Package index • streamMetabolizer

Plotting

plot_DO_preds(): Plot dissolved oxygen predictions
plot_distribs(): Plot the prior/posterior distributions of a parameter
plot_metab_data(): Plot metabolism input data
plot_metab_preds(): Plot metabolism predictions

Other

calc_DO_deficit() deprecated: Calculate a vector of dissolved oxygen deficits
calc_DO_sat(): Calculate equilibrium oxygen saturation
calc_air_pressure(): Calculate 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 using the NASA solar insolation method.
calc_is_daytime() deprecated: Determine whether datetimes occur during daylight
calc_light(): Calculate modeled light from solar.time
calc_light_merged(): Merge modeled and observed PAR into a time series
calc_solar_insolation(): Model solar insolation on a horizontal surface
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 UTC to local time
convert_UTC_to_solartime(): Convert DateTime from UTC to local solar time
convert_k600_to_kGAS(): Convert K600 to a gas-specific exchange velocity
convert_kGAS_to_k600(): Convert a gas-specific exchange velocity to K600
convert_localtime_to_UTC(): Convert 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 calculates a one-day DO time series
data_metab(): Get a demo dataset for modeling metabolism
get_data(): Extract model fitting data
get_data_daily(): Extract daily model fitting data
get_fit(): Extract the internal fitted model
get_fitting_time(): Extract model fitting time
get_info(): Extract user-supplied model metadata
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 daily metabolism parameter names
get_params(): Extract metabolism model parameters
get_specs(): Extract model fitting specifications
get_version(): Extract the streamMetabolizer version used to fit a 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_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(): Fit a Bayesian metabolism model
metab_inputs(): Describe the requirements for an argument to metab()
metab_mle-class: Metabolism model fitted by maximum likelihood estimation
metab_mle(): Fit a metabolism model by maximum likelihood
metab_model-class: Metabolism model class
metab_model(): Create a metabolism model object
metab_model_interface: Functions implemented by compatible metabolism models
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(): Describe model input data types
mm_filter_valid_days(): Remove entries in data
mm_get_timestep(): Calculate timesteps 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(): Construct a model name from 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(): Validate model input data
mm_validate_name(): Check the validity of a model name
predict_DO(): Predict dissolved oxygen 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 daily data for K modeling
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 streamMetabolizer
to_degrees(): Convert radians to degrees
to_radians(): Convert degrees to radians