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_outflows(): Add outflows to Aeme object
add_output(): Add model output to Aeme object
add_param(): Add model parameters to Aeme object
aed_options(): Options for the AED biogeochemistry setup in build_aeme()
aed_phyto_pars: Example dataframe of parameters for phytoplankton in the GLM-AED model.
aed_succession_index(): Compute a system-level phytoplankton succession index
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
as.data.frame(<aeme_grouped_var>): Convert a grouped variable to a long-format data frame
assess_aeme() assess_model(): Assess model performance
assess_spin_up(): Assess model sensitivity to initial conditions and required spin-up
bardsley(): Bardsley Coefficient (B) fit function
bias(): Mean bias fit function
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_sed_temp(): GLM sediment-temperature parameters from observed temperature profiles
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(): Check if object is a valid Aeme object
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_loads(): Sanity-check lake loading against simple hydrological benchmarks
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_simstrat_par(): Check Simstrat par file for common issues
check_var_in_output(): Check if a variable is present in the model output
cli_inform_safe(): Inform messages respecting the global AEME.inform option
cli_safe(): Inform messages respecting the global AEME.inform option
collapse_met_daily(): Collapse a sub-daily meteo data frame to a daily time step
`configuration<-`(): Set the configuration slot of an Aeme object
configuration(): Access the configuration slot of an Aeme object
convert_do(): Convert dissolved oxygen between mg/L and percent saturation
d2(): Willmott Index of Agreement (d)
diag_aeme(): Diagnose the three baseline budgets (water, heat, nutrient) at once
diag_heat_budget(): Whole-lake heat budget vs observations: net deficit/surplus, or just surface/bottom redistribution?
diag_nutrient_budget(): Per-variable BGC bias vs observations
diag_water_balance(): Water level bias and drift, against observations and against the model's own starting point
dy_cd_exe_path(): Locate an installed DYRESM-CAEDYM executable
dy_cd_parameters: Example dataset of parameters for the DYRESM-CAEDYM model
effective_configuration(): Model configuration with the model parameters applied
ensemble_summary() as.data.frame(<aeme_ensemble_summary>): Summarise an AEME ensemble across members
estimate_lake_wlev(): Estimate Lake Water Levels with Nudging
estimate_sed_zones(): Estimate sediment zones based on hypsograph
estimate_surface_temperature(): Estimate Surface Temperature Using Energy Balance Model
estimate_zone_fluxes(): Estimate zone-specific sediment fluxes from hypsograph
expand_met(): Expand a minimal set of meteorology inputs to a complete set of variables suitable for all models
expand_zone_ratios(): Convert zone-ratio and zone-offset parameters to per-zone values
extrap_hyps(): Extend hypsometry to a greater elevation using linear extrapolation
find_dy_cd_cfg(): Detect the DYRESM-CAEDYM configuration file within a directory
find_glm_nml(): Detect the GLM hydrodynamic nml file within a directory
nse_loss() kge_loss() kge_prime_loss() log_kge_loss(): Minimise-oriented (loss) variants of NSE / KGE fit functions
flux_to_evap(): Convert latent heat flux to evaporation depth
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_aeme_path(): Get the path to the AEME data
get_config_value(): Get a configuration value from the aeme object. If the key is not present, return the default value.
get_date_index(): Get date index for each model in the AEME object
get_deriv_inputs(): Get derived variables needed for simulation
get_dy_cd_param(): Get one or more parameter values from a DYRESM-CAEDYM configuration
get_glm_param(): Get one or more parameter values from a GLM-AED nml file
get_glm_sed_params(): Get number of sediment zones in GLM-AED model
get_glm_sed_zones(): Get number of sediment zones in GLM-AED model
get_gotm_param(): Get one or more parameter values from a GOTM-WET gotm.yaml file
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_initial_conditions(): Get the stored initial-conditions specification
get_lake(): Get lake data from Aeme object
get_lake_dir(): Get the directory of the lake model setup
get_mean_sea_level_pressure(): Return mean sea level pressure given air temperature, elevation and station pressure.
get_met(): Get meteorological data from Aeme object
get_met_vars(): Get the names and units for the meteorological variables
get_model_config_files(): Get model configuration files paths
get_model_controls(): Get model controls
get_model_dir(): Get the model directory for a given AEME and model.
