Function reference • streamMetabolizer

All functions

calc_DO_deficit(): Deprecated: Calculate a vector of dissolved oxygen deficits

calc_DO_sat(): Calculates the equilibrium saturation concentration of oxygen in water at the supplied conditions

calc_air_pressure(): Calculates the average air pressure for a site

calc_bins(): Assign continuous values in a vector to discrete bins

calc_declination_angle(): Calculate declination angle as in Yard et al. (2005)

calc_depth(): Estimate depth from discharge and hydraulic geometry coefficients

calc_hour_angle(): Calculate hour angle as in http://education.gsfc.nasa.gov/experimental/July61999siteupdate/inv99Project.Site/Pages/solar.insolation.html.

calc_is_daytime(): Determines if specified datetime is during the daytime Returns T/F indicating whether a datetime occurs during the daytime (sunlight hours)

calc_light(): Calculate modeled light from solar.time

calc_light_merged(): Merge modeled and observed PAR into a single timeseries

calc_solar_insolation(): Model solar insolation on a horizontal surface (W/m2 == J/s/m2) as in http://education.gsfc.nasa.gov/experimental/July61999siteupdate/inv99Project.Site/Pages/solar.insolation.html

calc_solar_time(): Calculate solar.time from local.time

calc_velocity(): Estimate velocity from discharge and hydraulic geometry coefficients

calc_zenith_angle(): Calculate zenith angle as in http://education.gsfc.nasa.gov/experimental/July61999siteupdate/inv99Project.Site/Pages/solar.insolation.html

convert_PAR_to_SW(): Convert from photosynthetically active to shortwave radiation

convert_SW_to_PAR(): Convert from shortwave to photosynthetically active radiation

convert_UTC_to_localtime(): Convert time from UTC to local time.

convert_UTC_to_solartime(): Convert DateTime from UTC to local solar time

convert_date_to_doyhr(): Convert a date to a day of year (1-366) with decimal hours

convert_doyhr_to_date(): Convert a a day of year (1-366) with decimal hours to a date

convert_k600_to_kGAS(): Returns the gas exchange velocity for gas of interest w/ no unit conversions

convert_kGAS_to_k600(): Returns the gas exchange velocity as k600 for gas of interest w/ no unit conversions

convert_localtime_to_UTC(): Convert time from local time to UTC.

convert_solartime_to_UTC(): Convert DateTime from local solar time to UTC

create_calc_DO(): Create a function to compute the numerical integration of a dDOdt function

create_calc_NLL(): Create a function to compute the negative log likelihood of a set of metabolism parameter values

create_calc_dDOdt(): Create a function that generates a 1-day timeseries of DO.mod

data_metab(): Get a demo dataset for modeling metabolism

get_data(): Extract the fitting data from a metabolism model.

get_data_daily(): Extract the daily fitting data, if any, from a metabolism model.

get_fit(): Extract the internal model from a metabolism model.

get_fitting_time(): Extract the amount of time that was required to fit the metabolism model.

get_info(): Extract the user-supplied metadata about a metabolism model.

get_log(): Return the log file[s] from a model run

get_mcmc(): Extract any MCMC model objects that were stored with the model

get_mcmc_data(): Extract any MCMC data list[s] that were stored with the model

get_param_names(): Extract the daily parameter names from a metabolism model.

get_params(): Extract the metabolism parameters (fitted and/or fixed) from a model.

get_specs(): Extract the fitting specifications from a metabolism model.

get_version(): Extract the version of streamMetabolizer that was used to fit the model.

load_french_creek(): Load a short dataset from French Creek

load_french_creek_std(): Load a short dataset from French Creek using Bob Hall's code

load_french_creek_std_mle(): Generate outputs using Bob's code for comparison

load_spring_creek(): Load a short dataset from Spring Creek

lookup_google_timezone(): Use Google API to determine local time zone

lookup_timezone(): Determine the local time zone from the coordinates

lookup_usgs_elevation(): Use USGS API (USGS Elevation Point Query Service) to determine approximate local elevation

metab(): Fit a metabolism model to data

metab_Kmodel-class: Interpolation model of daily K for metabolism

metab_Kmodel(): Combine a time series of K estimates to predict consistent values

metab_bayes-class: Metabolism model fitted by Bayesian MCMC

metab_bayes(): Basic Bayesian metabolism model fitting function

metab_inputs(): Describe the requirements for an argument to metab()

metab_mle-class: Metabolism model fitted by maximum likelihood estimation

metab_mle(): Maximum likelihood metabolism model fitting function

metab_model-class: A metabolism model class.

metab_model(): Create a metab_model object.

metab_model_interface: Functions implemented by any streamMetabolizer-compatible metabolism model.

metab_night-class: Reaeration model fitted by nighttime regression

metab_night(): Nighttime regression for K estimation

metab_night_predict_1ply(): Helper to predict_DO.metab_model

metab_sim-class: Data simulator

metab_sim(): Simulate dissolved oxygen data from input data

mm_data(): Return the data types that may be used by metab_models using the metab_model_interface.

mm_filter_valid_days(): Remove entries in data

mm_get_timestep(): Return the average timestep in days

mm_is_valid_day(): Validate one day of data, returning a vector of error strings if needed

mm_model_by_ply(): Split and label data into >=24-hr days for fitting daily metabolism

mm_model_by_ply_prototype(): A prototype for the model_fun argument to mm_model_by_ply

mm_name(): Find the name of a model by its features

mm_parse_name(): Parse a model name into its features

mm_predict_DO_1ply(): Helper to predict_DO.metab_model

mm_predict_metab_1ply(): Helper to predict_metab.metab_model

mm_valid_names(): Get the valid names for a given model type or types

mm_validate_data(): Evaluate whether the data argument is properly formatted.

mm_validate_name(): Check the validity of a model name

plot_DO_preds(): Plot predictions produced with predict_DO

plot_distribs(): Plot the prior/posterior distributions of a parameter

plot_metab_preds(): Plot predictions produced with predict_DO

predict_DO(): Predict DO from a fitted model.

predict_metab(): Predict metabolism from a fitted model.

predict_metab(<metab_Kmodel>): Override generic predict_metab for metab_Kmodel, which can't predict metab

prepdata_Kmodel(): Prepare data_daily by aggregating any daily data, renaming K600.daily to K600.daily.obs, & setting data_daily$weight to reflect user weights & filters

print(<logs_metab>): Print metab logs

print(<specs>): Display the specs object

revise(): Change or add named elements of a list

show(<metab_model>): Display the metab_model object

show(<specs>): Display the specs object

sim_Kb(): Simulate a lnK ~ lnQ relationship in the Kb format

sim_pred_Kb(): Predict ln(K600) as Kb-style function of discharge

specs(): Generate a coherent list of model specs

streamMetabolizer-deprecated: Deprecated Functions in package streamMetabolizer

streamMetabolizer streamMetabolizer-package: Functions for calculating ecosystem metabolism in streams

to_degrees(): Convert radians to degrees

to_radians(): Convert degrees to radians