# Soil Gas Analysis and Flux Modeling

## Documentation for package ‘ConFluxPro’ version 1.3.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A B C D E F G H L M N P R S U

## -- A --

alternate | Run parameter variation
alternate_model | Run parameter variation
as_cfp_dat | Model input data
as_cfp_dat.cfp_dat | Model input data

## -- B --

base_dat | Example cfp_dat object
bootstrap_error | Estimate model uncertainty
bootstrap_error.cfp_altres | Estimate model uncertainty
bootstrap_error.cfp_dat | Estimate model uncertainty
bootstrap_error.cfp_fgmod | Estimate model uncertainty
bootstrap_error.cfp_pfmod | Estimate model uncertainty

## -- C --

calculate_bootstrap_error | Estimate model uncertainty
calculate_bootstrap_error.cfp_pfmod | Estimate model uncertainty
cfp_altapply | Apply a function over a list of models
cfp_dat | Model input data
cfp_DSD0_optim | Extract elements from an object
cfp_evenness_factor | Extract elements from an object
cfp_fgmod | Model frame for fg_flux
cfp_fgres | Model result of fg_flux
cfp_funs | Extract elements from an object
cfp_gasdata | Soil gas concentration data
cfp_gasdata.cfp_dat | Soil gas concentration data
cfp_gasdata.data.frame | Soil gas concentration data
cfp_gases | Extract elements from an object
cfp_id_cols | Extract elements from an object
cfp_known_flux_factor | Extract elements from an object
cfp_layered_profile | Object for layered soil profiles
cfp_layers_altmap | Extract elements from an object
cfp_layers_different | Extract elements from an object
cfp_layers_from | Extract elements from an object
cfp_layers_map | Model layers
cfp_layers_map.cfp_dat | Model layers
cfp_layers_map.data.frame | Model layers
cfp_modes | Extract elements from an object
cfp_n_runs | Extract elements from an object
cfp_og_model | Extract elements from an object
cfp_og_model.cfp_altres | Extract elements from an object
cfp_param | Extract elements from an object
cfp_parameter | Get parameter descriptions and units
cfp_params_df | Extract elements from an object
cfp_pfmod | Model frame for pro_flux
cfp_pfres | Model result of pro_flux
cfp_profile | Object for soil profiles
cfp_runmap_type | Extract elements from an object
cfp_run_map | Create a run plan for parameter variation
cfp_soilphys | Soil physical parameters data
cfp_soilphys.cfp_dat | Soil physical parameters data
cfp_soilphys.data.frame | Soil physical parameters data
cfp_zero_flux | Extract elements from an object
cfp_zero_limits | Extract elements from an object
check_soilphys | Check for complete and correct soil physical parameters
combine_models | Combine models
combine_models.cfp_altres | Combine models
combine_models.list | Combine models
combine_models_by_reference | Combine models
complete_soilphys | (Re-)calculate soil physical parameters

## -- D --

D0_massman | Calculate D0
deepflux | Extract flux rates from deep soil
depth_structure | Unique layers depths
depth_structure.cfp_dat | Unique layers depths
depth_structure.cfp_layered_profile | Unique layers depths
depth_structure.cfp_profile | Unique layers depths
discretize_depth | Interpolate over depth to layered profile
discretize_depth.cfp_profile | Interpolate over depth to layered profile
discretize_depth.data.frame | Interpolate over depth to layered profile
DSD0 | Calculate DSD0
DSD0_currie | Calculate DSD0
DSD0_linear | Calculate DSD0
DSD0_millington_quirk | Calculate DSD0
DSD0_moldrup | Calculate DSD0

## -- E --

efflux | Extract efflux rates
efflux.cfp_altres | Extract efflux rates
efflux.cfp_fgres | Extract efflux rates
efflux.cfp_pfres | Extract efflux rates
error_concentration | Estimate model error
error_concentration.cfp_altres | Estimate model error
error_concentration.cfp_fgres | Estimate model error
error_concentration.cfp_pfres | Estimate model error
error_efflux | Estimate model error
error_efflux.cfp_altres | Estimate model error
error_efflux.cfp_fgres | Estimate model error
error_efflux.cfp_pfres | Estimate model error
error_funs | Estimate model error
evaluate_models | Evaluate model runs for calibration
evaluate_models.cfp_altres | Evaluate model runs for calibration
extractors | Extract elements from an object

## -- F --

fg_flux | Flux-gradient method
fg_flux.cfp_dat | Flux-gradient method
fg_flux.cfp_fgmod | Flux-gradient method
fg_flux.cfp_fgres | Flux-gradient method
filter | Filter profiles
filter.cfp_dat | Filter profiles
flux | Re-run model

## -- G --

gasdata | Example soil CO2 concentrations

## -- H --

harm | Harmonic mean

## -- L --

layers_map | Example cfp_layers_map object

## -- M --

make_bootstrap_model | Estimate model uncertainty
make_bootstrap_model.cfp_pfmod | Estimate model uncertainty

## -- N --

nrmse | (Normalized) root mean square error
n_groups | Get number of groups/profiles
n_profiles | Get number of groups/profiles

## -- P --

plot_profile | Plot profiles
production | Extract production rates
pro_flux | Inverse model of production profiles
pro_flux.cfp_dat | Inverse model of production profiles
pro_flux.cfp_pfmod | Inverse model of production profiles
pro_flux.cfp_pfres | Inverse model of production profiles

## -- R --

rmse | (Normalized) root mean square error
run_map | run_map

## -- S --

scale_min_median | Scale a vector by its min and median
season | Get season of a date-time
sobol_calc_indices | Calculate sobol indices
sobol_run_map | Create a run plan for sobol indice calculation
sobol_run_map.cfp_dat | Create a run plan for sobol indice calculation
sobol_run_map.cfp_run_map | Create a run plan for sobol indice calculation
soildiff | Example soil diffusion models
soilphys | Example cfp_soilphys object
soiltemp | Example soil temperature
soilwater | Example soil water content

## -- U --

unique_gases | Get the unique gases of an object