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Merge pull request #45 from James-Thorson/devel
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Devel
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@James-Thorson
James-Thorson authored Jul 25, 2017
2 parents e4df36f + ecfb4c1 commit 7477d7f
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3 changes: 2 additions & 1 deletion NAMESPACE
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@@ -1,4 +1,4 @@
# Generated by roxygen2 (4.1.1): do not edit by hand
# Generated by roxygen2: do not edit by hand

export(Build_TMB_Fn)
export(Coherence)
Expand All @@ -14,6 +14,7 @@ export(Summarize_Covariance)
export(calc_coherence)
export(calc_cov)
export(calc_synchrony)
export(calculate_proportion)
export(plot_cov)
export(plot_eigen)
importFrom(grDevices,colorRampPalette)
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38 changes: 24 additions & 14 deletions R/Data_Fn.R
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Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,7 @@
#' @param Aniso OPTIONAL, whether to assume isotropy (Aniso=0) or geometric anisotropy (Aniso=1)
#' @param RhoConfig OPTIONAL, vector of form c("Beta1"=0,"Beta2"=0,"Epsilon1"=0,"Epsilon2"=0) specifying whether either intercepts (Beta1 and Beta2) or spatio-temporal variation (Epsilon1 and Epsilon2) is structured among time intervals (0: each year as fixed effect; 1: each year as random following IID distribution; 2: each year as random following a random walk; 3: constant among years as fixed effect; 4: each year as random following AR1 process)
#' @param t_yz OPTIONAL, matrix specifying combination of levels of \code{t_iz} to use when calculating different indices of abundance or range shifts
#' @param Options OPTIONAL, a vector of form c('SD_site_density'=0,'SD_site_logdensity'=0,'Calculate_Range'=0,'Calculate_evenness'=0,'Calculate_effective_area'=0,'Calculate_Cov_SE'=0,'Calculate_Synchrony'=0,'Calculate_Coherence'=0), where Calculate_Range=1 turns on calculation of center of gravity, and Calculate_effective_area=1 turns on calculation of effective area occupied
#' @param Options OPTIONAL, a vector of form c('SD_site_logdensity'=0,'Calculate_Range'=0,'Calculate_effective_area'=0,'Calculate_Cov_SE'=0,'Calculate_Synchrony'=0,'Calculate_proportion'=0), where Calculate_Range=1 turns on calculation of center of gravity, and Calculate_effective_area=1 turns on calculation of effective area occupied
#' @param yearbounds_zz OPTIONAL, matrix with two columns, giving first and last years for defining one or more periods (rows) used to calculate changes in synchrony over time (only used if \code{Options['Calculate_Synchrony']=1})
