R/create_biology_prm.R
In r4atlantis/ratlantis: R package for developing, executing, and assessing Atlantis ecosystem models
#' create_biology_prm function
#'
#' This function creates the biology prm file needed for Atlantis
#' @param species_data_location where csv file with species data is located (defaults to
#' working directory).
#' @param species_info_groups_csv name of csv file with species data.
#' \itemize{
#' \item {The following column headers are required
#' (all provided by merging generate_group_parameter function):
#' \itemize{
#' \item{atlantis_type}
#' \item{group_name}
#' \item{group_code}
#' \item{TL_final}
#' \item{mean_M}
#' \item{max_age}
#' \item {min_age_reprod}
#' \item {mean_a} {average coefficient from length-weight relationship}
#' \item {mean_b} {average exponent from length-weight relationship}
#' \item {mean_Loo}
#' \item {mean_K}
#' \item {min_depth}
#' \item{max_depth}
#' \item{larval_duration}
#' \item{planktivore}{only used for vertebrates}
#' \item{bear_live_young}{only used for vertebrates, (0 = no, 1 = yes) }
#' \item{parental_care} {does the vertebrate group provides parental care for
#' young until maturity; 0 = no, 1 = yes, -1 = semelparous so die after reproduction}
#' \item{feed_while_spawning}{for vertebrates and age-structured inverts}
#' \item{assessed}
#' \item{cover}
#' \item{silicon_dep}
#' }
#' }
#' \item {The following columns are optional (will be filled in by function if not
#' provided):
#' \itemize{
#' \item{num_of_age_classes}
#' \item{catch_grazer} {is the group an opportunistic catch grazers (thief)?
#' defaults to no = 0}
#' \item{ca}
#' \item{cb}
#' \item{juv_eff}
#' \item{adult_eff}
#' \item{predator} {1 = yes, 0 = no, defaults based trophic level, needed for all
#' groups}
#' \item{jack_a}
#' \item{jack_b}
#' \item{optional for all living:
#' \itemize{
#' \item{flag_dem}{Preferred 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}
#' \item{ph_sensitive}{is species growth or non predation mortality is sensitive
#' to pH, defaults to 0}
#' \item{ph_sensitive_fecund}{is species fecundity sensitive to pH, defaults
#' to 0}
#' \item{salinity_impacts_nutrition}{Whether the species nutritional value is
#' sensitive to salinity or pH (mainly an issue for phytoplankton), default to
#' 0}
#' \item{ph_impacts_availablity}{# Whether the species availability to
#' predators is sensitive to pH (mainly behaviour in fish), defaults to 0}
#' \item{ph_impacts_growth_and_death}{# Whether the species growth or non-
#' predation mortality is sensitive to pH, defaults to 0}
#' \item{ph_impact_form}{Form 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}
#' \item{monod_inflection_point}{Monod inflection point for pH impact function,
#' defaults to 0}
#' \item{optimal_pH_for_nonlinear_function}{Optimal pH for nonlinear pH
#' impact function, defaults to 0}
#' \item{ph_correction_scalar}{Correction scalar pH for nonlinear pH impact
#' function, defaults to 1}
#' \item{ph_function_coeff}{Coefficient pH for nonlinear pH impact function,
#' defaults to 1}
#' \item{ph_function_base}{Base coefficient pH for nonlinear pH impact function, defaults to 1}
#' \item{ph_correction_scalar2}{Correction scalar pH for nonlinear pH impact function, defaults to 1}
#' \item{salinity_sensitive}{Whether the species is sensitive to salinity, defaults to 0}
#' \item{salinity_correction_scalar}{# Correction scalar salt for nonlinear salinity
#' impact function, defaults to 1}
#' }
#' }
#' \item{optional for primary producers:
#' \itemize{
#' \item{lysis_rate} {only primary producers defaults to 0}
#' }
#' }
#' \item{optional for macrophytes:
#' \itemize{
#' \item{extra_mortality_macrophytes} {due to scour or nutrient input for mar, defaults to 0}
#' }
#' }
#' \item{optional for catch grazers:
#' \itemize{
#' \item{prop_catch_available}{Availabilty of catch to opportunistic catch grazers (thieves);
#' should be space separated vector with entry for each other functional group; defaults to 0}
#' \item{prop_catch_exploitable}{How 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}
#' }
#' }
#'
#' \item{needed for all that horizontally migrate
#' \itemize{
#' \item{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.}
#' \item{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)}
#' \item{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)}
#' \item{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)}
#' \item{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)}
#' \item{migrate_times_juv} {days entering and leaving models, separated by a space
#' (defaults to leave 364, enter 1)}
#' \item{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}
#' \item{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}
#' \item{return_stock_ad} {defaults to 0, integer number identifying specific stock adult or pool migrants will return to; 0
#' spreads uniformly across model}
#' \item{return_stock_juv} {defaults to 0, integer number identifying specific stock juvenile migrants will return to; 0
#' spreads uniformly across model}
#' \item{migrants_return_ad} {proportion of migrating adult or pool biomass that return to the model domain, defaults to 1}
#' \item{migrants_return_juv} {proportion of migrating adult or pool biomass that return to the model domain, defaults to 1}
#' \item{prop_increase_migrant_size_ad}{Proportional increases in size while outside model domain for adults,
#' defaults to 0}
#' \item{prop_increase_migrant_size_juv}{Proportional increases in size while outside model domain for juveniles,
#' defaults to 0}
#' \item{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}
#' }
#' }
#' \item{optional for all stage structured inverts:
#' \itemize{
#' \item{seperate}{1 = 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}
#' }
#' }
#' \item{optional for all vertebrates:
#' \itemize{
#' \item{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)}
#' \item{flag_q10}{Switch 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}
#' \item{habitat_depend}{defaults to 0, dependent on demersal habitat: 0 = no,
#' 1 = yes 0, defaults to 0}
#' \item{channel}{indicating whether vertebrate group seeks channels during low
#' tide - in tidal models}
#' \item{Kcov_juv} {Exponent of refuge relationship with biogenic habitat, defaults to
#' 3, verts only}
#' \item{Kcov_ad} {Exponent of refuge relationship with biogenic habitat, defaults to
#' 3, verts only}
#' \item{Bcov_juv} {Coefficient of refuge relationship with biogenic habitat, defaults
#' to .6, verts only}
#' \item{Bcov_ad} {Coefficient of refuge relationship with biogenic habitat, defaults
#' to .6, verts only}
#' \item{Acov_juv} {scalar for relationship with biogenic habitat, defaults to 1, verts only}
#' \item{Acov_ad} {scalar for relationship with biogenic habitat, defaults to 1, verts only}
#' \item{swim_speed}{defaults to 12500 for fish and sharks, 15000 for birds, 20000 for sharks mammals}
#' \item{min_move_temp} {defaults to minimum temp in model}
#' \item{max_move_temp} {defaults to maximum temp in model}
#' \item{prefer_allocate_reserves}{Vertebrate preference for rebuilding reserves over structure;
#' defaults to 4 for fish, 3 for sharks, 3.5 for mammals, and 5 for birds}
#' \item{min_length_reproduction}{if not provided, uses mininum age at reproduction and
#' length weight relationship to estimate}
#' \item{ fish_respiration_scaling_coefficient} {scaling of respiration vs weight, defaults .025 for fish, .021
#' for mammals, .024 for birds, .014 for all others}
#' \item{ fish_respiration_scaling_exponent} {exponent of respiration vs weight, defaults to .8}
#' \item{minimim_oxygen_vertebrates}{minimum tolerated oxygen level for age
#' structured groups (typically vertebrates)}
#' \item{spawning_formulation_constant} {constant in spawning formulation, defaults to guild values}
#' \item{spawning_formulation_fraction} {defaults to guild values}
#' \item{stock_recruitment_scalar} {recruitment parameter for diffferent stocks of verts, defaults to 1
#' for all stocks}
#' \item{recovery_multiplier}{Recruitment modifiers to encourage recovery of
#' stocks, defaults to 1}
#' \item{recover_start_date}{day when recovery will start, only used when recruit_group_code
#' is set to 8, defaults to 999 for dummy value}
#' \item{min_spawn_temp} {defaults to minimum temp in model}
#' \item{max_spawn_temp} {defaults to maximum temp in model}
#' \item{min_spawn_salinity} {defaults to minimum temp in model}
#' \item{max_spawn_salinity} {defaults to maximum temp in model}
#' \item{stock_structure}{defaults to 1 for each box, not sure what this is, needs to
#' be 1 entry for each box separated by space}
#' }
#' }
#' \item{optional for all vertebrates and stage structured inverts:
#' \itemize{
#' \item{ext_reprod} {does group reproduce outside model area? 1 = yes, 0 = no,
#' required for all vertebrates and stage-structured invertebrates, defaults to 0}
#' \item{local_recruit} {defaults to 0,
#' 1 = demersal and piscivorous fish recruit at parental locations, 0 = independent distribution}
#' item{flag_temp_sensitive}{Temperature sensitivty; defaults to 0 = no, 1 = yes}
#' \item{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 12 for birds and mammal, 10 for fish and sharks}
#' \item{recruits_per_individual_per_year}{needed for vertebrates and stage-structured invertebrates, but only used for
#' groups with recruit_group_code = 10 or 12; defaults to 1 (stable population) for each stock; represents biomass of new recruit for
#' stage-structured inverts}
#' \item{primary_production_impact_recruitment}{Coefficient relating primary
#' production to recruitment, linked to recruit_group_code 2, defaults to
#' 999 for dummy value that is not used}
#' \item{ricker_alpha}{parameter needed for recruit_group_code 9, defaults to
#' 999 here for dummy value}
#' \item{ricker_beta}{parameter needed for recruit_group_code 9, defaults to
#' 999 here for dummy value}
#' \item{beverton_holt_alpha}{parameter needed for recruit_group_code 3, defaults to
#' 999 here for dummy value}
#' \item{beverton_holt_beta}{parameter needed for recruit_group_code 3, defaults to
#' 999 here for dummy value}
#' \item{structural and reserve weight of recruits is calculated internally;
#' results are output to "parameters_for_age_classes_of_groups.csv"}
#' }
#' }
#' \item{optional for all fish:
#' \itemize{
#' \item{other_fish_mortality} {mortality due to fish not included
#' in model), value per quarter, separated by a space; defaults to 0}
#' \item{mammal_bird_mortality} {Static seabird and mammal induced mortality of
#' each fish group, per quarter, separated by a space; defaults to 0}
#' }
#' }
#' \item{optional for all predators:
#' \itemize{
#' \item{gape_lower_limit} {defaults to .01, lower Gape size for predators, to determine available prey fish groups. Required for all
#' predators}
#' \item{gape_upper_limit} {defaults to 1, upper Gape size for predators, to determine available prey fish groups. Required for all
#' predators}
#' \item{population_refuge}{Seed 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}
#' \item{saturation_level}{Saturation levels for consumer food intake. only used by model for predcase = 4; defaults to 1 for filler}
#' \item{search_volume_invert}{Search volume for invertebrate predators -
#' used by size specific Holling type III (predcase 5); defaults to 999 here for filler value }
#' \item{search_volume_coefficient}{Search volume coefficient for vertebrate predators-
#' used by size specific Holling type III (predcase 5);
#' defaults to planktivorous = 2, pelagic piscivores = 5, demersal/reef = 1}
#' \item{search_volume_exponent}{Search 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}
#' \item{handling_time_invert}{handling time for invertebrate predators -
#' used by size specific Holling type III (predcase 5); defaults to 999 here for filler value }
#' \item{handling_time_coefficient}{handling time coefficient for vertebrate predators-
#' used by size specific Holling type III (predcase 5);
#' ; defaults to 999 here for filler value }
#' \item{handling_time_exponent}{handling time exponenent for vertebrate predators -
#' used by size specific Holling type III (predcase 5);
#' ; defaults to 999 here for filler value }
#' }
#' }
#' \item{optional for all consumers:
#' \itemize{
#' \item{active} { 2 = no preference, 1 = day, 0 = night,defaults to 2, needed
#' for all consumers}
#' \item {sediment_penetration_depth}{Depth 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 }
#' \item {assimilation_efficiency_on_plants}{defaults to .5 for invertebrates,
#' .1 for vertebrates}
#' \item {assimilation_efficiency_on_live_food_and_carrion}{defaults to .5 for invertebrates,
#' .1 for vertebrates}
#' \item {assimilation_efficiency_on_labile_detritus}{defaults to .3 for bacteria,
#' .2 for filter feeders, and .1 for everything else}
#' \item {assimilation_efficiency_on_refractory_detritus}{defaults to .5 for bacteria,
#' .3 for filter feeders, and .1 for everything else}
#' \item{food_lost_to_detritus}{Fraction of non-assimilated lost to detritus, defaults to 0}
#' \item{labile_detritus_lost_to_detritus}{Fraction of non-assimilate from
#' labile detrital food lost to detritu, defaults to 0}
#' \item{refractory_detritus_lost_to_detritus}{Fraction of non-assimilate from
#' refractory detrital food lost to detritus, defaults to 0}
#' \item{mortality_contribution_to_detritus}{Fraction of mortality that goes to
#' detritus, defaults to .3}
#' }
#' }
#' \item{k_tur} {defaults to .1}{needed for epibenthic groups that are mobile or infaunal (SM_INF, LG_INF, MOB_EP_OTHER)}
#' \item{k_irr} {defaults to 1, needed for epibenthic groups that are infaunal
#' (SM_INF, LG_INF))}
#' \item{temp_coefft_a} {defaults to .851, needed for all living things,
#' Coefficient A in Gary Griffith temperature function}
#' \item{q10} {defaults to 2, Exponent in temperature effect on rate parameters}
#' \item{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.}
#' \item{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.}
#' \item{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.}
#' \item{wc} {defaults to .01}
#' \item{turned_on} {defaults to 1 (=yes, 0=no) groups$IsTurnedOn=1}
#' \item{overwinter} {defaults to 0}
#' \item{max}{space restrictions for basal (epibenthic and some infauna) groups, defaults to
#' 5000}
#' \item{low}{Threshold spatial factors for filter feeders if using ERSEM formulation, Little space limitation (pop too small) }
#' \item{thresh}{Threshold spatial factors for filter feeders if using ERSEM formulation }
#' \item{sat}{Threshold spatial factors for filter feeders if using ERSEM formulation, Interference to uptake due to shading }
#' \item{home_range} {defaults to 1, all epxcept primary producers}
#' \item{overlap} {defaults to 1, all except primary producers}
#' \item{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)}
#' \item{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}
#' \item{linear_mortality} {tuning parameter needed for each stage for all living organisms; defaults to 0}
#' \item{quadratic_mortality} {tuning parameter needed for each stage for all living organisms; defaults to 0}
#' \item{juvenile_quadratic_mortality} {tuning parameter, defaults to 0, needed for stage-structured inverts
#' and vertebrates}
#' \item{starve} {mortality due to starvation, only for vertebrates, defaults to 0}
#' \item{oxygen_depth_mortality} {tuning parameter, Half oxygen mortality depth, inverts except
#' primary producers,defaults to .001}
#' \item{ambient_oxygen_mortality} {tuning parameter, oxygen dependent mortality due to ambient conditions, inverts except
#' primary producers, defaults to .01}
#' \item{lethal_oxygen_level} {lethal oxgyen level, inverts except primary producers,defaults to .5}
#' \item{limiting_oxygen_level} {limiting oxygen level, inverts except primary producers, defults to 10}
#' \item{other_fish_mortality} {fish only, defaults to 0 (mortatlity due to fish not included
#' in model), value for each season, separated by a space (defaults to 0)}
#' \item{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}
#' \item{FSP} {defaults to guild values, verts only}
#' \item{vert_stock_struct} {verts only, defaults to 1,input as number for each box
#' separated by a space}
#' \item{pop_ratio_stock} {defaults to 1}
#' \item{remin_contrib}{ for small_infaunal, defaults to 0}
#' \item{in_WC} {defaults to 0}
#' \item{in_sed} {defaults to 0}
#' \item{epi} {default to 0}
#' \item{vertically_migrates} {defaults to 0}
#' \item{horizontally_migrates} {defaults to 0}
#' \item{fished} {defaults to 0, is it targeted in fisheries}
#' \item{impacted} {defaults to 0, is it impacted by fisheries}
#' \item{TAC} {defaults to 0, is it controlled by a TAC}
#' \item{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}
#' \item{KI} {default to 0, light saturation, needed for primary producers}
#' \item{KS} {default to 0, Half-sat const for PL growth on Si mg Si m-3}
#' \item{KF} {default to 0, Half-sat const for PL growth on Micro-nutrient}
#' \item{KN} {default to 0, Primary producer nutrient requirements }
#' \item{num_of_genotypes}{defaults to 1}
#' \item{num_of_stages}{defaults to 2 for vertebrates, 1 for others}
#' \item{num_of_stocks}{defaults to 1}
#' \item{num_of_spawns}{{defaults to 1}}
#' \item{num_of_age_class_size}{set by internal function using maximum age and
#' number of cohorts}
#' \item{cultured}{defaults to 0}
#' }
#' }
#' }
# need to add file here wiht mum, clearance, and other values. for now these just default
# to value in group_code to keep everything clean
# @param invert_mum_and_clearance_csv name of csv file that must contain the
# following column headers
# \itemize{
# \item{group_code}
# \item{mum}
# \item{clearance}
# \item{KI}{Light saturation}
# \item{KN}{Half-sat const for PL growth on Micro-nutrient}
# \item{KS}{Half-sat const for PL growth on Si mg Si m-3}
# \item{KF}{Half-sat const for PL growth on Micro-nutrient}
# item{max}{space restrictions for basal (epibenthic and some infauna) groups}
# \item{in_WC} {defaults to 0}
# \item{in_sed} {defaults to 0}
# \item{epi} {default to 0}
# \item{vertically_migrates} {defaults to 0}
# \item{horizontally_migrates} {defaults to 0}
# }
#' @param flag_data_csv csv file containing major flag values for model
#' @details This function creates the biology prm file needed by Atlantis.
