Package index • AEME

All functions

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.

align_depth_data(): Align observation depth data with model data

assess_model(): Assess model performance

build_aeme(): Build model configuration directories

catchment_yields: Catchment yields

check_model_output(): Check model output

check_obs_var(): Check if a variable is present in the observations for the model time period

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

expand_met(): Expand a minimal set of meteorology inputs to a complete set of variables suitable for all models

extrap_hyps(): Extend hypsmetry to a greater elevation using linear extrapolation

generate_hypsograph(): Generate a hypsograph curve

get_lake_dir(): Get the directory of the lake model setup

get_model_controls(): Get model controls

get_model_outfile(): Get model output file

get_mod_obs_vars(): Get the variables that are both in the observation and model output

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(): Get observation variable names

get_output_vars(): Get the output variables from an AEME object

get_var(): Get variable from aeme

get_var_indices(): Get variable indices

glm_aed_parameters: Example dataframe used for calibrating the biogeochemistry in the GOTM-WET model.

gotm_wet_parameters: Example dataframe used for calibrating the biogeochemistry in 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.

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

load_configuration(): Load model configuration to the aeme object

load_output(): Load AEME output to the aeme object

model_controls: Model controls

model_layer_structure: Reference data frame for model layer structure.

names(<Aeme>): Update names Method

observations(<Aeme>): Access observations slot

`observations<-`(<Aeme>): Set observations in Aeme object

`observations<-`(): Set observations in Aeme object

observations(): Access observations slot

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

plot(<Aeme>,<ANY>): 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_zoops(): Plot phytoplankton variables

read_nml(): read in a GLM simulation *.nml file

remove_output(): Remove output from AEME object

retrieve_params(): Retrieve parameters for each model

run_aeme(): Run aquatic model ensemble

set_gotm_grid(): Set grid for GOTM model

set_nml(): sets values in nml object

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

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_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