#' @param CheckForErrors OPTIONAL, whether to check for errors in input (NOTE: when CheckForErrors=TRUE, the function will throw an error if it detects a problem with inputs. However, failing to throw an error is no guaruntee that the inputs are all correct)

Expand All @@ -50,7 +50,18 @@ Data_Fn <-
function( Version, FieldConfig, OverdispersionConfig=c("eta1"=0,"eta2"=0), ObsModel=c("PosDist"=1,"Link"=0), b_i, a_i, c_i, s_i, t_iz,
a_xl, MeshList, GridList, Method, v_i=rep(0,length(b_i)), PredTF_i=rep(0,length(b_i)), X_xj=NULL, X_xtp=NULL, Q_ik=NULL,
Aniso=1, RhoConfig=c("Beta1"=0,"Beta2"=0,"Epsilon1"=0,"Epsilon2"=0), t_yz=NULL, CheckForErrors=TRUE, yearbounds_zz=NULL,
Options=c('SD_site_density'=0,'SD_site_logdensity'=0,'Calculate_Range'=0,'Calculate_evenness'=0,'Calculate_effective_area'=0,'Calculate_Cov_SE'=0,'Calculate_Synchrony'=0,'Calculate_Coherence'=0) ){
Options=c('SD_site_logdensity'=0,'Calculate_Range'=0,'Calculate_effective_area'=0,'Calculate_Cov_SE'=0,'Calculate_Synchrony'=0,'Calculate_proportion'=0) ){

# Specify default values for `Options`
Options2use = c('SD_site_density'=0,'SD_site_logdensity'=0,'Calculate_Range'=0,'Calculate_evenness'=0,'Calculate_effective_area'=0,
'Calculate_Cov_SE'=0,'Calculate_Synchrony'=0,'Calculate_Coherence'=0,'Calculate_proportion'=0)

# Replace defaults for `Options` with provided values (if any)
for( i in 1:length(Options)){
if(tolower(names(Options)[i]) %in% tolower(names(Options2use))){
Options2use[[match(tolower(names(Options)[i]),tolower(names(Options2use)))]] = Options[[i]]
}
}

# Coerce t_iz to be a matrix
if( !is.matrix(t_iz) ) t_iz = matrix(t_iz,ncol=1)
Expand Down Expand Up @@ -105,10 +116,9 @@ function( Version, FieldConfig, OverdispersionConfig=c("eta1"=0,"eta2"=0), ObsMo
print(OverdispersionConfig_input)

# by default, add nothing as Z_xl
if( Options['Calculate_Range']==FALSE ){
if( Options2use['Calculate_Range']==FALSE ){
Z_xm = matrix(0, nrow=nrow(a_xl), ncol=ncol(a_xl) ) # Size so that it works for Version 3g-3j
}
if(Options['Calculate_Range']==TRUE ){
}else{
Z_xm = MeshList$loc_x
message( "Calculating range shift for stratum #1:",colnames(a_xl[1]))
}
Expand All @@ -127,7 +137,7 @@ function( Version, FieldConfig, OverdispersionConfig=c("eta1"=0,"eta2"=0), ObsMo
if( length(OverdispersionConfig)!=2 ) stop("length(OverdispersionConfig)!=2")
if( length(ObsModel)!=2 ) stop("length(ObsModel)!=2")
if( ncol(yearbounds_zz)!=2 ) stop("yearbounds_zz must have two columns")
if( Options['Calculate_Coherence']==1 & ObsModel[2]==0 ) stop("Calculating coherence only makes sense when 'ObsModel[2]=1'")
if( Options2use['Calculate_Coherence']==1 & ObsModel[2]==0 ) stop("Calculating coherence only makes sense when 'ObsModel[2]=1'")