#' @keywords biology prm
#' @export
create_biology_prm <- function(species_data_location = getwd(), species_info_groups_csv,
flag_data_csv){
species_input <- read.csv(paste(species_data_location, "/", species_info_groups_csv, sep=""),
header = T, strip.white = T)
flag_data <- read.csv(paste(species_data_location, "/",flag_data_csv, sep=""),
header=T)
#grab map info from flag_data
NumberofHabitats <- as.numeric(as.character(flag_data[flag_data$Flag == "#NumberofHabitats","Value"]))
MaxDepth <- as.numeric(as.character(flag_data[flag_data$Flag == "#MaxDepth","Value"]))
MinDepth <- as.numeric(as.character(flag_data[flag_data$Flag == "#MinDepth","Value"]))
NumberofBoxes <- as.numeric(as.character(flag_data[flag_data$Flag == "#NumberofBoxes","Value"]))
NumberofDepthLayers <- as.numeric(as.character(flag_data[flag_data$Flag == "#NumberofDepthLayers","Value"]))
MinTemp <- as.numeric(as.character(flag_data[flag_data$Flag == "#MinTemp","Value"]))
MaxTemp <- as.numeric(as.character(flag_data[flag_data$Flag == "#MaxTemp","Value"]))
MinSalt <- as.numeric(as.character(flag_data[flag_data$Flag == "#MinSalt","Value"]))
MaxSalt <- as.numeric(as.character(flag_data[flag_data$Flag == "#MaxSalt","Value"]))
#constant across all groups
Ntoall <- 0.175438596 #ratio of N to all other elements
drytowet <- 20 #ratio of wet to dry weight
sNtN <- 0.273972603 #ratio of structural N to total N
rNtN <- 0.726027397 #ratio of reserve N to total N
gtot <- 1000000 #ratio of metric tons to grams
#start making other columns in loop
species_input$T_max_from_M <- log(.01)/-species_input$mean_M
species_input$M_from_T_max <- log(.01)/-species_input$max_age
species_input$ypa_FUNC <- NA
species_input$mat_FUNC <- NA
#set number of age classes if not provided by user
if( "num_of_age_classes" %!in% names(species_input)){
for (i in 1:nrow(species_input)){
if(species_input$atlantis_type[i] %in% c("bird", "fish", "mammal", "shark")){
species_input$num_of_age_classes[i] <- 10
}else {species_input$num_of_age_classes[i] <- 1}
}
} else {
#make sure user provided all values
if( !is.numeric(species_input$num_of_age_classes)){
stop(message = "Provided number of age classes are not all numeric")
}
if( any(is.na(species_input$num_of_age_classes))){
stop(message = "Provided number of age classes contains an NA")
}
}
#use independent M estimate if it exists to calculate years per class
# for vertebrate groups
for (i in 1:nrow(species_input)){
if(species_input$atlantis_type[i] %in% c("bird", "fish", "mammal", "shark")){
if(is.na(species_input$mean_M[i]) == T){
species_input$ypa_FUNC[i] <- species_input$max_age[i]/species_input$num_of_age_classes[i]
}
else{species_input$ypa_FUNC[i] <- species_input$T_max_from_M[i]/species_input$num_of_age_classes[i]}
}
}
#for vertebrates, determine age class where maturity starts
for (i in 1:nrow(species_input)){
if(species_input$atlantis_type[i] %in% c("bird", "fish", "mammal", "shark")){
species_input$mat_FUNC[i]=min(ceiling(species_input$min_age_reprod[i]/species_input$ypa_FUNC[i]), species_input$num_of_age_classes[i])
}
#set maturity at 0 for inverts, other that are just pools
else{species_input$mat_FUNC[i]=0}
}
#energetics from Hanson 1997 (Horne 2010)
#maximum feeding rate (clearance) based on allometric relationships between weight and feeding
#see Anderson 2010 for example
cageneral <- .3
cbgeneral <- .7
if( "ca" %!in% names(species_input)){
species_input$ca <- cageneral
}
if( "cb" %!in% names(species_input)){
species_input$cb <- cbgeneral
}
#calculate mum and clearance for vertebrates, also need weights, all for average individual in each size class
#for classes 1-10
#produce separate table with info on size classses for vertebrates
#list variables to be included here
to_be_included <- c("atlantis_type", "AgeClass", "ActualAge", "WetWeight",
"StructN", "ResN", "mum", "clearance", "Decay", "PropAgeDist", "PropJuv", "PropAdults",
"PropBiomass", "PropSpawning", "length")
#make matrix to hold data
#take number of ages classes plus a 0 class for all vertebrate
mean_individual_morphology <- matrix(NA, sum(sum(species_input[species_input$atlantis_type
%in% c("bird", "fish", "mammal", "shark"),]$num_of_age_classes),
length(species_input[species_input$atlantis_type %in% c("bird", "fish", "mammal", "shark"),]$group_code)),
length(to_be_included)+1)
mean_individual_morphology <- as.data.frame(mean_individual_morphology)
names(mean_individual_morphology)=c("group_code", to_be_included)
#loop over species, variables, and age classes
#consider recruits as 0 age class
#to create this, loop over group_code, age classes, and use counter
counter <- 1
for(i in 1:nrow(species_input)){
#add one for larval group
if(species_input$atlantis_type[i] %in% c("bird", "fish", "mammal", "shark")){
for (j in 1:(species_input[species_input$group_code ==
species_input$group_code[i], "num_of_age_classes"]+1)){
mean_individual_morphology$atlantis_type[counter] =
as.character(species_input[species_input$group_code ==
species_input$group_code[i], "atlantis_type"])
mean_individual_morphology$group_code[counter] <- as.character(species_input$group_code[i])
mean_individual_morphology$AgeClass[counter] <- j-1
counter <- counter+1
}}
}
#fill in information with loops
#do age classes and wet weights for verts
#for each age class, this finds actual age, uses VB equation to estimate L, and
#then use length-weight relationship to estimate wet weight
for (i in 1:nrow(mean_individual_morphology)){
if(mean_individual_morphology$atlantis_type[i] %in% c("bird", "fish", "mammal", "shark")){
mean_individual_morphology$ActualAge[i] <- as.numeric(mean_individual_morphology$AgeClass[i]*
species_input[species_input$group_code == mean_individual_morphology$group_code[i], "ypa_FUNC"])
if(mean_individual_morphology$AgeClass[i] > 0){
mean_individual_morphology$WetWeight[i] <- species_input[species_input$group_code ==
mean_individual_morphology$group_code[i], "mean_a"]*
(species_input[species_input$group_code == mean_individual_morphology$group_code[i],
"mean_Loo"]*(1-exp(-1
*species_input[species_input$group_code == mean_individual_morphology$group_code[i],
"mean_K"]*
mean_individual_morphology$ActualAge[i]
)))^species_input[species_input$group_code == mean_individual_morphology$group_code[i],
"mean_b"]
mean_individual_morphology$length[i] <- (mean_individual_morphology$WetWeight[i]/
species_input[species_input$group_code == mean_individual_morphology$group_code[i],
"mean_a"])^(1/species_input[species_input$group_code == mean_individual_morphology$group_code[i],
"mean_b"])
if(mean_individual_morphology$atlantis_type[i] %in% c("fish", "shark")){
mean_individual_morphology$Decay[i]<- exp(-1*species_input[species_input$group_code
== mean_individual_morphology$group_code[i], "mean_M"]*
(mean_individual_morphology$AgeClass[i]-1)*species_input[species_input$group_code
== mean_individual_morphology$group_code[i], "ypa_FUNC"])
} else if(mean_individual_morphology$atlantis_type[i] == "mammal"){
#need to add silers group_code
mean_individual_morphology$Decay[i] <- exp(-1*species_input[species_input$group_code
== mean_individual_morphology$group_code[i], "mean_M"]*
(mean_individual_morphology$AgeClass[i]-1)*species_input[species_input$group_code
== mean_individual_morphology$group_code[i], "ypa_FUNC"])
}else if(mean_individual_morphology$atlantis_type[i] == "bird"){
#birds shoudl be constant
mean_individual_morphology$Decay[i] <- exp(-1*species_input[species_input$group_code ==
mean_individual_morphology$group_code[i], "mean_M"]*
(mean_individual_morphology$AgeClass[i]-1)*species_input[species_input$group_code ==
mean_individual_morphology$group_code[i], "ypa_FUNC"])
}
} else {
mean_individual_morphology$WetWeight[i] <- species_input[species_input$group_code ==
mean_individual_morphology$group_code[i], "mean_a"] *
(species_input[species_input$group_code == mean_individual_morphology$group_code[i],
"mean_Loo"]*(1-exp(-1
*species_input[species_input$group_code == mean_individual_morphology$group_code[i], "mean_K"]*
species_input[species_input$group_code == mean_individual_morphology$group_code[i],
"larval_duration"]/365
)))^species_input[species_input$group_code == mean_individual_morphology$group_code[i],
"mean_b"]
}
}
}
mean_individual_morphology$StructN <- mean_individual_morphology$WetWeight*Ntoall/drytowet*sNtN*1000
mean_individual_morphology$ResN <- mean_individual_morphology$WetWeight*Ntoall/drytowet*rNtN*1000
#mum and clearance for verts
for (i in 1:nrow(mean_individual_morphology)){
if(mean_individual_morphology$AgeClass[i] > 0){
mean_individual_morphology$clearance[i] <- species_input[species_input$group_code ==
mean_individual_morphology$group_code[i],
"ca"]*(mean_individual_morphology$StructN[i] +
mean_individual_morphology$ResN[i])^species_input[species_input$group_code == mean_individual_morphology$group_code[i], "cb"] * .8 * 3.3
mean_individual_morphology$mum[i] <- 10 * mean_individual_morphology$clearance[i]
mean_individual_morphology$PropAgeDist[i] <- mean_individual_morphology$Decay[i]/
sum(mean_individual_morphology[mean_individual_morphology$AgeClass > 0 & mean_individual_morphology$group_code == mean_individual_morphology$group_code[i],
"Decay"])
if(mean_individual_morphology$AgeClass[i] < species_input[species_input$group_code ==
mean_individual_morphology$group_code[i], "mat_FUNC"]){
mean_individual_morphology$PropJuv[i] <- mean_individual_morphology$Decay[i]/
sum(mean_individual_morphology[mean_individual_morphology$AgeClass > 0 & mean_individual_morphology$group_code == mean_individual_morphology$group_code[i] &
mean_individual_morphology$AgeClass < species_input[species_input$group_code == mean_individual_morphology$group_code[i], "mat_FUNC"],
"Decay"])
mean_individual_morphology$PropAdults[i] = 0
if(mean_individual_morphology$AgeClass[i] < (species_input[species_input$group_code == mean_individual_morphology$group_code[i], "mat_FUNC"] - 1)){
mean_individual_morphology$PropSpawning[i] = 0}
else{mean_individual_morphology$PropSpawning[i] = .2}
} else{
mean_individual_morphology$PropJuv[i] <- 0
mean_individual_morphology$PropAdults[i] <- mean_individual_morphology$Decay[i]/
sum(mean_individual_morphology[mean_individual_morphology$AgeClass>0 & mean_individual_morphology$group_code == mean_individual_morphology$group_code[i]&
mean_individual_morphology$AgeClass >= species_input[species_input$group_code == mean_individual_morphology$group_code[i], "mat_FUNC"],
"Decay"])
if(mean_individual_morphology$AgeClass[i] == species_input[species_input$group_code == mean_individual_morphology$group_code[i], "mat_FUNC"]){
mean_individual_morphology$PropSpawning[i] = .8}
else{mean_individual_morphology$PropSpawning[i] = 1}
}
} else{
mean_individual_morphology$mum[i] <- (mean_individual_morphology$StructN[i]+
mean_individual_morphology$ResN[i])/(species_input[species_input$group_code == mean_individual_morphology$group_code[i], "larval_duration"]/365)/365
}
}
#figure out invert mum and clearance formulas, KI, KN, KS, KF
#for now, use values from other models
#invert_mum_clearance <- read.csv("invert_mum_and_clearance.csv")
# mean_individual_morphology <- merge (mean_individual_morphology, invert_mum_clearance,
# all.x=T, all.y=T)
#merge not vert species in model with species_input sheet
# invert_params <- merge(unique(species_input[
#species_input$atlantis_type %!in% c("fish", "mammal", "bird", "shark"),c(
# "group_code", "atlantis_type")]), INVERTSHET)
#merge this info into mean_individual_morphology
mean_individual_morphology <- merge (unique(species_input[,c("group_code", "atlantis_type")]),
mean_individual_morphology,all.x = T,
all.y = T)
mean_individual_morphology$clearance[is.na(mean_individual_morphology$clearance)] <- 1
mean_individual_morphology$mum[is.na(mean_individual_morphology$mum)] <- 1
#parameters needed for availability calculator
if ("juv_eff" %!in% names(species_input)) {species_input$juv_eff <- .1}
if ("adult_eff" %!in% names(species_input)) {species_input$adult_eff <- .1}
for (i in 1:nrow(species_input)){
average_individual <- mean_individual_morphology[mean_individual_morphology$group_code ==
species_input$group_code[i],]
average_juvenile=mean_individual_morphology[mean_individual_morphology$group_code ==
species_input$group_code[i] &
mean_individual_morphology$AgeClass<species_input$mat_FUNC[i]
& mean_individual_morphology$AgeClass!=0,]
average_adult=mean_individual_morphology[mean_individual_morphology$group_code ==
species_input$group_code[i]&
mean_individual_morphology$AgeClass>=species_input$mat_FUNC[i],]
#juvenile calculations
species_input$avgjuvN[i] <- sum(average_juvenile$WetWeight*average_juvenile$PropJuv) *
Ntoall * 1000/drytowet
species_input$JuvGrowthRate[i] <- sum(average_juvenile$mum * average_juvenile$PropJuv) /
species_input$avgjuvN[i]
species_input$Juvclearance[i] <- sum(average_juvenile$clearance * average_juvenile$PropJuv)
#adult calculations
species_input$avgadultN[i] <- sum(average_adult$WetWeight*average_adult$PropAdult)*Ntoall*1000/drytowet
species_input$AdultGrowthRate[i] <- sum(average_adult$mum*average_adult$PropAdult)/species_input$avgadultN[i]
species_input$Adultclearance[i] <- sum(average_adult$clearance*average_adult$PropAdult)
}
species_input$JuvSj <- .3*species_input$JuvGrowthRate/species_input$juv_eff
species_input$AdultSj <- .3*species_input$AdultGrowthRate/species_input$adult_eff
#make columns for type of recruitment, local recruitment, and year class variation
if ("recruit_group_code" %!in% names (species_input)){
species_input$recruit_group_code <- NA
species_input$recruit_group_code[species_input$atlantis_type %in% c("bird", "mammal")] <- 12
species_input$recruit_group_code[species_input$atlantis_type %in% c("fish", "shark")] <- 10
}
if ("local_recruit" %!in% names (species_input)){
species_input$local_recruit <- 0
}
if ("reprod_strength" %!in% names (species_input)){
species_input$reprod_strength <- NA
species_input$reprod_strength[species_input$atlantis_type %in% c("bird", "mammal")] <- 0
species_input$reprod_strength[species_input$atlantis_type %in% c("fish", "shark")] <- 0
}
if( "predator" %!in% names(species_input)){
species_input$predator <- NA
species_input$predator[species_input$TL_final > 2.5] <- 1
species_input$predator[is.na(species_input$predator)] <- 0
}
if( "pred_case" %!in% names(species_input)){
species_input$pred_case <- NA
species_input$pred_case[species_input$predator == 1] <- 0
}
if("horizontally_migrates" %!in% names(species_input)){
species_input$horizontally_migrates <- 1
}
if( "jack_a" %!in% names(species_input)){
species_input$jack_a <- 0
}
if( "jack_b" %!in% names(species_input)){
species_input$jack_b <- 0
}
if( "recovery_multiplier" %!in% names(species_input)){
species_input$recovery_multiplier <- NA
species_input$recovery_multiplier[species_input$atlantis_type %in% c("fish",
"mammal",
"bird", "shark")] <- 999
}
if( "recover_start_date" %!in% names(species_input)){
species_input$recover_start_date <- NA
species_input$recover_start_date[species_input$atlantis_type %in% c("fish",
"mammal",
"bird", "shark")] <- 999
}
if( "flag_dem" %!in% names(species_input)){
species_input$flag_dem <-1
}
if( "flag_q10" %!in% names(species_input)){
species_input$q10 <-1
}
if( "flag_temp_sensitive" %!in% names(species_input)){
species_input$flag_temp_sensitive <- 0
}
# if( "flag_hab_depend" %!in% names(species_input)){
# species_input$flag_hab_depend <- 0
# }
if( "channel" %!in% names(species_input)){
species_input$flag_channel <- 0
}
if( "active" %!in% names(species_input)){
species_input$active <- 2
}
if( "k_tur" %!in% names(species_input)){
species_input$k_tur <- .1
}
if( "k_irr" %!in% names(species_input)){
species_input$k_irr <- 1
}
if( "temp_coefft_a" %!in% names(species_input)){
species_input$temp_coefft_a <- .851
}
if( "q10" %!in% names(species_input)){
species_input$q10 <- 2
}
if( "q10_method" %!in% names(species_input)){
species_input$q10_method <- 0
}
if( "q10_optimal_temp" %!in% names(species_input)){
species_input$q10_optimal_temp <- 0
}
if( "q10_correction" %!in% names(species_input)){
species_input$q10_correction <- 0
}
if( "wc" %!in% names(species_input)){
species_input$wc <- 0.01
}
if("turned_on" %!in% names(species_input)){
species_input$turned_on <- 1
}
if("low" %!in% names(species_input)){
species_input$low <- 500
}
if("thresh" %!in% names(species_input)){
species_input$thresh <- 2500
}
if("sat" %!in% names(species_input)){
species_input$sat <- NA
species_input$sat[species_input$atlantis_type %in% c("fish")] <- 4000
}
if("Kcov_juv" %!in% names(species_input)){
species_input$Kcov_juv <- NA
species_input$Kcov_juv[species_input$atlantis_type %in% c("fish", "mammal", "shark",
"bird")] <- 3
}
if("Kcov_ad" %!in% names(species_input)){
species_input$Kcov_ad <- NA
species_input$Kcov_ad[species_input$atlantis_type %in% c("fish", "mammal", "shark",
"bird")] <- 3
}
if("Bcov_juv" %!in% names(species_input)){
species_input$Bcov_juv <- NA
species_input$Bcov_juv[species_input$atlantis_type %in% c("fish", "mammal", "shark",
"bird")] <- .6
}
if("Bcov_ad" %!in% names(species_input)){
species_input$Bcov_ad <- NA
species_input$Bcov_ad[species_input$atlantis_type %in% c("fish", "mammal", "shark",
"bird")] <- .6
}
if("Acov_juv" %!in% names(species_input)){
species_input$Acov_juv <- NA
species_input$Acov_juv[species_input$atlantis_type %in% c("fish", "mammal", "shark",
"bird")] <- 1
}
if("Acov_ad" %!in% names(species_input)){
species_input$Acov_juv <- NA
species_input$Acov_juv[species_input$atlantis_type %in% c("fish", "mammal", "shark",
"bird")] <- 1
}
if("swim_speed" %!in% names(species_input)){
species_input$swim_speed <- NA
species_input$swim_speed[species_input$atlantis_type %in% c("fish", "shark")] <- 12500
species_input$swim_speed[species_input$atlantis_type %in% c("mammal")] <- 20000
species_input$swim_speed[species_input$atlantis_type %in% c("bird")] <- 15000
}
if("home_range" %!in% names(species_input)){
species_input$home_range <- 1
}
if("overlap" %!in% names(species_input)){
species_input$overlap <- 1
}
if("migrates_out_of_model" %!in% names(species_input)){
species_input$migrates_out_of_model <- NA
species_input$migrates_out_of_model[species_input$horizontally_migrates == 1] <- 0
}
if("migrates_out_times_ad" %!in% names(species_input)){
species_input$migrates_out_times_ad <- 364
}
if("migrates_out_times_juv" %!in% names(species_input)){
species_input$migrates_out_times_juv <- 364
}
if("migrates_in_times_juv" %!in% names(species_input)){
species_input$migrates_in_times_juv <- 0
}
if("migrates_in_times_ad" %!in% names(species_input)){
species_input$migrates_in_times_ad <- 0
}
if("migrate_period_ad" %!in% names(species_input)){
species_input$migrate_period_ad <- NA
species_input$migrate_period_ad[species_input$horizontally_migrates == 0] <- 0
species_input$migrate_period_ad[species_input$horizontally_migrates != 0] <- 1
}
if("migrate_period_juv" %!in% names(species_input)){
species_input$migrate_period_juv <- NA
species_input$migrate_period_juv[species_input$horizontally_migrates == 0] <- 0
species_input$migrate_period_juv[species_input$horizontally_migrates != 0] <- 1
}
if("return_stock_ad" %!in% names(species_input)){
species_input$return_stock_ad <- 0
}
if("return_stock_juv" %!in% names(species_input)){
species_input$return_stock_juv <- 0
}
if("migrants_return_ad" %!in% names(species_input)){
species_input$migrants_return_ad <- 1
}
if("migrants_return_juv" %!in% names(species_input)){
species_input$migrants_return_juv <- 1
}
if("prop_increase_migrant_size_ad" %!in% names(species_input)){
species_input$prop_increase_migrant_size_ad <- 0
}
if("prop_increase_migrant_size_juv" %!in% names(species_input)){
species_input$prop_increase_migrant_size_juv <- 0
}
if("fsp" %!in% names(species_input)){
species_input$fsp <- 0
}
if("stock_availabilty" %!in% names(species_input)){
species_input$stock_availability <- 1
}
if("stock_availabilty_juv" %!in% names(species_input)){
species_input$stock_availability_juv <- 1
}
if("gape_lower_limit" %!in% names(species_input)){
species_input$gape_lower_limit <- NA
species_input$gape_lower_limit[species_input$predator == 1] <- .01
}
if("gape_upper_limit" %!in% names(species_input)){
species_input$gape_upper_limit <- NA
species_input$gape_upper_limit[species_input$predator == 1] <- 1
}
if("population_refuge" %!in% names(species_input)){
species_input$population_refuge <- NA
species_input$population_refuge[species_input$predator == 1] <- 1
}
if("saturation_level" %!in% names(species_input)){
species_input$saturation_level <- NA
species_input$saturation_level[species_input$predator == 1] <- 1
}
if("search_volume_invert" %!in% names(species_input)){
species_input$search_volume_invert <- NA
species_input$search_volume_invert[species_input$predator == 1 &
species_input$atlantis_type %!in% c("fish",
"mammal", "bird", "shark")] <- 999
}
if("search_volume_coefficient" %!in% names(species_input)){
species_input$search_volume_coefficient <- NA
species_input$search_volume_coefficient[species_input$predator == 1 &
species_input$atlantis_type %in% c("fish",
"mammal", "bird", "shark")
& species_input$TL_final < 3.1] <- 2
species_input$search_volume_coefficient[species_input$predator == 1 &
species_input$atlantis_type %in% c("fish",
"mammal", "bird", "shark")
& species_input$TL_final >= 3.1] <- 5
}
if("search_volume_exponent" %!in% names(species_input)){
species_input$search_volume_exponent <- NA
species_input$search_volume_exponent[species_input$predator == 1 &
species_input$atlantis_type %in% c("bird", "shark")] <- .5
species_input$search_volume_exponent[species_input$predator == 1 &
species_input$atlantis_type %in% c("fish",
"mammal")] <- .35
}
if("handling_time_invert" %!in% names(species_input)){
species_input$handling_time_invert <- NA
species_input$handling_time_invert[species_input$predator == 1 &
species_input$atlantis_type %!in% c("fish",
"mammal", "bird", "shark")] <- 999
}
if("handling_time_coefficient" %!in% names(species_input)){
species_input$handling_time_coefficient <- NA
species_input$handling_time_coefficient[species_input$predator == 1 &
species_input$atlantis_type %in% c("fish",
"mammal", "bird", "shark")] <- 999
}
