Starting values and parameters
Source:vignettes/articles/starting-values-parameters.Rmd
starting-values-parameters.RmdPlease see vignette("general-background") for a general
overview of arrR. For a quick tutorial of how to use
arrR, please see
vignette("get-started").
To see a full list all needed starting values and parameters, simply
run check_parameters(). Both starting values and parameters
must be provided as a named lists. The package contains a set of default
values you can easily access (default_parameters,
default_starting).
Starting values
| Name | Function | Describtion |
|---|---|---|
| bg_biomass | setup_seafloor() | Starting belowground biomass |
| ag_biomass | setup_seafloor() | Starting aboveground biomass |
| nutrients_pool | setup_seafloor() | Starting nutrients pool |
| detritus_pool | setup_seafloor() | Starting detritus biomass |
| pop_n | setup_fishpop() | Number of fish individuals |
| pop_mean_size | setup_fishpop() | Mean fish individual size |
| pop_sd_size | setup_fishpop() | Standard deviation fish individual size |
Parameters
| Name | Function | Describtion |
|---|---|---|
| bg_biomass_min | rcpp_seagrass_growth() | Minimum belowground biomass |
| bg_biomass_max | rcpp_seagrass_growth() | Maximum belowground biomass |
| bg_v_max | rcpp_seagrass_growth() | Maximum belowground uptake rate |
| bg_k_m | rcpp_seagrass_growth() | Half-saturation belowground nutrient uptake |
| bg_gamma | rcpp_seagrass_growth() | Nutrient content percent per dry weight belowground biomass |
| ag_biomass_min | rcpp_seagrass_growth() | Minimum aboveground biomass |
| ag_biomass_max | rcpp_seagrass_growth() | Maximum aboveground biomass |
| ag_v_max | rcpp_seagrass_growth() | Maximum aboveground uptake rate |
| ag_k_m | rcpp_seagrass_growth() | Half-saturation aboveground nutrient uptake |
| ag_gamma | rcpp_seagrass_growth() | Nutrient content percent per dry weight aboveground biomass |
| seagrass_thres | rcpp_seagrass_growth() | Midpoint or threshold of allocation function |
| seagrass_slope | rcpp_seagrass_growth() | Slope of allocation function |
| seagrass_slough | rcpp_seagrass_growth() | Sloughed fraction of biomass |
| nutrients_diffusion | rcpp_diffuse_values() | Fraction of nutrients that is diffused across neighboring cells |
| nutrients_loss | rcpp_nutr_output() | Fraction of nutrients that exits the system each timestep |
| detritus_mineralization | rcpp_mineralization() | Fraction of detrital biomass that is mineralized |
| detritus_diffusion | rcpp_diffuse_values() | Fraction of detrital biomass that is diffused across neighboring cells |
| detritus_fish_decomp | rcpp_mineralization() | Fraction of fish detrital biomass that is decomposited |
| detritus_fish_diffusion | rcpp_diffuse_values() | Fraction of fish detrital biomass that is diffused across neighboring cells |
| detritus_loss | rcpp_nutr_output() | Fraction of detritus pool that exits the system each timestep |
| move_mean | rcpp_move_rand(), rcpp_move_behav() | Mean movement distance |
| move_sd | rcpp_move_rand() | Standard deviation of movement distance |
| move_border | rcpp_move_behav() | Distance to the AR until individuals are considered to be at the AR |
| move_reef | rcpp_move_behav() | Movement distance directly at the AR |
| move_return | rcpp_move_behav() | Movement distance for returning to the AR |
| pop_reserves_max | rcpp_fishpop_growth(), rcpp_mortality() | Fraction of total biomass that individuals can store as reserves |
| pop_reserves_thres_lo | run_simulation() | Lower boundary of reservers at which individuals leave AR to forage |
| pop_reserves_thres_hi | run_simulation() | Upper boundary of reservers at which individuals leave AR to forage |
| pop_reserves_consump | rcpp_fishpop_growth() | Fraction of reserves that individuals can consume each timestep |
| pop_a | rcpp_fishpop_growth() | Length-weight relationship |
| pop_b | rcpp_fishpop_growth() | Length-weight relationship |
| pop_k | rcpp_fishpop_growth() | Growth coefficient |
| pop_linf | rcpp_fishpop_growth(), rcpp_mortality() | Maximum body length |
| pop_n_body | rcpp_fishpop_growth(), rcpp_mortality() | Nutrient ratio of individual body mass |
| resp_intercept | rcpp_respiration() | Intercept of respiration function |
| resp_slope | rcpp_respiration() | Slope of respiration function |
| resp_temp_low | rcpp_respiration() | Low water temperature for respiration |
| resp_temp_optm | rcpp_respiration() | Optimum water temperature for respiration |
| resp_temp_max | rcpp_respiration() | Maximum water temperature for respiration |