inputs: Inputs and outputs

Description

These functions are one of two mechanisms to add the information about which input files to load in a spades call and the information about which output files to save. The other way is to pass them as arguments to a simInit call.

inputArgs and outputArgs are ways to specify any arguments that are needed for file loading and file saving. This is still somewhat experimental.

Usage

inputs(object)
# S4 method for .simList
inputs(object)
inputs(object) <- value
# S4 method for .simList
inputs(object) <- value
outputs(object)
# S4 method for .simList
outputs(object)
outputs(object) <- value
# S4 method for .simList
outputs(object) <- value
inputArgs(object)
# S4 method for .simList
inputArgs(object)
inputArgs(object) <- value
# S4 method for .simList
inputArgs(object) <- value
outputArgs(object)
# S4 method for .simList
outputArgs(object)
outputArgs(object) <- value
# S4 method for .simList
outputArgs(object) <- value

Arguments

object

A simList simulation object.

value

The object to be stored at the slot. See Details.

Value

Returns or sets the value(s) of the input or output slots in the simList object.

inputs

inputs accepts a data.frame, with up to 7 columns. Columns are:

`file`	required, a character string indicating the file path. There is no default.
`objectName`	optional, character string indicating the name of the object that the loaded file will be assigned to in the `simList`. This object can therefore be accessed with `sim$xxx` in any module, where `objectName = "xxx"`. Defaults to the filename without file extension or directory information.
`fun`	optional, a character string indicating the function to use to load that file. Defaults to the known extentions in `SpaDES` (found by examining `.fileExtensions()`). The `package` and `fun` can be jointly specified here as `"packageName::functionName"`, e.g., `"raster::raster"`.
`package`	optional character string indicating the package in which to find the `fun`);
`loadTime`	optional numeric, indicating when in simulation time the file should be loaded. The default is the highest priority at `start(sim)`, i.e., at the very start.
`interval`	optional numeric, indicating at what interval should this same exact file be reloaded from disk, e.g,. 10 would mean every 10 time units. The default is NA or no interval, i.e, load the file only once as described in `loadTime`
`arguments`	is a list of lists of named arguments, one list for each `fun`. For example, if `fun="raster"`, `arguments = list(native = TRUE)` will pass the argument "native = TRUE" to raster. 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`.

Currently, only file is required. All others will be filled with defaults if not specified.

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

outputs

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")).

Details

Accessor functions for the inputs and outputs slots in a simList object.

Examples

Run this code

# NOT RUN {
#######################
# inputs
#######################

# Start with a basic empty simList
sim <- simInit()

test <- 1:10
library(igraph) # for %>%
tmpdir <- file.path(tempdir(), "inputs") %>% checkPath(create = TRUE)
tmpFile <- file.path(tmpdir, "test.rds")
saveRDS(test, file = tmpFile)
inputs(sim) <- data.frame(file = tmpFile) # using only required column, "file"
inputs(sim) # see that it is not yet loaded, but when it is scheduled to be loaded
simOut <- spades(sim)
inputs(simOut) # confirm it was loaded
simOut$test

# can put data.frame for inputs directly inside simInit call
allTifs <- dir(system.file("maps", package = "SpaDES"),
               full.names = TRUE, pattern = "tif")

# next: objectNames are taken from the filenames (without the extension)
# This will load all 5 tifs in the SpaDES sample directory, using
#   the raster fuction in the raster package, all at time = 0
if (require("rgdal", quietly = TRUE)) {
  sim <- simInit(
    inputs = data.frame(
      files = allTifs,
      functions = "raster",
      package = "raster",
      loadTime = 0,
      stringsAsFactors = FALSE)
    )

  ##############################
  #A fully described inputs object, including arguments:
  files <- dir(system.file("maps", package = "SpaDES"),
               full.names = TRUE, pattern = "tif")
  # arguments must be a list of lists. This may require I() to keep it as a list
  #   once it gets coerced into the data.frame.
  arguments = I(rep(list(native = TRUE), length(files)))
  filelist = data.frame(
     objectName = paste0("Maps", 1:5),
     files = files,
     functions = "raster::raster",
     arguments = arguments,
     loadTime = 0,
     intervals = c(rep(NA, length(files) - 1), 10)
  )
  inputs(sim) <- filelist
  spades(sim)
}


# Clean up after
unlink(tmpdir, recursive = TRUE)

#######################
# 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="second10.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"))
  all.equal(newRas, ras) # Should be TRUE
}
# Clean up after
unlink(tmpdir, recursive = TRUE)
# }

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