Functions for calculating ecosystem metabolism in streams

This package uses inverse modeling to estimate aquatic photosynthesis and respiration (collectively, metabolism) from time series data on dissolved oxygen, water temperature, depth, and light. The package assists with data preparation, handles data gaps during modeling, and provides tabular and graphical reports of model outputs. Several time-honored methods are implemented along with many promising new variants that produce more accurate and precise metabolism estimates.

Details

See http://usgs-r.github.io/streamMetabolizer for vignettes on the web.

Calculate new input variables

• calc_depth

• calc_DO_sat

• calc_light

Convert existing input variables

• convert_date_to_doyhr

• convert_localtime_to_UTC

• convert_UTC_to_solartime

• convert_k600_to_kGAS

• convert_PAR_to_SW

Model metabolism

• mm_name 1. Choose a model structure

• specs 2. Set the specifications

• metab 3. Fit the model

Inspect model results

• predict_metab

• predict_DO

• plot_metab_preds

• plot_DO_preds

• get_params

• get_fit

• get_mcmc (Bayesian models only)

• get_fitting_time

Inspect model inputs/properties

• get_specs

• get_data

• get_data_daily

• get_info

• get_version