createMultiSiteSettings.RdCreate a MultiSettings object containing (identical) run blocks for multiple different sites
createMultiSiteSettings(templateSettings, siteIds)A Settings object that will be
the template for the resulting MultiSettings.
The site IDs to be used in the resulting MultiSettings.
May be a vector or a data frame with a mandatory id column and
optionally other columns to be copied into run$site. See details.
A MultiSettings object with the same settings as
templateSettings but replicated run$site blocks,
one for each specified site ID.
Starts with a template settings object, and duplicates the run$site
block once for each specified site ID. The resulting MultiSettings is thus
identical to the input, except ready to run for each site in the vector
of site IDs.
If siteIds is a data frame with a column named id,
each resulting run$site block will contain all the site parameters
(lat, lon, site name, etc) that are specified in its other columns.
dontrun <- function() { # Added by Alexey Shiklomanov
# so this doesn't run and break the build
# This isn't necessarily a fully working settings object.
# Enough to get the idea though.
# Note it has a $run block with settings that will be shared across all sites
template <- Settings(list(
info = structure(list(
notes = NULL, userid = "1000000005", username = "Ryan Kelly",
date = "2016/07/13 13:23:46 -0400"),
.Names = c("notes", "userid", "username", "date")),
database = structure(list(
bety = structure(
list(user = "bety", password = "bety", host = "psql-pecan.bu.edu",
dbname = "bety", driver = "PostgreSQL", write = "TRUE"),
.Names = c("user", "password", "host", "dbname", "driver", "write")),
fia = structure(
list(user = "bety", password = "bety", host = "psql-pecan.bu.edu",
dbname = "fia5", driver = "PostgreSQL", write = "true"),
.Names = c("user", "password", "host", "dbname", "driver", "write"))),
.Names = c("bety", "fia")),
pfts = structure(list(
pft = structure(
list(comment = NULL, name = "temperate.Evergreen_Hardwood",
constants = structure(list(num = "1"), .Names = "num")),
.Names = c("comment", "name", "constants")),
pft = structure(
list(name = "temperate.Hydric",
constants = structure(list(num = "2"), .Names = "num")),
.Names = c("name", "constants"))),
.Names = c("pft", "pft")),
meta.analysis = structure(list(
iter = "3000", random.effects = list(on = FALSE, use_ghs = TRUE),
update = "AUTO", threshold = "1.2"),
.Names = c("iter", "random.effects", "update", "threshold")),
ensemble = structure(list(size = "1", variable = "NPP"),
.Names = c("size", "variable")),
model = structure(list(id = "2000000005",
edin = "/home/rykelly/pecan/RK_files/ED2IN/ED2IN.rgit.mandifore_04",
config.header = structure(list(
radiation = structure(list(lai_min = "0.01"), .Names = "lai_min"),
ed_misc = structure(list(output_month = "12"),
.Names = "output_month")),
.Names = c("radiation", "ed_misc")),
phenol.scheme = "0", prerun = "module load hdf5/1.8.11",
binary = "/usr2/postdoc/rykelly/ED2/ED/build/ed_2.1-opt"),
.Names = c("id", "edin", "config.header", "phenol.scheme", "prerun",
"binary")),
host = structure(list(name = "geo.bu.edu", user = "rykelly",
folder = "/projectnb/dietzelab/pecan.data/output/rykelly",
qsub = "qsub -V -N @NAME@ -o @STDOUT@ -e @STDERR@ -S /bin/bash",
qsub.jobid = "Your job ([0-9]+) .*",
qstat = "qstat -j @JOBID@ || echo DONE",
prerun = "module load udunits R/R-3.0.0_gnu-4.4.6",
dbfiles = "/projectnb/dietzelab/pecan.data/input",
modellauncher = structure(list(
binary = "/usr2/postdoc/rykelly/pecan/utils/modellauncher/modellauncher",
qsub.extra = "-pe omp 20"),
.Names = c("binary", "qsub.extra"))),
.Names = c("name", "user", "folder", "qsub", "qsub.jobid", "qstat",
"prerun", "dbfiles", "modellauncher")),
run = structure(list(
inputs = structure(list(
met = structure(list(source = "NARR", output = "ED2"),
.Names = c("source", "output")),
lu = structure(list(id = "294",
path = "/projectnb/dietzelab/EDI/ed_inputs/glu/"),
.Names = c("id", "path")),
soil = structure(list(id = "297",
path = "/projectnb/dietzelab/EDI/faoOLD/FAO_"),
.Names = c("id", "path")),
thsum = structure(list(id = "295",
path = "/projectnb/dietzelab/EDI/ed_inputs/"),
.Names = c("id", "path")),
veg = structure(list(id = "296",
path = "/projectnb/dietzelab/EDI/oge2OLD/OGE2_"),
.Names = c("id", "path")),
pss = structure(list(source = "FIA"), .Names = "source")),
.Names = c("met", "lu", "soil", "thsum", "veg", "pss")),
start.date = "2004/01/01",
end.date = "2004/01/31"),
.Names = c("inputs", "start.date", "end.date"))
))
sitegroupId <- 1000000002
startDate <- "2000/01/01"
endDate <- "2015/12/31"
nSite <- 10
outDir <- "~/multisite_setup_test"
template <- setDates(template, startDate = startDate, endDate = endDate)
template <- setOutDir(template, outDir)
multiRunSettings <- createSitegroupMultiSettings(
template,
sitegroupId = sitegroupId,
nSite = nSite)
dir.create(outDir, showWarnings = FALSE)
write.settings(multiRunSettings, outputfile = "pecan.xml")
} # dontrun