Accessor functions for the outputs slots in a simList object.
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) <- valueA simList object from which to extract element(s) or
in which to replace element(s).
The object to be stored at the slot. See Details.
These functions are one of three mechanisms to add information about which output files to save.
As arguments to a simInit call. Specifically, inputs or outputs.
See ?simInit.
With the outputs(simList) function call.
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.
The automatic file type handling only adds the correct extension from a given
fun and package. It does not do the inverse, from a given extension find the
correct fun and package.
simInitoutputs 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")).
#######################
# 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))
#> Setting:
#> options(
#> spades.outputPath = '/tmp/RtmpAzfvD1/outputs'
#> )
#> Paths set to:
#> options(
#> rasterTmpDir = '/tmp/RtmpAzfvD1/SpaDES/scratch/raster'
#> reproducible.cachePath = '/tmp/RtmpAzfvD1/myProject/cache'
#> spades.inputPath = '/tmp/RtmpAzfvD1/myProject/inputs'
#> spades.outputPath = '/tmp/RtmpAzfvD1/outputs'
#> spades.modulePath = '/tmp/RtmpAzfvD1/myProject/modules'
#> spades.scratchPath = '/tmp/RtmpAzfvD1/SpaDES/scratch'
#> )
#> terra::terraOptions(tempdir = '/tmp/RtmpAzfvD1/SpaDES/scratch/terra'
#> Using setDTthreads(1). To change: 'options(spades.DTthreads = X)'.
outputs(sim) # To see what will be saved, when, what filename
#> objectName file fun package
#> 1 tempObj /tmp/RtmpAzfvD1/outputs/tempObj_year10.rds saveRDS base
#> saveTime saved arguments
#> 1 10 NA NA
sim <- spades(sim)
#> Aug19 19:59:30 Using setDTthreads(1). To change: 'options(spades.DTthreads = X)'.
#> Aug19 19:59:30 chckpn total elpsd: 0.00096 secs | 0 checkpoint init 0
#> Aug19 19:59:30 save total elpsd: 0.0026 secs | 0 save init 0
#> Aug19 19:59:30 prgrss total elpsd: 0.0044 secs | 0 progress init 0
#> Aug19 19:59:30 load total elpsd: 0.0059 secs | 0 load init 0
#> Aug19 19:59:30 save total elpsd: 0.0073 secs | 10 save spades 10
#> simList saved in
#> SpaDES.core:::.pkgEnv$.sim
#> It will be deleted at next spades() call.
outputs(sim) # To see that it was saved, when, what filename
#> objectName file fun package
#> 1 tempObj /tmp/RtmpAzfvD1/outputs/tempObj_year10.rds saveRDS base
#> saveTime saved arguments
#> 1 10 TRUE NA
# Also can add using assignment after a simList object has been made
sim <- simInit(objects = c("tempObj"), paths = list(outputPath = tmpdir))
#> Setting:
#> options(
#> spades.outputPath = '/tmp/RtmpAzfvD1/outputs'
#> )
#> Paths set to:
#> options(
#> rasterTmpDir = '/tmp/RtmpAzfvD1/SpaDES/scratch/raster'
#> reproducible.cachePath = '/tmp/RtmpAzfvD1/myProject/cache'
#> spades.inputPath = '/tmp/RtmpAzfvD1/myProject/inputs'
#> spades.outputPath = '/tmp/RtmpAzfvD1/outputs'
#> spades.modulePath = '/tmp/RtmpAzfvD1/myProject/modules'
#> spades.scratchPath = '/tmp/RtmpAzfvD1/SpaDES/scratch'
#> )
#> terra::terraOptions(tempdir = '/tmp/RtmpAzfvD1/SpaDES/scratch/terra'
#> Using setDTthreads(1). To change: 'options(spades.DTthreads = X)'.
outputs(sim) <- data.frame(objectName = "tempObj", saveTime = 1:10)
sim <- spades(sim)
#> Aug19 19:59:30 Using setDTthreads(1). To change: 'options(spades.DTthreads = X)'.