if("handling_time_exponent" %!in% names(species_input)){
species_input$handling_time_exponent <- NA
species_input$handling_time_exponent[species_input$predator == 1 &
species_input$atlantis_type %in% c("fish",
"mammal", "bird", "shark")] <- 999
}
if("pr" %!in% names(species_input)){
species_input$pr <- NA
species_input$pr[species_input$atlantis_type %in% c("fish", "mammal")] <- 3
species_input$pr[species_input$atlantis_type %in% c("bird", "shark")] <- 5
}
if("min_length_reprod" %!in% names(species_input)){
species_input$min_length_reprod <- 0
}
if(" fish_respiration_scaling_coefficient" %!in% names(species_input)){
species_input$ fish_respiration_scaling_coefficient <- NA
species_input$ fish_respiration_scaling_coefficient[species_input$atlantis_type == "fish"] <- .025
species_input$ fish_respiration_scaling_coefficient[species_input$atlantis_type == "mammal"] <- .021
species_input$ fish_respiration_scaling_coefficient[species_input$atlantis_type == "bird"] <- .024
species_input$ fish_respiration_scaling_coefficient[species_input$atlantis_type %!in% c("fish", "mammal", "bird")] <- .014
}
if("prefer_allocate_reserves" %!in% names(species_input)){
species_input$prefer_allocate_reserves <- NA
species_input$prefer_allocate_reserves[species_input$atlantis_type == "fish"] <- 4
species_input$prefer_allocate_reserves[species_input$atlantis_type == "shark"] <- 2
species_input$prefer_allocate_reserves[species_input$atlantis_type == "mammal"] <- 3.5
species_input$prefer_allocate_reserves[species_input$atlantis_type == "bird"] <- 5
}
if(" fish_respiration_scaling_exponent" %!in% names(species_input)){
species_input$ fish_respiration_scaling_exponent <- .8
}
if("lysis_rate" %!in% names(species_input)){
species_input$lysis_rate <- NA
species_input$lysis_rate[species_input$atlantis_type %in% c("phytoben", "microphytobenthos",
"seagrass", "lg_phy", "sm_phy")] <- 0
}
if("starve" %!in% names(species_input)){
species_input$prefer_allocate_reserves <- NA
species_input$starve[species_input$atlantis_type %in% c("fish", "mammal", "bird",
"shark")] <- 0
}
if("oxygen_depth_mortality" %!in% names(species_input)){
species_input$oxygen_depth_mortality <- NA
species_input$oxygen_depth_mortality[species_input$atlantis_type %!in%
c("fish", "mammal", "bird", "shark",
"microphytobenthos", "phytoben",
"sm_phy", "lg_phy", "dinoflag",
"seagrass")] <- 0.001
}
if("ambient_oxygen_mortality" %!in% names(species_input)){
species_input$ambient_oxygen_mortality <- NA
species_input$ambient_oxygen_mortality[species_input$atlantis_type %!in%
c("fish", "mammal", "bird", "shark",
"microphytobenthos", "phytoben",
"sm_phy", "lg_phy", "dinoflag",
"seagrass")] <- 0.01
}
if("lethal_oxygen_level" %!in% names(species_input)){
species_input$lethal_oxygen_level <- NA
species_input$lethal_oxygen_level[species_input$atlantis_type %!in%
c("fish", "mammal", "bird", "shark",
"microphytobenthos", "phytoben",
"sm_phy", "lg_phy", "dinoflag",
"seagrass")] <- 0.5
}
if("limiting_oxygen_level" %!in% names(species_input)){
species_input$limiting_oxygen_level <- NA
species_input$limiting_oxygen_level[species_input$atlantis_type %!in%
c("fish", "mammal", "bird", "shark",
"microphytobenthos", "phytoben",
"sm_phy", "lg_phy", "dinoflag",
"seagrass")] <- 10
}
if("minimim_oxygen_vertebrates" %!in% names(species_input)){
species_input$minimim_oxygen_vertebrates <-NA
species_input$minimim_oxygen_vertebrates[species_input$atlantis_type %in%
c("fish", "mammal", "bird",
"shark")] <- 0
}
if("other_fish_mortality" %!in% names(species_input)){
species_input$other_fish_mortality <-NA
species_input$other_fish_mortality[species_input$atlantis_type %in%
c("fish")] <- c("0 0 0 0")
}
if("mammal_bird_mortality" %!in% names(species_input)){
species_input$mammal_bird_mortality <-NA
species_input$mammal_bird_mortality[species_input$atlantis_type %in%
c("fish")] <- c("0 0 0 0")
}
if("mS_SB" %!in% names(species_input)){
species_input$mS_SB <- c("0, 0, 0, 0")
}
if("spawning_formulation_constant" %!in% names(species_input)){
species_input$spawning_formulation_constant <- NA
species_input$spawning_formulation_constant[species_input$atlantis_type == "shark"] <- 2763.3
species_input$spawning_formulation_constant[species_input$atlantis_type == "fish" &
species_input$TL_final <= 2.5] <- 31.93
species_input$spawning_formulation_constant[species_input$atlantis_type == "fish" &
species_input$TL_final > 2.5] <- 569.65
species_input$spawning_formulation_constant[species_input$atlantis_type == "bird"] <- 193.9
species_input$spawning_formulation_constant[species_input$atlantis_type == "mammal"] <- 38376.9
}
if("spawning_formulation_fraction" %!in% names(species_input)){
species_input$spawning_formulation_fraction <- NA
species_input$spawning_formulation_fraction[species_input$atlantis_type == "shark"] <- .27
species_input$spawning_formulation_fraction[species_input$atlantis_type == "fish" &
species_input$TL_final <= 2.5] <- .246
species_input$spawning_formulation_fraction[species_input$atlantis_type == "fish" &
species_input$TL_final > 2.5] <- .425
species_input$spawning_formulation_fraction[species_input$atlantis_type == "bird"] <- .2
species_input$spawning_formulation_fraction[species_input$atlantis_type == "mammal"] <- .16
}
if("FSP" %!in% names(species_input)){
species_input$FSP <- 0
}
if("min_spawn_temp" %!in% names(species_input)){
species_input$min_spawn_temp <- NA
species_input$min_spawn_temp[species_input$atlantis_type %in% c("fish",
"mammal",
"bird",
"shark")] <- MinTemp
}
if("min_spawn_salinity" %!in% names(species_input)){
species_input$min_spawn_salinity <- NA
species_input$min_spawn_salinity[species_input$atlantis_type %in% c("fish",
"mammal",
"bird",
"shark")] <- MinSalt
}
if("max_move_temp" %!in% names(species_input)){
species_input$max_move_temp <- MaxTemp
}
if("min_move_temp" %!in% names(species_input)){
species_input$min_move_temp <- MinTemp
}
if("max_spawn_temp" %!in% names(species_input)){
species_input$max_spawn_temp <- NA
species_input$max_spawn_temp [species_input$atlantis_type %in% c("fish",
"mammal",
"bird",
"shark")] <- MaxTemp
}
if("max_spawn_salinity" %!in% names(species_input)){
species_input$max_spawn_salinity <- NA
species_input$max_spawn_salinity[species_input$atlantis_type %in% c("fish",
"mammal",
"bird",
"shark")] <- MaxSalt
}
if("stock_structure" %!in% names(species_input)){
species_input$stock_structure <- NA
species_input$stock_structure <- gsub(",", rep = "", toString(rep(1,NumberofBoxes)))
}
if("vert_stock_struct" %!in% names(species_input)){
species_input$vert_stock_struct <- 1
}
if("pop_ratio_stock" %!in% names(species_input)){
species_input$pop_ratio_stock <- 1
}
if("remin_contrib" %!in% names(species_input)){
species_input$remin_contrib <- 0
}
if("vertically_migrates" %!in% names(species_input)){
species_input$vertically_migrates <- 0
}
if("density_depend" %!in% names(species_input)){
species_input$density_depend <- NA
species_input$density_depend[species_input$atlantis_type %in%
c("bird", "fish", "mammal", "shark")] <- 0
species_input$density_depend[species_input$atlantis_type %!in%
c("bird", "fish", "mammal", "shark") & species_input$horizontally_migrates ==
1] <- 4
}
if("in_WC" %!in% names(species_input)){
species_input$in_WC <- 0
}
if("in_sed" %!in% names(species_input)){
species_input$in_sed <- 0
}
if("epi" %!in% names(species_input)){
species_input$epi <- 0
}
if("fished" %!in% names(species_input)){
species_input$fished <- 0
}
if("seperate" %!in% names(species_input)){
species_input$seperate <- 0
}
if("ext_reprod" %!in% names(species_input)){
species_input$ext_reprod <- 0
}
if("impacted" %!in% names(species_input)){
species_input$impacted <- 0
}
if("TAC" %!in% names(species_input)){
species_input$TAC <- 0
}
if("KI" %!in% names(species_input)){
species_input$KI <- 0
}
if("KS" %!in% names(species_input)){
species_input$KS <- 0
}
if("KF" %!in% names(species_input)){
species_input$KF <- 0
}
if("KN" %!in% names(species_input)){
species_input$KN <- 0
}
if("overwinter" %!in% names(species_input)){
species_input$overwinter <- 0
}
if("num_of_genotypes" %!in% names(species_input)){
species_input$num_of_genotypes <- 1
}
if("num_of_stages" %!in% names(species_input)){
species_input$num_of_stages <- NA
species_input$num_of_stages[species_input$atlantis_type %in% c("fish","shark",
"mammal", "bird")] <- 2
species_input$num_of_stages[is.na(species_input$num_of_stages)] <- 1
}
if("linear_mortality" %!in% names(species_input)){
species_input$linear_mortality <- NA
for (i in 1:nrow (species_input)){
if(species_input$atlantis_type[i] %!in% c("lab_det",
"ref_det",
"carrion")){
species_input$linear_mortality[i] <- gsub(",", rep = "", toString(rep(0, species_input$num_of_stages[i])))
}
}
}
if("quadratic_mortality" %!in% names(species_input)){
species_input$quadratic_mortality <- NA
for (i in 1:nrow (species_input)){
if(species_input$atlantis_type[i] %!in% c("lab_det",
"ref_det",
"carrion")){
species_input$quadratic_mortality[i] <- gsub(",", rep = "",
toString(rep(0, species_input$num_of_stages[i])))
}
}
}
if("extra_mortality_macrophytes" %!in% names(species_input)){
species_input$extra_mortality_macrophytes <- NA
species_input$extra_mortality_macrophytes[species_input$atlantis_type %!in% c("phytoben", "seagrass")] <- 0
}
if("num_of_stocks" %!in% names(species_input)){
species_input$num_of_stocks <- 1
}
if("stock_recruitment_scalar" %!in% names(species_input)){
species_input$stock_recruitment_scalar <- NA
for (i in 1:nrow(species_input)){
if(species_input$atlantis_type[i] %in% c("fish",
"mammal", "bird", "shark")){
species_input$stock_recruitment_scalar[i] <- gsub(",", rep = "", toString(rep(1, species_input$num_of_stocks[i])))
}
}
}
if("recruits_per_individual_per_year" %!in% names(species_input)){
species_input$recruits_per_individual_per_year <- NA
for(i in 1:nrow(species_input)){
if(is.na(species_input$recruit_group_code[i]) == F){
species_input$recruits_per_individual_per_year[i] <- gsub(",", rep = "", toString(rep(1, species_input$num_of_stocks[i])))
}
}
}
if("primary_production_impact_recruitment" %!in% names(species_input)){
species_input$primary_production_impact_recruitment <- NA
species_input$primary_production_impact_recruitment[species_input$num_of_stages > 1] <- 999
}
if("ricker_alpha" %!in% names(species_input)){
species_input$ricker_alpha <- NA
species_input$ricker_alpha[species_input$num_of_stages > 1] <- 999
}
if("ricker_beta" %!in% names(species_input)){
species_input$ricker_beta <- NA
species_input$ricker_beta[species_input$num_of_stages > 1] <- 999
}
if("beverton_holt_alpha" %!in% names(species_input)){
species_input$beverton_holt_alpha <- NA
species_input$beverton_holt_alpha[species_input$num_of_stages > 1] <- 999
}
if("beverton_holt_beta" %!in% names(species_input)){
species_input$beverton_holt_beta <- NA
species_input$beverton_holt_beta[species_input$num_of_stages > 1] <- 999
}
if("num_of_spawns" %!in% names(species_input)){
species_input$num_of_spawns <- 1
}
if("cultured" %!in% names(species_input)){
species_input$cultured <- 0
}
if("habitat_depend" %!in% names(species_input)){
species_input$habitat_depend <- 0
}
if("ph_sensitive" %!in% names(species_input)){
species_input$ph_sensitive <- 0
}
if("ph_sensitive_fecund" %!in% names(species_input)){
species_input$ph_sensitive_fecund <- 0
}
if("salinity_impacts_nutrition" %!in% names(species_input)){
species_input$salinity_impacts_nutrition <- 0
}
if("ph_impacts_availability" %!in% names(species_input)){
species_input$ph_impacts_availability <- 0
}
if("ph_impacts_growth_and_death" %!in% names(species_input)){
species_input$ph_impacts_growth_and_death <- 0
}
if("ph_impact_form" %!in% names(species_input)){
species_input$ph_impact_form <- 0
}
if("monod_inflection_point" %!in% names(species_input)){
species_input$monod_inflection_point <- 0
}
if("optimal_pH_for_nonlinear_function" %!in% names(species_input)){
species_input$optimal_pH_for_nonlinear_function <- 0
}
if("ph_correction_scalar" %!in% names(species_input)){
species_input$ph_correction_scalar <- 1
}
if("ph_function_coeff" %!in% names(species_input)){
species_input$ph_function_coeff <- 1
}
if("ph_function_base" %!in% names(species_input)){
species_input$ph_function_base <- 1
}
if("ph_correction_scalar2" %!in% names(species_input)){
species_input$ph_correction_scalar2 <- 1
}
if("salinity_sensitive" %!in% names(species_input)){
species_input$salinity_sensitive <- 0
}
if("salinity_correction_scalar" %!in% names(species_input)){
species_input$salinity_correction_scalar <- 1
}
if("max" %!in% names(species_input)){
species_input$max <- 5000
}
if("catch_grazer" %!in% names(species_input)){
species_input$catch_grazer <- 0
}
if("prop_catch_available" %!in% names(species_input)){
species_input$prop_catch_available <- NA
species_input$prop_catch_available[species_input$catch_grazer == 1] <-
gsub(",", rep = "", toString(rep(0,nrow(species_input))))
}
if("prop_catch_exploitable" %!in% names(species_input)){
species_input$prop_catch_exploitable <- NA
species_input$prop_catch_exploitable[species_input$catch_grazer == 1] <-
gsub(",", rep = "", toString(rep(0,nrow(species_input))))
}
if("sediment_penetration_depth" %!in% names(species_input)){
species_input$sediment_penetration_depth <- NA
species_input$sediment_penetration_depth[species_input$atlantis_type %!in%
c("phytoben", "microphytobenthos",
"seagrass", "lg_phy", "sm_phy")] <- .001
species_input$sediment_penetration_depth[species_input$atlantis_type %in%
c("lg_inf")] <- .1
species_input$sediment_penetration_depth[species_input$atlantis_type %in%
c("fish", "mammal", "shark", "bird")] <- 1
}
if("assimilation_efficiency_on_plants" %!in% names(species_input)){
species_input$assimilation_efficiency_on_plants <- NA
species_input$assimilation_efficiency_on_plants[species_input$atlantis_type %!in%
c("phytoben", "microphytobenthos",
"seagrass", "lg_phy", "sm_phy")] <- .5
species_input$assimilation_efficiency_on_plants[species_input$atlantis_type %in%
c("fish", "mammal", "shark", "bird")] <- .1
}
if("assimilation_efficiency_on_live_food_and_carrion" %!in% names(species_input)){
species_input$assimilation_efficiency_on_live_food_and_carrion <- NA
species_input$assimilation_efficiency_on_live_food_and_carrion[species_input$atlantis_type %!in%
c("phytoben", "microphytobenthos",
"seagrass", "lg_phy", "sm_phy")] <- .5
species_input$assimilation_efficiency_on_live_food_and_carrion[species_input$atlantis_type %in%
c("fish", "mammal", "shark", "bird")] <- .1
}
if("assimilation_efficiency_on_labile_detritus" %!in% names(species_input)){
species_input$assimilation_efficiency_on_labile_detritus <- NA
species_input$assimilation_efficiency_on_labile_detritus[species_input$atlantis_type %!in%
c("phytoben", "microphytobenthos",
"seagrass", "lg_phy", "sm_phy")] <- .1
species_input$assimilation_efficiency_on_labile_detritus[species_input$atlantis_type %in%
c("sed_ep_ff")] <- .2
species_input$assimilation_efficiency_on_labile_detritus[species_input$atlantis_type %in%
c("pl_bact", "sed_bact")] <- .3
}
if("assimilation_efficiency_on_refractory_detritus" %!in% names(species_input)){
species_input$assimilation_efficiency_on_refractory_detritus <- NA
species_input$assimilation_efficiency_on_refractory_detritus[species_input$atlantis_type %!in%
c("phytoben", "microphytobenthos",
"seagrass", "lg_phy", "sm_phy")] <- .1
species_input$assimilation_efficiency_on_refractory_detritus[species_input$atlantis_type %in%
c("sed_ep_ff")] <- .3
species_input$assimilation_efficiency_on_refractory_detritus[species_input$atlantis_type %in%
c("pl_bact", "sed_bact")] <- .5
}
if("food_lost_to_detritus" %!in% names(species_input)){
species_input$food_lost_to_detritus <- NA
species_input$food_lost_to_detritus[species_input$atlantis_type %!in%
c("phytoben", "microphytobenthos",
"seagrass", "lg_phy", "sm_phy")] <- 0
}
if("labile_detritus_lost_to_detritus" %!in% names(species_input)){
species_input$labile_detritus_lost_to_detritus <- NA
species_input$labile_detritus_lost_to_detritus[species_input$atlantis_type %!in%
c("phytoben", "microphytobenthos",
"seagrass", "lg_phy", "sm_phy")] <- 0
}
if("refractory_detritus_lost_to_detritus" %!in% names(species_input)){
species_input$refractory_detritus_lost_to_detritus <- NA
species_input$refractory_detritus_lost_to_detritus[species_input$atlantis_type %!in%
c("phytoben", "microphytobenthos",
"seagrass", "lg_phy", "sm_phy")] <- 0
}
if("mortality_contribution_to_detritus" %!in% names(species_input)){
species_input$mortality_contribution_to_detritus <- NA
species_input$mortality_contribution_to_detritus[species_input$atlantis_type %!in%
c("phytoben", "microphytobenthos",
"seagrass", "lg_phy", "sm_phy")] <- .3
}
#add index
species_input=species_input[order(species_input$atlantis_type, species_input$group_code),]
species_input$index=seq(from=0, to=(nrow(species_input)-1))
#write files for eventual review
write.csv(species_input, "final_group_paramaters_used_in_model.csv")
write.csv(mean_individual_morphology, "parameters_for_age_classes_of_groups.csv")
# start producing actual input files
species_input$group_code <- toupper(species_input$group_code)
mean_individual_morphology$group_code <- toupper(mean_individual_morphology$group_code)
#PRODUCE GROUPS FILE
groups <- data.frame("Code" = species_input$group_code,
"Index" = species_input$index,
"IsTurnedOn" = species_input$turned_on,
"Name" = species_input$group_code,
"LongName" = species_input$group_code,
"NumCohorts" = species_input$num_of_age_classes,
"NumGeneTypes" = species_input$num_of_genotypes,
"NumStages" = species_input$num_of_stages,
"NumSpawns" = species_input$num_of_spawns,
"NumAgeClassSize" = species_input$ypa_FUNC,
"NumStocks" = species_input$num_of_stocks,
"VerticallyMigrates" = species_input$vertically_migrates,
"HorizontallyMigrates" = species_input$horizontally_migrates,
"IsFished" = species_input$fished,
"IsImpacted" = species_input$impacted,
"isTAC" = species_input$TAC,
"GroupType" = toupper(species_input$atlantis_type),
"IsPredator" = species_input$predator,
"IsCover" = species_input$cover,
"IsSiliconDep" = species_input$silicon_dep,
"IsAssessed" = species_input$assessed,
"IsCatchGrazer" = species_input$catch_grazer,
"OverWinters" = species_input$overwinter,
"isCultured" = species_input$cultured,
"isHabDepend" = species_input$habitat_depend)
write.csv(groups, "set_as_groups.csv", row.names = F)
#produce biology.prm file
sink("Biology_prm.prm")
cat("#Biology prm file for Deep-C model \n")
cat(paste("#",Sys.Date(), "\n"))
#group_codes for reference
cat("#list group_codes for reference \n")
for (i in 1:nrow(species_input)){cat(paste("#", as.character(species_input$group_name[i]),
as.character(species_input$group_code[i]), "\n"))}
#start adding flags, check https://wiki.csiro.au/display/Atlantis/Finding+all+the+options+for+the+flags
#read in file with general flags (not tied to groups), this has explanations on it
cat("\n")
#use default values for flags
for (i in 1:nrow(flag_data)){
cat(paste(as.character(flag_data[i,1]), as.character(flag_data[i,2]), sep=" "))
cat("\n")
}
#Array indicating cells effected by coastal degradation (this assumes no degradation)
cat (paste ("Box_degraded", NumberofBoxes,"\n", sep=" "))
cat (rep(0,NumberofBoxes))
cat("\n")
#Set option for regional reporting here, defaults to no regions
cat(paste("regID ", NumberofBoxes, "\n", sep=" "))
cat(rep(0,NumberofBoxes))
cat("\n")
# Differential scaling with depth (must be as many entries as
# number of water column layers * number of changes)
cat(paste("vertTchange_mult ", NumberofDepthLayers, "\n", sep=""))
cat(rep(1,NumberofDepthLayers))
cat("\n")
# Differential scaling with depth (must be as many entries as
# number of water column layers * number of changes)
cat(paste("vertSchange_mult ", NumberofDepthLayers, "\n", sep=""))
cat(rep(1,NumberofDepthLayers))
cat("\n")
# Differential scaling with depth (must be as many entries as
# number of water column layers * number of changes)
cat(paste("vertpHchange_mult ", NumberofDepthLayers, "\n", sep=""))
cat(rep(1,NumberofDepthLayers))
cat("\n")
#start putting in flags for each group
#design is to make one block per group since comparisons easier to see
#in excel
for (i in 1:nrow(species_input)){
cat(paste("# parameters for ", species_input$group_code[i]), "\n")
#for all living
if (species_input$atlantis_type[i] %!in% c("lab_det", "carrion",
"ref_det")){
#flagdem <- flag_dem
if(species_input$num_of_stages[i] > 1){
if (species_input$atlantis_type[i] %in% c("fish", "bird", "mammal",
"shark")){
cat(paste("flagdem",as.character(species_input$group_code[i]), " ",
species_input$flag_dem[i],"\n", sep=""))
} else {
cat(paste("flagdem",as.character(species_input$group_code[i]), " ",
species_input$flagdem[i],"\n", sep=""))
cat(paste("flagdem j",as.character(species_input$group_code[i]), " ",
species_input$flagdem[i],"\n", sep=""))
}} else {
cat(paste("flagdem",as.character(species_input$group_code[i]), " ",
species_input$flag_dem[i],"\n", sep=""))
}
#temperature
cat(paste("temp_coefftA_",as.character(species_input$group_code[i]), " ",
species_input$temp_coefft_a[i],"\n", sep=""))
cat(paste("q10_",as.character(species_input$group_code[i]), " ",
species_input$q10[i],"\n", sep=""))
cat(paste("q10_method_",as.character(species_input$group_code[i]), " ",
species_input$q10_method[i],"\n", sep=""))
cat(paste("q10_optimal_temp_",as.character(species_input$group_code[i]), " ",
species_input$q10_optimal_temp[i],"\n", sep=""))
cat(paste("q10_correction_",as.character(species_input$group_code[i]), " ",
species_input$q10_correction[i],"\n", sep=""))
cat(paste("flagpHsensitive_",as.character(species_input$group_code[i]), " ",
species_input$ph_sensitive[i],"\n", sep=""))
cat(paste("flagfecundsensitive_",as.character(species_input$group_code[i]),
" ", species_input$ph_sensitive_fecund[i],"\n", sep=""))
cat(paste("flagnutvaleffect_",as.character(species_input$group_code[i]), " ",
species_input$salinity_impacts_nutrition[i],"\n", sep=""))
cat(paste("flagpredavaileffect_",as.character(species_input$group_code[i]),
" ", species_input$ph_impacts_availability[i],"\n", sep=""))
cat(paste("flagcontract_tol_",as.character(species_input$group_code[i]),
