Man pages for USGS-R/streamMetabolizer
Models for Estimating Aquatic Photosynthesis and Respiration
| add_specs_class | Add the metabolism model specifications class to a list |
| bayes_1ply | Make daily metabolism estimates from input parameters |
| bayes_allply | Make daily metabolism estimates from input parameters using a... |
| 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... |
| calc_DO_deficit | Deprecated: Calculate a vector of dissolved oxygen deficits |
| calc_DO_sat | Calculates the equilibrium saturation concentration of oxygen... |
| calc_hour_angle | Calculate hour angle as in... |
| calc_is_daytime | Determines if specified datetime is during the daytime... |
| 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 ==... |
| calc_solar_time | Calculate solar.time from local.time |
| calc_sun_rise_set | Calculates the time of sunrise and sunset |
| calc_velocity | Estimate velocity from discharge and hydraulic geometry... |
| calc_zenith_angle | Calculate zenith angle as in... |
| compress_msgs | Compress warnings and errors in to a single column |
| 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... |
| convert_kGAS_to_k600 | Returns the gas exchange velocity as k600 for gas of interest... |
| convert_localtime_to_UTC | Convert time from local time to UTC. |
| convert_PAR_to_SW | Convert from photosynthetically active to shortwave radiation |
| convert_solartime_to_UTC | Convert DateTime from local solar time to UTC |
| 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 |
| create_calc_dDOdt | Create a function that generates a 1-day timeseries of DO.mod |
| create_calc_DO | Create a function to compute the numerical integration of a... |
| create_calc_NLL | Create a function to compute the negative log likelihood of a... |
| data_metab | Get a demo dataset for modeling metabolism |
| define_pkg_env | Define a package environment for storing data specific to a... |
| format_mcmc_mat_nosplit | Format MCMC output into a list of data.frames |
| format_mcmc_mat_split | Format MCMC output into a one-row data.frame |
| get_data | Extract the fitting data from a metabolism model. |
| get_data_daily | Extract the daily fitting data, if any, from a metabolism... |
| get_fit | Extract the internal model from a metabolism model. |
| get_fitting_time | Extract the amount of time that was required to fit the... |
| 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... |
| 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... |
| get_specs | Extract the fitting specifications from a metabolism model. |
| get_version | Extract the version of streamMetabolizer that was used to fit... |
| Kmodel_aggregate_day | Aggregate unit values to daily values |
| Kmodel_allply | Fit a K 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... |
| metab | Fit a metabolism model to data |
| metab_bayes | Basic Bayesian metabolism model fitting function |
| metab_bayes-class | Metabolism model fitted by Bayesian MCMC |
| metab_inputs | Describe the requirements for an argument to metab() |
| metab_Kmodel | Combine a time series of K estimates to predict consistent... |
| metab_Kmodel-class | Interpolation model of daily K for metabolism |
| metab_mle | Maximum likelihood metabolism model fitting function |
| metab_mle-class | Metabolism model fitted by maximum likelihood estimation |
| metab_model | Create a metab_model object. |
| metab_model-class | A metabolism model class. |
| metab_model_interface | Functions implemented by any 'streamMetabolizer'-compatible... |
| metab_night | Nighttime regression for K estimation |
| metab_night-class | Reaeration model fitted by nighttime regression |
| metab_night_predict_1ply | Helper to predict_DO.metab_model |
| metab_sim | Simulate dissolved oxygen data from input data |
| metab_sim-class | Data simulator |
| mle_1ply | Make daily metabolism estimates from input parameters |
| mm_check_mcmc_file | Use an engine-specific function to check the model syntax |
| mm_check_mcmc_files | Check the syntax of all Bayesian model files in the package |
| mm_data | Return the data types that may be used by metab_models using... |
| mm_filter_dates | Filter unit or daily data by inclusive start & end dates |
| mm_filter_hours | Limit to a specific time range on each date |
| mm_filter_valid_days | Remove entries in data |
| mm_generate_mcmc_file | Generate the models in inst/models/bayes |
| mm_generate_mcmc_files | Generate MCMC code files with all of the desired combinations... |
| mm_get_timestep | Return the average timestep in days |
| mm_is_valid_day | Validate one day of data, returning a vector of error strings... |
| mm_locate_filename | Look for a model file |
| mm_model_by_ply | Split and label data into >=24-hr days for fitting daily... |
| 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_sd_to_ci | Convert SD columns into CI columns in a data.frame |
| mm_validate_data | Evaluate whether the data argument is properly formatted. |
| mm_validate_name | Check the validity of a model name |
| mm_valid_names | Get the valid names for a given model type or types |
| nightreg_1ply | Make daily reaeration estimates from input parameters |
| plot_distribs | Plot the prior/posterior distributions of a parameter |
| plot_DO_preds | Plot predictions produced with predict_DO |
| 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... |
| prepdata_bayes | Prepare data for passing to Stan |
| prepdata_Kmodel | Prepare data_daily by aggregating any daily data, renaming... |
| pretty_print_ddat | Format and print a summary of data frame of daily values |
| print.logs_metab | Print metab logs |
| print_specs | Display the specs object |
| print.specs | Display the specs object |
| revise | Change or add named elements of a list |
| runstan_bayes | Run Stan on a formatted data ply |
| show-metab_model-method | Display the metab_model object |
| show-specs-method | Display the specs object |
| sim_get_par | Get a parameter from data_daily, specs, or both |
| 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 | Functions for calculating ecosystem metabolism in streams |
| streamMetabolizer-deprecated | Deprecated Functions in package streamMetabolizer |
| summarize_stopwarn_msgs | Summarize a vector of warning or error messages |
| to_degrees | Convert radians to degrees |
| to_radians | Convert degrees to radians |
| unitted_deprecate_warn | Warn about deprecation of a units-related argument or... |
| zz_build_docs | Generate doc text for the 'metab()' documentation |
| zz_tabular | Format a data.frame for inclusion in a roxygen header |
