create_biology_prm: create_biology_prm function

In jsgosnell/ratlantis: R package for developing, executing, and assessing Atlantis ecosystem models

Description

This function creates the biology prm file needed for Atlantis

Usage

create_biology_prm(species_data_location = getwd(), species_info_groups_csv,
  flag_data_csv)

Arguments

species_data_location	where csv file with species data is located (defaults to working directory).
species_info_groups_csv	name of csv file with species data. The following column headers are required (all provided by merging generate_group_parameter function): atlantis_type group_name group_code TL_final mean_M max_age min_age_reprod mean_a average coefficient from length-weight relationship mean_b average exponent from length-weight relationship mean_Loo mean_K min_depth max_depth larval_duration planktivoreonly used for vertebrates bear_live_youngonly used for vertebrates, (0 = no, 1 = yes) parental_care does the vertebrate group provides parental care for young until maturity; 0 = no, 1 = yes, -1 = semelparous so die after reproduction feed_while_spawningfor vertebrates and age-structured inverts assessed cover silicon_dep The following columns are optional (will be filled in by function if not provided): num_of_age_classes catch_grazer is the group an opportunistic catch grazers (thief)? defaults to no = 0 ca cb juv_eff adult_eff recruit_group_code flag recruit, needed for verts and stage structured invertebrates, Vertebrate reproduction related flags. The flagrecruit entries refer to the recruitment function used. 1=const, 2=dependent on prim producers (Chla), 3=Beverton-Holt, 4=lognormal, 5=dependent on all plankton groups not just Chla, 6=Bev-Holt with lognormal variation added, 7=Bev-Holt with encourage recovery 8=Bev-Holt with perscribed recovery, 9=Ricker, 10=Standard Bev-Holt (no explict use of spawn included) 11=pupping/calving linearly dependent on maternal condition, 12=pupping/calving a fixed number per adult spawning, 13=forced timeseries of recruitment, defaults to predator 1 = yes, 0 = no, defaults based trophic level, needed for all groups jack_a jack_b recover_mult recover_start PP optional for all living: flag_demPreferred location trend (0 is top, 1 is demersal (?))); whether to weight vertical distributions towards surface or bottom layers when in depths where there were less than complete set of depth layers. defaults to 1 ph_sensitiveis species growth or non predation mortality is sensitive to pH, defaults to 0 ph_sensitive_fecundis species fecundity sensitive to pH, defaults to 0 salinity_impacts_nutritionWhether the species nutritional value is sensitive to salinity or pH (mainly an issue for phytoplankton), default to 0 ph_impacts_availablity# Whether the species availability to predators is sensitive to pH (mainly behaviour in fish), defaults to 0 ph_impacts_growth_and_death# Whether the species growth or non- predation mortality is sensitive to pH, defaults to 0 ph_impact_formForm of the pH effects model applied for the group, defaults to 0, 0 = no effect, 0 = monod, 0 = nonlinear (humped form as of Hinga 0000), 0 = linear monod_inflection_pointMonod inflection point for pH impact function, defaults to 0 optimal_pH_for_nonlinear_functionOptimal pH for nonlinear pH impact function, defaults to 0 ph_correction_scalarCorrection scalar pH for nonlinear pH impact function, defaults to 1 ph_function_coeffCoefficient pH for nonlinear pH impact function, defaults to 1 ph_function_baseBase coefficient pH for nonlinear pH impact function, defaults to 1 ph_correction_scalar2Correction scalar pH for nonlinear pH impact function, defaults to 1 salinity_sensitiveWhether the species is sensitive to salinity, defaults to 0 salinity_correction_scalar# Correction scalar salt for nonlinear salinity impact function, defaults to 1 optional for primary producers: lysis_rate only primary producers defaults to 0 optional for macrophytes: extra_mortality_macrophytes due to scour or nutrient input for mar, defaults to 0 optional for catch grazers: prop_catch_availableAvailabilty of catch to opportunistic catch grazers (thieves); should be space separated vector with entry for each other functional group; defaults to 0 prop_catch_exploitableHow much of each catch is exploitable by opportunistic catch grazers (thieves); should be space separated vector with entry for each other functional group; defaults to 0 needed for all that horizontally migrate migrates_out_of_model defaults to 0, needed for all that horizontally migrate. Maximum number of times juvenile OR adult stages must leave the model domain). For example if juvenile FVT leave once,but adults leave 3 times then enter 3 here. Hard group_code assumes juvenile inverts do not leave model. migrates_out_times_ad Migration dates (days of the year) for adults of groups with stages or for pools moving out of model domain - must be as many entries in these arrays as there are in the flagjXXXMigrate entry for that group, separated by a space. Note an entry of 0 for the flag still requires a single entry for the array (defaults to 364) migrates_in_times_ad Migration dates (days of the year) for adults of groups with stages or for pools returning to the model domain - must be as many entries in these arrays as there are in the migrates_out_model entry for that group, separated by a space. Note an entry of 0 for the flag still requires a single entry for the array (defaults to 0) migrates_out_times_juv Migration dates (days of the year) for juveniles of groups with stages moving out of model domain - must be as many entries in these arrays as there are in the flagjXXXMigrate entry for that group, separated by a space. Note an entry of 0 for the flag still requires a single entry for the array (defaults to 364) migrates_in_times_juv Migration dates (days of the year) for juveniles of groups with stages returning to the model domain - must be as many entries in these arrays as there are in the migrates_out_model entry for that group, separated by a space. Note an entry of 0 for the flag still requires a single entry for the array (defaults to 0) migrate_times_juv days entering and leaving models, separated by a space (defaults to leave 364, enter 1) migrate_period_ad defaults to 1 for those with horizontal migration, period of time adults of groups wiht stages of pools exit or enter model over; put to 0 to stop migration migrate_period_juv defaults to 1 for those wiht horizontal migration, period of time juveniles of groups with stages exit or enter model over; put to 0 to stop migration return_stock_ad defaults to 0, integer number identifying specific stock adult or pool migrants will return to; 0 spreads uniformly across model return_stock_juv defaults to 0, integer number identifying specific stock juvenile migrants will return to; 0 spreads uniformly across model migrants_return_ad proportion of migrating adult or pool biomass that return to the model domain, defaults to 1 migrants_return_juv proportion of migrating adult or pool biomass that return to the model domain, defaults to 1 prop_increase_migrant_size_adProportional increases in size while outside model domain for adults, defaults to 0 prop_increase_migrant_size_juvProportional increases in size while outside model domain for juveniles, defaults to 0 density_depend is movement of group density-dependent, 0 = off, 1 = sedentary, 2 = on, 3 = sticky, 4 = no explicit movement, defaults to 0 for vertebrates, 4 for others; needed for all that horizontally migrate optional for all stage structured inverts: seperate1 = seperate groups (or single pool), 0 = age structured single group, defaults to 0; at this point can only handle one recruit type for these groups optional for all vertebrates: reprod_strength# Vertebrate reproduction strength flags (1=very strong year classes possible, relative strength set using recruitRange and 0=only moderate variation in year class strength possible, mainly for top predators with few young per reproductive event, relative strength set using recruitRangeFlat. defaults to 0) flag_q10Switch indicating whether or not efficiency of assimilation is temperature dependent, defaults 1; 0 = no (same efficiency regardless), 1 = poorer when cooler, 2 = poorer when warmer habitat_dependdefaults to 0, dependent on demersal habitat: 0 = no, 1 = yes 0, defaults to 0 channelindicating whether vertebrate group seeks channels during low tide - in tidal models Kcov_juv Exponent of refuge relationship with biogenic habitat, defaults to 3, verts only Kcov_ad Exponent of refuge relationship with biogenic habitat, defaults to 3, verts only