sam: SAMによる資源計算を実施する

In ShotaNishijima/frasam: Fisheries Research Agency (FRA) provides an R package for analyzing the State-space Assessment Model (SAM)

SAMによる資源計算を実施する

Description

SAMによる資源計算を実施する

Usage

sam(
  dat,
  last.catch.zero = FALSE,
  cpp.file.name = "sam2",
  tmb.run = FALSE,
  abund = c("B"),
  rec.age = 0,
  min.age = rep(0, length(abund)),
  max.age = rep(0, length(abund)),
  plus.group = TRUE,
  alpha = 1,
  b.est = FALSE,
  b.fix = rep(NA, length(abund)),
  varC = 0,
  varN = 0,
  varF = 0,
  varN.fix = NULL,
  est.method = "ml",
  SR = "BH",
  AR = 0,
  rho.mode = 2,
  q.init = NULL,
  sdFsta.init = NULL,
  sdLogN.init = NULL,
  sdLogObs.init = NULL,
  rho.init = NULL,
  a.init = NULL,
  b.init = NULL,
  ref.year = 1:5,
  bias.correct = TRUE,
  bias.correct.sd = FALSE,
  get.random.vcov = FALSE,
  silent = FALSE,
  remove.Fprocess.year = NULL,
  RW.Forder = 0,
  map.add = NULL,
  p0.list = NULL,
  scale = 1000,
  gamma = 10,
  sel.def = "max",
  use.index = NULL,
  upper = NULL,
  lower = NULL,
  index.key = NULL,
  index.b.key = NULL,
  b_random = FALSE,
  b_range = NULL,
  lambda = 0,
  FreeADFun = FALSE,
  add_random = NULL,
  lambda_Mesnil = 0,
  tmbdata = NULL,
  map = NULL,
  model_wm = c(FALSE, FALSE),
  w0_factor = c("none", "SSB")[1],
  weight_factor = c("none", "N_total")[1],
  family_w = c("lognormal", "gamma")[2],
  maturity_factor = c("none", "cohort_plus")[1],
  scale_number = 1000,
  weight_weight = NULL,
  maturity_weight = NULL,
  g_fix = NULL,
  CV_w_fix = NULL,
  w_link = "log",
  sep_omicron = TRUE,
  growth_regime = NULL,
  catch_prop = NULL,
  no_est = FALSE,
  getJointPrecision = FALSE,
  loopnum = 2
)

Arguments

dat	samに使用するdataでrvpaと同じフォーマットで利用可能
rec.age	加入年齢 (default: 0)
min.age	Indexの最低年齢 (frasyr::vpa()と同じで最小の年齢を0とする)
max.age	Indexの最高年齢 (frasyr::vpa()と同じで最小の年齢を0とする)
SR	再生産関係："RW", "BH", "RI", "HS", "Mesnil", or "Const"
index.key	Indexのsigmaの制約
model_wm	weightとmaturityの成長をモデリングするかどうか

ShotaNishijima/frasam documentation built on Sept. 9, 2024, 8:43 p.m.