install.packages("devtools")

## if any of the below fails, just go with the CRAN version via 
## install.packages()

## First restart R (Ctrl + Shift + F10 on Windows or CMD + Shift + F10 on Mac)

remotes::install_github("r-lib/rlang")
devtools::install_github("hadley/tidyverse")
devtools::install_github("r-lib/devtools")

## Again, restart R (Ctrl + Shift + F10 on Windows or CMD + Shift + F10 on Mac)

remotes::install_github("r-lib/remotes")
devtools::install_github("r-lib/usethis")
devtools::install_github("ropenscilabs/available")

## Restart R (Ctrl + Shift + F10 on Windows or CMD + Shift + F10 on Mac)

devtools::install_github("r-lib/testthat")
devtools::install_github("r-lib/pkgdown")
devtools::install_github("klutometis/roxygen")
devtools::install_github("r-lib/roxygen2", force = TRUE)
remotes::install_github('rstudio/rmarkdown')
devtools::install_github("r-lib/usethis")

## Restart R (Ctrl + Shift + F10 on Windows or CMD + Shift + F10 on Mac)

devtools::install_github("mangothecat/goodpractice")
devtools::install_github("ropensci/codemetar")
devtools::install_github("ropensci/spelling")

## Restart R (Ctrl + Shift + F10 on Windows or CMD + Shift + F10 on Mac)

devtools::install_github("geomorphR/geomorph", ref = "Stable")
devtools::install_github("liamrevell/phytools")
devtools::install_github("mwpennell/geiger-v2")
devtools::install_github("MomX/Momocs")
devtools::install_github("ropensci/workloopR", force = TRUE)

## Restart R (Ctrl + Shift + F10 on Windows or CMD + Shift + F10 on Mac)

devtools::install_github("mjskay/tidybayes")
devtools::install_github("easystats/easystats")
remotes::install_github("mlr-org/mlr")
remotes::install_github("mlr-org/mlr3")
devtools::install_github('topepo/caret/pkg/caret')

## Restart R (Ctrl + Shift + F10 on Windows or CMD + Shift + F10 on Mac)

devtools::install_github("tidymodels/tidymodels")

## Restart R (Ctrl + Shift + F10 on Windows or CMD + Shift + F10 on Mac)

remotes::install_github("ropensci/beautier", dependencies = TRUE)
remotes::install_github("ropensci/tracerer", dependencies = TRUE)
remotes::install_github("ropensci/beastier", dependencies = TRUE)
remotes::install_github("ropensci/mauricer", dependencies = TRUE)
remotes::install_github("ropensci/babette", dependencies = TRUE)

## Restart R (Ctrl + Shift + F10 on Windows or CMD + Shift + F10 on Mac)

beastier::install_beast2()
beastier:::is_beast2_installed()

## Restart R (Ctrl + Shift + F10 on Windows or CMD + Shift + F10 on Mac)

devtools::install_github("thierrymoudiki/crossval")

## Restart R (Ctrl + Shift + F10 on Windows or CMD + Shift + F10 on Mac)

## Get the rest from CRAN (if not already installed)
packages=c(
  "tidyverse", #munging
  "plyr",
  "dplyr",
  "reshape",
  "reshape2",
  "magrittr",
  "abind",
  "forcats",
  "class",
  "xlsx",
  "ggplot2", #plotting
  "ggridges",
  "ggmcmc",
  "gghighlight",
  "cowplot",
  "patchwork",
  "lattice",
  "leaflet",
  "viridis", #colors
  "RColorBrewer",
  "ape", #phylo
  "geiger",
  "phytools",
  "castor",
  "geomorph",
  "Momocs",
  "dendextend",
  "convevol",
  "sensiPhy",
  "caper",
  'evolqg',
  'RRphylo',
  'phangorn',
  'distory',
  'PhylogeneticEM',
  "ouch",
  #'surface', ## removed from CRAN, get this one from the archive
  'MCMCglmm', #models
  "tidymodels",
  'hglm',
  'AGHmatrix',
  "MuMIn",
  "rstan", 
  "rstanarm", 
  "brms", 
  "shinystan", 
  "bayesplot", 
  "rstantools",
  "loo",
  "lsmeans",
  "emmeans",
  "tidybayes",
  "mcmcse",
  "sjstats",
  "nFactors",
  "fANCOVA",
  "spatstat",
  "caret",
  "mda",
  "crossval",
  "glmulti",
  "spatialEco",
  "nimble",
  "cluster", #patterns
  "splitstackshape",
  "boot", #parallel-processing
  "snow",
  "snowfall",
  "pracma", #math&shapes
  "rgl",
  "alphashape3d",
  "ptinpoly",
  "sp",
  "Hmisc", #other
  "goodpractice",
  "codemetar",
  "pkgdown",
  "spelling"
)
## Load or install&load all
package.check<-lapply(packages,FUN=function(x){   #apply to the list of packages
  if(!require(x,character.only=TRUE)){            #if any is not installed
    install.packages(x,dependencies=TRUE)         #install it
    library(x,character.only=TRUE)                #otherwise load it
  }
})
## verify they are loaded
search()

## for surface:
# install.packages("Y:/Dropbox/downloads/r-packages/surface_0.4.tar.gz", 
#                  repos = NULL, type = "source")


##### H2Oai #####
## Taken from: https://h2o-release.s3.amazonaws.com/h2o/rel-yu/1/index.html 
# The following two commands remove any previously installed H2O packages for R.
if ("package:h2o" %in% search()) { detach("package:h2o", unload=TRUE) }
if ("h2o" %in% rownames(installed.packages())) { remove.packages("h2o") }

# Next, we download packages that H2O depends on.
pkgs <- c("RCurl","jsonlite")
for (pkg in pkgs) {
  if (! (pkg %in% rownames(installed.packages()))) { install.packages(pkg) }
}

# Now we download, install and initialize the H2O package for R.
install.packages("h2o", type="source", 
                 repos="https://h2o-release.s3.amazonaws.com/h2o/rel-yu/1/R")

# Finally, let's load H2O and start up an H2O cluster
library(h2o)
h2o.init()