Man pages for USGS-R/streamMetabolizer
Models for Estimating Aquatic Photosynthesis and Respiration

add_specs_classAdd the metabolism model specifications class to a list
bayes_1plyMake daily metabolism estimates from input parameters
bayes_allplyMake daily metabolism estimates from input parameters using a...
calc_air_pressureCalculates the average air pressure for a site
calc_binsAssign continuous values in a vector to discrete bins
calc_declination_angleCalculate declination angle as in Yard et al. (2005)
calc_depthEstimate depth from discharge and hydraulic geometry...
calc_DO_deficitDeprecated: Calculate a vector of dissolved oxygen deficits
calc_DO_satCalculates the equilibrium saturation concentration of oxygen...
calc_hour_angleCalculate hour angle as in...
calc_is_daytimeDetermines if specified datetime is during the daytime...
calc_lightCalculate modeled light from solar.time
calc_light_mergedMerge modeled and observed PAR into a single timeseries
calc_solar_insolationModel solar insolation on a horizontal surface (W/m2 ==...
calc_solar_timeCalculate solar.time from local.time
calc_sun_rise_setCalculates the time of sunrise and sunset
calc_velocityEstimate velocity from discharge and hydraulic geometry...
calc_zenith_angleCalculate zenith angle as in...
compress_msgsCompress warnings and errors in to a single column
convert_date_to_doyhrConvert a date to a day of year (1-366) with decimal hours
convert_doyhr_to_dateConvert a a day of year (1-366) with decimal hours to a date
convert_k600_to_kGASReturns the gas exchange velocity for gas of interest w/ no...
convert_kGAS_to_k600Returns the gas exchange velocity as k600 for gas of interest...
convert_localtime_to_UTCConvert time from local time to UTC.
convert_PAR_to_SWConvert from photosynthetically active to shortwave radiation
convert_solartime_to_UTCConvert DateTime from local solar time to UTC
convert_SW_to_PARConvert from shortwave to photosynthetically active radiation
convert_UTC_to_localtimeConvert time from UTC to local time.
convert_UTC_to_solartimeConvert DateTime from UTC to local solar time
create_calc_dDOdtCreate a function that generates a 1-day timeseries of DO.mod
create_calc_DOCreate a function to compute the numerical integration of a...
create_calc_NLLCreate a function to compute the negative log likelihood of a...
data_metabGet a demo dataset for modeling metabolism
define_pkg_envDefine a package environment for storing data specific to a...
format_mcmc_mat_nosplitFormat MCMC output into a list of data.frames
format_mcmc_mat_splitFormat MCMC output into a one-row data.frame
get_dataExtract the fitting data from a metabolism model.
get_data_dailyExtract the daily fitting data, if any, from a metabolism...
get_fitExtract the internal model from a metabolism model.
get_fitting_timeExtract the amount of time that was required to fit the...
get_infoExtract the user-supplied metadata about a metabolism model.
get_logReturn the log file[s] from a model run
get_mcmcExtract any MCMC model objects that were stored with the...
get_mcmc_dataExtract any MCMC data list[s] that were stored with the model
get_param_namesExtract the daily parameter names from a metabolism model.
get_paramsExtract the metabolism parameters (fitted and/or fixed) from...
get_specsExtract the fitting specifications from a metabolism model.
get_versionExtract the version of streamMetabolizer that was used to fit...
Kmodel_aggregate_dayAggregate unit values to daily values
Kmodel_allplyFit a K model
load_french_creekLoad a short dataset from French Creek
load_french_creek_stdLoad a short dataset from French Creek using Bob Hall's code
load_french_creek_std_mleGenerate outputs using Bob's code for comparison
load_spring_creekLoad a short dataset from Spring Creek
lookup_google_timezoneUse Google API to determine local time zone
lookup_timezoneDetermine the local time zone from the coordinates
lookup_usgs_elevationUse USGS API (USGS Elevation Point Query Service) to...
