This is particularly useful to build plots using the tidyverse, e.g., ggplot2.

# S3 method for simLists
as.data.table(x, vals, objectsFromSim = NULL, objectsFromOutputs = NULL, ...)

Arguments

x An R object. A (named) list of object names to extract from each simList, or a named list of quoted expressions to calculate for each simList, or a mix of character and quoted expressions. Character vector of objects to extract from the simLists. If omitted, it will extract all objects from each simList in order to calculate the vals. This may have a computational cost. If NA, then no objects will be accessed from the simList. Objects identified here will only be as they are in the simList, i.e., at end(sim). List of (named) character vectors of objects to load from the outputs(sim) prior to evaluating vals. If there already is an object with that same name in the simList, then it will be overwritten with the object loaded from outputs(sim). If there are many objects with the same name, specifically from several saveTime values in the outputs(sim), these will all be loaded, one at a time, vals evaluated one at a time, and each of the values will be returned from each saveTime. A column, saveTime, will be part of the returned data.table. For cases where more than one object is required at a given saveTime, all should be identified here, without time specified. This function will take all identified objects from the same time period. Additional arguments. Currently unused.

See examples.

Examples


if (FALSE) {
tmpdir <- file.path(tempdir(), "examples")
# Make 3 simLists -- set up scenarios
endTime <- 2

# Example of changing parameter values
# Make 3 simLists with some differences between them
mySim <- lapply(c(10, 20, 30), function(nFires) {
simInit(
times = list(start = 0.0, end = endTime, timeunit = "year"),
params = list(
.globals = list(stackName = "landscape", burnStats = "nPixelsBurned"),
# Turn off interactive plotting
caribouMovement = list(.plotInitialTime = NA),
randomLandscapes = list(.plotInitialTime = NA, .useCache = "init")
),
paths = list(modulePath = system.file("sampleModules", package = "SpaDES.core"),
outputPath = tmpdir),
# Save final state of landscape and caribou
outputs = data.frame(
objectName = c(rep("landscape", endTime), "caribou", "caribou"),
saveTimes = c(seq_len(endTime), unique(c(ceiling(endTime / 2), endTime))),
stringsAsFactors = FALSE
)
)
})

planTypes <- c("sequential") # try others! ?future::plan
sims <- experiment2(sim1 = mySim[[1]], sim2 = mySim[[2]], sim3 = mySim[[3]],
replicates = 3)

# Try pulling out values from simulation experiments
# 2 variables
df1 <- as.data.table(sims, vals = c("nPixelsBurned", NCaribou = quote(length(caribou$x1)))) # Now use objects that were saved to disk at different times during spades call df1 <- as.data.table(sims, vals = c("nPixelsBurned", NCaribou = quote(length(caribou$x1))),
objectsFromOutputs = list(nPixelsBurned = NA, NCaribou = "caribou"))

# now calculate 4 different values, some from data saved at different times
# Define new function -- this calculates perimeter to area ratio
fn <- quote({
landscape$Fires[landscape$Fires[] == 0] <- NA;
a <- boundaries(landscape$Fires, type = "inner"); a[landscape$Fires[] > 0 & a[] == 1] <- landscape$Fires[landscape$Fires[] > 0 & a[] == 1];
peri <- table(a[]);
area <- table(landscape$Fires[]); keep <- match(names(area),names(peri)); mean(peri[keep]/area) }) df1 <- as.data.table(sims, vals = c("nPixelsBurned", perimToArea = fn, meanFireSize = quote(mean(table(landscape$Fires[])[-1])),
caribouPerHaFire = quote({
NROW(caribou) /
mean(table(landscape$Fires[])[-1]) })), objectsFromOutputs = list(NA, c("landscape"), c("landscape"), c("landscape", "caribou")), objectsFromSim = "nPixelsBurned") if (interactive()) { # with an unevaluated string library(ggplot2) p <- lapply(unique(df1$vals), function(var) {
ggplot(df1[vals == var,],
aes(x = saveTime, y = value, group = simList, color = simList)) +
stat_summary(geom = "point", fun.y = mean) +
stat_summary(geom = "line", fun.y = mean) +
stat_summary(geom = "errorbar", fun.data = mean_se, width = 0.2) +
ylab(var)
})

# Arrange all 4 -- could use gridExtra::grid.arrange -- easier
pushViewport(viewport(layout = grid.layout(2, 2)))
vplayout <- function(x, y) viewport(layout.pos.row = x, layout.pos.col = y)
print(p[[1]], vp = vplayout(1, 1))
print(p[[2]], vp = vplayout(1, 2))
print(p[[3]], vp = vplayout(2, 1))
print(p[[4]], vp = vplayout(2, 2))
}
}