fnc_write: Function to reduce data output from automated LWFB90-Runs

In rhabel/modLWFB90: R-package for applying LWF-Brook90 directly from FVA-BW servers

Function to reduce data output from automated LWFB90-Runs

Description

LWFBrook90 creates a lot of output files. In order to keep data storage to a minimum, both run_LWFB90 and run_multisite_LWFB90 provide an output_fun - argument that can be used to reduce the output and directly write it to a database. This is what this function is made for.

LWFBrook90 creates a lot of output files. In order to keep data storage to a minimum, both run_LWFB90 and run_multisite_LWFB90 provide an output_fun - argument that can be used to reduce the output and directly write it. This is what this function is made for. It writes .rds files with the desired output for each point. fnc_write_to_sql can be used to convert these files into a SQLite-DB.
This "step-in-between" is necessary because SQLite does not support parallel writing.

Usage

fnc_write(x, layercols = NA, dailycols = NA, dir_name = NA)

fnc_write(x, layercols = NA, dailycols = NA, dir_name = NA)

Arguments

x	one of the intermediate producs of run_LWFB90 or run_multisite_LWFB90, which is further processed internally. Can't be adjusted.
layercols	a sting containing the desired output products. Full list of possible output columns can be find on the help page of run_LWFB90 under Layer outputs
dailycols	same as layercols but for daily output. For possible options see run_LWFB90
dir_name	directory for tmp files, if NA (default), output will be returned to console
db_name	name and file path of the SQL-database

Value

Returns the desired output to the database directly.

writes output to

Examples

df.ids <- test_ids_bze

meta <- data.frame("ID_custom" = df.ids$ID_custom,
                   modelled = 0,
                   err.code = "no error",
                   sim_dur_s = NA_integer_)

ls.soil <- fnc_get_soil(df.ids,
                        soil_option = "BZE",
                        PTF_to_use = "WESSOLEK")

ls.parms <- fnc_get_params(df.ids = df.ids,
                           tree_species = "spruce")

ls.clim <- fnc_get_clim(df.ids = df.ids,
                        mindate = as.Date("2002-01-01"),
                        maxdate = as.Date("2003-12-31"))

# keep info which points have no soil info...
no_soil_data <- which(unlist(lapply(ls.soil, is.null))==T)
with_soil_data <- which(unlist(lapply(ls.soil, is.null))==F)
meta[no_soil_data, "err.code"] <- "no soil data"

# ...but remove for modelling...
ls.parms <- ls.parms[with_soil_data]
ls.soil <- ls.soil[with_soil_data]
ls.clim <- ls.clim[with_soil_data]

res <- run_multisite_LWFB90(options_b90 = set_optionsLWFB90(),

                            param_b90 = ls.parms,
                            soil = ls.soil,
                            climate = ls.clim,

                            output = -1,

                            cores = parallel::detectCores()-1,

                            rtrn_output = F,
                            rtrn_input = F,

                            timelimit = 15,

                            output_fun = fnc_write,
                            dailycols = c("rfal", "tran"),
                            dir_name= "./tmp/")

meta <- fnc_check_errors(res = res, meta = meta)

# can be written to sql as follows (see fnc_write_to_sql)
if(!dir.exists("./tmp/meta/")){
  dir.create("./tmp/meta/", recursive = T)
}

saveRDS(meta, file = "./tmp/meta/meta.rds")

# write to db
fnc_write_to_sql(db_name = "./tmp/testdb.sqlite",
                 dir_tmp = "./tmp/")

# check results
con <- dbConnect(drv = RSQLite::SQLite(), dbname =  "./tmp/testdb.sqlite")
dbListTables(conn = con)
dbGetQuery(con,
           "SELECT * FROM meta")
dbDisconnect(con)

# # delete example tmp file
# unlink("./tmp/", recursive = T)

rhabel/modLWFB90 documentation built on Nov. 21, 2024, 3:28 a.m.