metabFit a metabolism model to data
metab_bayesBasic Bayesian metabolism model fitting function
metab_bayes-classMetabolism model fitted by Bayesian MCMC
metab_inputsDescribe the requirements for an argument to metab()
metab_KmodelCombine a time series of K estimates to predict consistent...
metab_Kmodel-classInterpolation model of daily K for metabolism
metab_mleMaximum likelihood metabolism model fitting function
metab_mle-classMetabolism model fitted by maximum likelihood estimation
metab_modelCreate a metab_model object.
metab_model-classA metabolism model class.
metab_model_interfaceFunctions implemented by any 'streamMetabolizer'-compatible...
metab_nightNighttime regression for K estimation
metab_night-classReaeration model fitted by nighttime regression
metab_night_predict_1plyHelper to predict_DO.metab_model
metab_simSimulate dissolved oxygen data from input data
metab_sim-classData simulator
mle_1plyMake daily metabolism estimates from input parameters
mm_check_mcmc_fileUse an engine-specific function to check the model syntax
mm_check_mcmc_filesCheck the syntax of all Bayesian model files in the package
mm_dataReturn the data types that may be used by metab_models using...
mm_filter_datesFilter unit or daily data by inclusive start & end dates
mm_filter_hoursLimit to a specific time range on each date
mm_filter_valid_daysRemove entries in data
mm_generate_mcmc_fileGenerate the models in inst/models/bayes
mm_generate_mcmc_filesGenerate MCMC code files with all of the desired combinations...
mm_get_timestepReturn the average timestep in days
mm_is_valid_dayValidate one day of data, returning a vector of error strings...
mm_locate_filenameLook for a model file
mm_model_by_plySplit and label data into >=24-hr days for fitting daily...
mm_model_by_ply_prototypeA prototype for the model_fun argument to mm_model_by_ply
mm_nameFind the name of a model by its features
mm_parse_nameParse a model name into its features
mm_predict_DO_1plyHelper to predict_DO.metab_model
mm_predict_metab_1plyHelper to predict_metab.metab_model
mm_sd_to_ciConvert SD columns into CI columns in a data.frame
mm_validate_dataEvaluate whether the data argument is properly formatted.
mm_validate_nameCheck the validity of a model name
mm_valid_namesGet the valid names for a given model type or types
nightreg_1plyMake daily reaeration estimates from input parameters
plot_distribsPlot the prior/posterior distributions of a parameter
plot_DO_predsPlot predictions produced with predict_DO
plot_metab_predsPlot predictions produced with predict_DO
predict_DOPredict DO from a fitted model.
predict_metabPredict metabolism from a fitted model.
predict_metab.metab_KmodelOverride generic predict_metab for metab_Kmodel, which can't...
prepdata_bayesPrepare data for passing to Stan
prepdata_KmodelPrepare data_daily by aggregating any daily data, renaming...
pretty_print_ddatFormat and print a summary of data frame of daily values
print.logs_metabPrint metab logs
print_specsDisplay the specs object
print.specsDisplay the specs object
reviseChange or add named elements of a list
runstan_bayesRun Stan on a formatted data ply
show-metab_model-methodDisplay the metab_model object
show-specs-methodDisplay the specs object
sim_get_parGet a parameter from data_daily, specs, or both
sim_KbSimulate a lnK ~ lnQ relationship in the Kb format
sim_pred_KbPredict ln(K600) as Kb-style function of discharge
specsGenerate a coherent list of model specs
streamMetabolizerFunctions for calculating ecosystem metabolism in streams
streamMetabolizer-deprecatedDeprecated Functions in package streamMetabolizer
summarize_stopwarn_msgsSummarize a vector of warning or error messages
to_degreesConvert radians to degrees
to_radiansConvert degrees to radians
zz_build_docsGenerate doc text for the 'metab()' documentation
zz_tabularFormat a data.frame for inclusion in a roxygen header
USGS-R/streamMetabolizer documentation built on Oct. 21, 2018, 12:09 p.m.