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###        Install all packages for 2019 QCBS R Symposium workshops          ####
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#### Workshop 1: Basics of effective and reproducible data visualization ####
# setwd("")
#
# Download: https://rstudio.com/wp-content/uploads/2015/03/ggplot2-cheatsheet.pdf

#####Install packages and libraries #####
# install packages that are not already installed
if (!require(datasets)) install.packages('datasets')
if (!require(ggplot2)) install.packages('ggplot2')
if (!require(plyr)) install.packages('plyr')
if (!require(ggpubr)) install.packages('ggpubr')

# potential errors for non windows users with these (non-essential)
if (!require(rvg)) install.packages('rvg')
if (!require(svglite)) install.packages('svglite')
if (!require(officer)) install.packages('officer')
if (!require(extrafont)) install.packages('extrafont')

library(ggplot2)
library(datasets)
library(plyr)
library(ggpubr)

# Installation for Windows only, not essential
library(rvg) 
library(svglite)
library(officer)
library(extrafont)


#### Workshop 2: Community Phylogenetics in R ####

# Check for needed packages, and install the missing ones
required.libraries <- c("ape", "picante", 
                        "pez", "phytools",
                        "vegan", "adephylo", 
                        "phylobase", "geiger", 
                        "mvMORPH", "OUwie", 
                        "hisse", "BAMMtools",
                        "phylosignal", "Biostrings",
                        "devtools","ggplot2", 
                        "kableExtra", "betapart", "gridExtra",
                        "reshape2")

needed.libraries <- required.libraries[!(required.libraries %in% installed.packages()[,"Package"])]
if(length(needed.libraries)) install.packages(needed.libraries)

# Load all required libraries at once
lapply(required.libraries, require, character.only = TRUE)

# Download files from Marc Cadotte's and Jonathan Davies' book 
# "Phylogenies in Ecology: A guide to concepts and methods":

dir.create("data/Jasper")
download.file("https://raw.githubusercontent.com/pedrohbraga/CommunityPhylogenetics-Workshop/master/data/Jasper/jasper_data.csv?token=ACBTNPKQWOFPQW7UT6Z7RCS5UDUMK", 
              "data/Jasper/jasper_data.csv")
download.file("https://raw.githubusercontent.com/pedrohbraga/CommunityPhylogenetics-Workshop/master/data/Jasper/jasper_tree.phy?token=ACBTNPNS2F5ZYYXLCMGMVCS5UDURO", 
              "data/Jasper/jasper_tree.phy")

Workshop HTML Markdown Page: https://pedrohbraga.github.io/CommunityPhylogenetics-Workshop/CommunityPhylogenetics-Workshop.html

#### Workshop 3: Mining species-level biodiversity information from published literature ####

Presentation: https://docs.google.com/presentation/d/1vUt8GdHCS9j3d_VEn-ftYsdayRgkzFIYKMSEGutoEVQ/edit
Examples: https://drive.google.com/open?id=1CNIIWZFXsTLdaL5f82hZX7R_4T-n1Prc
Exercise 1: https://drive.google.com/file/d/1Sp_4oaXPpZvAsC1ymA_aKJxPoWF6KuFX/view?usp=sharing
Exercise 2: https://drive.google.com/file/d/1o32RbKgGjaP6MFtc4UZnilt7-F0uMElL/view?usp=sharing

#### Workshop 4: Touchdown your research! ####

Presentation: https://insileco.github.io/ResearchDown/#1
Requirements: https://github.com/inSileco/ResearchDown#requirements

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