if( any(yearbounds_zz<0) | any(yearbounds_zz>=max(n_t)) ) stop("yearbounds_zz exceeds bounds for modeled years")
if( ncol(t_yz)!=ncol(t_iz) ) stop("t_yz and t_iz must have same number of columns")
if( n_c!=length(unique(c_i)) ) stop("n_c doesn't equal the number of levels in c_i")
Expand Down Expand Up @@ -158,25 +168,25 @@ function( Version, FieldConfig, OverdispersionConfig=c("eta1"=0,"eta2"=0), ObsMo
# CMP_xmax should be >100 and CMP_breakpoint should be 1 for Tweedie model
Options_vec = c("Aniso"=Aniso, "R2_interpretation"=0, "Rho_betaTF"=ifelse(RhoConfig[["Beta1"]]|RhoConfig[["Beta2"]],1,0), "Alpha"=0, "AreaAbundanceCurveTF"=0, "CMP_xmax"=200, "CMP_breakpoint"=1, "Method"=switch(Method,"Mesh"=0,"Grid"=1,"Spherical_mesh"=0) )
if(Version%in%c("VAST_v1_1_0","VAST_v1_0_0")){
Return = list( "n_i"=n_i, "n_s"=c(MeshList$anisotropic_spde$n.spde,n_x)[Options_vec['Method']+1], "n_x"=n_x, "n_t"=n_t, "n_c"=n_c, "n_j"=n_j, "n_p"=n_p, "n_k"=n_k, "n_l"=n_l, "n_m"=ncol(Z_xm), "Options_vec"=Options_vec, "FieldConfig"=FieldConfig_input, "ObsModel"=ObsModel, "Options"=Options, "b_i"=b_i, "a_i"=a_i, "c_i"=c_i, "s_i"=s_i, "t_i"=t_iz-min(t_iz[,1]), "a_xl"=a_xl, "X_xj"=X_xj, "X_xtp"=X_xtp, "Q_ik"=Q_ik, "Z_xm"=Z_xm, "spde"=list(), "spde_aniso"=list() )
Return = list( "n_i"=n_i, "n_s"=c(MeshList$anisotropic_spde$n.spde,n_x)[Options_vec['Method']+1], "n_x"=n_x, "n_t"=n_t, "n_c"=n_c, "n_j"=n_j, "n_p"=n_p, "n_k"=n_k, "n_l"=n_l, "n_m"=ncol(Z_xm), "Options_vec"=Options_vec, "FieldConfig"=FieldConfig_input, "ObsModel"=ObsModel, "Options"=Options2use, "b_i"=b_i, "a_i"=a_i, "c_i"=c_i, "s_i"=s_i, "t_i"=t_iz-min(t_iz[,1]), "a_xl"=a_xl, "X_xj"=X_xj, "X_xtp"=X_xtp, "Q_ik"=Q_ik, "Z_xm"=Z_xm, "spde"=list(), "spde_aniso"=list() )
}
if(Version%in%c("VAST_v1_4_0","VAST_v1_3_0","VAST_v1_2_0")){
Return = list( "n_i"=n_i, "n_s"=c(MeshList$anisotropic_spde$n.spde,n_x)[Options_vec['Method']+1], "n_x"=n_x, "n_t"=n_t, "n_c"=n_c, "n_j"=n_j, "n_p"=n_p, "n_k"=n_k, "n_v"=n_v, "n_f_input"=OverdispersionConfig_input[1], "n_l"=n_l, "n_m"=ncol(Z_xm), "Options_vec"=Options_vec, "FieldConfig"=FieldConfig_input, "ObsModel"=ObsModel, "Options"=Options, "b_i"=b_i, "a_i"=a_i, "c_i"=c_i, "s_i"=s_i, "t_i"=t_iz-min(t_iz[,1]), "v_i"=match(v_i,sort(unique(v_i)))-1, "a_xl"=a_xl, "X_xj"=X_xj, "X_xtp"=X_xtp, "Q_ik"=Q_ik, "Z_xm"=Z_xm, "spde"=list(), "spde_aniso"=list() )
Return = list( "n_i"=n_i, "n_s"=c(MeshList$anisotropic_spde$n.spde,n_x)[Options_vec['Method']+1], "n_x"=n_x, "n_t"=n_t, "n_c"=n_c, "n_j"=n_j, "n_p"=n_p, "n_k"=n_k, "n_v"=n_v, "n_f_input"=OverdispersionConfig_input[1], "n_l"=n_l, "n_m"=ncol(Z_xm), "Options_vec"=Options_vec, "FieldConfig"=FieldConfig_input, "ObsModel"=ObsModel, "Options"=Options2use, "b_i"=b_i, "a_i"=a_i, "c_i"=c_i, "s_i"=s_i, "t_i"=t_iz-min(t_iz[,1]), "v_i"=match(v_i,sort(unique(v_i)))-1, "a_xl"=a_xl, "X_xj"=X_xj, "X_xtp"=X_xtp, "Q_ik"=Q_ik, "Z_xm"=Z_xm, "spde"=list(), "spde_aniso"=list() )