" ", species_input$ph_impacts_growth_and_death[i],"\n", sep=""))
cat(paste("pHsensitive_model_",as.character(species_input$group_code[i]),
" ", species_input$ph_impact_form[i],"\n", sep=""))
cat(paste("KN_pH_",as.character(species_input$group_code[i]),
" ", species_input$monod_inflection_point[i],"\n", sep=""))
cat(paste("optimal_pH_",as.character(species_input$group_code[i]),
" ", species_input$optimal_pH_for_nonlinear_function[i],"\n", sep=""))
cat(paste("pH_correction_",as.character(species_input$group_code[i]),
" ", species_input$ph_correction_scalar[i],"\n", sep=""))
cat(paste("pH_constA_",as.character(species_input$group_code[i]),
" ", species_input$ph_function_coeff[i],"\n", sep=""))
cat(paste("pH_constB_",as.character(species_input$group_code[i]),
" ", species_input$ph_function_base[i],"\n", sep=""))
cat(paste("contract_tol_",as.character(species_input$group_code[i]),
" ", species_input$ph_correction_scalar2[i],"\n", sep=""))
cat(paste("flagSaltSensitive_",as.character(species_input$group_code[i]),
" ", species_input$salinity_sensitive[i],"\n", sep=""))
cat(paste("salt_correction_",as.character(species_input$group_code[i]),
" ", species_input$salinity_correction_scalar[i],"\n", sep=""))
if(species_input$num_of_stages[i] > 1){
cat(paste(as.character(species_input$group_code[i]), "_mL ", species_input$num_of_stages[i],
"\n", sep=""))
cat(paste(species_input$linear_mortality[i], "\n", sep="" ))
} else {
cat(paste(as.character(species_input$group_code[i]), "_mL ",
species_input$linear_mortality[i],sep="" ))
}
if(species_input$num_of_stages[i] > 1){
cat(paste(as.character(species_input$group_code[i]), "_mQ ", species_input$num_of_stages[i],
"\n", sep=""))
cat(paste(species_input$quadratic_mortality[i], "\n", sep="" ))
} else {
cat(paste(as.character(species_input$group_code[i]), "_mQ ",
species_input$quadratic_mortality[i],sep="" ))
}
if(species_input$atlantis_type[i] %in% c("phytoben", "seagrass")){
cat(paste("mS_", as.character(species_input$group_code[i]), "_T15 ",
species_input$extra_mortality_macrophyte[i],"\n", sep="" ))
}
if(species_input$atlantis_type[i] %in% c("fish", "mammal", "bird", "shark")){
cat(paste("mStarve_", as.character(species_input$group_code[i]), " ",
species_input$starve[i],"\n", sep="" ))
}
if(species_input$atlantis_type[i] %!in% c("fish", "mammal", "bird", "shark",
"microphytobenthos", "phytoben", "sm_phy", "lg_phy", "dinoflag",
"seagrass")){
cat(paste("mD_", as.character(species_input$group_code[i]), " ",
species_input$oxygen_depth_mortality[i],"\n", sep="" ))
cat(paste("mO_", as.character(species_input$group_code[i]), " ",
species_input$ambient_oxygen_mortality[i],"\n", sep="" ))
cat(paste("KO2_", as.character(species_input$group_code[i]), " ",
species_input$lethal_oxygen_level[i],"\n", sep="" ))
cat(paste("KO2lim_", as.character(species_input$group_code[i]), " ",
species_input$limiting_oxygen_level[i],"\n", sep="" ))
}
}
#for all except pelagic bacteria
if (species_input$atlantis_type[i] != "pl_bact"){
cat(paste(as.character(species_input$group_code[i]), "_mindepth ",species_input$min_depth[i],"\n", sep=""))
cat(paste(as.character(species_input$group_code[i]), "_maxdepth ",species_input$max_depth[i],"\n", sep=""))
}
#for all predators
if (species_input$predator[i] == 1){
cat(paste("predcase_", as.character(species_input$group_code[i]), " ",
species_input$pred_case[i], "\n", sep=""))
cat(paste("KLP_", as.character(species_input$group_code[i]), " ",
species_input$gape_lower_limit[i], "\n", sep=""))
cat(paste("KUP_", as.character(species_input$group_code[i]), " ",
species_input$gape_upper_limit[i], "\n", sep=""))
cat(paste("KL_", as.character(species_input$group_code[i]), " ",
species_input$population_refuge[i], "\n", sep=""))
cat(paste("KU_", as.character(species_input$group_code[i]), " ",
species_input$saturation_level[i], "\n", sep=""))
if (species_input$atlantis_type[i] %!in% c("fish", "mammal", "bird", "shark")){
cat(paste("vl_", as.character(species_input$group_code[i]), " ",
species_input$search_volume_invert[i], "\n", sep=""))
cat(paste("ht_", as.character(species_input$group_code[i]), " ",
species_input$handling_time_invert[i], "\n", sep=""))
}else{
cat(paste("vla_", as.character(species_input$group_code[i]), "_T15 ",
species_input$search_volume_coefficient[i], "\n", sep=""))
cat(paste("vlb_", as.character(species_input$group_code[i]), " ",
species_input$search_volume_exponent[i], "\n", sep=""))
cat(paste("hta_", as.character(species_input$group_code[i]), " ",
species_input$handling_time_coefficient[i], "\n", sep=""))
cat(paste("htb_", as.character(species_input$group_code[i]), " ",
species_input$handling_time_exponent[i], "\n", sep=""))
}
}
#for all consumeer
if(species_input$atlantis_type[i] %!in% c("phytoben", "microphytobenthos",
"seagrass", "lg_phy", "sm_phy")){
cat(paste("flag",as.character(species_input$group_code[i]), "day ",
species_input$active[i],"\n", sep = ""))
if (species_input$atlantis_type[i] %!in% c("fish", "mammal", "bird", "shark") |
species_input$num_of_stages[i] == 1){
cat(paste("mum_", as.character(species_input$group_code[i]), "_T15 ",
mean_individual_morphology[mean_individual_morphology$group_code ==
species_input$group_code[i], "mum"], "\n", sep=""))
cat(paste("C_", as.character(species_input$group_code[i]), "_T15 ",
mean_individual_morphology[mean_individual_morphology$group_code ==
species_input$group_code[i], "clearance"], "\n", sep=""))
} else {
#clearance
cat(paste("C_", as.character(species_input$group_code[i]), " ",
species_input$num_of_age_classes[i], "\n", sep=""))
cat(mean_individual_morphology[mean_individual_morphology$group_code ==
species_input$group_code[i] &
mean_individual_morphology$AgeClass>0,"clearance"])
cat("\n")
#mum
cat(paste("mum_", as.character(species_input$group_code[i]), " ",
species_input$num_of_age_classes[i], "\n", sep=""))
cat(mean_individual_morphology[mean_individual_morphology$group_code ==
species_input$group_code[i] & mean_individual_morphology$AgeClass>0,"mum"])
cat("\n")
}
cat(paste("KDEP_", as.character(species_input$group_code[i]), " ",
species_input$sediment_penetration_depth[i],"\n", sep=""))
cat(paste("EPlant_", as.character(species_input$group_code[i]), " ",
species_input$assimilation_efficiency_on_plants[i],"\n", sep=""))
cat(paste("E_", as.character(species_input$group_code[i]), " ",
species_input$assimilation_efficiency_on_live_food_and_carrion[i],"\n", sep=""))
cat(paste("EDL_", as.character(species_input$group_code[i]), " ",
species_input$assimilation_efficiency_on_labile_detritus[i],"\n", sep=""))
cat(paste("EDR_", as.character(species_input$group_code[i]), " ",
species_input$assimilation_efficiency_on_refractory_detritus[i],"\n", sep=""))
cat(paste("FDG_", as.character(species_input$group_code[i]), " ",
species_input$food_lost_to_detritus[i],"\n", sep=""))
cat(paste("FDGDL_", as.character(species_input$group_code[i]), " ",
species_input$labile_detritus_lost_to_detritus[i],"\n", sep=""))
cat(paste("FDGDR_", as.character(species_input$group_code[i]), " ",
species_input$refractory_detritus_lost_to_detritus[i],"\n", sep=""))
cat(paste("FDM_", as.character(species_input$group_code[i]), " ",
species_input$mortality_contribution_to_detritus[i],"\n", sep=""))
}
#for all catch grazers
if(species_input$catch_grazer[i] == 1){
cat(paste("pFC",as.character(species_input$group_code[i]), " ",
nrow(species_input),"\n", sep = ""))
cat(as.character(species_input$prop_catch_available[i]))
cat("\n")
cat(paste("PropCatch_",as.character(species_input$group_code[i]), " ",
nrow(species_input),"\n", sep = ""))
cat(as.character(species_input$prop_catch_exploitable[i]))
cat("\n")
}
#for primary producers
if(species_input$atlantis_type[i] %in% c("phytoben", "microphytobenthos",
"seagrass", "lg_phy", "sm_phy")){
cat(paste("mum_", as.character(species_input$group_code[i]), "_T15 ",
mean_individual_morphology[mean_individual_morphology$group_code ==
species_input$group_code[i], "mum"],
"\n", sep=""))
cat(paste("KI_", as.character(species_input$group_code[i]), "_T15 ",
species_input$KI[i], "\n", sep=""))
cat(paste("KN_", as.character(species_input$group_code[i]), "_T15 ",
species_input$KN[i], "\n", sep=""))
cat(paste("KS_", as.character(species_input$group_code[i]), "_T15 ",
species_input$KS[i], "\n", sep=""))
cat(paste("KF_", as.character(species_input$group_code[i]), "_T15 ",
species_input$KS[i], "\n", sep=""))
cat(paste("KLYS_", as.character(species_input$group_code[i]), " ",
species_input$lysis_rate[i], "\n", sep=""))
}
#for all fish
if(species_input$atlantis_type[i] %in% c("fish")){
cat(paste("mS_FD", as.character(species_input$group_code[i]), " 4",
"\n", sep=""))
cat(as.character(species_input$other_fish_mortality[i]))
cat("\n")
cat(paste("mS_SB", as.character(species_input$group_code[i]), " 4",
"\n", sep=""))
cat(as.character(species_input$mammal_bird_mortality[i]))
cat("\n")
}
#all except primary producers
if(species_input$atlantis_type[i] %!in% c("phytoben", "microphytobenthos",
"seagrass", "lg_phy", "sm_phy")){
cat(paste(as.character(species_input$group_code[i]), "_homerange ",species_input$home_range[i],"\n", sep=""))
cat(paste(as.character(species_input$group_code[i]), "_overlap ",species_input$overlap[i],"\n", sep=""))
}
#for mobile epibenthic groups that are mobile or infaunal
if(species_input$atlantis_type[i] %in% c("sm_inf", "lg_inf", "mob_ep_other")){
cat(paste("KTUR_",as.character(species_input$group_code[i]), " ",
species_input$k_tur[i]))
}
#for epibenthic infaunal groups
if(species_input$atlantis_type[i] %in% c("sm_inf", "lg_inf")){
cat(paste("KIRR_",as.character(species_input$group_code[i]), " ",
species_input$k_irr[i], sep = ""))
}
#for epibenthic and large and small infaunal groups
if(species_input$atlantis_type[i] %in% c("sed_ep_ff", "sed_ep_other", "mob_ep_other", "phytoben", "microphytobenthos", "seagrass", "sm_inf", "lg_inf")){
cat(paste(as.character(species_input$group_code[i]), "max ",species_input$max[i],"\n", sep=""))
}
#for filter feeders
if(species_input$atlantis_type[i] %in% c("SED_EP_FF")){
cat(paste(as.character(species_input$group_code[i]), "_low ", ,species_input$low[i], "\n", sep=""))
cat(paste(as.character(species_input$group_code[i]), "thresh ",species_input$thresh[i],"\n", sep=""))
cat(paste(as.character(species_input$group_code[i]), "_sat ",species_input$sat[i],"\n", sep=""))
}
#for species that horizontally migrate
if(species_input$horizontally_migrates[1] == 1){
cat(paste(as.character(species_input$group_code[i]), "_ddepend_move"," ",
species_input$density_depend[i], "\n", sep=""))
if(species_input$num_of_stages[i] > 1){
if (species_input$atlantis_type[i] %in% c("fish", "bird", "mammal",
"shark")){
cat(paste("flag", as.character(species_input$group_code[i]), "Migrate"," ",
species_input$migrates_out_of_model[i], "\n", sep=""))
} else {
cat(paste("flag", as.character(species_input$group_code[i]), "Migrate"," ", species_input$migrates_out_of_model[i], "\n", sep=""))
cat(paste("flagj", as.character(species_input$group_code[i]), "Migrate"," ", species_input$migrates_out_of_model[i], "\n", sep=""))
}} else {
cat(paste("flag", as.character(species_input$group_code[i]), "Migrate"," ",
species_input$migrates_out_of_model[i], "\n", sep=""))
}
if(species_input$num_of_stages[i] > 1){
cat(paste("j", as.character(species_input$group_code[i]), "_Migrate_Time 1",
"\n", sep=""))
cat(as.character(species_input$migrates_out_times_juv[i]))
cat("\n")
cat(paste("j", as.character(species_input$group_code[i]), "_Migrate_Return 1",
"\n", sep=""))
cat(as.character(species_input$migrates_in_times_juv[i]))
cat("\n")
cat(paste("j", as.character(species_input$group_code[i]), "_Migrate_Period 1",
"\n", sep=""))
cat(as.character(species_input$migrate_period_juv[i]))
cat("\n")
cat(paste("j", as.character(species_input$group_code[i]), "_ReturnStock 1",
"\n", sep=""))
cat(as.character(species_input$return_stock_juv[i]))
cat("\n")
cat(paste("j", as.character(species_input$group_code[i]), "_FSM 1",
"\n", sep=""))
cat(as.character(species_input$migrants_return_juv[i]))
cat("\n")
cat(paste("j", as.character(species_input$group_code[i]), "_FSMG 1",
"\n", sep=""))
cat(as.character(species_input$prop_increase_migrant_size_juv[i]))
cat("\n")
cat(paste(as.character(species_input$group_code[i]), "_Migrate_Time 1",
"\n", sep=""))
cat(as.character(species_input$migrates_out_times_ad[i]))
cat("\n")
cat(paste(as.character(species_input$group_code[i]), "_Migrate_Return 1",
"\n", sep=""))
cat(as.character(species_input$migrates_in_times_ad[i]))
cat("\n")
cat(paste(as.character(species_input$group_code[i]), "_Migrate_Period 1",
"\n", sep=""))
cat(as.character(species_input$migrate_period_ad[i]))
cat("\n")
cat(paste(as.character(species_input$group_code[i]), "_ReturnStock 1",
"\n", sep=""))
cat(as.character(species_input$return_stock_ad[i]))
cat("\n")
cat(paste(as.character(species_input$group_code[i]), "_FSM 1",
"\n", sep=""))
cat(as.character(species_input$migrants_return_ad[i]))
cat("\n")
cat(paste(as.character(species_input$group_code[i]), "_FSMG 1",
"\n", sep=""))
cat(as.character(species_input$prop_increase_migrant_size_ad[i]))
cat("\n")
} else {
cat(paste(as.character(species_input$group_code[i]), "_Migrate_Time 1",
"\n", sep=""))
cat(as.character(species_input$migrates_out_times_ad[i]))
cat("\n")
cat(paste(as.character(species_input$group_code[i]), "_Migrate_Return 1",
"\n", sep=""))
cat(as.character(species_input$migrates_in_times_ad[i]))
cat("\n")
cat(paste(as.character(species_input$group_code[i]), "_Migrate_Period 1",
"\n", sep=""))
cat(as.character(species_input$migrate_period_ad[i]))
cat("\n")
cat(paste(as.character(species_input$group_code[i]), "_ReturnStock 1",
"\n", sep=""))
cat(as.character(species_input$return_stock_ad[i]))
cat("\n")
cat(paste(as.character(species_input$group_code[i]), "_FSM 1",
"\n", sep=""))
cat(as.character(species_input$migrants_return_ad[i]))
cat("\n")
cat(paste(as.character(species_input$group_code[i]), "_FSMG 1",
"\n", sep=""))
cat(as.character(species_input$prop_increase_migrant_size_ad[i]))
cat("\n")
}
}
#for all vertebrates and stage-structured inverts
if (species_input$atlantis_type[i] %in% c("fish", "mammal", "bird", "shark") |
species_input$num_of_stages[i] > 1){
#flagrecruit <- flag_recruit
if (species_input$atlantis_type[i] %in% c("fish", "mammal", "bird", "shark")){
cat(paste("flagrecruit",as.character(species_input$group_code[i]), " ",
species_input$recruit_group_code[i], "\n", sep=""))
} else{
cat(paste("flagrecruit",as.character(species_input$group_code[i]), " ",
species_input$recruit_group_code[i], "\n", sep=""))
cat(paste("flagseperate",as.character(species_input$group_code[i]), " ",
species_input$seperate[i], "\n", sep=""))
}
cat(paste("KDENR_",as.character(species_input$group_code[i]), " ",species_input$num_of_stocks[i],
"\n", sep=""))
cat(paste(species_input$recruits_per_individual_per_year[i], "\n", sep=""))
cat(paste("PP_", as.character(species_input$group_code[i]), " ",
species_input$primary_production_impact_recruitment[i], "\n", sep=""))
cat(paste("Ralpha_", as.character(species_input$group_code[i]), " ",
species_input$ricker_alpha[i], "\n", sep=""))
cat(paste("Rbeta_", as.character(species_input$group_code[i]), " ",
species_input$ricker_beta[i], "\n", sep=""))
cat(paste("BHalpha_", as.character(species_input$group_code[i]), " ",
species_input$beverton_holt_alpha[i], "\n", sep=""))
cat(paste("BHbeta_", as.character(species_input$group_code[i]), " ",
species_input$beverton_holt_beta[i], "\n", sep=""))
#external reproduction
cat(paste("flagext_reprod",as.character(species_input$group_code[i]), " ",
species_input$ext_reprod[i], "\n", sep=""))
#local recruit
cat(paste("flaglocalrecruit",as.character(species_input$group_code[i]), " ", species_input$local_recruit[i], "\n", sep=""))
cat(paste("feed_while_spawn",as.character(species_input$group_code[i]), " ", species_input$feed_while_spawning[i], "\n", sep=""))
cat(paste("flagtempsensitive",as.character(species_input$group_code[i]),
" ",species_input$flag_temp_sensitive[i],"\n", sep=""))
cat(paste(as.character(species_input$group_code[i]), "_AgeClassSize", " ", max(1, round(species_input$ypa_FUNC[i])), "\n", sep=""))
cat(paste(as.character(species_input$group_code[i]), "_age_mat", " ", species_input$mat_FUNC[i], "\n", sep=""))
cat(paste("FSPB_", as.character(species_input$group_code[i]), " ", species_input$NumofAgeClasses[i], "\n", sep=""))
cat(mean_individual_morphology[mean_individual_morphology$group_code==species_input$group_code[i] & mean_individual_morphology$AgeClass>0,
"PropSpawning"])
cat("\n")
cat(paste("KSWR_", as.character(species_input$group_code[i]), " ",
mean_individual_morphology[mean_individual_morphology$group_code
== species_input$group_code[i] & mean_individual_morphology$AgeClass==1,
"StructN"], "\n", sep=""))
cat(paste("KWWR_", as.character(species_input$group_code[i]), " ",
mean_individual_morphology[mean_individual_morphology$group_code
== species_input$group_code[i] & mean_individual_morphology$AgeClass==1,
"ResN"], "\n", sep=""))
cat("\n")
}
#for all vertebrates
if (species_input$atlantis_type[i] %in% c("fish", "mammal", "bird", "shark")){
cat(paste("flagplankfish",as.character(species_input$group_code[i]), " ", species_input$planktivore[i], "\n", sep=""))
cat(paste("flagrecpeak",as.character(species_input$group_code[i]), " ", species_input$reprod_strength[i], "\n", sep=""))
cat(paste("flagbearlive",as.character(species_input$group_code[i]), " ", species_input$bear_live_young[i], "\n", sep=""))
cat(paste("flagmother",as.character(species_input$group_code[i]), " ", species_input$parental_care[i], "\n", sep=""))
cat(paste("flaq10eff",as.character(species_input$group_code[i]), " ",species_input$flag_q10[i],"\n", sep=""))
cat(paste("flaghabdepend",as.character(species_input$group_code[i]), " ",species_input$habitat_depend[i],"\n", sep=""))
cat(paste("flagchannel",as.character(species_input$group_code[i]), " ",species_input$channel[i],"\n", sep=""))
cat(paste("Kcov_juv_",as.character(species_input$group_code[i]), " ",species_input$Kcov_juv[i],"\n", sep=""))
cat(paste("Bcov_juv_",as.character(species_input$group_code[i]), " ",species_input$Bcov_juv[i],"\n", sep=""))
cat(paste("Acov_juv_",as.character(species_input$group_code[i]), " ",species_input$Acov_juv[i],"\n", sep=""))
cat(paste("Kcov_ad_",as.character(species_input$group_code[i]), " ",species_input$Kcov_ad[i],"\n", sep=""))
cat(paste("Bcov_ad_",as.character(species_input$group_code[i]), " ",species_input$Bcov_ad[i],"\n", sep=""))
cat(paste("Acov_ad_",as.character(species_input$group_code[i]), " ",species_input$Acov_ad[i],"\n", sep=""))
cat(paste("Speed_",as.character(species_input$group_code[i]), " ",species_input$swim_speed[i],"\n", sep=""))
cat(paste(as.character(species_input$group_code[i]), "_min_move_temp ",species_input$min_move_temp[i],"\n", sep=""))
cat(paste(as.character(species_input$group_code[i]), "_max_move_temp ",species_input$max_move_temp[i],"\n", sep=""))
cat(paste(as.character(species_input$group_code[i]), "_min_move_salt ",species_input$min_move_salt[i],"\n", sep=""))
cat(paste(as.character(species_input$group_code[i]), "_max_move_salt",species_input$max_move_salt[i],"\n", sep=""))
cat(paste("pSTOCK_", as.character(species_input$group_code[i]), " 1","\n", sep=""))
cat(as.character(species_input$stock_availability[i]))
cat("\n")
cat(paste("pSTOCK_j", as.character(species_input$group_code[i]), " 1","\n", sep=""))
cat(as.character(species_input$stock_availability_juv[i]))
cat("\n")
cat(paste("pR_", as.character(species_input$group_code[i]), " ",
species_input$prefer_allocate_reserves[i],"\n", sep=""))
cat(paste("li_a_", as.character(species_input$group_code[i]), " ",
species_input$mean_a[i],"\n", sep=""))
cat(paste("li_b_", as.character(species_input$group_code[i]), " ",
species_input$mean_b[i],"\n", sep=""))
if("min_length_reproduction" %!in% names(species_input)){
cat(paste("min_li_mat_", as.character(species_input$group_code[i]), " ",
minnona(mean_individual_morphology[mean_individual_morphology$group_code
== species_input$group_code[i] &
mean_individual_morphology$Prop_Adult > 0,
"length"]),"\n", sep=""))
}else {cat(paste("min_li_mat_", as.character(species_input$group_code[i]), " ",
species_input$min_length_reproduction[i]), "\n", sep="")
}
cat(paste("KA_", as.character(species_input$group_code[i]), " ",
species_input$fish_respiration_scaling_coefficient[i], "\n", sep=""))
cat(paste("KB_", as.character(species_input$group_code[i]), " ",
species_input$fish_respiration_scaling_exponent[i], "\n", sep=""))
cat(paste(as.character(species_input$group_code[i]), "_min_O2 ",
species_input$minimim_oxygen_vertebrates[i], "\n", sep = ""))
cat(paste("KSPA_", as.character(species_input$group_code[i]), " ",
species_input$spawning_formulation_constant[i], "\n", sep = ""))
cat(paste("FSP_", as.character(species_input$group_code[i]), " ",
species_input$spawning_formulation_fraction[i], "\n", sep = ""))
cat(paste("recSTOCK_"), as.character(species_input$group_code[i]), " ",
species_input$num_of_stocks[i], "\n", sep = "")
cat(paste(species_input$stock_recruitment_scalar[i], "\n", sep="" ))
cat(paste("recover_mult_", as.character(species_input$group_code[i]), " ",
species_input$recovery_multiplier[i], "\n", sep = ""))
cat(paste("recover_start_", as.character(species_input$group_code[i]), " ",
species_input$recover_start_date[i], "\n", sep = ""))
cat(paste(as.character(species_input$group_code[i]), "_min_spawn_temp ",species_input$min_spawn_temp[i],"\n", sep=""))
cat(paste(as.character(species_input$group_code[i]), "_max_spawn_temp ",species_input$max_spawn_temp[i],"\n", sep=""))
cat(paste(as.character(species_input$group_code[i]), "_min_spawn_temp ",species_input$min_spawn_salinity[i],"\n", sep=""))
cat(paste(as.character(species_input$group_code[i]), "_max_spawn_temp ",species_input$max_spawn_salinity[i],"\n", sep=""))
cat (paste (as.character(species_input$group_code[i]), "_stock_struct ", NumberofBoxes,"\n", sep=""))
cat(paste(species_input$stock_structure[i]), "\n")
}
cat("\n")
}
sink()
}
r4atlantis/ratlantis documentation built on May 26, 2019, 6:40 p.m.