#> Aug19 19:59:30 chckpn total elpsd: 0.00097 secs | 0 checkpoint init 0
#> Aug19 19:59:30 save total elpsd: 0.0026 secs | 0 save init 0
#> Aug19 19:59:30 prgrss total elpsd: 0.0043 secs | 0 progress init 0
#> Aug19 19:59:30 load total elpsd: 0.0058 secs | 0 load init 0
#> Aug19 19:59:30 save total elpsd: 0.0073 secs | 1 save spades 10
#> Aug19 19:59:30 save total elpsd: 0.012 secs | 2 save later 10
#> Aug19 19:59:30 save total elpsd: 0.017 secs | 3 save later 10
#> Aug19 19:59:30 save total elpsd: 0.022 secs | 4 save later 10
#> Aug19 19:59:30 save total elpsd: 0.026 secs | 5 save later 10
#> Aug19 19:59:30 save total elpsd: 0.031 secs | 6 save later 10
#> Aug19 19:59:30 save total elpsd: 0.036 secs | 7 save later 10
#> Aug19 19:59:30 save total elpsd: 0.04 secs | 8 save later 10
#> Aug19 19:59:30 save total elpsd: 0.045 secs | 9 save later 10
#> Aug19 19:59:30 save total elpsd: 0.05 secs | 10 save later 10
#> simList saved in
#> SpaDES.core:::.pkgEnv$.sim
#> It will be deleted at next spades() call.
outputs(sim) # To see that it was saved, when, what filename.
#> objectName saveTime file fun
#> 1 tempObj 1 /tmp/RtmpAzfvD1/outputs/tempObj_year01.rds saveRDS
#> 2 tempObj 2 /tmp/RtmpAzfvD1/outputs/tempObj_year02.rds saveRDS
#> 3 tempObj 3 /tmp/RtmpAzfvD1/outputs/tempObj_year03.rds saveRDS
#> 4 tempObj 4 /tmp/RtmpAzfvD1/outputs/tempObj_year04.rds saveRDS
#> 5 tempObj 5 /tmp/RtmpAzfvD1/outputs/tempObj_year05.rds saveRDS
#> 6 tempObj 6 /tmp/RtmpAzfvD1/outputs/tempObj_year06.rds saveRDS
#> 7 tempObj 7 /tmp/RtmpAzfvD1/outputs/tempObj_year07.rds saveRDS
#> 8 tempObj 8 /tmp/RtmpAzfvD1/outputs/tempObj_year08.rds saveRDS
#> 9 tempObj 9 /tmp/RtmpAzfvD1/outputs/tempObj_year09.rds saveRDS
#> 10 tempObj 10 /tmp/RtmpAzfvD1/outputs/tempObj_year10.rds saveRDS
#> package saved arguments
#> 1 base TRUE NA
#> 2 base TRUE NA
#> 3 base TRUE NA
#> 4 base TRUE NA
#> 5 base TRUE NA
#> 6 base TRUE NA
#> 7 base TRUE NA
#> 8 base TRUE NA
#> 9 base TRUE NA
#> 10 base TRUE NA
# 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))
#> Setting:
#> options(
#> spades.outputPath = '/tmp/RtmpAzfvD1/outputs'
#> )
#> Paths set to:
#> options(
#> rasterTmpDir = '/tmp/RtmpAzfvD1/SpaDES/scratch/raster'
#> reproducible.cachePath = '/tmp/RtmpAzfvD1/myProject/cache'
#> spades.inputPath = '/tmp/RtmpAzfvD1/myProject/inputs'
#> spades.outputPath = '/tmp/RtmpAzfvD1/outputs'
#> spades.modulePath = '/tmp/RtmpAzfvD1/myProject/modules'
#> spades.scratchPath = '/tmp/RtmpAzfvD1/SpaDES/scratch'
#> )
#> terra::terraOptions(tempdir = '/tmp/RtmpAzfvD1/SpaDES/scratch/terra'
#> Using setDTthreads(1). To change: 'options(spades.DTthreads = X)'.
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)
#> Aug19 19:59:30 Using setDTthreads(1). To change: 'options(spades.DTthreads = X)'.