}
if(Version%in%c("VAST_v1_6_0","VAST_v1_5_0")){
Return = list( "n_i"=n_i, "n_s"=c(MeshList$anisotropic_spde$n.spde,n_x)[Options_vec['Method']+1], "n_x"=n_x, "n_t"=n_t, "n_c"=n_c, "n_j"=n_j, "n_p"=n_p, "n_k"=n_k, "n_v"=n_v, "n_f_input"=OverdispersionConfig_input[1], "n_l"=n_l, "n_m"=ncol(Z_xm), "Options_vec"=Options_vec, "FieldConfig"=FieldConfig_input, "ObsModel"=ObsModel, "Options"=Options, "b_i"=b_i, "a_i"=a_i, "c_i"=c_i, "s_i"=s_i, "t_i"=t_iz-min(t_iz[,1]), "v_i"=match(v_i,sort(unique(v_i)))-1, "PredTF_i"=PredTF_i, "a_xl"=a_xl, "X_xj"=X_xj, "X_xtp"=X_xtp, "Q_ik"=Q_ik, "Z_xm"=Z_xm, "spde"=list(), "spde_aniso"=list() )
Return = list( "n_i"=n_i, "n_s"=c(MeshList$anisotropic_spde$n.spde,n_x)[Options_vec['Method']+1], "n_x"=n_x, "n_t"=n_t, "n_c"=n_c, "n_j"=n_j, "n_p"=n_p, "n_k"=n_k, "n_v"=n_v, "n_f_input"=OverdispersionConfig_input[1], "n_l"=n_l, "n_m"=ncol(Z_xm), "Options_vec"=Options_vec, "FieldConfig"=FieldConfig_input, "ObsModel"=ObsModel, "Options"=Options2use, "b_i"=b_i, "a_i"=a_i, "c_i"=c_i, "s_i"=s_i, "t_i"=t_iz-min(t_iz[,1]), "v_i"=match(v_i,sort(unique(v_i)))-1, "PredTF_i"=PredTF_i, "a_xl"=a_xl, "X_xj"=X_xj, "X_xtp"=X_xtp, "Q_ik"=Q_ik, "Z_xm"=Z_xm, "spde"=list(), "spde_aniso"=list() )
}
if(Version%in%c("VAST_v1_7_0")){
Return = list( "n_i"=n_i, "n_s"=c(MeshList$anisotropic_spde$n.spde,n_x)[Options_vec['Method']+1], "n_x"=n_x, "n_t"=n_t, "n_c"=n_c, "n_j"=n_j, "n_p"=n_p, "n_k"=n_k, "n_v"=n_v, "n_l"=n_l, "n_m"=ncol(Z_xm), "Options_vec"=Options_vec, "FieldConfig"=FieldConfig_input, "OverdispersionConfig"=OverdispersionConfig_input, "ObsModel"=ObsModel, "Options"=Options, "b_i"=b_i, "a_i"=a_i, "c_i"=c_i, "s_i"=s_i, "t_i"=t_iz-min(t_iz[,1]), "v_i"=match(v_i,sort(unique(v_i)))-1, "PredTF_i"=PredTF_i, "a_xl"=a_xl, "X_xj"=X_xj, "X_xtp"=X_xtp, "Q_ik"=Q_ik, "Z_xm"=Z_xm, "spde"=list(), "spde_aniso"=list() )
Return = list( "n_i"=n_i, "n_s"=c(MeshList$anisotropic_spde$n.spde,n_x)[Options_vec['Method']+1], "n_x"=n_x, "n_t"=n_t, "n_c"=n_c, "n_j"=n_j, "n_p"=n_p, "n_k"=n_k, "n_v"=n_v, "n_l"=n_l, "n_m"=ncol(Z_xm), "Options_vec"=Options_vec, "FieldConfig"=FieldConfig_input, "OverdispersionConfig"=OverdispersionConfig_input, "ObsModel"=ObsModel, "Options"=Options2use, "b_i"=b_i, "a_i"=a_i, "c_i"=c_i, "s_i"=s_i, "t_i"=t_iz-min(t_iz[,1]), "v_i"=match(v_i,sort(unique(v_i)))-1, "PredTF_i"=PredTF_i, "a_xl"=a_xl, "X_xj"=X_xj, "X_xtp"=X_xtp, "Q_ik"=Q_ik, "Z_xm"=Z_xm, "spde"=list(), "spde_aniso"=list() )
}
if(Version%in%c("VAST_v1_8_0")){
