View source: R/make_metab_config.R
make_metab_config | R Documentation |
Quick-make function for manual making of a model config file
make_metab_config(site, 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()")
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
|
end_date |
NA or datetime, to be coerced with |
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 |
If a data source is given as NA, the 'priority local' timeseries option will be selected.
If a data source is given as a character, the character will be used to
specify the src
argument to choose_data_source
with
codetype='ts'.
If a data source is given as NULL, the variable will be set to 'unused var'.
For the most flexibility, each parameter whose definition begins with Data
Source may 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
.
## Not run:
make_metab_config('nwis_08062500')
make_metab_config('nwis_08062500', sitetime='calcLon', doobs='nwis',
dosat='calcGGbts', depth='calcDischHarvey', wtr='nwis', par='calcSw')
## End(Not run)
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