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#' create_biology_prm function
#'
#' This function creates the biology prm file needed for Atlantis
#' @param species_data_location where csv file with species data is located (defaults to
#' working directory).
#' @param species_info_groups_csv name of csv file with species data.
#' \itemize{
#' \item {The following column headers are required
#' (all provided by merging generate_group_parameter function):
#' \itemize{
#' \item{atlantis_type}
#' \item{group_name}
#' \item{group_code}
#' \item{TL_final}
#' \item{mean_M}
#' \item{max_age}
#' \item {min_age_reprod}
#' \item {mean_a} {average coefficient from length-weight relationship}
#' \item {mean_b} {average exponent from length-weight relationship}
#' \item {mean_Loo}
#' \item {mean_K}
#' \item {min_depth}
#' \item{max_depth}
#' \item{larval_duration}
#' \item{planktivore}{only used for vertebrates}
#' \item{bear_live_young}{only used for vertebrates, (0 = no, 1 = yes) }
#' \item{parental_care} {does the vertebrate group provides parental care for
#' young until maturity; 0 = no, 1 = yes, -1 = semelparous so die after reproduction}
#' \item{feed_while_spawning}{for vertebrates and age-structured inverts}
#' \item{assessed}
#' \item{cover}
#' \item{silicon_dep}
#' }
#' }
#' \item {The following columns are optional (will be filled in by function if not
#' provided):
#' \itemize{
#' \item{num_of_age_classes}
#' \item{catch_grazer} {is the group an opportunistic catch grazers (thief)?
#' defaults to no = 0}
#' \item{ca}
#' \item{cb}
#' \item{juv_eff}
#' \item{adult_eff}
#' \item{predator} {1 = yes, 0 = no, defaults based trophic level, needed for all
#' groups}
#' \item{jack_a}
#' \item{jack_b}
#' \item{optional for all living:
#' \itemize{
#' \item{flag_dem}{Preferred 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}
#' \item{ph_sensitive}{is species growth or non predation mortality is sensitive
#' to pH, defaults to 0}
#' \item{ph_sensitive_fecund}{is species fecundity sensitive to pH, defaults
#' to 0}
#' \item{salinity_impacts_nutrition}{Whether the species nutritional value is
#' sensitive to salinity or pH (mainly an issue for phytoplankton), default to
#' 0}
#' \item{ph_impacts_availablity}{# Whether the species availability to
#' predators is sensitive to pH (mainly behaviour in fish), defaults to 0}
#' \item{ph_impacts_growth_and_death}{# Whether the species growth or non-
#' predation mortality is sensitive to pH, defaults to 0}
#' \item{ph_impact_form}{Form 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}
#' \item{monod_inflection_point}{Monod inflection point for pH impact function,
#' defaults to 0}
#' \item{optimal_pH_for_nonlinear_function}{Optimal pH for nonlinear pH
#' impact function, defaults to 0}
#' \item{ph_correction_scalar}{Correction scalar pH for nonlinear pH impact
#' function, defaults to 1}
#' \item{ph_function_coeff}{Coefficient pH for nonlinear pH impact function,
#' defaults to 1}
#' \item{ph_function_base}{Base coefficient pH for nonlinear pH impact function, defaults to 1}
#' \item{ph_correction_scalar2}{Correction scalar pH for nonlinear pH impact function, defaults to 1}
#' \item{salinity_sensitive}{Whether the species is sensitive to salinity, defaults to 0}
#' \item{salinity_correction_scalar}{# Correction scalar salt for nonlinear salinity
#' impact function, defaults to 1}
#' }
#' }
#' \item{optional for primary producers:
#' \itemize{
#' \item{lysis_rate} {only primary producers defaults to 0}
#' }
#' }
#' \item{optional for macrophytes:
#' \itemize{
#' \item{extra_mortality_macrophytes} {due to scour or nutrient input for mar, defaults to 0}
#' }
#' }
#' \item{optional for catch grazers:
#' \itemize{
#' \item{prop_catch_available}{Availabilty of catch to opportunistic catch grazers (thieves);
#' should be space separated vector with entry for each other functional group; defaults to 0}
#' \item{prop_catch_exploitable}{How 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}
#' }
#' }
#'
#' \item{needed for all that horizontally migrate
#' \itemize{
#' \item{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.}
#' \item{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)}
#' \item{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)}
#' \item{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)}
#' \item{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)}
#' \item{migrate_times_juv} {days entering and leaving models, separated by a space
#' (defaults to leave 364, enter 1)}
#' \item{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}
#' \item{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}
#' \item{return_stock_ad} {defaults to 0, integer number identifying specific stock adult or pool migrants will return to; 0
#' spreads uniformly across model}
#' \item{return_stock_juv} {defaults to 0, integer number identifying specific stock juvenile migrants will return to; 0
#' spreads uniformly across model}
#' \item{migrants_return_ad} {proportion of migrating adult or pool biomass that return to the model domain, defaults to 1}
#' \item{migrants_return_juv} {proportion of migrating adult or pool biomass that return to the model domain, defaults to 1}
#' \item{prop_increase_migrant_size_ad}{Proportional increases in size while outside model domain for adults,
#' defaults to 0}
#' \item{prop_increase_migrant_size_juv}{Proportional increases in size while outside model domain for juveniles,
#' defaults to 0}
#' \item{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}
#' }
#' }
#' \item{optional for all stage structured inverts:
#' \itemize{
#' \item{seperate}{1 = 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}
#' }
#' }
#' \item{optional for all vertebrates:
#' \itemize{
#' \item{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)}
#' \item{flag_q10}{Switch 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}
#' \item{habitat_depend}{defaults to 0, dependent on demersal habitat: 0 = no,
#' 1 = yes 0, defaults to 0}
#' \item{channel}{indicating whether vertebrate group seeks channels during low
#' tide - in tidal models}
#' \item{Kcov_juv} {Exponent of refuge relationship with biogenic habitat, defaults to
#' 3, verts only}
#' \item{Kcov_ad} {Exponent of refuge relationship with biogenic habitat, defaults to
#' 3, verts only}
#' \item{Bcov_juv} {Coefficient of refuge relationship with biogenic habitat, defaults
#' to .6, verts only}
#' \item{Bcov_ad} {Coefficient of refuge relationship with biogenic habitat, defaults
#' to .6, verts only}
#' \item{Acov_juv} {scalar for relationship with biogenic habitat, defaults to 1, verts only}
#' \item{Acov_ad} {scalar for relationship with biogenic habitat, defaults to 1, verts only}
#' \item{swim_speed}{defaults to 12500 for fish and sharks, 15000 for birds, 20000 for sharks mammals}
#' \item{min_move_temp} {defaults to minimum temp in model}
#' \item{max_move_temp} {defaults to maximum temp in model}
#' \item{prefer_allocate_reserves}{Vertebrate preference for rebuilding reserves over structure;
#' defaults to 4 for fish, 3 for sharks, 3.5 for mammals, and 5 for birds}
#' \item{min_length_reproduction}{if not provided, uses mininum age at reproduction and
#' length weight relationship to estimate}
#' \item{ fish_respiration_scaling_coefficient} {scaling of respiration vs weight, defaults .025 for fish, .021
#' for mammals, .024 for birds, .014 for all others}
#' \item{ fish_respiration_scaling_exponent} {exponent of respiration vs weight, defaults to .8}
#' \item{minimim_oxygen_vertebrates}{minimum tolerated oxygen level for age
#' structured groups (typically vertebrates)}
#' \item{spawning_formulation_constant} {constant in spawning formulation, defaults to guild values}
#' \item{spawning_formulation_fraction} {defaults to guild values}
#' \item{stock_recruitment_scalar} {recruitment parameter for diffferent stocks of verts, defaults to 1
#' for all stocks}
#' \item{recovery_multiplier}{Recruitment modifiers to encourage recovery of
#' stocks, defaults to 1}
#' \item{recover_start_date}{day when recovery will start, only used when recruit_group_code
#' is set to 8, defaults to 999 for dummy value}
#' \item{min_spawn_temp} {defaults to minimum temp in model}
#' \item{max_spawn_temp} {defaults to maximum temp in model}
#' \item{min_spawn_salinity} {defaults to minimum temp in model}
#' \item{max_spawn_salinity} {defaults to maximum temp in model}
#' \item{stock_structure}{defaults to 1 for each box, not sure what this is, needs to
#' be 1 entry for each box separated by space}
#' }
#' }
#' \item{optional for all vertebrates and stage structured inverts:
#' \itemize{
#' \item{ext_reprod} {does group reproduce outside model area? 1 = yes, 0 = no,
#' required for all vertebrates and stage-structured invertebrates, defaults to 0}
#' \item{local_recruit} {defaults to 0,
#' 1 = demersal and piscivorous fish recruit at parental locations, 0 = independent distribution}
#' item{flag_temp_sensitive}{Temperature sensitivty; defaults to 0 = no, 1 = yes}
#' \item{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 12 for birds and mammal, 10 for fish and sharks}
#' \item{recruits_per_individual_per_year}{needed for vertebrates and stage-structured invertebrates, but only used for
#' groups with recruit_group_code = 10 or 12; defaults to 1 (stable population) for each stock; represents biomass of new recruit for
#' stage-structured inverts}
#' \item{primary_production_impact_recruitment}{Coefficient relating primary
#' production to recruitment, linked to recruit_group_code 2, defaults to
#' 999 for dummy value that is not used}
#' \item{ricker_alpha}{parameter needed for recruit_group_code 9, defaults to
#' 999 here for dummy value}
#' \item{ricker_beta}{parameter needed for recruit_group_code 9, defaults to
#' 999 here for dummy value}
#' \item{beverton_holt_alpha}{parameter needed for recruit_group_code 3, defaults to
#' 999 here for dummy value}
#' \item{beverton_holt_beta}{parameter needed for recruit_group_code 3, defaults to
#' 999 here for dummy value}
#' \item{structural and reserve weight of recruits is calculated internally;
#' results are output to "parameters_for_age_classes_of_groups.csv"}
#' }
#' }
#' \item{optional for all fish:
#' \itemize{
#' \item{other_fish_mortality} {mortality due to fish not included
#' in model), value per quarter, separated by a space; defaults to 0}
#' \item{mammal_bird_mortality} {Static seabird and mammal induced mortality of
#' each fish group, per quarter, separated by a space; defaults to 0}
#' }
#' }
#' \item{optional for all predators:
#' \itemize{
#' \item{gape_lower_limit} {defaults to .01, lower Gape size for predators, to determine available prey fish groups. Required for all
#' predators}
#' \item{gape_upper_limit} {defaults to 1, upper Gape size for predators, to determine available prey fish groups. Required for all
#' predators}
#' \item{population_refuge}{Seed 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}
#' \item{saturation_level}{Saturation levels for consumer food intake. only used by model for predcase = 4; defaults to 1 for filler}
#' \item{search_volume_invert}{Search volume for invertebrate predators -
#' used by size specific Holling type III (predcase 5); defaults to 999 here for filler value }
#' \item{search_volume_coefficient}{Search volume coefficient for vertebrate predators-
#' used by size specific Holling type III (predcase 5);
#' defaults to planktivorous = 2, pelagic piscivores = 5, demersal/reef = 1}
#' \item{search_volume_exponent}{Search 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}
#' \item{handling_time_invert}{handling time for invertebrate predators -
#' used by size specific Holling type III (predcase 5); defaults to 999 here for filler value }
#' \item{handling_time_coefficient}{handling time coefficient for vertebrate predators-
#' used by size specific Holling type III (predcase 5);
#' ; defaults to 999 here for filler value }
#' \item{handling_time_exponent}{handling time exponenent for vertebrate predators -
#' used by size specific Holling type III (predcase 5);
#' ; defaults to 999 here for filler value }
#' }
#' }
#' \item{optional for all consumers:
#' \itemize{
#' \item{active} { 2 = no preference, 1 = day, 0 = night,defaults to 2, needed
#' for all consumers}
#' \item {sediment_penetration_depth}{Depth 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 }
#' \item {assimilation_efficiency_on_plants}{defaults to .5 for invertebrates,
#' .1 for vertebrates}
#' \item {assimilation_efficiency_on_live_food_and_carrion}{defaults to .5 for invertebrates,
#' .1 for vertebrates}
#' \item {assimilation_efficiency_on_labile_detritus}{defaults to .3 for bacteria,
#' .2 for filter feeders, and .1 for everything else}
#' \item {assimilation_efficiency_on_refractory_detritus}{defaults to .5 for bacteria,
#' .3 for filter feeders, and .1 for everything else}
#' \item{food_lost_to_detritus}{Fraction of non-assimilated lost to detritus, defaults to 0}
#' \item{labile_detritus_lost_to_detritus}{Fraction of non-assimilate from
#' labile detrital food lost to detritu, defaults to 0}
#' \item{refractory_detritus_lost_to_detritus}{Fraction of non-assimilate from
#' refractory detrital food lost to detritus, defaults to 0}
#' \item{mortality_contribution_to_detritus}{Fraction of mortality that goes to
#' detritus, defaults to .3}
#' }
#' }
#' \item{k_tur} {defaults to .1}{needed for epibenthic groups that are mobile or infaunal (SM_INF, LG_INF, MOB_EP_OTHER)}
#' \item{k_irr} {defaults to 1, needed for epibenthic groups that are infaunal
#' (SM_INF, LG_INF))}
#' \item{temp_coefft_a} {defaults to .851, needed for all living things,
#' Coefficient A in Gary Griffith temperature function}
#' \item{q10} {defaults to 2, Exponent in temperature effect on rate parameters}
#' \item{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.}
#' \item{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.}
#' \item{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.}
#' \item{wc} {defaults to .01}
#' \item{turned_on} {defaults to 1 (=yes, 0=no) groups$IsTurnedOn=1}
#' \item{overwinter} {defaults to 0}
#' \item{max}{space restrictions for basal (epibenthic and some infauna) groups, defaults to
#' 5000}
#' \item{low}{Threshold spatial factors for filter feeders if using ERSEM formulation, Little space limitation (pop too small) }
#' \item{thresh}{Threshold spatial factors for filter feeders if using ERSEM formulation }
#' \item{sat}{Threshold spatial factors for filter feeders if using ERSEM formulation, Interference to uptake due to shading }
#' \item{home_range} {defaults to 1, all epxcept primary producers}
#' \item{overlap} {defaults to 1, all except primary producers}
#' \item{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)}
#' \item{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}
#' \item{linear_mortality} {tuning parameter needed for each stage for all living organisms; defaults to 0}
#' \item{quadratic_mortality} {tuning parameter needed for each stage for all living organisms; defaults to 0}
#' \item{juvenile_quadratic_mortality} {tuning parameter, defaults to 0, needed for stage-structured inverts
#' and vertebrates}
#' \item{starve} {mortality due to starvation, only for vertebrates, defaults to 0}
#' \item{oxygen_depth_mortality} {tuning parameter, Half oxygen mortality depth, inverts except
#' primary producers,defaults to .001}
#' \item{ambient_oxygen_mortality} {tuning parameter, oxygen dependent mortality due to ambient conditions, inverts except
#' primary producers, defaults to .01}
#' \item{lethal_oxygen_level} {lethal oxgyen level, inverts except primary producers,defaults to .5}
#' \item{limiting_oxygen_level} {limiting oxygen level, inverts except primary producers, defults to 10}
#' \item{other_fish_mortality} {fish only, defaults to 0 (mortatlity due to fish not included
#' in model), value for each season, separated by a space (defaults to 0)}
#' \item{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}
#' \item{FSP} {defaults to guild values, verts only}
#' \item{vert_stock_struct} {verts only, defaults to 1,input as number for each box
#' separated by a space}
#' \item{pop_ratio_stock} {defaults to 1}
#' \item{remin_contrib}{ for small_infaunal, defaults to 0}
#' \item{in_WC} {defaults to 0}
#' \item{in_sed} {defaults to 0}
#' \item{epi} {default to 0}
#' \item{vertically_migrates} {defaults to 0}
#' \item{horizontally_migrates} {defaults to 0}
#' \item{fished} {defaults to 0, is it targeted in fisheries}
#' \item{impacted} {defaults to 0, is it impacted by fisheries}
#' \item{TAC} {defaults to 0, is it controlled by a TAC}
#' \item{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}
#' \item{KI} {default to 0, light saturation, needed for primary producers}
#' \item{KS} {default to 0, Half-sat const for PL growth on Si mg Si m-3}
#' \item{KF} {default to 0, Half-sat const for PL growth on Micro-nutrient}
#' \item{KN} {default to 0, Primary producer nutrient requirements }
#' \item{num_of_genotypes}{defaults to 1}
#' \item{num_of_stages}{defaults to 2 for vertebrates, 1 for others}
#' \item{num_of_stocks}{defaults to 1}
#' \item{num_of_spawns}{{defaults to 1}}
#' \item{num_of_age_class_size}{set by internal function using maximum age and
#' number of cohorts}
#' \item{cultured}{defaults to 0}
#' }
#' }
#' }
# need to add file here wiht mum, clearance, and other values. for now these just default
# to value in group_code to keep everything clean
# @param invert_mum_and_clearance_csv name of csv file that must contain the
# following column headers
# \itemize{
# \item{group_code}
# \item{mum}
# \item{clearance}
# \item{KI}{Light saturation}
# \item{KN}{Half-sat const for PL growth on Micro-nutrient}
# \item{KS}{Half-sat const for PL growth on Si mg Si m-3}
# \item{KF}{Half-sat const for PL growth on Micro-nutrient}
# item{max}{space restrictions for basal (epibenthic and some infauna) groups}
# \item{in_WC} {defaults to 0}
# \item{in_sed} {defaults to 0}
# \item{epi} {default to 0}
# \item{vertically_migrates} {defaults to 0}
# \item{horizontally_migrates} {defaults to 0}
# }
#' @param flag_data_csv csv file containing major flag values for model
#' @details This function creates the biology prm file needed by Atlantis.