Return = list( "n_i"=n_i, "n_s"=c(MeshList$anisotropic_spde$n.spde,n_x)[Options_vec['Method']+1], "n_x"=n_x, "n_t"=n_t, "n_c"=n_c, "n_j"=n_j, "n_p"=n_p, "n_k"=n_k, "n_v"=n_v, "n_l"=n_l, "n_m"=ncol(Z_xm), "Options_vec"=Options_vec, "FieldConfig"=FieldConfig_input, "OverdispersionConfig"=OverdispersionConfig_input, "ObsModel"=ObsModel, "Options"=Options, "b_i"=b_i, "a_i"=a_i, "c_i"=c_i, "s_i"=s_i, "t_i"=t_iz-min(t_iz[,1]), "v_i"=match(v_i,sort(unique(v_i)))-1, "PredTF_i"=PredTF_i, "a_xl"=a_xl, "X_xj"=X_xj, "X_xtp"=X_xtp, "Q_ik"=Q_ik, "Z_xm"=Z_xm, "spde"=list(), "spde_aniso"=list(), "M0"=GridList$M0, "M1"=GridList$M1, "M2"=GridList$M2 )
Return = list( "n_i"=n_i, "n_s"=c(MeshList$anisotropic_spde$n.spde,n_x)[Options_vec['Method']+1], "n_x"=n_x, "n_t"=n_t, "n_c"=n_c, "n_j"=n_j, "n_p"=n_p, "n_k"=n_k, "n_v"=n_v, "n_l"=n_l, "n_m"=ncol(Z_xm), "Options_vec"=Options_vec, "FieldConfig"=FieldConfig_input, "OverdispersionConfig"=OverdispersionConfig_input, "ObsModel"=ObsModel, "Options"=Options2use, "b_i"=b_i, "a_i"=a_i, "c_i"=c_i, "s_i"=s_i, "t_i"=t_iz-min(t_iz[,1]), "v_i"=match(v_i,sort(unique(v_i)))-1, "PredTF_i"=PredTF_i, "a_xl"=a_xl, "X_xj"=X_xj, "X_xtp"=X_xtp, "Q_ik"=Q_ik, "Z_xm"=Z_xm, "spde"=list(), "spde_aniso"=list(), "M0"=GridList$M0, "M1"=GridList$M1, "M2"=GridList$M2 )
}
if(Version%in%c("VAST_v1_9_0")){
Return = list( "n_i"=n_i, "n_s"=c(MeshList$anisotropic_spde$n.spde,n_x)[Options_vec['Method']+1], "n_x"=n_x, "n_t"=n_t, "n_c"=n_c, "n_j"=n_j, "n_p"=n_p, "n_k"=n_k, "n_v"=n_v, "n_l"=n_l, "n_m"=ncol(Z_xm), "Options_vec"=Options_vec, "FieldConfig"=FieldConfig_input, "OverdispersionConfig"=OverdispersionConfig_input, "ObsModel"=ObsModel, "Options"=Options, "yearbounds_zz"=yearbounds_zz, "b_i"=b_i, "a_i"=a_i, "c_i"=c_i, "s_i"=s_i, "t_i"=t_iz-min(t_iz[,1]), "v_i"=match(v_i,sort(unique(v_i)))-1, "PredTF_i"=PredTF_i, "a_xl"=a_xl, "X_xj"=X_xj, "X_xtp"=X_xtp, "Q_ik"=Q_ik, "Z_xm"=Z_xm, "spde"=list(), "spde_aniso"=list(), "M0"=GridList$M0, "M1"=GridList$M1, "M2"=GridList$M2 )
Return = list( "n_i"=n_i, "n_s"=c(MeshList$anisotropic_spde$n.spde,n_x)[Options_vec['Method']+1], "n_x"=n_x, "n_t"=n_t, "n_c"=n_c, "n_j"=n_j, "n_p"=n_p, "n_k"=n_k, "n_v"=n_v, "n_l"=n_l, "n_m"=ncol(Z_xm), "Options_vec"=Options_vec, "FieldConfig"=FieldConfig_input, "OverdispersionConfig"=OverdispersionConfig_input, "ObsModel"=ObsModel, "Options"=Options2use, "yearbounds_zz"=yearbounds_zz, "b_i"=b_i, "a_i"=a_i, "c_i"=c_i, "s_i"=s_i, "t_i"=t_iz-min(t_iz[,1]), "v_i"=match(v_i,sort(unique(v_i)))-1, "PredTF_i"=PredTF_i, "a_xl"=a_xl, "X_xj"=X_xj, "X_xtp"=X_xtp, "Q_ik"=Q_ik, "Z_xm"=Z_xm, "spde"=list(), "spde_aniso"=list(), "M0"=GridList$M0, "M1"=GridList$M1, "M2"=GridList$M2 )
}
if(Version%in%c("VAST_v2_6_0","VAST_v2_5_0","VAST_v2_4_0","VAST_v2_3_0","VAST_v2_2_0","VAST_v2_1_0","VAST_v2_0_0")){