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_obs_vars(): Show the observation variables present in an Aeme object
get_output_vars(): Get the output variables from an AEME object
get_simstrat_param(): Get one or more parameter values from a Simstrat-AED2 simstrat.par file
get_station_pressure(): Return station pressure from mean sea level pressure.
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
get_wbal_param(): Get water balance parameters
glm_aed_parameters: Example dataframe used for calibrating the biogeochemistry in the GLM-AED model.
glm_aed_parameter_library: Parameter library for the GLM-AED model.
glm_config_to_aeme(): Reconstruct an Aeme object from a GLM-AED model configuration
glm_exe_path(): Locate an installed GLM executable
glm_extra_vars: GLM-AED sediment, flux and diagnostic output variables
glm_sed_params(): Generate GLM Sediment Parameters
glm_to_aeme(): Load a GLM nml file and convert to aeme object
gotm_wet_exe_path(): Locate an installed GOTM-WET executable
gotm_wet_parameters: Example dataset of parameters for the GOTM-WET model
guess_aeme_vars(): Match variable to AEME variable names
`inflows<-`(): Set the inflows slot of an Aeme object
inflows(): Access the inflows slot of an Aeme object
`input<-`(): Set the input slot of an Aeme object
input(): Access the input slot of an Aeme object
input_model_parameters(): Input model parameters
insert_aeme(): Insert default aeme list code snippet.
install_dy_cd(): Install DYRESM-CAEDYM executables for AEME
install_glm_aed(): Install a GLM executable for AEME
install_gotm_wet(): Install a GOTM-WET executable for AEME
install_models(): Install the latest available binary for every AEME model
install_simstrat_aed(): Install a Simstrat-AED executable for AEME
install_simstrat_aed2(): Install a Simstrat-AED2 executable for AEME
is_aeme_output(): Is x a model-output list (standardised or raw)?
is_aeme_output_raw(): Is x a raw (raw_output = TRUE) model-output list?
is_model_error(): Check if object is a model output error
is_strat(): Check if water temperature profile is stratified
is_zone_ratio() zone_base_name(): Identify zone-ratio and zone-offset parameters
key_naming: Model variable naming
kge(): Kling-Gupta Efficiency (KGE) fit function
kge_prime(): Modified Kling-Gupta Efficiency (KGE') fit function
`lake<-`(): Set the lake slot of an Aeme object
lake(): Access the lake slot of an Aeme object
lake_obs_to_aeme(): Format lake observation data to AEME format
latent_heat_flux(): Latent heat flux from a lake surface
list_dy_cd_versions(): List available DYRESM-CAEDYM versions
list_glm_versions(): List available GLM versions
list_gotm_wet_versions(): List available GOTM-WET versions
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
list_simstrat_aed2_versions(): List available Simstrat-AED2 versions
list_simstrat_aed_versions(): List available Simstrat-AED versions
load_configuration(): Load model configuration to the aeme object
load_output(): Load AEME output to the aeme object
log_kge(): Log-transformed Kling-Gupta Efficiency fit function
lookup_aeme_vars(): View AEME variables
mae(): Mean Absolute Error (MAE) fit function
model_controls: Model controls
model_layer_structure: Reference data frame for model layer structure.