#> Aug19 19:59:30 chckpn total elpsd: 0.00099 secs | 0 checkpoint init 0
#> Aug19 19:59:30 save total elpsd: 0.0027 secs | 0 save init 0
#> Aug19 19:59:30 prgrss total elpsd: 0.0045 secs | 0 progress init 0
#> Aug19 19:59:30 load total elpsd: 0.006 secs | 0 load init 0
#> Aug19 19:59:30 save total elpsd: 0.0074 secs | 1 save spades 10
#> Aug19 19:59:30 save total elpsd: 0.013 secs | 2 save later 10
#> Aug19 19:59:30 save total elpsd: 0.018 secs | 4 save later 10
#> Aug19 19:59:30 save total elpsd: 0.023 secs | 6 save later 10
#> Aug19 19:59:30 save total elpsd: 0.027 secs | 7 save later 10
#> Aug19 19:59:30 save total elpsd: 0.032 secs | 10 save later 10
#> simList saved in
#> SpaDES.core:::.pkgEnv$.sim
#> It will be deleted at next spades() call.
outputs(sim)
#> objectName saveTime fun package
#> 1 tempObj 1 saveRDS base
#> 2 tempObj 4 saveRDS base
#> 3 tempObj2 2 saveRDS base
#> 4 tempObj2 6 saveRDS base
#> 5 tempObj2 7 saveRDS base
#> 6 df1 10 write.csv utils
#> file saved arguments
#> 1 /tmp/RtmpAzfvD1/outputs/tempObj_year01.rds TRUE NA
#> 2 /tmp/RtmpAzfvD1/outputs/tempObj_year04.rds TRUE NA
#> 3 /tmp/RtmpAzfvD1/outputs/tempObj2_year02.rds TRUE NA
#> 4 /tmp/RtmpAzfvD1/outputs/tempObj2_year06.rds TRUE NA
#> 5 /tmp/RtmpAzfvD1/outputs/tempObj2_year07.rds TRUE NA
#> 6 /tmp/RtmpAzfvD1/outputs/df1_year10.csv TRUE FALSE
# read one back in just to test it all worked as planned
newObj <- read.csv(dir(tmpdir, pattern = "year10.csv", full.name = TRUE))
newObj
#> col1 col2
#> 1 1 val 1
#> 2 2 val 2
#> 3 3 val 3
#> 4 4 val 4
#> 5 5 val 5
#> 6 6 val 6
#> 7 7 val 7
#> 8 8 val 8
#> 9 9 val 9
#> 10 10 val 10
# using saving with SpaDES-aware methods
# To see current ones SpaDES can do
.saveFileExtensions()
#> exts fun package
#> 1 rds saveRDS base
#> 2 qs qsave qs
#> 5 grd writeRaster raster
#> 4 csv write.csv utils
#> 3 txt write.table utils
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
}
#> Setting:
#> options(
#> spades.outputPath = '/tmp/RtmpAzfvD1/outputs'
#> )
#> Paths set to:
#> options(
#> rasterTmpDir = '/tmp/RtmpAzfvD1/SpaDES/scratch/raster'
#> reproducible.cachePath = '/tmp/RtmpAzfvD1/myProject/cache'
#> spades.inputPath = '/tmp/RtmpAzfvD1/myProject/inputs'
#> spades.outputPath = '/tmp/RtmpAzfvD1/outputs'
#> spades.modulePath = '/tmp/RtmpAzfvD1/myProject/modules'
#> spades.scratchPath = '/tmp/RtmpAzfvD1/SpaDES/scratch'
#> )
#> terra::terraOptions(tempdir = '/tmp/RtmpAzfvD1/SpaDES/scratch/terra'
#> Using setDTthreads(1). To change: 'options(spades.DTthreads = X)'.
#> Aug19 19:59:30 Using setDTthreads(1). To change: 'options(spades.DTthreads = X)'.
#> Aug19 19:59:30 chckpn total elpsd: 0.00093 secs | 0 checkpoint init 0
#> Aug19 19:59:30 save total elpsd: 0.0025 secs | 0 save init 0
#> Aug19 19:59:30 prgrss total elpsd: 0.0042 secs | 0 progress init 0
#> Aug19 19:59:30 load total elpsd: 0.0057 secs | 0 load init 0
#> Aug19 19:59:30 save total elpsd: 0.0071 secs | 10 save spades 10
#> simList saved in
#> SpaDES.core:::.pkgEnv$.sim
#> It will be deleted at next spades() call.
#> [1] TRUE
# Clean up after
unlink(tmpdir, recursive = TRUE)