SpaDES.core (version 1.0.9)

outputs: Simulation outputs

Description

Accessor functions for the outputs slots in a simList object.

Usage

outputs(sim)
# S4 method for simList
outputs(sim)
outputs(sim) <- value
# S4 method for simList
outputs(sim) <- value
outputArgs(sim)
# S4 method for simList
outputArgs(sim)
outputArgs(sim) <- value
# S4 method for simList
outputArgs(sim) <- value

outputs function or argument in <code>simInit</code>

outputs accepts a data.frame similar to the inputs data.frame, but with up to 6 columns.

objectName	required, character string indicating the name of the object in the simList that will be saved to disk (without the sim$ prefix).
file	optional, a character string indicating the file path to save to. The default is to concatenate objectName with the model timeunit and saveTime, separated by underscore, '_'. So a default filename would be "Fires_year1.rds".
fun	optional, a character string indicating the function to use to save that file. The default is saveRDS
package	optional character string indicating the package in which to find the fun);
saveTime	optional numeric, indicating when in simulation time the file should be saved. The default is the lowest priority at end(sim), i.e., at the very end.
arguments	is a list of lists of named arguments, one list for each fun. For example, if fun = "write.csv", arguments = list(row.names = TRUE) will pass the argument row.names = TRUE to write.csv If there is only one list, then it is assumed to apply to all files and will be recycled as per normal R rules of recycling for each fun.

See the modules vignette for more details (browseVignettes("SpaDES.core")).

Details

These functions are one of three mechanisms to add information about which output files to save.

1. As arguments to a simInit call. Specifically, inputs or outputs. See ?simInit.

2. With the outputs(simList) function call.

3. By adding a function called .inputObjects inside a module, which will be executed during the simInit call. This last way is the most "modular" way to create default data sets for your model.

See below for more details.

Examples

# NOT RUN {
#######################
# outputs
#######################

library(igraph) # for %>%
tmpdir <- file.path(tempdir(), "outputs") %>% checkPath(create = TRUE)
tmpFile <- file.path(tmpdir, "temp.rds")
tempObj <- 1:10

# Can add data.frame of outputs directly into simInit call
sim <- simInit(objects = c("tempObj"),
               outputs = data.frame(objectName = "tempObj"),
               paths = list(outputPath = tmpdir))
outputs(sim) # To see what will be saved, when, what filename
sim <- spades(sim)
outputs(sim) # To see that it was saved, when, what filename

# Also can add using assignment after a simList object has been made
sim <- simInit(objects = c("tempObj"), paths = list(outputPath = tmpdir))
outputs(sim) <- data.frame(objectName = "tempObj", saveTime = 1:10)
sim <- spades(sim)
outputs(sim) # To see that it was saved, when, what filename.

# can do highly variable saving
tempObj2 <- paste("val", 1:10)
df1 <- data.frame(col1 = tempObj, col2 = tempObj2)
sim <- simInit(objects = c("tempObj", "tempObj2", "df1"),
  paths = list(outputPath = tmpdir))
outputs(sim) = data.frame(
     objectName = c(rep("tempObj", 2), rep("tempObj2", 3), "df1"),
     saveTime = c(c(1,4), c(2,6,7), end(sim)),
     fun = c(rep("saveRDS", 5), "write.csv"),
     package = c(rep("base", 5), "utils"),
     stringsAsFactors = FALSE)
# since write.csv has a default of adding a column, x, with rownames, must add additional
#   argument for 6th row in data.frame (corresponding to the write.csv function)
outputArgs(sim)[[6]] <- list(row.names = FALSE)
sim <- spades(sim)
outputs(sim)

# read one back in just to test it all worked as planned
newObj <- read.csv(dir(tmpdir, pattern = "year10.csv", full.name = TRUE))
newObj

# using saving with SpaDES-aware methods
# To see current ones SpaDES can do
.saveFileExtensions()

library(raster)
if (require(rgdal)) {
  ras <- raster(ncol = 4, nrow = 5)
  ras[] <- 1:20

  sim <- simInit(objects = c("ras"), paths = list(outputPath = tmpdir))
  outputs(sim) = data.frame(
    file = "test",
    fun = "writeRaster",
    package = "raster",
    objectName = "ras",
    stringsAsFactors = FALSE)

  outputArgs(sim)[[1]] <- list(format = "GTiff") # see ?raster::writeFormats
  simOut <- spades(sim)
  outputs(simOut)
  newRas <- raster(dir(tmpdir, full.name = TRUE, pattern = ".tif")[1])
  all.equal(newRas, ras) # Should be TRUE
}
# Clean up after
unlink(tmpdir, recursive = TRUE)
# }