link-citations: true
colorlinks: true
---

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<img src="images/trombone.png" alt="image" hidden/>

```{r DoNotModify, include=FALSE}
### Utilities. Do not modify.
# Installation of packages if necessary
InstallPackages <- function(Packages) {
  InstallPackage <- function(Package) {
    if (!Package %in% installed.packages()[, 1]) {
      install.packages(Package, repos="https://cran.rstudio.com/")
    }
  }
  invisible(sapply(Packages, InstallPackage))
}

# Basic packages
InstallPackages(c("bookdown", "formatR", "kableExtra", "magick", "ragg"))

# kableExtra must be loaded 
if (knitr::opts_knit$get("rmarkdown.pandoc.to") == "docx") {
  # Word output (https://stackoverflow.com/questions/35144130/in-knitr-how-can-i-test-for-if-the-output-will-be-pdf-or-word)
  # Do not use autoformat (https://github.com/haozhu233/kableExtra/issues/308)
  options(kableExtra.auto_format = FALSE)
}
library("kableExtra")

# Chunk font size hook: allows size='small' or any valid Latex font size in chunk options
def.chunk.hook  <- knitr::knit_hooks$get("chunk")
knitr::knit_hooks$set(chunk = function(x, options) {
  x <- def.chunk.hook(x, options)
  ifelse(options$size != "normalsize", paste0("\n \\", options$size,"\n\n", x, "\n\n \\normalsize"), x)
})

# Figures with side captions
if (rmarkdown::metadata$largemargins)
  knitr::opts_chunk$set(fig.env='SCfigure')
```

```{r Options, include=FALSE}
### Customized options for this document
# Add necessary packages here
Packages <- c( "tidyverse")
# Install them
InstallPackages(Packages)
# Create packages.bib file to reference them as @R-package
knitr::write_bib(Packages, file="packages.bib")

# knitr options
knitr::opts_chunk$set(
  cache=FALSE, # Cache chunk results
  echo = TRUE, # Show/Hide R chunks
  warning=FALSE, # Show/Hide warnings
  # Figure alignment and size
  fig.align='center', out.width='80%', fig.asp=.75,
  # Graphic devices (ragg_png is better than standard png)
  dev = c("ragg_png", "pdf"),
  # Code chunk format
  tidy=TRUE, tidy.opts=list(blank=FALSE, width.cutoff=60),
  size="scriptsize", knitr.graphics.auto_pdf = TRUE
  )
options(width=60)

# ggplot style
library("tidyverse")
theme_set(theme_bw())
theme_update(panel.background=element_rect(fill="transparent", colour=NA),
             plot.background=element_rect(fill="transparent", colour=NA))
knitr::opts_chunk$set(dev.args=list(bg="transparent"))

# Random seed
set.seed(973)
```

# Introduction {#intro}


Plant functional traits are the features (morphological, physiological, phenological) that represent ecological strategies and determine *describe?* how plants respond to environmental factors, affect other trophic levels and influence ecosystem properties. 
Variation in plant functional traits, and trait syndromes, has proven useful for tackling many important ecological questions at a range of scales, giving rise to a demand for standardized ways to measure ecologically meaningful plant traits. 
The importance of these topics dictates the urgent need for more and better data, and increases the value of standardized protocols for quantifying trait variation of different species, in particular for traits with power to predict plant- and ecosystem-level processes, and for traits that can be measured relatively easily (Pérez-Harguindeguy et al., 2013)

This handbook presents the different protocols used in EcoFoG's ecophysio lab.
We therefore suggest the methodological principles for a more open and transparent science.
This handbook not only includes updated methods for the trait measurements, but also includes the excel worksheets for data collection and links toward detailed tutorial or user's guide for all methods used in this lab.
This handbook will be associated with an R package [EcophyCofog][EcophyCofog Package] containing some useful homemade functions to deal with some devices output. 

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\mainmatter