Package index • AEME

All functions

add_deriv_output(): Add derived output variables to model output
add_hum_vars(): Add humidity variables to meteorological data frame
add_hypsograph(): Add hypsograph to Aeme object
add_inflow(): Set inflow data from Aeme object
add_inflows(): Add inflows to Aeme object
add_met(): Add meteorological data to Aeme object
add_obs(): Add observations to Aeme object
add_output(): Add model output to Aeme object
add_param(): Add model parameters to Aeme object
Aeme Aeme-class: Aeme Class
aeme_constructor(): Constructor function for Aeme class
aeme_parameters: Example dataframe used for calibrating AEME models.
aeme_parameters_bgc: Example dataframe used for calibrating the biogeochemistry in the AEME models.
aeme_to_inflow(): Convert AEME model outputs to inflow format
align_depth_data(): Align observation depth data with model data
assess_model(): Assess model performance
build_aeme(): Build model configuration directories
calc_humidity_vars(): Calculate humidity-related variables using GOTM formulas
calc_lake_vol(): Calculate the volume of a lake using bathymetry data or a hypsograph
calc_tli3(): Calculate TLI 3
calc_tli4(): Calculate TLI 4
calc_tli_chla(): Calculate TLI chlorophyll component
calc_tli_n(): Calculate TLI nitrogen component
calc_tli_p(): Calculate TLI phosphorus component
calc_tli_secchi(): Calculate TLI secchi component
catchment_yields: Catchment yields
check_AEME_pkg(): Check if the package is working correctly
check_aeme_vars(): Check AEME variable names
check_glm_nml(): Check GLM nml for common issues
check_gotm_yaml(): Check GOTM YAML configuration file for common issues
check_model(): Check model name and return standardized code
check_model_output(): Check model output
check_obs_var(): Check if a variable is present in the observations for the model time period
check_path(): Check and manage file paths
check_var_in_output(): Check if a variable is present in the model output
configuration(<Aeme>): Access configuration slot
`configuration<-`(<Aeme>): Set configuration in Aeme object
`configuration<-`(): Set configuration in Aeme object
configuration(): Access configuration slot
convert_do(): Convert dissolved oxygen between mg/L and percent saturation
dy_cd_parameters: Example dataset of parameters for the DYRESM-CAEDYM model
estimate_lake_wlev(): Estimate Lake Water Levels with Nudging
estimate_surface_temperature(): Estimate Surface Temperature Using Energy Balance Model
expand_met(): Expand a minimal set of meteorology inputs to a complete set of variables suitable for all models
extrap_hyps(): Extend hypsometry to a greater elevation using linear extrapolation
generate_hypsograph(): Generate a hypsograph curve
generate_var_map_code(): Generate variable mapping code for lake observation data
get_aed_sed_const2d_param(): Get AED sed_const2d parameters
get_aeme_parameters(): Make parameters dataframe for AEME
get_date_index(): Get date index for each model in the AEME object
get_deriv_inputs(): Get derived variables needed for simulation
get_glm_sed_zones(): Get number of sediment zones in GLM-AED model
get_hm_palette(): Get default heatmap palette for a variable
get_hypsograph(): Get hypsograph from Aeme object
get_inflows(): Get inflow data from Aeme object
get_lake(): Get lake data from Aeme object
get_lake_dir(): Get the directory of the lake model setup
get_met(): Get meteorological data from Aeme object
get_model_config_files(): Get model configuration files paths
get_model_controls(): Get model controls
get_model_outfile(): Get model output file
get_model_version(): Get model version
get_mod_obs_vars(): Get modeled observation variables
get_nml_value(): gets a nml value according to an arg_name
get_obs(): Get observations for a given variable from an Aeme object
get_obs_column_names(): Get column names for the observational data frame
get_output_vars(): Get the output variables from an AEME object
get_var(): Get variable from aeme
get_vars_sim(): Get all variables to be simulated, including those that are derived from others.
get_var_indices(): Get variable indices
get_wbal_components(): Get water balance components from AEME object
glm_aed_parameters: Example dataframe used for calibrating the biogeochemistry in the GLM-AED model.
glm_sed_params(): Generate GLM Sediment Parameters
glm_to_aeme(): Load a GLM nml file and convert to aeme object
gotm_wet_parameters: Example dataset of parameters for the GOTM-WET model
inflows(<Aeme>): Access inflows slot
`inflows<-`(<Aeme>): Set inflows in Aeme object
`inflows<-`(): Set inflows in Aeme object
inflows(): Access inflows slot
input(<Aeme>): Access input slot
`input<-`(<Aeme>): Set input in Aeme object
`input<-`(): Set input in Aeme object
input(): Access input slot
input_model_parameters(): Input model parameters
insert_aeme(): Insert default aeme list code snippet.
