Make_Map: Makes the Map argument for TMB, which is used to turn off...

In aaronmberger/Geo_dGLMM_habitat: Package for conducting spatial estimation of CPUE index standardization (fisheries, ecology, etc).

Usage

Make_Map(VesselConfig, TmbData, FieldConfig, CovConfig, CovConception, ObsModel, Aniso)

Arguments

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)

Examples

##---- 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)
  }

aaronmberger/Geo_dGLMM_habitat documentation built on May 10, 2019, 3:20 a.m.