# Uninstall and reinstall developer branch from GitHub

# 1. If rCTM is already installed, uninstall rCTM
if ("rCTM" %in% installed.packages()) {
  remove.packages('rCTM')
}

# 2. If rCTM is loaded and in the memory, forget rCTM
if ("rCTM" %in% (.packages())){
  detach("package:rCTM", unload=TRUE) 
}

# 3a. If devtools is not already installed, install it
if (! ("devtools" %in% installed.packages())) {
  install.packages('devtools')
}

# 3. Install package from developer branch of GitHub
devtools::install_github("https://github.com/tilbud/rCTM/tree/JimH-dev")

# 4. Load most current version in the memory
library(rCTM)

# Check and install dependencies

# A column vector listing the packages needed
dependencies <- c("tidyverse", 
                  "gganimate", 
                  "gifski",
                  "png")

# Iterate through the necessary packages
for (i in 1:length(dependencies)) {
  print(paste(dependencies[i], " ...", sep=""))
  # If the package is not in the installed package ...
  if (! (dependencies[i] %in% installed.packages())) {
    # .. install it.
    install.packages(dependencies[i])
  } else {
    print("... already installed.")
  }
}

# Run rMEM with Cohorts example
memCohortExample <- runMemWithCohorts(startYear=2015, relSeaLevelRiseInit=0.3, relSeaLevelRiseTotal=100,
                                      initElv=21.9, meanSeaLevel=7.4, meanHighWater=16.9, meanHighHighWater=25.4, meanHighHighWaterSpring=31.2, 
                                      suspendedSediment=3e-05, lunarNodalAmp=2.5, bMax=0.25, 
                                      zVegMin=-24.7, zVegMax=44.4, zVegPeak=22.1,
                                      plantElevationType="orthometric", rootToShoot=2,
                                      rootTurnover=0.5, rootDepthMax=30, omDecayRate=0.8,
                                      recalcitrantFrac=0.2, settlingVelocity=2.8,
                                      coreYear = 2050)

# look at the structure of the function output
str(memCohortExample)

# Look at the three tables making up the output
head(memCohortExample$annualTimeSteps)
head(memCohortExample$cohorts)
head(memCohortExample$core)

# run the animate cohorts function
# This will take a few minutes to run and then save an animation of accumulating cohorts
animateCohorts(cohorts=memCohortExample$cohorts,
               scenario=memCohortExample$annualTimeSteps,
               filename="MEM-Try_191212.gif")