names(<Aeme>): Names method for Aeme objects
new_aeme(): Create a new, minimal Aeme object
new_grouped_var(): Construct a "grouped" (non depth x time) model output variable
nmae(): Normalized Mean Absolute Error (NMAE)
nse(): Nash-Sutcliffe Efficiency (NSE) fit function
o2_at_sat(): Estimate oxygen saturation concentration
`observations<-`(): Set the observations slot of an Aeme object
observations(): Access the observations slot of an Aeme object
open_nc_safe(): Safely open a NetCDF file
`outflows<-`(): Set the outflows slot of an Aeme object
outflows(): Access the outflows slot of an Aeme object
`output<-`(): Set the output slot of an Aeme object
output(): Access the output slot of an Aeme object
`parameters<-`(): Set the parameters slot of an Aeme object
parameters(): Access the parameters slot of an Aeme object
param_colnames(): Get AEME parameters data frame column names
encode_param() decode_param_full() decode_param(): Encode and decode full parameter names
pbias(): Percent Bias (PBIAS) fit function
plot(<Aeme>): Plot method for Aeme objects
plot(<aeme_grouped_var>): Plot a grouped variable as a line plot, coloured by its non-time dimensions (e.g. one line per zone)
plot(<kw_regime>): Plot a Kw regime suggestion
plot_assess(): Plot model performance metrics
plot_car(): Plot carbon variables
plot_ensemble(): Plot AEME ensemble output
plot_est_wbal(): Plot estimated water balance diagnostics from an aeme object.
plot_flows(): Plot inflows and/or outflows
plot_fluxes(): Plot fluxes
plot_glm_config(): Visualise GLM-AED model configuration
plot_glm_diagnostics(): Plot GLM-AED diagnostic variables to debug unrealistic oxygen values
plot_glm_output(): Plot a variable from a raw read_glm_output()/read_model_outputs() list
plot_hyps(): Plot hypsograph
plot_loads(): Plot lake loading summary
plot_met_tile(): Plot a tile plot of meteorological data
plot_model_output(): Plot a variable from model output – an Aeme object or a raw output list
plot_nit(): Plot nitrogen variables
plot_obs(): Plot observations
plot_output(): Plot AEME output
plot_output_base(): Base plotting function for AEME output
plot_phs(): Plot phytoplankton variables
plot_phytos(): Plot phytoplankton variables
plot_resid(): Plot model residuals
plot_spin_up(): Plot a spin-up assessment
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 Components
plot_wbal_summaries(): Plot Water Balance Summaries
plot_wbal_ts(): Plot Water Balance Components as Timeseries
plot_weir_calibration(): Visualise calibrated weir parameters (C, h_inv) from calc_water_balance().
plot_wlev(): Plot lake water level
plot_zoops(): Plot phytoplankton variables
precip_status(): Get current precipitation status in Aeme object
print(<kw_regime>): Print a Kw regime suggestion
print(<model_controls>): Print a model controls table
print(<nml>): Print an nml 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_aeme_parquet(): Read from a Parquet store written by write_aeme_parquet()
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_hypsograph(): Load model hypsograph from configuration
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
read_simstrat_dat(): Read Simstrat's raw text output directly
read_simstrat_dat_file(): Read a single Simstrat <var>_out.dat output file
read_simstrat_dat_wlev(): Read Simstrat lake water level from the raw text output
read_simstrat_output(): Read Simstrat-AED2 netCDF output
read_simstrat_wlev(): Read Simstrat-AED2 lake water level output
recommend_calib_plan(): Turn a diagnosis into concrete calibration suggestions
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
reset_wbal_param(): Reset water balance parameters
rmse(): Root Mean Square Error (RMSE) fit function
run_aeme(): Run aquatic model ensemble
run_aeme_ensemble(): Run an ensemble of parameter sets
run_dy_cd() run_glm_aed() run_gotm_wet() run_simstrat_aed2() run_simstrat_aed(): Run AEME models
run_glm_aed_diagnostics(): Run GLM-AED diagnostics
run_model_test(): Run a single what-if model scenario from a path alone
r_pearson(): Pearson Correlation Coefficient (r)
r_spearman(): Spearman Rank Correlation Coefficient (rs)