#' @keywords biology prm
#' @export
create_biology_prm <- function(species_data_location = getwd(), species_info_groups_csv,
flag_data_csv){
species_input <- read.csv(paste(species_data_location, "/", species_info_groups_csv, sep=""),
header = T, strip.white = T)
flag_data <- read.csv(paste(species_data_location, "/",flag_data_csv, sep=""),
header=T)
#grab map info from flag_data
NumberofHabitats <- as.numeric(as.character(flag_data[flag_data$Flag == "#NumberofHabitats","Value"]))
MaxDepth <- as.numeric(as.character(flag_data[flag_data$Flag == "#MaxDepth","Value"]))
MinDepth <- as.numeric(as.character(flag_data[flag_data$Flag == "#MinDepth","Value"]))
NumberofBoxes <- as.numeric(as.character(flag_data[flag_data$Flag == "#NumberofBoxes","Value"]))
NumberofDepthLayers <- as.numeric(as.character(flag_data[flag_data$Flag == "#NumberofDepthLayers","Value"]))
MinTemp <- as.numeric(as.character(flag_data[flag_data$Flag == "#MinTemp","Value"]))
MaxTemp <- as.numeric(as.character(flag_data[flag_data$Flag == "#MaxTemp","Value"]))
MinSalt <- as.numeric(as.character(flag_data[flag_data$Flag == "#MinSalt","Value"]))
MaxSalt <- as.numeric(as.character(flag_data[flag_data$Flag == "#MaxSalt","Value"]))
#constant across all groups
Ntoall <- 0.175438596 #ratio of N to all other elements
drytowet <- 20 #ratio of wet to dry weight
sNtN <- 0.273972603 #ratio of structural N to total N
rNtN <- 0.726027397 #ratio of reserve N to total N
gtot <- 1000000 #ratio of metric tons to grams
#start making other columns in loop
species_input$T_max_from_M <- log(.01)/-species_input$mean_M
species_input$M_from_T_max <- log(.01)/-species_input$max_age
species_input$ypa_FUNC <- NA
species_input$mat_FUNC <- NA
#set number of age classes if not provided by user
if( "num_of_age_classes" %!in% names(species_input)){
for (i in 1:nrow(species_input)){
if(species_input$atlantis_type[i] %in% c("bird", "fish", "mammal", "shark")){
species_input$num_of_age_classes[i] <- 10
}else {species_input$num_of_age_classes[i] <- 1}
}
} else {
#make sure user provided all values
if( !is.numeric(species_input$num_of_age_classes)){
stop(message = "Provided number of age classes are not all numeric")
}
if( any(is.na(species_input$num_of_age_classes))){
stop(message = "Provided number of age classes contains an NA")
}
}
#use independent M estimate if it exists to calculate years per class
# for vertebrate groups
for (i in 1:nrow(species_input)){
if(species_input$atlantis_type[i] %in% c("bird", "fish", "mammal", "shark")){
if(is.na(species_input$mean_M[i]) == T){
species_input$ypa_FUNC[i] <- species_input$max_age[i]/species_input$num_of_age_classes[i]
}
else{species_input$ypa_FUNC[i] <- species_input$T_max_from_M[i]/species_input$num_of_age_classes[i]}
}
}
#for vertebrates, determine age class where maturity starts
for (i in 1:nrow(species_input)){
if(species_input$atlantis_type[i] %in% c("bird", "fish", "mammal", "shark")){
species_input$mat_FUNC[i]=min(ceiling(species_input$min_age_reprod[i]/species_input$ypa_FUNC[i]), species_input$num_of_age_classes[i])
}
#set maturity at 0 for inverts, other that are just pools
else{species_input$mat_FUNC[i]=0}
}
#energetics from Hanson 1997 (Horne 2010)
#maximum feeding rate (clearance) based on allometric relationships between weight and feeding
#see Anderson 2010 for example
cageneral <- .3
cbgeneral <- .7
if( "ca" %!in% names(species_input)){
species_input$ca <- cageneral
}
if( "cb" %!in% names(species_input)){
species_input$cb <- cbgeneral
}
#calculate mum and clearance for vertebrates, also need weights, all for average individual in each size class
#for classes 1-10
#produce separate table with info on size classses for vertebrates
#list variables to be included here
to_be_included <- c("atlantis_type", "AgeClass", "ActualAge", "WetWeight",
"StructN", "ResN", "mum", "clearance", "Decay", "PropAgeDist", "PropJuv", "PropAdults",
"PropBiomass", "PropSpawning", "length")
#make matrix to hold data
#take number of ages classes plus a 0 class for all vertebrate
mean_individual_morphology <- matrix(NA, sum(sum(species_input[species_input$atlantis_type
%in% c("bird", "fish", "mammal", "shark"),]$num_of_age_classes),
length(species_input[species_input$atlantis_type %in% c("bird", "fish", "mammal", "shark"),]$group_code)),
length(to_be_included)+1)
mean_individual_morphology <- as.data.frame(mean_individual_morphology)
names(mean_individual_morphology)=c("group_code", to_be_included)
#loop over species, variables, and age classes
#consider recruits as 0 age class
#to create this, loop over group_code, age classes, and use counter
counter <- 1
for(i in 1:nrow(species_input)){
#add one for larval group
if(species_input$atlantis_type[i] %in% c("bird", "fish", "mammal", "shark")){
for (j in 1:(species_input[species_input$group_code ==
species_input$group_code[i], "num_of_age_classes"]+1)){
mean_individual_morphology$atlantis_type[counter] =
as.character(species_input[species_input$group_code ==
species_input$group_code[i], "atlantis_type"])
mean_individual_morphology$group_code[counter] <- as.character(species_input$group_code[i])
mean_individual_morphology$AgeClass[counter] <- j-1
counter <- counter+1
}}
}
#fill in information with loops
#do age classes and wet weights for verts
#for each age class, this finds actual age, uses VB equation to estimate L, and
#then use length-weight relationship to estimate wet weight
for (i in 1:nrow(mean_individual_morphology)){
if(mean_individual_morphology$atlantis_type[i] %in% c("bird", "fish", "mammal", "shark")){
mean_individual_morphology$ActualAge[i] <- as.numeric(mean_individual_morphology$AgeClass[i]*
species_input[species_input$group_code == mean_individual_morphology$group_code[i], "ypa_FUNC"])
if(mean_individual_morphology$AgeClass[i] > 0){
mean_individual_morphology$WetWeight[i] <- species_input[species_input$group_code ==
mean_individual_morphology$group_code[i], "mean_a"]*
(species_input[species_input$group_code == mean_individual_morphology$group_code[i],
"mean_Loo"]*(1-exp(-1
*species_input[species_input$group_code == mean_individual_morphology$group_code[i],
"mean_K"]*
mean_individual_morphology$ActualAge[i]
)))^species_input[species_input$group_code == mean_individual_morphology$group_code[i],
"mean_b"]
mean_individual_morphology$length[i] <- (mean_individual_morphology$WetWeight[i]/
species_input[species_input$group_code == mean_individual_morphology$group_code[i],
"mean_a"])^(1/species_input[species_input$group_code == mean_individual_morphology$group_code[i],
"mean_b"])
if(mean_individual_morphology$atlantis_type[i] %in% c("fish", "shark")){
mean_individual_morphology$Decay[i]<- exp(-1*species_input[species_input$group_code
== mean_individual_morphology$group_code[i], "mean_M"]*
(mean_individual_morphology$AgeClass[i]-1)*species_input[species_input$group_code
== mean_individual_morphology$group_code[i], "ypa_FUNC"])
} else if(mean_individual_morphology$atlantis_type[i] == "mammal"){
#need to add silers group_code
mean_individual_morphology$Decay[i] <- exp(-1*species_input[species_input$group_code
== mean_individual_morphology$group_code[i], "mean_M"]*
(mean_individual_morphology$AgeClass[i]-1)*species_input[species_input$group_code
== mean_individual_morphology$group_code[i], "ypa_FUNC"])
}else if(mean_individual_morphology$atlantis_type[i] == "bird"){
#birds shoudl be constant
mean_individual_morphology$Decay[i] <- exp(-1*species_input[species_input$group_code ==
mean_individual_morphology$group_code[i], "mean_M"]*
(mean_individual_morphology$AgeClass[i]-1)*species_input[species_input$group_code ==
mean_individual_morphology$group_code[i], "ypa_FUNC"])
}
} else {
mean_individual_morphology$WetWeight[i] <- species_input[species_input$group_code ==
mean_individual_morphology$group_code[i], "mean_a"] *
(species_input[species_input$group_code == mean_individual_morphology$group_code[i],
"mean_Loo"]*(1-exp(-1
*species_input[species_input$group_code == mean_individual_morphology$group_code[i], "mean_K"]*
species_input[species_input$group_code == mean_individual_morphology$group_code[i],
"larval_duration"]/365
)))^species_input[species_input$group_code == mean_individual_morphology$group_code[i],
"mean_b"]
}
}
}
mean_individual_morphology$StructN <- mean_individual_morphology$WetWeight*Ntoall/drytowet*sNtN*1000
mean_individual_morphology$ResN <- mean_individual_morphology$WetWeight*Ntoall/drytowet*rNtN*1000
#mum and clearance for verts
for (i in 1:nrow(mean_individual_morphology)){
if(mean_individual_morphology$AgeClass[i] > 0){
mean_individual_morphology$clearance[i] <- species_input[species_input$group_code ==
mean_individual_morphology$group_code[i],
"ca"]*(mean_individual_morphology$StructN[i] +
mean_individual_morphology$ResN[i])^species_input[species_input$group_code == mean_individual_morphology$group_code[i], "cb"] * .8 * 3.3
mean_individual_morphology$mum[i] <- 10 * mean_individual_morphology$clearance[i]
mean_individual_morphology$PropAgeDist[i] <- mean_individual_morphology$Decay[i]/
sum(mean_individual_morphology[mean_individual_morphology$AgeClass > 0 & mean_individual_morphology$group_code == mean_individual_morphology$group_code[i],
"Decay"])
if(mean_individual_morphology$AgeClass[i] < species_input[species_input$group_code ==
mean_individual_morphology$group_code[i], "mat_FUNC"]){
mean_individual_morphology$PropJuv[i] <- mean_individual_morphology$Decay[i]/
sum(mean_individual_morphology[mean_individual_morphology$AgeClass > 0 & mean_individual_morphology$group_code == mean_individual_morphology$group_code[i] &
mean_individual_morphology$AgeClass < species_input[species_input$group_code == mean_individual_morphology$group_code[i], "mat_FUNC"],
"Decay"])
mean_individual_morphology$PropAdults[i] = 0
if(mean_individual_morphology$AgeClass[i] < (species_input[species_input$group_code == mean_individual_morphology$group_code[i], "mat_FUNC"] - 1)){
mean_individual_morphology$PropSpawning[i] = 0}
else{mean_individual_morphology$PropSpawning[i] = .2}
} else{
mean_individual_morphology$PropJuv[i] <- 0
mean_individual_morphology$PropAdults[i] <- mean_individual_morphology$Decay[i]/
sum(mean_individual_morphology[mean_individual_morphology$AgeClass>0 & mean_individual_morphology$group_code == mean_individual_morphology$group_code[i]&
mean_individual_morphology$AgeClass >= species_input[species_input$group_code == mean_individual_morphology$group_code[i], "mat_FUNC"],
"Decay"])
if(mean_individual_morphology$AgeClass[i] == species_input[species_input$group_code == mean_individual_morphology$group_code[i], "mat_FUNC"]){
mean_individual_morphology$PropSpawning[i] = .8}
else{mean_individual_morphology$PropSpawning[i] = 1}
}
} else{
mean_individual_morphology$mum[i] <- (mean_individual_morphology$StructN[i]+
mean_individual_morphology$ResN[i])/(species_input[species_input$group_code == mean_individual_morphology$group_code[i], "larval_duration"]/365)/365
}
}
#figure out invert mum and clearance formulas, KI, KN, KS, KF
#for now, use values from other models
#invert_mum_clearance <- read.csv("invert_mum_and_clearance.csv")
# mean_individual_morphology <- merge (mean_individual_morphology, invert_mum_clearance,
# all.x=T, all.y=T)
#merge not vert species in model with species_input sheet
# invert_params <- merge(unique(species_input[
#species_input$atlantis_type %!in% c("fish", "mammal", "bird", "shark"),c(
# "group_code", "atlantis_type")]), INVERTSHET)
#merge this info into mean_individual_morphology
mean_individual_morphology <- merge (unique(species_input[,c("group_code", "atlantis_type")]),
mean_individual_morphology,all.x = T,
all.y = T)
mean_individual_morphology$clearance[is.na(mean_individual_morphology$clearance)] <- 1
mean_individual_morphology$mum[is.na(mean_individual_morphology$mum)] <- 1
#parameters needed for availability calculator
if ("juv_eff" %!in% names(species_input)) {species_input$juv_eff <- .1}
if ("adult_eff" %!in% names(species_input)) {species_input$adult_eff <- .1}
for (i in 1:nrow(species_input)){
average_individual <- mean_individual_morphology[mean_individual_morphology$group_code ==
species_input$group_code[i],]
average_juvenile=mean_individual_morphology[mean_individual_morphology$group_code ==
species_input$group_code[i] &
mean_individual_morphology$AgeClass<species_input$mat_FUNC[i]
& mean_individual_morphology$AgeClass!=0,]
average_adult=mean_individual_morphology[mean_individual_morphology$group_code ==
species_input$group_code[i]&
mean_individual_morphology$AgeClass>=species_input$mat_FUNC[i],]
#juvenile calculations
species_input$avgjuvN[i] <- sum(average_juvenile$WetWeight*average_juvenile$PropJuv) *
Ntoall * 1000/drytowet
species_input$JuvGrowthRate[i] <- sum(average_juvenile$mum * average_juvenile$PropJuv) /
species_input$avgjuvN[i]
species_input$Juvclearance[i] <- sum(average_juvenile$clearance * average_juvenile$PropJuv)
#adult calculations
species_input$avgadultN[i] <- sum(average_adult$WetWeight*average_adult$PropAdult)*Ntoall*1000/drytowet
species_input$AdultGrowthRate[i] <- sum(average_adult$mum*average_adult$PropAdult)/species_input$avgadultN[i]
species_input$Adultclearance[i] <- sum(average_adult$clearance*average_adult$PropAdult)
}
species_input$JuvSj <- .3*species_input$JuvGrowthRate/species_input$juv_eff
species_input$AdultSj <- .3*species_input$AdultGrowthRate/species_input$adult_eff
#make columns for type of recruitment, local recruitment, and year class variation
if ("recruit_group_code" %!in% names (species_input)){
species_input$recruit_group_code <- NA
species_input$recruit_group_code[species_input$atlantis_type %in% c("bird", "mammal")] <- 12
species_input$recruit_group_code[species_input$atlantis_type %in% c("fish", "shark")] <- 10
}
if ("local_recruit" %!in% names (species_input)){
species_input$local_recruit <- 0
}
if ("reprod_strength" %!in% names (species_input)){
species_input$reprod_strength <- NA
species_input$reprod_strength[species_input$atlantis_type %in% c("bird", "mammal")] <- 0
species_input$reprod_strength[species_input$atlantis_type %in% c("fish", "shark")] <- 0
}
if( "predator" %!in% names(species_input)){
species_input$predator <- NA
species_input$predator[species_input$TL_final > 2.5] <- 1
species_input$predator[is.na(species_input$predator)] <- 0
}
if( "pred_case" %!in% names(species_input)){
species_input$pred_case <- NA
species_input$pred_case[species_input$predator == 1] <- 0
}
if("horizontally_migrates" %!in% names(species_input)){
species_input$horizontally_migrates <- 1
}
if( "jack_a" %!in% names(species_input)){
species_input$jack_a <- 0
}
if( "jack_b" %!in% names(species_input)){
species_input$jack_b <- 0
}
if( "recovery_multiplier" %!in% names(species_input)){
species_input$recovery_multiplier <- NA
species_input$recovery_multiplier[species_input$atlantis_type %in% c("fish",
"mammal",
"bird", "shark")] <- 999
}
if( "recover_start_date" %!in% names(species_input)){
species_input$recover_start_date <- NA
species_input$recover_start_date[species_input$atlantis_type %in% c("fish",
"mammal",
"bird", "shark")] <- 999
}
if( "flag_dem" %!in% names(species_input)){
species_input$flag_dem <-1
}
if( "flag_q10" %!in% names(species_input)){
species_input$q10 <-1
}
if( "flag_temp_sensitive" %!in% names(species_input)){
species_input$flag_temp_sensitive <- 0
}
# if( "flag_hab_depend" %!in% names(species_input)){
# species_input$flag_hab_depend <- 0
# }
if( "channel" %!in% names(species_input)){
species_input$flag_channel <- 0
}
if( "active" %!in% names(species_input)){
species_input$active <- 2
}
if( "k_tur" %!in% names(species_input)){
species_input$k_tur <- .1
}
if( "k_irr" %!in% names(species_input)){
species_input$k_irr <- 1
}
if( "temp_coefft_a" %!in% names(species_input)){
species_input$temp_coefft_a <- .851
}
if( "q10" %!in% names(species_input)){
species_input$q10 <- 2
}
if( "q10_method" %!in% names(species_input)){
species_input$q10_method <- 0
}
if( "q10_optimal_temp" %!in% names(species_input)){
species_input$q10_optimal_temp <- 0
}
if( "q10_correction" %!in% names(species_input)){
species_input$q10_correction <- 0
}
if( "wc" %!in% names(species_input)){
species_input$wc <- 0.01
}
if("turned_on" %!in% names(species_input)){
species_input$turned_on <- 1
}
if("low" %!in% names(species_input)){
species_input$low <- 500
}
if("thresh" %!in% names(species_input)){
species_input$thresh <- 2500
}
if("sat" %!in% names(species_input)){
species_input$sat <- NA
species_input$sat[species_input$atlantis_type %in% c("fish")] <- 4000
}
if("Kcov_juv" %!in% names(species_input)){
species_input$Kcov_juv <- NA
species_input$Kcov_juv[species_input$atlantis_type %in% c("fish", "mammal", "shark",
"bird")] <- 3
}
if("Kcov_ad" %!in% names(species_input)){
species_input$Kcov_ad <- NA
species_input$Kcov_ad[species_input$atlantis_type %in% c("fish", "mammal", "shark",
"bird")] <- 3
}
if("Bcov_juv" %!in% names(species_input)){
species_input$Bcov_juv <- NA
species_input$Bcov_juv[species_input$atlantis_type %in% c("fish", "mammal", "shark",
"bird")] <- .6
}
if("Bcov_ad" %!in% names(species_input)){
species_input$Bcov_ad <- NA
species_input$Bcov_ad[species_input$atlantis_type %in% c("fish", "mammal", "shark",
"bird")] <- .6
}
if("Acov_juv" %!in% names(species_input)){
species_input$Acov_juv <- NA
species_input$Acov_juv[species_input$atlantis_type %in% c("fish", "mammal", "shark",
"bird")] <- 1
}
if("Acov_ad" %!in% names(species_input)){
species_input$Acov_juv <- NA
species_input$Acov_juv[species_input$atlantis_type %in% c("fish", "mammal", "shark",
"bird")] <- 1
}
if("swim_speed" %!in% names(species_input)){
species_input$swim_speed <- NA
species_input$swim_speed[species_input$atlantis_type %in% c("fish", "shark")] <- 12500
species_input$swim_speed[species_input$atlantis_type %in% c("mammal")] <- 20000
species_input$swim_speed[species_input$atlantis_type %in% c("bird")] <- 15000
}
if("home_range" %!in% names(species_input)){
species_input$home_range <- 1
}
if("overlap" %!in% names(species_input)){
species_input$overlap <- 1
}
if("migrates_out_of_model" %!in% names(species_input)){
species_input$migrates_out_of_model <- NA
species_input$migrates_out_of_model[species_input$horizontally_migrates == 1] <- 0
}
if("migrates_out_times_ad" %!in% names(species_input)){
species_input$migrates_out_times_ad <- 364
}
if("migrates_out_times_juv" %!in% names(species_input)){
species_input$migrates_out_times_juv <- 364
}
if("migrates_in_times_juv" %!in% names(species_input)){
species_input$migrates_in_times_juv <- 0
}
if("migrates_in_times_ad" %!in% names(species_input)){
species_input$migrates_in_times_ad <- 0
}
if("migrate_period_ad" %!in% names(species_input)){
species_input$migrate_period_ad <- NA
species_input$migrate_period_ad[species_input$horizontally_migrates == 0] <- 0
species_input$migrate_period_ad[species_input$horizontally_migrates != 0] <- 1
}
if("migrate_period_juv" %!in% names(species_input)){
species_input$migrate_period_juv <- NA
species_input$migrate_period_juv[species_input$horizontally_migrates == 0] <- 0
species_input$migrate_period_juv[species_input$horizontally_migrates != 0] <- 1
}
if("return_stock_ad" %!in% names(species_input)){
species_input$return_stock_ad <- 0
}
if("return_stock_juv" %!in% names(species_input)){
species_input$return_stock_juv <- 0
}
if("migrants_return_ad" %!in% names(species_input)){
species_input$migrants_return_ad <- 1
}
if("migrants_return_juv" %!in% names(species_input)){
species_input$migrants_return_juv <- 1
}
if("prop_increase_migrant_size_ad" %!in% names(species_input)){
species_input$prop_increase_migrant_size_ad <- 0
}
if("prop_increase_migrant_size_juv" %!in% names(species_input)){
species_input$prop_increase_migrant_size_juv <- 0
}
if("fsp" %!in% names(species_input)){
species_input$fsp <- 0
}
if("stock_availabilty" %!in% names(species_input)){
species_input$stock_availability <- 1
}
if("stock_availabilty_juv" %!in% names(species_input)){
species_input$stock_availability_juv <- 1
}
if("gape_lower_limit" %!in% names(species_input)){
species_input$gape_lower_limit <- NA
species_input$gape_lower_limit[species_input$predator == 1] <- .01
}
if("gape_upper_limit" %!in% names(species_input)){
species_input$gape_upper_limit <- NA
species_input$gape_upper_limit[species_input$predator == 1] <- 1
}
if("population_refuge" %!in% names(species_input)){
species_input$population_refuge <- NA
species_input$population_refuge[species_input$predator == 1] <- 1
}
if("saturation_level" %!in% names(species_input)){
species_input$saturation_level <- NA
species_input$saturation_level[species_input$predator == 1] <- 1
}
if("search_volume_invert" %!in% names(species_input)){
species_input$search_volume_invert <- NA
species_input$search_volume_invert[species_input$predator == 1 &
species_input$atlantis_type %!in% c("fish",
"mammal", "bird", "shark")] <- 999
}
if("search_volume_coefficient" %!in% names(species_input)){
species_input$search_volume_coefficient <- NA
species_input$search_volume_coefficient[species_input$predator == 1 &
species_input$atlantis_type %in% c("fish",
"mammal", "bird", "shark")
& species_input$TL_final < 3.1] <- 2
species_input$search_volume_coefficient[species_input$predator == 1 &
species_input$atlantis_type %in% c("fish",
"mammal", "bird", "shark")
& species_input$TL_final >= 3.1] <- 5
}
if("search_volume_exponent" %!in% names(species_input)){
species_input$search_volume_exponent <- NA
species_input$search_volume_exponent[species_input$predator == 1 &
species_input$atlantis_type %in% c("bird", "shark")] <- .5
species_input$search_volume_exponent[species_input$predator == 1 &
species_input$atlantis_type %in% c("fish",
"mammal")] <- .35
}
if("handling_time_invert" %!in% names(species_input)){
species_input$handling_time_invert <- NA
species_input$handling_time_invert[species_input$predator == 1 &
species_input$atlantis_type %!in% c("fish",
"mammal", "bird", "shark")] <- 999
}
if("handling_time_coefficient" %!in% names(species_input)){
species_input$handling_time_coefficient <- NA
species_input$handling_time_coefficient[species_input$predator == 1 &
species_input$atlantis_type %in% c("fish",
"mammal", "bird", "shark")] <- 999