Bcov_juv Coefficient of refuge relationship with biogenic habitat, defaults to .6, verts only Bcov_ad Coefficient of refuge relationship with biogenic habitat, defaults to .6, verts only Acov_juv scalar for relationship with biogenic habitat, defaults to 1, verts only Acov_ad scalar for relationship with biogenic habitat, defaults to 1, verts only swim_speeddefaults to 12500 for fish and sharks, 15000 for birds, 20000 for sharks mammals min_move_temp defaults to minimum temp in model max_move_temp defaults to maximum temp in model prefer_allocate_reservesVertebrate preference for rebuilding reserves over structure; defaults to 4 for fish, 3 for sharks, 3.5 for mammals, and 5 for birds min_length_reproductionif not provided, uses mininum age at reproduction and length weight relationship to estimate fish_respiration_scaling_coefficient scaling of respiration vs weight, defaults .025 for fish, .021 for mammals, .024 for birds, .014 for all others fish_respiration_scaling_exponent exponent of respiration vs weight, defaults to .8 optional for all vertebrates and stage structured inverts: ext_reprod does group reproduce outside model area? 1 = yes, 0 = no, required for all vertebrates and stage-structured invertebrates, defaults to 0 local_recruit defaults to 0, 1 = demersal and piscivorous fish recruit at parental locations, 0 = independent distribution itemflag_temp_sensitiveTemperature sensitivty; defaults to 0 = no, 1 = yes #' optional for all predators: gape_lower_limit defaults to .01, lower Gape size for predators, to determine available prey fish groups. Required for all predators gape_upper_limit defaults to 1, upper Gape size for predators, to determine available prey fish groups. Required for all predators population_refugeSeed bank/population refuge based on consumer intake, if available food below this feeding slows/stops so can't eat out all food. only used by model for predcase =4; defaults to 1 for filler saturation_levelSaturation levels for consumer food intake. only used by model for predcase = 4; defaults to 1 for filler search_volume_invertSearch volume for invertebrate predators - used by size specific Holling type III (predcase 5); defaults to 999 here for filler value search_volume_coefficientSearch volume coefficient for vertebrate predators- used by size specific Holling type III (predcase 5); defaults to planktivorous = 2, pelagic piscivores = 5, demersal/reef = 1 search_volume_exponentSearch volume exponenent for vertebrate predators - used by size specific Holling type III (predcase 5); defaults to .5 for birds and sharks and .35 for mammals and fish handling_time_inverthandling time for invertebrate predators - used by size specific Holling type III (predcase 5); defaults to 999 here for filler value handling_time_coefficienthandling time coefficient for vertebrate predators- used by size specific Holling type III (predcase 5); ; defaults to 999 here for filler value handling_time_exponenthandling time exponenent for vertebrate predators - used by size specific Holling type III (predcase 5); ; defaults to 999 here for filler value optional for all consumers: active 2 = no preference, 1 = day, 0 = night,defaults to 2, needed for all consumers sediment_penetration_depthDepth consumers can dig into, are found down to in the sediment; defaults to .1 for lg_inf; .1 for fish, mammals, sharks, and birds; and .001 for others assimilation_efficiency_on_plantsdefaults to .5 for invertebrates, .1 for vertebrates assimilation_efficiency_on_live_food_and_carriondefaults to .5 for invertebrates, .1 for vertebrates assimilation_efficiency_on_labile_detritusdefaults to .3 for bacteria, .2 for filter feeders, and .1 for everything else assimilation_efficiency_on_refractory_detritusdefaults to .5 for bacteria, .3 for filter feeders, and .1 for everything else flag_X_day k_tur defaults to .1needed for epibenthic groups that are mobile or infaunal (SM_INF, LG_INF, MOB_EP_OTHER) k_irr defaults to 1, needed for epibenthic groups that are infaunal (SM_INF, LG_INF)) temp_coefft_a defaults to .851, needed for all living things, Coefficient A in Gary Griffith temperature function q10 defaults to 2, Exponent in temperature effect on rate parameters q10_method defaults to 0, method of calculating Q10 0 is the 'normal' way of calculating it. 1 is the 