sat_vapour_pressure(): Saturation vapour pressure
score_ensemble(): Skill scores for an AEME ensemble
set_aed_sed_const2d(): Setup AED aed_sed_const2d sediment model parameters
set_aed_totals(): Setup AED aed_totals parameters
set_dy_cd_inflows(): Set inflow data for a DYRESM-CAEDYM simulation directory
set_dy_cd_init(): Set initial conditions for a DYRESM-CAEDYM simulation
set_dy_cd_outflows(): Set outflow data for a DYRESM-CAEDYM simulation directory
set_dy_cd_param(): Set one or more parameter values in a DYRESM-CAEDYM configuration
set_glm_aed_models(): Set GLM-AED Models
set_glm_inflows(): Set inflow data for a GLM-AED simulation directory
set_glm_init(): Set initial conditions for a GLM-AED simulation
set_glm_outflows(): Set outflow data for a GLM-AED simulation directory
set_glm_outflow_config(): Fine-grained control of the GLM-AED &outflow configuration
set_glm_param(): Set one or more parameter values in a GLM-AED nml file
set_gotm_grid(): Set grid for GOTM model
set_gotm_inflows(): Set inflow data for a GOTM-WET simulation directory
set_gotm_init(): Set initial conditions for a GOTM-WET simulation
set_gotm_outflows(): Set outflow data for a GOTM-WET simulation directory
set_gotm_param(): Set one or more parameter values in a GOTM-WET gotm.yaml file
set_inflows(): Set inflow data from Aeme object
set_initial_conditions(): Set initial conditions for AEME models
set_model_controls(): Set model controls for AEME object
set_nml(): sets values in nml object
set_output_time_step(): Set the model output temporal frequency
set_output_vars(): Restrict a model's written output to the variables of interest
set_precip(): Set precipitation as either meteorological input or inflow
set_simstrat_inflows(): Set inflow data for a Simstrat-AED2 simulation directory
set_simstrat_init(): Set initial conditions for a Simstrat simulation
set_simstrat_outflows(): Set outflow data for a Simstrat-AED2 simulation directory
set_simstrat_param(): Set one or more parameter values in a Simstrat-AED2 simstrat.par file
set_sim_period(): Apply a suggested simulation period to an Aeme object
set_time(): Set time parameters for an Aeme object
set_vars_sim(): Set simulation variables in model controls
set_wbal_param(): Set water balance parameters
show(<Aeme>): Print Aeme object to the console
simstrat_aed2_exe_path(): Locate an installed Simstrat-AED2 executable
simstrat_aed2_parameters: Example dataframe used for calibrating the Simstrat-AED2 model.
simstrat_aed2_parameter_library: Simstrat-AED2 parameter library
simstrat_aed_exe_path(): Locate an installed Simstrat-AED executable
standardise_glm_output(): Standardise a raw GLM-AED output list onto AEME's common depth grid
standardise_inflow(): Standardise inflow variable names and units for AEME
standardise_met(): Standardise meteorological variable names and units for AEME
suggest_kw_regime(): Suggest a light extinction (Kw) regime for GLM
suggest_sim_period(): Choose a simulation period from what the data can support
summarise_loads(): Summarise lake loading from inflows
summarise_obs(): Summarise what the observations actually contain
summary(<Aeme>): Summarise an Aeme object
summary(<nml>): Summarise an nml object
`time<-`(): Set the time slot of an Aeme object
time(): Access the time slot of an Aeme object
toggle_models(): Toggle between model display names and codes
update_init(): Update initial conditions in AEME object based on lake observations.
upgrade_aeme(): Upgrade an Aeme object to the current AEME version
`water_balance<-`(): Set the water_balance slot of an Aeme object
water_balance(): Access the water_balance slot of an Aeme object
write_aeme_parquet(): Export an Aeme object's model output to a partitioned Parquet store
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_simstrat_nc(): Consolidate Simstrat-AED2/AED text output into a single netCDF file
write_yaml(): Write a yaml object to file
yaml_to_aeme() deprecated: Convert aeme.yaml file to list
zone_offset_param(): Parameterise zoned parameters as an anchor value plus offsets
zone_ratio_param(): Parameterise zoned parameters as an anchor value plus ratios