}
if("handling_time_exponent" %!in% names(species_input)){
species_input$handling_time_exponent <- NA
species_input$handling_time_exponent[species_input$predator == 1 &
species_input$atlantis_type %in% c("fish",
"mammal", "bird", "shark")] <- 999
}
if("pr" %!in% names(species_input)){
species_input$pr <- NA
species_input$pr[species_input$atlantis_type %in% c("fish", "mammal")] <- 3
species_input$pr[species_input$atlantis_type %in% c("bird", "shark")] <- 5
}
if("min_length_reprod" %!in% names(species_input)){
species_input$min_length_reprod <- 0
}
if(" fish_respiration_scaling_coefficient" %!in% names(species_input)){
species_input$ fish_respiration_scaling_coefficient <- NA
species_input$ fish_respiration_scaling_coefficient[species_input$atlantis_type == "fish"] <- .025
species_input$ fish_respiration_scaling_coefficient[species_input$atlantis_type == "mammal"] <- .021
species_input$ fish_respiration_scaling_coefficient[species_input$atlantis_type == "bird"] <- .024
species_input$ fish_respiration_scaling_coefficient[species_input$atlantis_type %!in% c("fish", "mammal", "bird")] <- .014
}
if("prefer_allocate_reserves" %!in% names(species_input)){
species_input$prefer_allocate_reserves <- NA
species_input$prefer_allocate_reserves[species_input$atlantis_type == "fish"] <- 4
species_input$prefer_allocate_reserves[species_input$atlantis_type == "shark"] <- 2
species_input$prefer_allocate_reserves[species_input$atlantis_type == "mammal"] <- 3.5
species_input$prefer_allocate_reserves[species_input$atlantis_type == "bird"] <- 5
}
if(" fish_respiration_scaling_exponent" %!in% names(species_input)){
species_input$ fish_respiration_scaling_exponent <- .8
}
if("lysis_rate" %!in% names(species_input)){
species_input$lysis_rate <- NA
species_input$lysis_rate[species_input$atlantis_type %in% c("phytoben", "microphytobenthos",
"seagrass", "lg_phy", "sm_phy")] <- 0
}
if("starve" %!in% names(species_input)){
species_input$prefer_allocate_reserves <- NA
species_input$starve[species_input$atlantis_type %in% c("fish", "mammal", "bird",
"shark")] <- 0
}
if("oxygen_depth_mortality" %!in% names(species_input)){
species_input$oxygen_depth_mortality <- NA
species_input$oxygen_depth_mortality[species_input$atlantis_type %!in%
c("fish", "mammal", "bird", "shark",
"microphytobenthos", "phytoben",
"sm_phy", "lg_phy", "dinoflag",
"seagrass")] <- 0.001
}
if("ambient_oxygen_mortality" %!in% names(species_input)){
species_input$ambient_oxygen_mortality <- NA
species_input$ambient_oxygen_mortality[species_input$atlantis_type %!in%
c("fish", "mammal", "bird", "shark",
"microphytobenthos", "phytoben",
"sm_phy", "lg_phy", "dinoflag",
"seagrass")] <- 0.01
}
if("lethal_oxygen_level" %!in% names(species_input)){
species_input$lethal_oxygen_level <- NA
species_input$lethal_oxygen_level[species_input$atlantis_type %!in%
c("fish", "mammal", "bird", "shark",
"microphytobenthos", "phytoben",
"sm_phy", "lg_phy", "dinoflag",
"seagrass")] <- 0.5
}
if("limiting_oxygen_level" %!in% names(species_input)){
species_input$limiting_oxygen_level <- NA
species_input$limiting_oxygen_level[species_input$atlantis_type %!in%
c("fish", "mammal", "bird", "shark",
"microphytobenthos", "phytoben",
"sm_phy", "lg_phy", "dinoflag",
"seagrass")] <- 10
}
if("minimim_oxygen_vertebrates" %!in% names(species_input)){
species_input$minimim_oxygen_vertebrates <-NA
species_input$minimim_oxygen_vertebrates[species_input$atlantis_type %in%
c("fish", "mammal", "bird",
"shark")] <- 0
}
if("other_fish_mortality" %!in% names(species_input)){
species_input$other_fish_mortality <-NA
species_input$other_fish_mortality[species_input$atlantis_type %in%
c("fish")] <- c("0 0 0 0")
}
if("mammal_bird_mortality" %!in% names(species_input)){
species_input$mammal_bird_mortality <-NA
species_input$mammal_bird_mortality[species_input$atlantis_type %in%
c("fish")] <- c("0 0 0 0")
}
if("mS_SB" %!in% names(species_input)){
species_input$mS_SB <- c("0, 0, 0, 0")
}
if("spawning_formulation_constant" %!in% names(species_input)){
species_input$spawning_formulation_constant <- NA
species_input$spawning_formulation_constant[species_input$atlantis_type == "shark"] <- 2763.3
species_input$spawning_formulation_constant[species_input$atlantis_type == "fish" &
species_input$TL_final <= 2.5] <- 31.93
species_input$spawning_formulation_constant[species_input$atlantis_type == "fish" &
species_input$TL_final > 2.5] <- 569.65
species_input$spawning_formulation_constant[species_input$atlantis_type == "bird"] <- 193.9
species_input$spawning_formulation_constant[species_input$atlantis_type == "mammal"] <- 38376.9
}
if("spawning_formulation_fraction" %!in% names(species_input)){
species_input$spawning_formulation_fraction <- NA
species_input$spawning_formulation_fraction[species_input$atlantis_type == "shark"] <- .27
species_input$spawning_formulation_fraction[species_input$atlantis_type == "fish" &
species_input$TL_final <= 2.5] <- .246
species_input$spawning_formulation_fraction[species_input$atlantis_type == "fish" &
species_input$TL_final > 2.5] <- .425
species_input$spawning_formulation_fraction[species_input$atlantis_type == "bird"] <- .2
species_input$spawning_formulation_fraction[species_input$atlantis_type == "mammal"] <- .16
}
if("FSP" %!in% names(species_input)){
species_input$FSP <- 0
}
if("min_spawn_temp" %!in% names(species_input)){
species_input$min_spawn_temp <- NA
species_input$min_spawn_temp[species_input$atlantis_type %in% c("fish",
"mammal",
"bird",
"shark")] <- MinTemp
}
if("min_spawn_salinity" %!in% names(species_input)){
species_input$min_spawn_salinity <- NA
species_input$min_spawn_salinity[species_input$atlantis_type %in% c("fish",
"mammal",
"bird",
"shark")] <- MinSalt
}
if("max_move_temp" %!in% names(species_input)){
species_input$max_move_temp <- MaxTemp
}
if("min_move_temp" %!in% names(species_input)){
species_input$min_move_temp <- MinTemp
}
if("max_spawn_temp" %!in% names(species_input)){
species_input$max_spawn_temp <- NA
species_input$max_spawn_temp [species_input$atlantis_type %in% c("fish",
"mammal",
"bird",
"shark")] <- MaxTemp
}
if("max_spawn_salinity" %!in% names(species_input)){
species_input$max_spawn_salinity <- NA
species_input$max_spawn_salinity[species_input$atlantis_type %in% c("fish",
"mammal",
"bird",
"shark")] <- MaxSalt
}
if("stock_structure" %!in% names(species_input)){
species_input$stock_structure <- NA
species_input$stock_structure <- gsub(",", rep = "", toString(rep(1,NumberofBoxes)))
}
if("vert_stock_struct" %!in% names(species_input)){
species_input$vert_stock_struct <- 1
}
if("pop_ratio_stock" %!in% names(species_input)){
species_input$pop_ratio_stock <- 1
}
if("remin_contrib" %!in% names(species_input)){
species_input$remin_contrib <- 0
}
if("vertically_migrates" %!in% names(species_input)){
species_input$vertically_migrates <- 0
}
if("density_depend" %!in% names(species_input)){
species_input$density_depend <- NA
species_input$density_depend[species_input$atlantis_type %in%
c("bird", "fish", "mammal", "shark")] <- 0
species_input$density_depend[species_input$atlantis_type %!in%
c("bird", "fish", "mammal", "shark") & species_input$horizontally_migrates ==
1] <- 4
}
if("in_WC" %!in% names(species_input)){
species_input$in_WC <- 0
}
if("in_sed" %!in% names(species_input)){
species_input$in_sed <- 0
}
if("epi" %!in% names(species_input)){
species_input$epi <- 0
}
if("fished" %!in% names(species_input)){
species_input$fished <- 0
}
if("seperate" %!in% names(species_input)){
species_input$seperate <- 0
}
if("ext_reprod" %!in% names(species_input)){
species_input$ext_reprod <- 0
}
if("impacted" %!in% names(species_input)){
species_input$impacted <- 0
}
if("TAC" %!in% names(species_input)){
species_input$TAC <- 0
}
if("KI" %!in% names(species_input)){
species_input$KI <- 0
}
if("KS" %!in% names(species_input)){
species_input$KS <- 0
}
if("KF" %!in% names(species_input)){
species_input$KF <- 0
}
if("KN" %!in% names(species_input)){
species_input$KN <- 0
}
if("overwinter" %!in% names(species_input)){
species_input$overwinter <- 0
}
if("num_of_genotypes" %!in% names(species_input)){
species_input$num_of_genotypes <- 1
}
if("num_of_stages" %!in% names(species_input)){
species_input$num_of_stages <- NA
species_input$num_of_stages[species_input$atlantis_type %in% c("fish","shark",
"mammal", "bird")] <- 2
species_input$num_of_stages[is.na(species_input$num_of_stages)] <- 1
}
if("linear_mortality" %!in% names(species_input)){
species_input$linear_mortality <- NA
for (i in 1:nrow (species_input)){
if(species_input$atlantis_type[i] %!in% c("lab_det",
"ref_det",
"carrion")){
species_input$linear_mortality[i] <- gsub(",", rep = "", toString(rep(0, species_input$num_of_stages[i])))
}
}
}
if("quadratic_mortality" %!in% names(species_input)){
species_input$quadratic_mortality <- NA
for (i in 1:nrow (species_input)){
if(species_input$atlantis_type[i] %!in% c("lab_det",
"ref_det",
"carrion")){
species_input$quadratic_mortality[i] <- gsub(",", rep = "",
toString(rep(0, species_input$num_of_stages[i])))
}
}
}
if("extra_mortality_macrophytes" %!in% names(species_input)){
species_input$extra_mortality_macrophytes <- NA
species_input$extra_mortality_macrophytes[species_input$atlantis_type %!in% c("phytoben", "seagrass")] <- 0
}
if("num_of_stocks" %!in% names(species_input)){
species_input$num_of_stocks <- 1
}
if("stock_recruitment_scalar" %!in% names(species_input)){
species_input$stock_recruitment_scalar <- NA
for (i in 1:nrow(species_input)){
if(species_input$atlantis_type[i] %in% c("fish",
"mammal", "bird", "shark")){
species_input$stock_recruitment_scalar[i] <- gsub(",", rep = "", toString(rep(1, species_input$num_of_stocks[i])))
}
}
}
if("recruits_per_individual_per_year" %!in% names(species_input)){
species_input$recruits_per_individual_per_year <- NA
for(i in 1:nrow(species_input)){
if(is.na(species_input$recruit_group_code[i]) == F){
species_input$recruits_per_individual_per_year[i] <- gsub(",", rep = "", toString(rep(1, species_input$num_of_stocks[i])))
}
}
}
if("primary_production_impact_recruitment" %!in% names(species_input)){
species_input$primary_production_impact_recruitment <- NA
species_input$primary_production_impact_recruitment[species_input$num_of_stages > 1] <- 999
}
if("ricker_alpha" %!in% names(species_input)){
species_input$ricker_alpha <- NA
species_input$ricker_alpha[species_input$num_of_stages > 1] <- 999
}
if("ricker_beta" %!in% names(species_input)){
species_input$ricker_beta <- NA
species_input$ricker_beta[species_input$num_of_stages > 1] <- 999
}
if("beverton_holt_alpha" %!in% names(species_input)){
species_input$beverton_holt_alpha <- NA
species_input$beverton_holt_alpha[species_input$num_of_stages > 1] <- 999
}
if("beverton_holt_beta" %!in% names(species_input)){
species_input$beverton_holt_beta <- NA
species_input$beverton_holt_beta[species_input$num_of_stages > 1] <- 999
}
if("num_of_spawns" %!in% names(species_input)){
species_input$num_of_spawns <- 1
}
if("cultured" %!in% names(species_input)){
species_input$cultured <- 0
}
if("habitat_depend" %!in% names(species_input)){
species_input$habitat_depend <- 0
}
if("ph_sensitive" %!in% names(species_input)){
species_input$ph_sensitive <- 0
}
if("ph_sensitive_fecund" %!in% names(species_input)){
species_input$ph_sensitive_fecund <- 0
}
if("salinity_impacts_nutrition" %!in% names(species_input)){
species_input$salinity_impacts_nutrition <- 0
}
if("ph_impacts_availability" %!in% names(species_input)){
species_input$ph_impacts_availability <- 0
}
if("ph_impacts_growth_and_death" %!in% names(species_input)){
species_input$ph_impacts_growth_and_death <- 0
}
if("ph_impact_form" %!in% names(species_input)){
species_input$ph_impact_form <- 0
}
if("monod_inflection_point" %!in% names(species_input)){
species_input$monod_inflection_point <- 0
}
if("optimal_pH_for_nonlinear_function" %!in% names(species_input)){
species_input$optimal_pH_for_nonlinear_function <- 0
}
if("ph_correction_scalar" %!in% names(species_input)){
species_input$ph_correction_scalar <- 1
}
if("ph_function_coeff" %!in% names(species_input)){
species_input$ph_function_coeff <- 1
}
if("ph_function_base" %!in% names(species_input)){
species_input$ph_function_base <- 1
}
if("ph_correction_scalar2" %!in% names(species_input)){
species_input$ph_correction_scalar2 <- 1
}
if("salinity_sensitive" %!in% names(species_input)){
species_input$salinity_sensitive <- 0
}
if("salinity_correction_scalar" %!in% names(species_input)){
species_input$salinity_correction_scalar <- 1
}
if("max" %!in% names(species_input)){
species_input$max <- 5000
}
if("catch_grazer" %!in% names(species_input)){
species_input$catch_grazer <- 0
}
if("prop_catch_available" %!in% names(species_input)){
species_input$prop_catch_available <- NA
species_input$prop_catch_available[species_input$catch_grazer == 1] <-
gsub(",", rep = "", toString(rep(0,nrow(species_input))))
}
if("prop_catch_exploitable" %!in% names(species_input)){
species_input$prop_catch_exploitable <- NA
species_input$prop_catch_exploitable[species_input$catch_grazer == 1] <-
gsub(",", rep = "", toString(rep(0,nrow(species_input))))
}
if("sediment_penetration_depth" %!in% names(species_input)){
species_input$sediment_penetration_depth <- NA
species_input$sediment_penetration_depth[species_input$atlantis_type %!in%
c("phytoben", "microphytobenthos",
"seagrass", "lg_phy", "sm_phy")] <- .001
species_input$sediment_penetration_depth[species_input$atlantis_type %in%
c("lg_inf")] <- .1
species_input$sediment_penetration_depth[species_input$atlantis_type %in%
c("fish", "mammal", "shark", "bird")] <- 1
}
if("assimilation_efficiency_on_plants" %!in% names(species_input)){
species_input$assimilation_efficiency_on_plants <- NA
species_input$assimilation_efficiency_on_plants[species_input$atlantis_type %!in%
c("phytoben", "microphytobenthos",
"seagrass", "lg_phy", "sm_phy")] <- .5
species_input$assimilation_efficiency_on_plants[species_input$atlantis_type %in%
c("fish", "mammal", "shark", "bird")] <- .1
}
if("assimilation_efficiency_on_live_food_and_carrion" %!in% names(species_input)){
species_input$assimilation_efficiency_on_live_food_and_carrion <- NA
species_input$assimilation_efficiency_on_live_food_and_carrion[species_input$atlantis_type %!in%
c("phytoben", "microphytobenthos",
"seagrass", "lg_phy", "sm_phy")] <- .5
species_input$assimilation_efficiency_on_live_food_and_carrion[species_input$atlantis_type %in%
c("fish", "mammal", "shark", "bird")] <- .1
}
if("assimilation_efficiency_on_labile_detritus" %!in% names(species_input)){
species_input$assimilation_efficiency_on_labile_detritus <- NA
species_input$assimilation_efficiency_on_labile_detritus[species_input$atlantis_type %!in%
c("phytoben", "microphytobenthos",
"seagrass", "lg_phy", "sm_phy")] <- .1
species_input$assimilation_efficiency_on_labile_detritus[species_input$atlantis_type %in%
c("sed_ep_ff")] <- .2
species_input$assimilation_efficiency_on_labile_detritus[species_input$atlantis_type %in%
c("pl_bact", "sed_bact")] <- .3
}
if("assimilation_efficiency_on_refractory_detritus" %!in% names(species_input)){
species_input$assimilation_efficiency_on_refractory_detritus <- NA
species_input$assimilation_efficiency_on_refractory_detritus[species_input$atlantis_type %!in%
c("phytoben", "microphytobenthos",
"seagrass", "lg_phy", "sm_phy")] <- .1
species_input$assimilation_efficiency_on_refractory_detritus[species_input$atlantis_type %in%
c("sed_ep_ff")] <- .3
species_input$assimilation_efficiency_on_refractory_detritus[species_input$atlantis_type %in%
c("pl_bact", "sed_bact")] <- .5
}
if("food_lost_to_detritus" %!in% names(species_input)){
species_input$food_lost_to_detritus <- NA
species_input$food_lost_to_detritus[species_input$atlantis_type %!in%
c("phytoben", "microphytobenthos",
"seagrass", "lg_phy", "sm_phy")] <- 0
}
if("labile_detritus_lost_to_detritus" %!in% names(species_input)){
species_input$labile_detritus_lost_to_detritus <- NA
species_input$labile_detritus_lost_to_detritus[species_input$atlantis_type %!in%
c("phytoben", "microphytobenthos",
"seagrass", "lg_phy", "sm_phy")] <- 0
}
if("refractory_detritus_lost_to_detritus" %!in% names(species_input)){
species_input$refractory_detritus_lost_to_detritus <- NA
species_input$refractory_detritus_lost_to_detritus[species_input$atlantis_type %!in%
c("phytoben", "microphytobenthos",
"seagrass", "lg_phy", "sm_phy")] <- 0
}
if("mortality_contribution_to_detritus" %!in% names(species_input)){
species_input$mortality_contribution_to_detritus <- NA
species_input$mortality_contribution_to_detritus[species_input$atlantis_type %!in%
c("phytoben", "microphytobenthos",
"seagrass", "lg_phy", "sm_phy")] <- .3
}
#add index
species_input=species_input[order(species_input$atlantis_type, species_input$group_code),]
species_input$index=seq(from=0, to=(nrow(species_input)-1))
#write files for eventual review
write.csv(species_input, "final_group_paramaters_used_in_model.csv")
write.csv(mean_individual_morphology, "parameters_for_age_classes_of_groups.csv")
# start producing actual input files
species_input$group_code <- toupper(species_input$group_code)
mean_individual_morphology$group_code <- toupper(mean_individual_morphology$group_code)
#PRODUCE GROUPS FILE
groups <- data.frame("Code" = species_input$group_code,
"Index" = species_input$index,
"IsTurnedOn" = species_input$turned_on,
"Name" = species_input$group_code,
"LongName" = species_input$group_code,
"NumCohorts" = species_input$num_of_age_classes,
"NumGeneTypes" = species_input$num_of_genotypes,
"NumStages" = species_input$num_of_stages,
"NumSpawns" = species_input$num_of_spawns,
"NumAgeClassSize" = species_input$ypa_FUNC,
"NumStocks" = species_input$num_of_stocks,
"VerticallyMigrates" = species_input$vertically_migrates,
"HorizontallyMigrates" = species_input$horizontally_migrates,
"IsFished" = species_input$fished,
"IsImpacted" = species_input$impacted,
"isTAC" = species_input$TAC,
"GroupType" = toupper(species_input$atlantis_type),
"IsPredator" = species_input$predator,
"IsCover" = species_input$cover,
"IsSiliconDep" = species_input$silicon_dep,
"IsAssessed" = species_input$assessed,
"IsCatchGrazer" = species_input$catch_grazer,
"OverWinters" = species_input$overwinter,
"isCultured" = species_input$cultured,
"isHabDepend" = species_input$habitat_depend)
write.csv(groups, "set_as_groups.csv", row.names = F)
#produce biology.prm file
sink("Biology_prm.prm")
cat("#Biology prm file for Deep-C model \n")
cat(paste("#",Sys.Date(), "\n"))
#group_codes for reference
cat("#list group_codes for reference \n")
for (i in 1:nrow(species_input)){cat(paste("#", as.character(species_input$group_name[i]),
as.character(species_input$group_code[i]), "\n"))}
#start adding flags, check https://wiki.csiro.au/display/Atlantis/Finding+all+the+options+for+the+flags
#read in file with general flags (not tied to groups), this has explanations on it
cat("\n")
#use default values for flags
for (i in 1:nrow(flag_data)){
cat(paste(as.character(flag_data[i,1]), as.character(flag_data[i,2]), sep=" "))
cat("\n")
}
#Array indicating cells effected by coastal degradation (this assumes no degradation)
cat (paste ("Box_degraded", NumberofBoxes,"\n", sep=" "))
cat (rep(0,NumberofBoxes))
cat("\n")
#Set option for regional reporting here, defaults to no regions
cat(paste("regID ", NumberofBoxes, "\n", sep=" "))
cat(rep(0,NumberofBoxes))
cat("\n")
# Differential scaling with depth (must be as many entries as
# number of water column layers * number of changes)
cat(paste("vertTchange_mult ", NumberofDepthLayers, "\n", sep=""))
cat(rep(1,NumberofDepthLayers))
cat("\n")
# Differential scaling with depth (must be as many entries as
# number of water column layers * number of changes)
cat(paste("vertSchange_mult ", NumberofDepthLayers, "\n", sep=""))
cat(rep(1,NumberofDepthLayers))
cat("\n")
# Differential scaling with depth (must be as many entries as
# number of water column layers * number of changes)
cat(paste("vertpHchange_mult ", NumberofDepthLayers, "\n", sep=""))
cat(rep(1,NumberofDepthLayers))
cat("\n")
#start putting in flags for each group
#design is to make one block per group since comparisons easier to see
#in excel
for (i in 1:nrow(species_input)){
cat(paste("# parameters for ", species_input$group_code[i]), "\n")
#for all living
if (species_input$atlantis_type[i] %!in% c("lab_det", "carrion",
"ref_det")){
#flagdem <- flag_dem
if(species_input$num_of_stages[i] > 1){
if (species_input$atlantis_type[i] %in% c("fish", "bird", "mammal",
"shark")){
cat(paste("flagdem",as.character(species_input$group_code[i]), " ",
species_input$flag_dem[i],"\n", sep=""))
} else {
cat(paste("flagdem",as.character(species_input$group_code[i]), " ",
species_input$flagdem[i],"\n", sep=""))
cat(paste("flagdem j",as.character(species_input$group_code[i]), " ",
species_input$flagdem[i],"\n", sep=""))
}} else {
cat(paste("flagdem",as.character(species_input$group_code[i]), " ",
species_input$flag_dem[i],"\n", sep=""))
}
#temperature
cat(paste("temp_coefftA_",as.character(species_input$group_code[i]), " ",
species_input$temp_coefft_a[i],"\n", sep=""))
cat(paste("q10_",as.character(species_input$group_code[i]), " ",
species_input$q10[i],"\n", sep=""))
cat(paste("q10_method_",as.character(species_input$group_code[i]), " ",
species_input$q10_method[i],"\n", sep=""))
cat(paste("q10_optimal_temp_",as.character(species_input$group_code[i]), " ",
species_input$q10_optimal_temp[i],"\n", sep=""))
cat(paste("q10_correction_",as.character(species_input$group_code[i]), " ",
species_input$q10_correction[i],"\n", sep=""))
cat(paste("flagpHsensitive_",as.character(species_input$group_code[i]), " ",
species_input$ph_sensitive[i],"\n", sep=""))
cat(paste("flagfecundsensitive_",as.character(species_input$group_code[i]),
" ", species_input$ph_sensitive_fecund[i],"\n", sep=""))
cat(paste("flagnutvaleffect_",as.character(species_input$group_code[i]), " ",
species_input$salinity_impacts_nutrition[i],"\n", sep=""))
cat(paste("flagpredavaileffect_",as.character(species_input$group_code[i]),
" ", species_input$ph_impacts_availability[i],"\n", sep=""))
cat(paste("flagcontract_tol_",as.character(species_input$group_code[i]),