'new' climate change method from Gary G. q10_optimal_temp defaults to 0, optimum temperature of each functional group - this is only read in for groups where the q10_method is 1. q10_correction defaults to 0, the q10 correction factor for each functional group - this is only read in for groups where the q10_method is 1. wc defaults to .01 turned_on defaults to 1 (=yes, 0=no) groups$IsTurnedOn=1 overwinter defaults to 0 maxspace restrictions for basal (epibenthic and some infauna) groups, defaults to 5000 lowThreshold spatial factors for filter feeders if using ERSEM formulation, Little space limitation (pop too small) threshThreshold spatial factors for filter feeders if using ERSEM formulation satThreshold spatial factors for filter feeders if using ERSEM formulation, Interference to uptake due to shading home_range defaults to 1, all epxcept primary producers overlap defaults to 1, all except primary producers stock_availability verts only, scalars to determine stock availablity for adults, defaults to 1 assuming no stocks considered (just one big group, should be vector the same length as number of stocks) stock_availability_juv verts only, scalars to determine availablity for juveniles, defaults to 1 assuming no stocks considered (just one big group), should be vector the same length as number of stocks linear_mortality tuning parameter needed for all living organisms, defaults to 0 juvenile_linear_mortality tuning parameter, defaults to 0, needed for stage-structured inverts and vertebrates quadratic_mortality tuning parameter, needed for all living except primary producers, defaults to 0 juvenile_quadratic_mortality tuning parameter, defaults to 0, needed for stage-structured inverts and vertebrates starve mortality due to starvation, only for vertebrates, defaults to 0 oxygen_depth_mortality tuning parameter, Half oxygen mortality depth, inverts except primary producers,defaults to .001 ambient_oxygen_mortality tuning parameter, oxygen dependent mortality due to ambient conditions, inverts except primary producers, defaults to .01 lethal_oxygen_level lethal oxgyen level, inverts except primary producers,defaults to .5 limiting_oxygen_level limiting oxygen level, inverts except primary producers, defults to 10 (min_02)verts only, defaults to 0 mS_FD verts only, defaults to 0 (mortatlity due to fish not included in model), value for each season, separated by a space (defaults to 0) mS_SB verts only, defaults to 0 (mortatlity due to birds and mammals not included in model), value for each season, separated by a space KSPA defaults to guild values, verts only FSM ddefaults to guild values, verts only FSP ddefaults to guild values, verts only rec_stock recruitment param for diffferent stocks of verts, defaults to 1 (no stocks) min_spawn_temp defaults to minimum temp in model max_spawn_temp defaults to maximum temp in model stock_struct verts only, defaults to 1, input as number for each box separated by a space vert_stock_struct verts only, defaults to 1,input as number for each box separated by a space pop_ratio_stock defaults to 1 remin_contrib for small_infaunal, defaults to 0 in_WC defaults to 0 in_sed defaults to 0 epi default to 0 vertically_migrates defaults to 0 horizontally_migrates defaults to 0 fished defaults to 0, is it targeted in fisheries impacted defaults to 0, is it impacted by fisheries TAC defaults to 0, is it controlled by a TAC pred_case needed for all predators, defaults to 0, Predation formulation switches. 0=Holling type II, 1=Holling type I, 2=Holling type III, 3=ECOSIM (currently disabled), 4=min-max, 5=Size specific Holling type III KI default to 0, light saturation, needed for primary producers KS default to 0, Half-sat const for PL growth on Si mg Si m-3 KF default to 0, Half-sat const for PL growth on Micro-nutrient KN default to 0, Primary producer nutrient requirements num_of_genotypesdefaults to 1 num_of_stagesdefaults to 2 for vertebrates, 1 for others num_of_stocksdefaults to 1 num_of_spawnsdefaults to 1 num_of_age_class_sizeset by internal function using maximum age and number of cohorts cultureddefaults to 0
flag_data_csv	csv file containing major flag values for model

Details

This function creates the biology prm file needed by Atlantis.

jsgosnell/ratlantis documentation built on May 20, 2019, 2:08 a.m.