Run_Example_AB.Rmd

---
title: "Running Biomass_core with a sample study area in Alberta, Canada"
author: "Eliot McIntire <eliotmcintire@gmail.com>"
date: "`r format(Sys.time(), '%d %B %Y')`"
editor_options:
  chunk_output_type: console
---

## Get the module

See [SpaDES-modules repository](https://github.com/PredictiveEcology/SpaDES-modules) to see how to download this and other SpaDES modules.

# Usage example

```{r setup}
workshopPath = "~/SpaDESWorkshop"
modulePath = file.path(workshopPath, "modules")
modulePath = "~/GitHub"
options(spades.modulePath = modulePath,
        reproducible.inputPaths = file.path(workshopPath, "cachedData"))
if (!require("Require")) {install.packages("Require"); library(Require)}
Require("SpaDES.core")
setPaths(modulePath = modulePath)

# Pick a study area



# Pick 5 species of tree
sppEquiv <- LandR::sppEquivalencies_CA
sppEquiv <- sppEquiv[Boreal %in% c("Pice_Gla", "Pice_Mar", "Pinu_Ban", "Pinu_Con", "Popu_Tre")]
```

## Using Landis txt files

This module is a port of the Landis II Biomass Extension to R.
It can use the Landis txt files as inputs. 
```{r LandisFiles}

out <- prepInputsMainInput()
LandisDefaultsURL <-
"https://raw.githubusercontent.com/LANDIS-II-Foundation/Extensions-Succession/master/biomass-succession-archive/trunk/tests/v6.0-2.0/biomass-succession_test.txt"
LandisFile <- "LandisParams.txt"
download.file(LandisDefaultsURL, destfile = LandisFile)
vals <- readLines(LandisFile)
file.edit(LandisFile)

parameters <- list(
  successionTimestep = as.integer(strsplit(grep("Timestep", vals, value = TRUE), "  ")[[1]][2])
)

```

## Setup simulation

```{r module usage example}

times <- list(start = 0, end = 1)

## Usage example
modules <- as.list(moduleName)
objects <- list()
paths <- getPaths()

successionTimestep <- 1L

## keep default values for most parameters
## (ommitted from this list)
parameters <- list(
  Biomass_core = list(
    ".plotInitialTime" = times$start
    , "sppEquivCol" = "Boreal"
    , "successionTimestep" = successionTimestep*10
    , ".saveInitialTime" = 1
    , ".useCache" = FALSE
    , ".useParallel" = FALSE
    , ".studyAreaName" = "RandomAB"
  )
)

mySim <- simInit(times = times, params = parameters, modules = modules, objects = objects, paths = paths)
mySimOut <- spades(mySim, debug = TRUE)
```