" ", species_input$ph_impacts_growth_and_death[i],"\n", sep=""))
cat(paste("pHsensitive_model_",as.character(species_input$group_code[i]),
" ", species_input$ph_impact_form[i],"\n", sep=""))
cat(paste("KN_pH_",as.character(species_input$group_code[i]),
" ", species_input$monod_inflection_point[i],"\n", sep=""))
cat(paste("optimal_pH_",as.character(species_input$group_code[i]),
" ", species_input$optimal_pH_for_nonlinear_function[i],"\n", sep=""))
cat(paste("pH_correction_",as.character(species_input$group_code[i]),
" ", species_input$ph_correction_scalar[i],"\n", sep=""))
cat(paste("pH_constA_",as.character(species_input$group_code[i]),
" ", species_input$ph_function_coeff[i],"\n", sep=""))
cat(paste("pH_constB_",as.character(species_input$group_code[i]),
" ", species_input$ph_function_base[i],"\n", sep=""))
cat(paste("contract_tol_",as.character(species_input$group_code[i]),
" ", species_input$ph_correction_scalar2[i],"\n", sep=""))
cat(paste("flagSaltSensitive_",as.character(species_input$group_code[i]),
" ", species_input$salinity_sensitive[i],"\n", sep=""))
cat(paste("salt_correction_",as.character(species_input$group_code[i]),
" ", species_input$salinity_correction_scalar[i],"\n", sep=""))
if(species_input$num_of_stages[i] > 1){
cat(paste(as.character(species_input$group_code[i]), "_mL ", species_input$num_of_stages[i],
"\n", sep=""))
cat(paste(species_input$linear_mortality[i], "\n", sep="" ))
} else {
cat(paste(as.character(species_input$group_code[i]), "_mL ",
species_input$linear_mortality[i],sep="" ))
}
if(species_input$num_of_stages[i] > 1){
cat(paste(as.character(species_input$group_code[i]), "_mQ ", species_input$num_of_stages[i],
"\n", sep=""))
cat(paste(species_input$quadratic_mortality[i], "\n", sep="" ))
} else {
cat(paste(as.character(species_input$group_code[i]), "_mQ ",
species_input$quadratic_mortality[i],sep="" ))
}
if(species_input$atlantis_type[i] %in% c("phytoben", "seagrass")){
cat(paste("mS_", as.character(species_input$group_code[i]), "_T15 ",
species_input$extra_mortality_macrophyte[i],"\n", sep="" ))
}
if(species_input$atlantis_type[i] %in% c("fish", "mammal", "bird", "shark")){
cat(paste("mStarve_", as.character(species_input$group_code[i]), " ",
species_input$starve[i],"\n", sep="" ))
}
if(species_input$atlantis_type[i] %!in% c("fish", "mammal", "bird", "shark",
"microphytobenthos", "phytoben", "sm_phy", "lg_phy", "dinoflag",
"seagrass")){
cat(paste("mD_", as.character(species_input$group_code[i]), " ",
species_input$oxygen_depth_mortality[i],"\n", sep="" ))
cat(paste("mO_", as.character(species_input$group_code[i]), " ",
species_input$ambient_oxygen_mortality[i],"\n", sep="" ))
cat(paste("KO2_", as.character(species_input$group_code[i]), " ",
species_input$lethal_oxygen_level[i],"\n", sep="" ))
cat(paste("KO2lim_", as.character(species_input$group_code[i]), " ",
species_input$limiting_oxygen_level[i],"\n", sep="" ))
}
}
#for all except pelagic bacteria
if (species_input$atlantis_type[i] != "pl_bact"){
cat(paste(as.character(species_input$group_code[i]), "_mindepth ",species_input$min_depth[i],"\n", sep=""))
cat(paste(as.character(species_input$group_code[i]), "_maxdepth ",species_input$max_depth[i],"\n", sep=""))
}
#for all predators
if (species_input$predator[i] == 1){
cat(paste("predcase_", as.character(species_input$group_code[i]), " ",
species_input$pred_case[i], "\n", sep=""))
cat(paste("KLP_", as.character(species_input$group_code[i]), " ",
species_input$gape_lower_limit[i], "\n", sep=""))
cat(paste("KUP_", as.character(species_input$group_code[i]), " ",
species_input$gape_upper_limit[i], "\n", sep=""))
cat(paste("KL_", as.character(species_input$group_code[i]), " ",
species_input$population_refuge[i], "\n", sep=""))
cat(paste("KU_", as.character(species_input$group_code[i]), " ",
species_input$saturation_level[i], "\n", sep=""))
if (species_input$atlantis_type[i] %!in% c("fish", "mammal", "bird", "shark")){
cat(paste("vl_", as.character(species_input$group_code[i]), " ",
species_input$search_volume_invert[i], "\n", sep=""))
cat(paste("ht_", as.character(species_input$group_code[i]), " ",
species_input$handling_time_invert[i], "\n", sep=""))
}else{
cat(paste("vla_", as.character(species_input$group_code[i]), "_T15 ",
species_input$search_volume_coefficient[i], "\n", sep=""))
cat(paste("vlb_", as.character(species_input$group_code[i]), " ",
species_input$search_volume_exponent[i], "\n", sep=""))
cat(paste("hta_", as.character(species_input$group_code[i]), " ",
species_input$handling_time_coefficient[i], "\n", sep=""))
cat(paste("htb_", as.character(species_input$group_code[i]), " ",
species_input$handling_time_exponent[i], "\n", sep=""))
}
}
#for all consumeer
if(species_input$atlantis_type[i] %!in% c("phytoben", "microphytobenthos",
"seagrass", "lg_phy", "sm_phy")){
cat(paste("flag",as.character(species_input$group_code[i]), "day ",
species_input$active[i],"\n", sep = ""))
if (species_input$atlantis_type[i] %!in% c("fish", "mammal", "bird", "shark") |
species_input$num_of_stages[i] == 1){
cat(paste("mum_", as.character(species_input$group_code[i]), "_T15 ",
mean_individual_morphology[mean_individual_morphology$group_code ==
species_input$group_code[i], "mum"], "\n", sep=""))
cat(paste("C_", as.character(species_input$group_code[i]), "_T15 ",
mean_individual_morphology[mean_individual_morphology$group_code ==
species_input$group_code[i], "clearance"], "\n", sep=""))
} else {
#clearance
cat(paste("C_", as.character(species_input$group_code[i]), " ",
species_input$num_of_age_classes[i], "\n", sep=""))
cat(mean_individual_morphology[mean_individual_morphology$group_code ==
species_input$group_code[i] &
mean_individual_morphology$AgeClass>0,"clearance"])
cat("\n")
#mum
cat(paste("mum_", as.character(species_input$group_code[i]), " ",
species_input$num_of_age_classes[i], "\n", sep=""))
cat(mean_individual_morphology[mean_individual_morphology$group_code ==
species_input$group_code[i] & mean_individual_morphology$AgeClass>0,"mum"])
cat("\n")
}
cat(paste("KDEP_", as.character(species_input$group_code[i]), " ",
species_input$sediment_penetration_depth[i],"\n", sep=""))
cat(paste("EPlant_", as.character(species_input$group_code[i]), " ",
species_input$assimilation_efficiency_on_plants[i],"\n", sep=""))
cat(paste("E_", as.character(species_input$group_code[i]), " ",
species_input$assimilation_efficiency_on_live_food_and_carrion[i],"\n", sep=""))
cat(paste("EDL_", as.character(species_input$group_code[i]), " ",
species_input$assimilation_efficiency_on_labile_detritus[i],"\n", sep=""))
cat(paste("EDR_", as.character(species_input$group_code[i]), " ",
species_input$assimilation_efficiency_on_refractory_detritus[i],"\n", sep=""))
cat(paste("FDG_", as.character(species_input$group_code[i]), " ",
species_input$food_lost_to_detritus[i],"\n", sep=""))
cat(paste("FDGDL_", as.character(species_input$group_code[i]), " ",
species_input$labile_detritus_lost_to_detritus[i],"\n", sep=""))
cat(paste("FDGDR_", as.character(species_input$group_code[i]), " ",
species_input$refractory_detritus_lost_to_detritus[i],"\n", sep=""))
cat(paste("FDM_", as.character(species_input$group_code[i]), " ",
species_input$mortality_contribution_to_detritus[i],"\n", sep=""))
}
#for all catch grazers
if(species_input$catch_grazer[i] == 1){
cat(paste("pFC",as.character(species_input$group_code[i]), " ",
nrow(species_input),"\n", sep = ""))
cat(as.character(species_input$prop_catch_available[i]))
cat("\n")
cat(paste("PropCatch_",as.character(species_input$group_code[i]), " ",
nrow(species_input),"\n", sep = ""))
cat(as.character(species_input$prop_catch_exploitable[i]))
cat("\n")
}
#for primary producers
if(species_input$atlantis_type[i] %in% c("phytoben", "microphytobenthos",
"seagrass", "lg_phy", "sm_phy")){
cat(paste("mum_", as.character(species_input$group_code[i]), "_T15 ",
mean_individual_morphology[mean_individual_morphology$group_code ==
species_input$group_code[i], "mum"],
"\n", sep=""))
cat(paste("KI_", as.character(species_input$group_code[i]), "_T15 ",
species_input$KI[i], "\n", sep=""))
cat(paste("KN_", as.character(species_input$group_code[i]), "_T15 ",
species_input$KN[i], "\n", sep=""))
cat(paste("KS_", as.character(species_input$group_code[i]), "_T15 ",
species_input$KS[i], "\n", sep=""))
cat(paste("KF_", as.character(species_input$group_code[i]), "_T15 ",
species_input$KS[i], "\n", sep=""))
cat(paste("KLYS_", as.character(species_input$group_code[i]), " ",
species_input$lysis_rate[i], "\n", sep=""))
}
#for all fish
if(species_input$atlantis_type[i] %in% c("fish")){
cat(paste("mS_FD", as.character(species_input$group_code[i]), " 4",
"\n", sep=""))
cat(as.character(species_input$other_fish_mortality[i]))
cat("\n")
cat(paste("mS_SB", as.character(species_input$group_code[i]), " 4",
"\n", sep=""))
cat(as.character(species_input$mammal_bird_mortality[i]))
cat("\n")
}
#all except primary producers
if(species_input$atlantis_type[i] %!in% c("phytoben", "microphytobenthos",
"seagrass", "lg_phy", "sm_phy")){
cat(paste(as.character(species_input$group_code[i]), "_homerange ",species_input$home_range[i],"\n", sep=""))
cat(paste(as.character(species_input$group_code[i]), "_overlap ",species_input$overlap[i],"\n", sep=""))
}
#for mobile epibenthic groups that are mobile or infaunal
if(species_input$atlantis_type[i] %in% c("sm_inf", "lg_inf", "mob_ep_other")){
cat(paste("KTUR_",as.character(species_input$group_code[i]), " ",
species_input$k_tur[i]))
}
#for epibenthic infaunal groups
if(species_input$atlantis_type[i] %in% c("sm_inf", "lg_inf")){
cat(paste("KIRR_",as.character(species_input$group_code[i]), " ",
species_input$k_irr[i], sep = ""))
}
#for epibenthic and large and small infaunal groups
if(species_input$atlantis_type[i] %in% c("sed_ep_ff", "sed_ep_other", "mob_ep_other", "phytoben", "microphytobenthos", "seagrass", "sm_inf", "lg_inf")){
cat(paste(as.character(species_input$group_code[i]), "max ",species_input$max[i],"\n", sep=""))
}
#for filter feeders
if(species_input$atlantis_type[i] %in% c("SED_EP_FF")){
cat(paste(as.character(species_input$group_code[i]), "_low ", ,species_input$low[i], "\n", sep=""))
cat(paste(as.character(species_input$group_code[i]), "thresh ",species_input$thresh[i],"\n", sep=""))
cat(paste(as.character(species_input$group_code[i]), "_sat ",species_input$sat[i],"\n", sep=""))
}
#for species that horizontally migrate
if(species_input$horizontally_migrates[1] == 1){
cat(paste(as.character(species_input$group_code[i]), "_ddepend_move"," ",
species_input$density_depend[i], "\n", sep=""))
if(species_input$num_of_stages[i] > 1){
if (species_input$atlantis_type[i] %in% c("fish", "bird", "mammal",
"shark")){
cat(paste("flag", as.character(species_input$group_code[i]), "Migrate"," ",
species_input$migrates_out_of_model[i], "\n", sep=""))
} else {
cat(paste("flag", as.character(species_input$group_code[i]), "Migrate"," ", species_input$migrates_out_of_model[i], "\n", sep=""))
cat(paste("flagj", as.character(species_input$group_code[i]), "Migrate"," ", species_input$migrates_out_of_model[i], "\n", sep=""))
}} else {
cat(paste("flag", as.character(species_input$group_code[i]), "Migrate"," ",
species_input$migrates_out_of_model[i], "\n", sep=""))
}
if(species_input$num_of_stages[i] > 1){
cat(paste("j", as.character(species_input$group_code[i]), "_Migrate_Time 1",
"\n", sep=""))
cat(as.character(species_input$migrates_out_times_juv[i]))
cat("\n")
cat(paste("j", as.character(species_input$group_code[i]), "_Migrate_Return 1",
"\n", sep=""))
cat(as.character(species_input$migrates_in_times_juv[i]))
cat("\n")
cat(paste("j", as.character(species_input$group_code[i]), "_Migrate_Period 1",
"\n", sep=""))
cat(as.character(species_input$migrate_period_juv[i]))
cat("\n")
cat(paste("j", as.character(species_input$group_code[i]), "_ReturnStock 1",
"\n", sep=""))
cat(as.character(species_input$return_stock_juv[i]))
cat("\n")
cat(paste("j", as.character(species_input$group_code[i]), "_FSM 1",
"\n", sep=""))
cat(as.character(species_input$migrants_return_juv[i]))
cat("\n")
cat(paste("j", as.character(species_input$group_code[i]), "_FSMG 1",
"\n", sep=""))
cat(as.character(species_input$prop_increase_migrant_size_juv[i]))
cat("\n")
cat(paste(as.character(species_input$group_code[i]), "_Migrate_Time 1",
"\n", sep=""))
cat(as.character(species_input$migrates_out_times_ad[i]))
cat("\n")
cat(paste(as.character(species_input$group_code[i]), "_Migrate_Return 1",
"\n", sep=""))
cat(as.character(species_input$migrates_in_times_ad[i]))
cat("\n")
cat(paste(as.character(species_input$group_code[i]), "_Migrate_Period 1",
"\n", sep=""))
cat(as.character(species_input$migrate_period_ad[i]))
cat("\n")
cat(paste(as.character(species_input$group_code[i]), "_ReturnStock 1",
"\n", sep=""))
cat(as.character(species_input$return_stock_ad[i]))
cat("\n")
cat(paste(as.character(species_input$group_code[i]), "_FSM 1",
"\n", sep=""))
cat(as.character(species_input$migrants_return_ad[i]))
cat("\n")
cat(paste(as.character(species_input$group_code[i]), "_FSMG 1",
"\n", sep=""))
cat(as.character(species_input$prop_increase_migrant_size_ad[i]))
cat("\n")
} else {
cat(paste(as.character(species_input$group_code[i]), "_Migrate_Time 1",
"\n", sep=""))
cat(as.character(species_input$migrates_out_times_ad[i]))
cat("\n")
cat(paste(as.character(species_input$group_code[i]), "_Migrate_Return 1",
"\n", sep=""))
cat(as.character(species_input$migrates_in_times_ad[i]))
cat("\n")
cat(paste(as.character(species_input$group_code[i]), "_Migrate_Period 1",
"\n", sep=""))
cat(as.character(species_input$migrate_period_ad[i]))
cat("\n")
cat(paste(as.character(species_input$group_code[i]), "_ReturnStock 1",
"\n", sep=""))
cat(as.character(species_input$return_stock_ad[i]))
cat("\n")
cat(paste(as.character(species_input$group_code[i]), "_FSM 1",
"\n", sep=""))
cat(as.character(species_input$migrants_return_ad[i]))
cat("\n")
cat(paste(as.character(species_input$group_code[i]), "_FSMG 1",
"\n", sep=""))
cat(as.character(species_input$prop_increase_migrant_size_ad[i]))
cat("\n")
}
}
#for all vertebrates and stage-structured inverts
if (species_input$atlantis_type[i] %in% c("fish", "mammal", "bird", "shark") |
species_input$num_of_stages[i] > 1){
#flagrecruit <- flag_recruit
if (species_input$atlantis_type[i] %in% c("fish", "mammal", "bird", "shark")){
cat(paste("flagrecruit",as.character(species_input$group_code[i]), " ",
species_input$recruit_group_code[i], "\n", sep=""))
} else{
cat(paste("flagrecruit",as.character(species_input$group_code[i]), " ",
species_input$recruit_group_code[i], "\n", sep=""))
cat(paste("flagseperate",as.character(species_input$group_code[i]), " ",
species_input$seperate[i], "\n", sep=""))
}
cat(paste("KDENR_",as.character(species_input$group_code[i]), " ",species_input$num_of_stocks[i],
"\n", sep=""))
cat(paste(species_input$recruits_per_individual_per_year[i], "\n", sep=""))
cat(paste("PP_", as.character(species_input$group_code[i]), " ",
species_input$primary_production_impact_recruitment[i], "\n", sep=""))
cat(paste("Ralpha_", as.character(species_input$group_code[i]), " ",
species_input$ricker_alpha[i], "\n", sep=""))
cat(paste("Rbeta_", as.character(species_input$group_code[i]), " ",
species_input$ricker_beta[i], "\n", sep=""))
cat(paste("BHalpha_", as.character(species_input$group_code[i]), " ",
species_input$beverton_holt_alpha[i], "\n", sep=""))
cat(paste("BHbeta_", as.character(species_input$group_code[i]), " ",
species_input$beverton_holt_beta[i], "\n", sep=""))
#external reproduction
cat(paste("flagext_reprod",as.character(species_input$group_code[i]), " ",
species_input$ext_reprod[i], "\n", sep=""))
#local recruit
cat(paste("flaglocalrecruit",as.character(species_input$group_code[i]), " ", species_input$local_recruit[i], "\n", sep=""))
cat(paste("feed_while_spawn",as.character(species_input$group_code[i]), " ", species_input$feed_while_spawning[i], "\n", sep=""))
cat(paste("flagtempsensitive",as.character(species_input$group_code[i]),
" ",species_input$flag_temp_sensitive[i],"\n", sep=""))
cat(paste(as.character(species_input$group_code[i]), "_AgeClassSize", " ", max(1, round(species_input$ypa_FUNC[i])), "\n", sep=""))
cat(paste(as.character(species_input$group_code[i]), "_age_mat", " ", species_input$mat_FUNC[i], "\n", sep=""))
cat(paste("FSPB_", as.character(species_input$group_code[i]), " ", species_input$NumofAgeClasses[i], "\n", sep=""))
cat(mean_individual_morphology[mean_individual_morphology$group_code==species_input$group_code[i] & mean_individual_morphology$AgeClass>0,
"PropSpawning"])
cat("\n")
cat(paste("KSWR_", as.character(species_input$group_code[i]), " ",
mean_individual_morphology[mean_individual_morphology$group_code
== species_input$group_code[i] & mean_individual_morphology$AgeClass==1,
"StructN"], "\n", sep=""))
cat(paste("KWWR_", as.character(species_input$group_code[i]), " ",
mean_individual_morphology[mean_individual_morphology$group_code
== species_input$group_code[i] & mean_individual_morphology$AgeClass==1,
"ResN"], "\n", sep=""))
cat("\n")
}
#for all vertebrates
if (species_input$atlantis_type[i] %in% c("fish", "mammal", "bird", "shark")){
cat(paste("flagplankfish",as.character(species_input$group_code[i]), " ", species_input$planktivore[i], "\n", sep=""))
cat(paste("flagrecpeak",as.character(species_input$group_code[i]), " ", species_input$reprod_strength[i], "\n", sep=""))
cat(paste("flagbearlive",as.character(species_input$group_code[i]), " ", species_input$bear_live_young[i], "\n", sep=""))
cat(paste("flagmother",as.character(species_input$group_code[i]), " ", species_input$parental_care[i], "\n", sep=""))
cat(paste("flaq10eff",as.character(species_input$group_code[i]), " ",species_input$flag_q10[i],"\n", sep=""))
cat(paste("flaghabdepend",as.character(species_input$group_code[i]), " ",species_input$habitat_depend[i],"\n", sep=""))
cat(paste("flagchannel",as.character(species_input$group_code[i]), " ",species_input$channel[i],"\n", sep=""))
cat(paste("Kcov_juv_",as.character(species_input$group_code[i]), " ",species_input$Kcov_juv[i],"\n", sep=""))
cat(paste("Bcov_juv_",as.character(species_input$group_code[i]), " ",species_input$Bcov_juv[i],"\n", sep=""))
cat(paste("Acov_juv_",as.character(species_input$group_code[i]), " ",species_input$Acov_juv[i],"\n", sep=""))
cat(paste("Kcov_ad_",as.character(species_input$group_code[i]), " ",species_input$Kcov_ad[i],"\n", sep=""))
cat(paste("Bcov_ad_",as.character(species_input$group_code[i]), " ",species_input$Bcov_ad[i],"\n", sep=""))
cat(paste("Acov_ad_",as.character(species_input$group_code[i]), " ",species_input$Acov_ad[i],"\n", sep=""))
cat(paste("Speed_",as.character(species_input$group_code[i]), " ",species_input$swim_speed[i],"\n", sep=""))
cat(paste(as.character(species_input$group_code[i]), "_min_move_temp ",species_input$min_move_temp[i],"\n", sep=""))
cat(paste(as.character(species_input$group_code[i]), "_max_move_temp ",species_input$max_move_temp[i],"\n", sep=""))
cat(paste(as.character(species_input$group_code[i]), "_min_move_salt ",species_input$min_move_salt[i],"\n", sep=""))
cat(paste(as.character(species_input$group_code[i]), "_max_move_salt",species_input$max_move_salt[i],"\n", sep=""))
cat(paste("pSTOCK_", as.character(species_input$group_code[i]), " 1","\n", sep=""))
cat(as.character(species_input$stock_availability[i]))
cat("\n")
cat(paste("pSTOCK_j", as.character(species_input$group_code[i]), " 1","\n", sep=""))
cat(as.character(species_input$stock_availability_juv[i]))
cat("\n")
cat(paste("pR_", as.character(species_input$group_code[i]), " ",
species_input$prefer_allocate_reserves[i],"\n", sep=""))
cat(paste("li_a_", as.character(species_input$group_code[i]), " ",
species_input$mean_a[i],"\n", sep=""))
cat(paste("li_b_", as.character(species_input$group_code[i]), " ",
species_input$mean_b[i],"\n", sep=""))
if("min_length_reproduction" %!in% names(species_input)){
cat(paste("min_li_mat_", as.character(species_input$group_code[i]), " ",
minnona(mean_individual_morphology[mean_individual_morphology$group_code
== species_input$group_code[i] &
mean_individual_morphology$Prop_Adult > 0,
"length"]),"\n", sep=""))
}else {cat(paste("min_li_mat_", as.character(species_input$group_code[i]), " ",
species_input$min_length_reproduction[i]), "\n", sep="")
}
cat(paste("KA_", as.character(species_input$group_code[i]), " ",
species_input$fish_respiration_scaling_coefficient[i], "\n", sep=""))
cat(paste("KB_", as.character(species_input$group_code[i]), " ",
species_input$fish_respiration_scaling_exponent[i], "\n", sep=""))
cat(paste(as.character(species_input$group_code[i]), "_min_O2 ",
species_input$minimim_oxygen_vertebrates[i], "\n", sep = ""))
cat(paste("KSPA_", as.character(species_input$group_code[i]), " ",
species_input$spawning_formulation_constant[i], "\n", sep = ""))
cat(paste("FSP_", as.character(species_input$group_code[i]), " ",
species_input$spawning_formulation_fraction[i], "\n", sep = ""))
cat(paste("recSTOCK_"), as.character(species_input$group_code[i]), " ",
species_input$num_of_stocks[i], "\n", sep = "")
cat(paste(species_input$stock_recruitment_scalar[i], "\n", sep="" ))
cat(paste("recover_mult_", as.character(species_input$group_code[i]), " ",
species_input$recovery_multiplier[i], "\n", sep = ""))
cat(paste("recover_start_", as.character(species_input$group_code[i]), " ",
species_input$recover_start_date[i], "\n", sep = ""))
cat(paste(as.character(species_input$group_code[i]), "_min_spawn_temp ",species_input$min_spawn_temp[i],"\n", sep=""))
cat(paste(as.character(species_input$group_code[i]), "_max_spawn_temp ",species_input$max_spawn_temp[i],"\n", sep=""))
cat(paste(as.character(species_input$group_code[i]), "_min_spawn_temp ",species_input$min_spawn_salinity[i],"\n", sep=""))
cat(paste(as.character(species_input$group_code[i]), "_max_spawn_temp ",species_input$max_spawn_salinity[i],"\n", sep=""))
cat (paste (as.character(species_input$group_code[i]), "_stock_struct ", NumberofBoxes,"\n", sep=""))
cat(paste(species_input$stock_structure[i]), "\n")
}
cat("\n")
}
sink()
}
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