get_metab_prep: Get a data.frame of metabolism input data

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

Get a data.frame of metabolism input data

Description

Quick-get function for manual getting of metabolism data

Usage

get_metab_prep(site, out = c("data", "data_daily", "info"), sitetime = NA,
  doobs = NA, dosat = NA, depth = NA, wtr = NA, par = NA,
  disch = NULL, veloc = NULL, sitedate = NULL, doinit = NULL,
  gpp = NULL, er = NULL, K600 = NULL, K600lwr = NULL, K600upr = NULL,
  gppinit = NULL, erinit = NULL, K600init = NULL, dischdaily = NULL,
  velocdaily = NULL, start_date = NA, end_date = NA, tag = "0.0.0",
  strategy = "get_metab_data", date = Sys.time(), model = "metab_mle",
  model_args = "list()", simplify_config = TRUE, simplify_out = TRUE,
  verbose = TRUE)

Arguments

site	site names
out	character vector of one or more elements of c('data','data_daily','info') to return
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
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
simplify_config	logical. If the implied config file has only one row, should the list be reduced to one element?
simplify_out	If out has only one element, should the list of lists be reduced to a list of data.frames?
verbose	logical. give progress messages?

Examples

## Not run: 
md <- get_metab_prep('nwis_08062500') # list of $data, $data_daily, $info
md <- get_metab_prep('nwis_08062500', simplify_config=FALSE) # list of lists
md <- get_metab_prep('nwis_08062500', out='data') # single data.frame
md <- get_metab_prep(c('nwis_08062500','nwis_01646500'), out='data') # list of data.frames
md <- get_metab_prep('nwis_08062500', sitedate=NA, K600=NA, 
  start_date="2014-03-10 04:00:00", end_date="2014-03-11 04:00:00") # short data.frames
md <- get_metab_prep('nwis_08062500', sitetime=NULL, doobs=NULL, dosat=NULL, depth=NULL, 
  wtr=NULL, par=NULL, sitedate=NA, K600='estBest', dischdaily=NA, model='metab_Kmodel')

## End(Not run)

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