Package index • ConFluxPro

Data formats

Structure your data to make it ready to run the models.

cfp_gasdata(): Soil gas concentration data

cfp_soilphys(): Soil physical parameters data

cfp_layers_map(): Model layers

cfp_dat() as_cfp_dat(): Model input data

Filter and combine models

filter(): Filter profiles

combine_models() combine_models_by_reference(): Combine models

Flux models

Run different models on your data.

fg_flux(): Flux-gradient method

pro_flux(): Inverse model of production profiles

flux(): Re-run model

Model results

Extract derived parameters from models.

efflux(): Extract efflux rates

production(): Extract production rates

deepflux(): Extract flux rates from deep soil

Calibration

Run a parameter variation to calibrate the models.

alternate() alternate_model(): Run parameter variation

cfp_run_map(): Create a run plan for parameter variation

evaluate_models(): Evaluate model runs for calibration

error_concentration() error_efflux(): Estimate model error

cfp_altapply(): Apply a function over a list of models

Uncertainty estimation

Estimate the uncertainty of the model result via a bootstrapping approach.

bootstrap_error() make_bootstrap_model() calculate_bootstrap_error(): Estimate model uncertainty

Model frames

Objects that define and hold the results of the models. These functions are mostly internal.

cfp_fgmod(): Model frame for fg_flux

cfp_fgres(): Model result of fg_flux

cfp_pfmod(): Model frame for pro_flux

cfp_pfres(): Model result of pro_flux

Profiles

Object types for soil profiles

cfp_profile(): Object for soil profiles

cfp_layered_profile(): Object for layered soil profiles

Data preparation

discretize_depth(): Interpolate over depth to layered profile

complete_soilphys(): (Re-)calculate soil physical parameters

check_soilphys(): Check for complete and correct soil physical parameters

Diffusion parameter

DSD0_millington_quirk() DSD0_moldrup() DSD0_currie() DSD0_linear(): Calculate DSD0

D0_massman(): Calculate D0

Extractors

cfp_og_model() cfp_id_cols() cfp_gases() cfp_modes() cfp_param() cfp_funs() cfp_zero_flux() cfp_zero_limits() cfp_DSD0_optim() cfp_evenness_factor() cfp_known_flux_factor() cfp_runmap_type() cfp_params_df() cfp_n_runs() cfp_layers_different() cfp_layers_from() cfp_layers_altmap(): Extract elements from an object

Mathematical formulas

rmse() nrmse(): (Normalized) root mean square error

harm(): Harmonic mean

scale_min_median(): Scale a vector by its min and median

Utility

cfp_parameter(): Get parameter descriptions and units

plot_profile(): Plot profiles

season(): Get season of a date-time

depth_structure(): Unique layers depths

unique_gases(): Get the unique gases of an object

n_groups() n_profiles(): Get number of groups/profiles

Sensitivity analysis

Sensitivity analysis for model input parameter. Experimental.

sobol_run_map() experimental: Create a run plan for sobol indice calculation

sobol_calc_indices() experimental: Calculate sobol indices

Example data

base_dat: Example cfp_dat object

gasdata: Example soil CO2 concentrations

layers_map: Example cfp_layers_map object

soildiff: Example soil diffusion models

soilphys: Example cfp_soilphys object

soiltemp: Example soil temperature

soilwater: Example soil water content

Deprecated functions

run_map() deprecated: run_map