#' Gadget defaults
#'
#' Some pre-baked defaults to use in setting up Gadget simulations
#'
#' @name gadget_defaults
NULL
#' @rdname gadget_defaults
#' @export
gad_mod_dir <- "gadget_model"
#' @rdname gadget_defaults
gadget_main_default <-
structure(
list(timefile = "time",
areafile = "Modelfiles/area",
printfiles = "; Required comment",
stockfiles = "",
tagfiles = "",
otherfoodfiles = "",
fleetfiles = "",
likelihoodfiles = ""),
class = c("gadget_main", "list"))
#' @rdname gadget_defaults
gadget_timefile_default <-
structure(
list(firstyear = NULL,
firststep = NULL,
lastyear = NULL,
laststep = NULL,
notimesteps = NULL),
class = c("gadget_time", "list")
)
#' @rdname gadget_defaults
gadget_areafile_default <-
structure(
list(areas = NULL,
size = NULL,
temperature = NULL),
class = c("gadget_area", "list")
)
#' @rdname gadget_defaults
gadget_stockfile_default <-
structure(
list(stockname = NULL,
livesonareas = NULL,
minage = NULL,
maxage = NULL,
minlength = NULL,
maxlength = NULL,
dl = NULL,
refweightfile = NULL,
growthandeatlengths = NULL,
doesgrow = 0,
naturalmortality = NULL,
iseaten = 0,
doeseat = 0,
initialconditions = NULL,
doesmigrate = 0,
doesmature = 0,
doesmove = 0,
doesrenew = 0,
doesspawn = 0,
doesstray = 0),
class = c("gadget_stock", "list")
)
#' @rdname gadget_defaults
gadget_tagfile_default <-
structure(
list(tagid = NULL,
stock = NULL,
tagarea = NULL,
endyear = NULL,
tagloss = NULL,
numbers = NULL),
class = c("gadget_tagfile", "list")
)
#' @rdname gadget_defaults
gadget_otherfood_default <-
structure(
list(foodname = NULL,
livesonareas = NULL,
lengths = NULL,
energycontent = NULL,
amount = NULL),
class = c("gadget_otherfood", "list")
)
#' Fleet Defaults
#'
#' Pre-baked default lists to use for reading in fleets
#'
#' @name fleet_defaults
NULL
#' @rdname fleet_defaults
totalfleet <-
structure(
list(totalfleet = "",
livesonareas = 1,
multiplicative = 1,
suitability = "",
amount = ""),
class = c("gadget_fleet", "list"))
#' @rdname fleet_defaults
numberfleet <- totalfleet
names(numberfleet)[1] <- "numberfleet"
#' @rdname fleet_defaults
linearfleet <- totalfleet
names(linearfleet)[1] <- "linearfleet"
#' @rdname fleet_defaults
effortfleet <- totalfleet
names(effortfleet)[1] <- "effortfleet"
#' @rdname fleet_defaults
quotafleet <-
structure(
list(quotafleet = "",
livesonareas = "",
multiplicative = "",
suitability = "",
quotafunction = "",
biomasslevel = "",
quotalevel = "",
amount = ""),
class = c("gadget_fleet", "list"))
fleet_types <-
c("totalfleet", "numberfleet", "linearfleet", "effortfleet", "quotafleet")
# defaults for likelihood components
penalty_likelihood <-
structure(list(
name = "penalty",
weight = 1,
type = "penalty",
data = data.frame(switch = "default", power = 2,
lower = 1000, upper = 1000)),
class = c("gadget_penalty_likelihood", "list"))
understocking_likelihood <-
structure(list(
name = "understocking",
weight = 1,
type = "understocking",
powercoeff = NULL
), class = c("gadget_understocking_likelihood", "list"))
catchdistribution_likelihood <-
structure(list(
name = "",
weight = 1,
type = "catchdistribution",
data = "",
`function` = "sumofsquares",
lag = NULL,
sigma = NULL,
param = NULL,
aggregationlevel = NULL,
overconsumption = NULL,
epsilon = NULL,
areaaggfile = "",
ageaggfile = "",
lenaggfile = "",
fleetnames = "",
stocknames = ""
), class = c("gadget_catchdistribution_likelihood", "list"))
catchstatistics_likelihood <-
structure(list(
name = "",
weight = 1,
type = "catchstatistics",
data = "",
`function` = "lengthcalcstddev",
overconsumption = 0,
areaaggfile = "",
lenaggfile = NULL,
ageaggfile = "",
fleetnames = "",
stocknames = ""
), class = c("gadget_catchstatistics_likelihood", "list"))
stockdistribution_likelihood <-
structure(list(
name = "",
weight = 1,
type = "stockdistribution",
data = "",
`function` = "sumofsquares",
aggregationlevel = NULL,
overconsumption = NULL,
epsilon = NULL,
areaaggfile = "",
