stage_metab_config: Write a metabolism modeling configuration file

In USGS-R/mda.streams: Data Preparation, Access, and Analysis Functions for the Powell Center Continental Stream Metabolism Project

Write a metabolism modeling configuration file

Description

Write a table (tsv) of configuration information for individual metabolism modeling jobs (one row/job per site-strategy combination). This tsv should reflect the full information needed to re-run a set of jobs. The jobs will probably, but not necessarily, be run on a Condor cluster.

Usage

stage_metab_config(tag, strategy, date = Sys.time(), model = "metab_mle",
  model_args = "list()", site = list_sites(c("doobs_nwis", "disch_nwis",
  "wtr_nwis")), sitetime = choose_data_source("sitetime", site),
  doobs = choose_data_source("doobs", site),
  dosat = choose_data_source("dosat", site),
  depth = choose_data_source("depth", site), wtr = choose_data_source("wtr",
  site), par = choose_data_source("par", site),
  disch = choose_data_source("disch", site, logic = "unused var"),
  veloc = choose_data_source("veloc", site, logic = "unused var"),
  sitedate = choose_data_source("sitedate", site, logic = "unused var"),
  doinit = choose_data_source("doinit", site, logic = "unused var"),
  gpp = choose_data_source("gpp", site, logic = "unused var"),
  er = choose_data_source("er", site, logic = "unused var"),
  K600 = choose_data_source("K600", site, logic = "unused var"),
  K600lwr = choose_data_source("K600lwr", site, logic = "unused var"),
  K600upr = choose_data_source("K600upr", site, logic = "unused var"),
  gppinit = choose_data_source("gppinit", site, logic = "unused var"),
  erinit = choose_data_source("erinit", site, logic = "unused var"),
  K600init = choose_data_source("K600init", site, logic = "unused var"),
  dischdaily = choose_data_source("dischdaily", site, logic = "unused var"),
  velocdaily = choose_data_source("velocdaily", site, logic = "unused var"),
  start_date = NA, end_date = NA, omit_incomplete = TRUE,
  filename = "./config.tsv")

Arguments

tag	character of form "1.0.2" that uniquely identifies this set of modeling runs.
strategy	character, or vector of length sites, describing this set of modeling runs in concise English.
date	POSIXct indicating the date of config construction. It is strongly recommended to use the default.
model	character. the name of the metabolism model to construct
model_args	character, in R language, specifying any arguments to pass to the model function
site	site names
sitetime	Data Source for mean solar time. See Data Source Format below.
doobs	Data Source for dissolved oxygen concentrations. See Data Source Format below.
dosat	Data Source for dissolved oxygen saturation concentrations. See Data Source Format below.
depth	Data Source for mean stream depth. See Data Source Format below.
wtr	Data Source for water temperature. See Data Source Format below.
par	Data Source for light (photosynthetically available radiation, PAR). See Data Source Format below.
disch	Data Source for unit-value stream discharge, for use in identifying daily priors or fixed values for K600. See Data Source Format below.
veloc	Data Source for unit-value flow velocity, for use in identifying daily priors or fixed values for K600. See Data Source Format below.
sitedate	Data Source for the dates of interest. See Data Source Format below.
doinit	Data Source for the first DO observation on each date to model, for use in data simulation. See Data Source Format below.
gpp	Data Source for daily gross primary productivity rates for use in data simulation. See Data Source Format below.
er	Data Source for ecosystem respiration rates for use in data simulation. See Data Source Format below.
K600	Data Source for reaeration rates for use in data simulation. See Data Source Format below.
K600lwr	Data Source for lower bound on reaeration rates for use in data simulation. See Data Source Format below.
K600upr	Data Source for upper bound on reaeration rates for use in data simulation. See Data Source Format below.
gppinit	Data Source for initial values of daily gross primary productivity rates for use in likelihood maximization. See Data Source Format below.
erinit	Data Source for initial values of ecosystem respiration rates for use in likelihood maximization. See Data Source Format below.
K600init	Data Source for initial values of reaeration rates for use in likelihood maximization. See Data Source Format below.
dischdaily	Data Source for daily mean stream discharge, for use in identifying daily priors or fixed values for K600. See Data Source Format below.
velocdaily	Data Source for daily mean flow velocity, for use in identifying daily priors or fixed values for K600. See Data Source Format below.
start_date	NA or datetime, to be coerced with as.POSIXct(start_date, tz="UTC"), at which to start the data passed to the metab model
end_date	NA or datetime, to be coerced with as.POSIXct(end_date, tz="UTC"), at which to end the data passed to the metab model
omit_incomplete	logical. If one or more datasets required for the specified config row is unavailable, should that row be omitted?
filename	character or NULL. If NULL, the function returns a data.frame, otherwise it writes that data.frame to the file specified by filename.

Value

file name of the config file

Data Source Format

Every parameter whose definition begins with Data Source should be supplied as a 4-column data.frame with column names c('type','site','src','logic'). These specify where to find the data for a given variable. The easiest way to create such a data.frame is usually with choose_data_source, though it may also be created manually.

The variables requiring Data Source specification, along with their expected units, are defined in the help file for mm_data.

Examples

## Not run: 
login_sb()
site="nwis_01646000"
cfg <- stage_metab_config(tag="0.0.1", strategy="try stage_metab_config", 
  model="metab_mle", site=site, filename=NULL,
  sitetime=choose_data_source("sitetime", site, logic="manual", src="calcLon", type="ts"),
  doobs=choose_data_source("doobs", site, logic="unused var"),
  dosat=choose_data_source("dosat", site, logic="unused var"),
  depth=choose_data_source("depth", site, logic="unused var"),
  wtr=choose_data_source("wtr", site, logic="unused var"),
  par=choose_data_source("par", site, logic="unused var"),
  K600=choose_data_source("K600", site, logic="nighttime", src="0.0.6", type="pred"),
  dischdaily=choose_data_source("dischdaily", site, logic="manual", src="calcDMean", type="ts"),
  velocdaily=choose_data_source("velocdaily", site, logic="manual", src="calcDMean", type="ts"),
  omit_incomplete=FALSE)
stage_metab_config(tag="0.0.1", strategy="try stage_metab_config", 
  site="nwis_01646000", filename=NULL)
stage_metab_config(tag="0.0.1", strategy="test write_metab_config", 
  site=list_sites()[24:33], filename=NULL,
  omit_incomplete=FALSE)
stage_metab_config(tag="0.0.1", strategy="test write_metab_config", 
  site=list_sites()[24:33], filename=NULL)
styxsites <- c("styx_001001","styx_001002","styx_001003")
mc <- stage_metab_config(tag="0.0.1", strategy="test styx config", 
  model="metab_sim", site=styxsites, filename=NULL, 
  doobs=choose_data_source("doobs", styxsites, logic="unused var"), omit_incomplete=FALSE)

## End(Not run)

USGS-R/mda.streams documentation built on June 3, 2023, 8:43 a.m.