1 | Make_Map(VesselConfig, TmbData, FieldConfig, CovConfig, CovConception, ObsModel, Aniso)
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VesselConfig |
Vector describing whether to include vessel effects |
TmbData |
named list generated by Data_Fn |
FieldConfig |
Vector describing what types of spatial variation to estimate |
CovConfig |
Vector describing covariates for spatial variation (advanced feature not used by default) |
CovConception |
Deprecated and FALSE by default |
ObsModel |
Integer for distribution of residual 'measurement' error (0=normal (log-link); 1=lognormal; 2=gamma; 4=ZANB; 5=ZINB; 11=lognormal-mixture; 12=gamma-mixture) |
Aniso |
Use geometric anisotropy for spatial variation (0=no, 1=yes) |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 | ##---- Should be DIRECTLY executable !! ----
##-- ==> Define data, use random,
##-- or do help(data=index) for the standard data sets.
## The function is currently defined as
function (VesselConfig, TmbData, FieldConfig, CovConfig, CovConception,
ObsModel, Aniso)
{
Map = list()
if (VesselConfig["Vessel"] == 0) {
Map[["nu1_v"]] = factor(rep(NA, TmbData$n_v))
Map[["nu2_v"]] = factor(rep(NA, TmbData$n_v))
Map[["logsigmaV1"]] = factor(NA)
Map[["logsigmaV2"]] = factor(NA)
}
if (VesselConfig["VesselYear"] == 0) {
Map[["nu1_vt"]] = factor(matrix(NA, nrow = TmbData$n_v,
ncol = TmbData$n_t))
Map[["nu2_vt"]] = factor(matrix(NA, nrow = TmbData$n_v,
ncol = TmbData$n_t))
Map[["logsigmaVT1"]] = factor(NA)
Map[["logsigmaVT2"]] = factor(NA)
}
if (FieldConfig["Omega1"] == 0) {
Map[["Omegainput1_s"]] = factor(rep(NA, TmbData$n_s))
Map[["logetaO1"]] = factor(NA)
}
if (FieldConfig["Epsilon1"] == 0) {
Map[["Epsiloninput1_st"]] = factor(matrix(NA, nrow = TmbData$n_s,
ncol = TmbData$n_t))
Map[["logetaE1"]] = factor(NA)
}
if (FieldConfig["Omega1"] == 0 & FieldConfig["Epsilon1"] ==
0)
Map[["logkappa1"]] = factor(NA)
if (FieldConfig["Omega2"] == 0) {
Map[["Omegainput2_s"]] = factor(rep(NA, TmbData$n_s))
Map[["logetaO2"]] = factor(NA)
}
if (FieldConfig["Epsilon2"] == 0) {
Map[["Epsiloninput2_st"]] = factor(matrix(NA, nrow = TmbData$n_s,
ncol = TmbData$n_t))
Map[["logetaE2"]] = factor(NA)
}
if (FieldConfig["Omega2"] == 0 & FieldConfig["Epsilon2"] ==
0)
Map[["logkappa2"]] = factor(NA)
if (sum(CovConfig) == 0 & CovConception == FALSE) {
Map[["gamma1_j"]] = factor(NA)
Map[["gamma2_j"]] = factor(NA)
}
if (ObsModel %in% c(0, 1, 2)) {
Map[["logSigmaM"]] = factor(c(1, NA, NA))
}
if (ObsModel %in% c(4, 5)) {
Map[["logSigmaM"]] = factor(c(1, NA, 2))
}
if (Aniso == 0 | all(FieldConfig == 0))
Map[["ln_H_input"]] = factor(rep(NA, 2))
return(Map)
}
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