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###        Install all packages for 2018 QCBS R Symposium workshops          ####
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# Marie-Hélène Brice
# 03-05-2018


# Packages for Survival analyses with R by Julie Landes 

pkgs_survi <- c("survival", "eha", "icenReg", 
                "MLEcens", "interval", "lme4", "plyr", 
                "Rcpp", "tidyr", "lubridate", "ggplot2", 
                "ggfortify", "reshape2", "MASS", "zoo", 
                "ssym", "GIGrvg", "numDeriv", "normalp", 
                "Formula", "perm", "Rcpp", "coda")

# For Icens
source("https://bioconductor.org/biocLite.R") ## try http:// if https:// URLs are not supported
biocLite("Icens")

# Packages for Beta diversity in space and time by Vincent Fugère & Katrine Turgeon

pkgs_beta <- c("adklakedata",
               "RCurl",
               "vegan",
               "gclus",
               "RColorBrewer",
               "ade4",
               "adespatial",
               "dplyr",
               "tidyr",
               "magrittr",
               "ggplot2")

# Packages for Geospatial analysis and cartography with R by Marie-Hélène Brice

pkgs_spatial <- c("sf",
                  "lwgeom",
                  "dplyr",
                  "RColorBrewer",
                  "raster",
                  "mapview")

# Packages for Phylogenetic Comparative Methods in R by Pedro Henrique Pereira Braga

pkgs_PhyloCompMethods <- c("devtools", 
                           "ape", "phytools", "picante", "geiger",
                           "apTreeshape", "caper", "pez", "OUwie", "adephylo")

## try http:// if https:// URLs are not supported
# source("https://bioconductor.org/biocLite.R")
biocLite("ggtree")


# Packages for eDNA metabarcoding: From raw data to RDA by Alexis Carteron & Simon Morvan

# source('http://bioconductor.org/biocLite.R')
biocLite('phyloseq')
biocLite('dada2')
pkgs_eDNA <- c('ggplot2', 'vegan', 'gtools')

# All packages

pkgs <- c(pkgs_survi, pkgs_beta, pkgs_spatial, pkgs_eDNA, pkgs_PhyloCompMethods)

pkgs <- pkgs[!duplicated(pkgs)]


# Which packages you don't already have

new.pkg <- pkgs[!(pkgs %in% installed.packages()[, "Package"])]

# Install!

if (length(new.pkg)) {
  install.packages(new.pkg, dependencies = TRUE)
} 

update.packages()