ageaggfile = "",
lenaggfile = "",
fleetnames = "",
stocknames = ""
), class = c("gadget_stockdistribution_likelihood", "list"))
surveyindices_likelihood <-
structure(list(
name = "",
weight = 1,
type = "surveyindices",
data = "",
sitype = "",
biomass = NULL
), class = c("gadget_surveyindices_likelihood", "list"))
si_lengths <-
modifyList(surveyindices_likelihood,
list(sitype = "lengths",
areaaggfile = "",
lenaggfile = "",
stocknames = ""))
si_ages <-
modifyList(surveyindices_likelihood,
list(sitype = "ages",
areaggfile = "",
lenaggfile = "",
stocknames = ""))
si_fleets <-
modifyList(surveyindices_likelihood,
list(sitype = "fleets",
areaggfile = "",
lenaggfile = "",
fleetnames = "",
stocknames = ""))
si_acoustic <-
modifyList(surveyindices_likelihood,
list(sitype = "acoustic",
areaaggfile = "",
surveynames = "",
stocknames = ""))
si_effort <-
modifyList(surveyindices_likelihood,
list(sitype = "effort",
areaaggfile = "",
fleetnames = "",
stocknames = ""))
surveydistribution_likelihood <-
structure(list(
name = "",
weight = 1,
type = "surveydistribution",
data = "",
areaaggfile = "",
lenaggfile = "",
ageaggfile = "",
stocknames = "",
fittype = "",
parameters = "",
suitability_parameters = "",
epsilon = 1,
likelihoodtype = "multinomial"
), class = c("gadget_surveydistribution_likelihood", "list"))
stomachcontent_likelihood <-
structure(list(
name = "",
weight = 1,
type = "stomachcontent",
`function` = "scsimple",
data = "",
epsilon = NULL,
areaaggfile = "",
predatornames = "",
predatorlengths = "",
lenaggfile = "",
preyaggfile = ""
), class = c("gadget_stomachconent_likelihood", "list"))
recaptures_likelihood <-
structure(list(
name = "",
weight = 1,
type = "recaptures",
data = "",
`function` = "poisson",
areaaggfile = "",
lenaggfile = "",
fleetnames = ""
), class = c("gadget_recaptures_likelihood", "list"))
recstatistics_likelihood <-
structure(list(
name = "",
weight = 1,
type = "recstatistics",
data = "",
`function` = "lengthcalcstddev",
areaaggfile = "",
fleetnames = ""
), class = c("gadget_recstatistics_likelihood", "list"))
migrationpenalty_likelihood <-
structure(list(
name = "",
weight = 1,
type = "migrationpenalty",
stockname = "",
powercoeffs = c(2, 1)
), class = c("gadget_migrationpenalty_likelihood", "list"))
migrationproportion_likelihood <-
structure(list(
name = "",
weight = 1,
type = "migrationproportion",
data = "",
`function` = "sumofsquares",
biomass = NULL,
areaaggfile = "",
stocknames = ""
), class = c("gadget_migrationproportion_likelhood", "list"))
catchinkilos_likelihood <-
structure(list(
name = "",
weight = 1,
type = "catchinkilos",
data = "",
`function` = "sumofsquares",
aggregationlevel = NULL,
epsilon = NULL,
areaaggfile = "",
fleetnames = "",
stocknames = ""
), class = c("gadget_catchinkilos_likelihood", "list"))
# optinfofile components
hooke_optinfo <-
list(
hookeiter = 50000,
hookeeps = 1e-04,
rho = 0.5,
lambda = 0
)
simann_optinfo <-
list(
simanniter = 2000,
scale = 1,
simanneps = 1e-03,
t = 3000000,
rt = 0.85,
nt = 2,
ns = 5,
vm = 1,
cstep = 2,
lratio = 0.3,
uratio = 0.7,
check = 4
)
bfgs_optinfo <-
list(
bfgsiter = 20000,
bfgseps = 0.01,
sigma = 0.01,
beta = 0.3,
gradacc = 1e-06,
gradstep = 0.5,
gradeps = 1e-10
)
pso_optinfo <-
list(
goal = 1e-06,
psoiter = 1e09
)
de_optinfo <-
list(
goal = 1e-06,
iter = 1e09
)
#' Switch defaults
#'
#' These are vectors of the switches that are used in when calling Gadget
#' from the command line, but you figured out a different way to implement this
#' You can probably delete these objects
#'
#' @name switches
single_switch <- c("s", "l", "n", "v", "h", "i", "opt", "main",
"p", "o", "print", "precision", "log", "loglevel",
"seed", "m", "printinitial", "printfinal", "maxratio")
#' @rdname switches
double_switch <- c("version", "help")
#' @rdname switches
file_switch <- single_switch[6:length(single_switch)]
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