is_model_error(): Check if object is a model output error
is_strat(): Check if water temperature profile is stratified
key_naming: Model variable naming
lake(<Aeme>): Access lake slot
`lake<-`(<Aeme>): Set lake in Aeme object
`lake<-`(): Set lake in Aeme object
lake(): Access lake slot
lake_obs_to_aeme(): Format lake observation data to AEME format
list_models(): Get a vector of available models
list_mod_obs_vars(): Get the variables that are both in the observation and model output
list_obs_vars(): Get observation variable names
load_configuration(): Load model configuration to the aeme object
load_output(): Load AEME output to the aeme object
lookup_aeme_vars(): View AEME variables
model_controls: Model controls
model_layer_structure: Reference data frame for model layer structure.
names(<Aeme>): Update names Method
o2_at_sat(): Estimate oxygen saturation concentration
observations(<Aeme>): Access observations slot
`observations<-`(<Aeme>): Set observations in Aeme object
`observations<-`(): Set observations in Aeme object
observations(): Access observations slot
open_nc_safe(): Safely open a NetCDF file
outflows(<Aeme>): Access outflows slot
`outflows<-`(<Aeme>): Set outflows in Aeme object
`outflows<-`(): Set outflows in Aeme object
outflows(): Access outflows slot
output(<Aeme>): Access output slot
`output<-`(<Aeme>): Set output in Aeme object
`output<-`(): Set output in Aeme object
output(): Access output slot
parameters(<Aeme>): Access parameters slot
`parameters<-`(<Aeme>): Set parameters in Aeme object
`parameters<-`(): Set parameters in Aeme object
parameters(): Access parameters slot
param_colnames(): Get AEME parameters data frame column names
plot(<Aeme>): Update summary Method
plot_flows(): Plot inflows and/or outflows
plot_fluxes(): Plot fluxes
plot_hyps(): Plot hypsograph
plot_met_tile(): Plot a tile plot of meteorological data
plot_nit(): Plot phytoplankton variables
plot_obs(): Plot observations
plot_output(): Plot AEME output
plot_phs(): Plot phytoplankton variables
plot_phytos(): Plot phytoplankton variables
plot_resid(): Plot model residuals
plot_ts(): Plot multi-variable timeseries
plot_var(): Plot AEME variable
plot_wbal(): Plot water balance components
plot_wbal_annual(): Plot annual water balance components
plot_wbal_comp(): Plot Water Balance Comparison
plot_wbal_summaries(): Plot Water Balance Summaries
plot_wlev(): Plot lake water level
plot_zoops(): Plot phytoplankton variables
precip_status(): Get current precipitation status in Aeme object
read_aed_param_csv() write_aed_param_csv(): Read and write AED parameter CSV files These functions handle reading and writing AED parameter CSV files, ensuring that single quotes are properly managed in column names and specific columns.
read_aeme_from_files(): Read an AEME object from files
read_dy_output(): Read DYRESM output
read_dy_wlev(): Read DYRESM water level output
read_glm_output(): Read GLM netCDF output
read_glm_wlev(): Read GLM lake water level output
read_gotm_flux_output(): Read GOTM flux output
read_gotm_output(): Read GOTM output
read_gotm_profile(): Read GOTM profile file
read_gotm_wlev(): Read GOTM water level output
read_model_config(): Read in model configuration files for a given model and lake directory
read_model_outputs(): Read model outputs and format to AEME standard
read_model_wlev(): Read water level from model output
read_nml(): read in a GLM simulation *.nml file
remove_inflow(): Remove inflow data from Aeme object
remove_outflow(): Remove outflow data from Aeme object
remove_output(): Remove output from AEME object
remove_param(): Remove parameter(s) from Aeme object
run_aeme(): Run aquatic model ensemble
run_dy_cd() run_glm_aed() run_gotm_wet(): Run AEME models
set_aed_sed_const2d(): Setup AED aed_sed_const2d sediment model parameters
set_glm_aed_models(): Set GLM-AED Models
set_gotm_grid(): Set grid for GOTM model
set_inflows(): Set inflow data from Aeme object
set_model_controls(): Set model controls for AEME object
set_nml(): sets values in nml object
set_precip(): Set precipitation as either meteorological input or inflow
set_time(): Set time parameters for an Aeme object
set_vars_sim(): Set simulation variables in model controls
show(<Aeme>): Print Aeme object to the console
summary(<Aeme>): Summarise an Aeme object
time(<Aeme>): Access time slot
`time<-`(<Aeme>): Set time in Aeme object
`time<-`(): Set time in Aeme object
time(): Access time slot
toggle_models(): Toggle between model display names and codes
update_init(): Update initial conditions in AEME object based on lake observations.
water_balance(<Aeme>): Access water_balance slot
`water_balance<-`(<Aeme>): Set water_balance in Aeme object
`water_balance<-`(): Set water_balance in Aeme object
water_balance(): Access water_balance slot
write_aeme_to_files(): Write an AEME object to files
write_configuration(): Write model configuration from the aeme object
write_nml(): write GLM .nml for a GLM simulation
write_yaml(): Write a yaml object to file
yaml_to_aeme(): Convert aeme.yaml file to list