Return = list( "n_i"=n_i, "n_s"=c(MeshList$anisotropic_spde$n.spde,n_x)[Options_vec['Method']+1], "n_x"=n_x, "n_t"=n_t, "n_c"=n_c, "n_j"=n_j, "n_p"=n_p, "n_k"=n_k, "n_v"=n_v, "n_l"=n_l, "n_m"=ncol(Z_xm), "Options_vec"=Options_vec, "FieldConfig"=FieldConfig_input, "OverdispersionConfig"=OverdispersionConfig_input, "ObsModel"=ObsModel, "Options"=Options, "yearbounds_zz"=yearbounds_zz, "b_i"=b_i, "a_i"=a_i, "c_i"=c_i, "s_i"=s_i, "t_iz"=t_iz-min(t_iz,na.rm=TRUE), "v_i"=match(v_i,sort(unique(v_i)))-1, "PredTF_i"=PredTF_i, "a_xl"=a_xl, "X_xj"=X_xj, "X_xtp"=X_xtp, "Q_ik"=Q_ik, "t_yz"=t_yz, "Z_xm"=Z_xm, "spde"=list(), "spde_aniso"=list(), "M0"=GridList$M0, "M1"=GridList$M1, "M2"=GridList$M2 )
if(Version%in%c("VAST_v2_7_0","VAST_v2_6_0","VAST_v2_5_0","VAST_v2_4_0","VAST_v2_3_0","VAST_v2_2_0","VAST_v2_1_0","VAST_v2_0_0")){
Return = list( "n_i"=n_i, "n_s"=c(MeshList$anisotropic_spde$n.spde,n_x)[Options_vec['Method']+1], "n_x"=n_x, "n_t"=n_t, "n_c"=n_c, "n_j"=n_j, "n_p"=n_p, "n_k"=n_k, "n_v"=n_v, "n_l"=n_l, "n_m"=ncol(Z_xm), "Options_vec"=Options_vec, "FieldConfig"=FieldConfig_input, "OverdispersionConfig"=OverdispersionConfig_input, "ObsModel"=ObsModel, "Options"=Options2use, "yearbounds_zz"=yearbounds_zz, "b_i"=b_i, "a_i"=a_i, "c_i"=c_i, "s_i"=s_i, "t_iz"=t_iz-min(t_iz,na.rm=TRUE), "v_i"=match(v_i,sort(unique(v_i)))-1, "PredTF_i"=PredTF_i, "a_xl"=a_xl, "X_xj"=X_xj, "X_xtp"=X_xtp, "Q_ik"=Q_ik, "t_yz"=t_yz, "Z_xm"=Z_xm, "spde"=list(), "spde_aniso"=list(), "M0"=GridList$M0, "M1"=GridList$M1, "M2"=GridList$M2 )
}
if( "spde" %in% names(Return) ) Return[['spde']] = MeshList$isotropic_spde$param.inla[c("M0","M1","M2")]
if( "spde_aniso" %in% names(Return) ) Return[['spde_aniso']] = list("n_s"=MeshList$anisotropic_spde$n.spde, "n_tri"=nrow(MeshList$anisotropic_mesh$graph$tv), "Tri_Area"=MeshList$Tri_Area, "E0"=MeshList$E0, "E1"=MeshList$E1, "E2"=MeshList$E2, "TV"=MeshList$TV-1, "G0"=MeshList$anisotropic_spde$param.inla$M0, "G0_inv"=INLA::inla.as.dgTMatrix(solve(MeshList$anisotropic_spde$param.inla$M0)) )
Expand Down
2 changes: 1 addition & 1 deletion R/Param_Fn.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -86,7 +86,7 @@ function( Version, DataList, RhoConfig=c("Beta1"=0,"Beta2"=0,"Epsilon1"=0,"Epsil
if(Version%in%c("VAST_v1_9_0","VAST_v1_8_0","VAST_v1_7_0","VAST_v1_6_0")){
Return = list("ln_H_input"=c(0,0), "beta1_ct"=NA, "gamma1_j"=rep(0,DataList$n_j), "gamma1_ctp"=array(0,dim=c(DataList$n_c,DataList$n_t,DataList$n_p)), "lambda1_k"=rep(0,DataList$n_k), "L1_z"=NA, "L_omega1_z"=NA, "L_epsilon1_z"=NA, "logkappa1"=log(0.9), "Beta_mean1"=0, "logsigmaB1"=log(1), "Beta_rho1"=0, "Epsilon_rho1"=0, "eta1_vf"=NA, "Omegainput1_sf"=NA, "Epsiloninput1_sft"=NA, "beta2_ct"=NA, "gamma2_j"=rep(0,DataList$n_j), "gamma2_ctp"=array(0,dim=c(DataList$n_c,DataList$n_t,DataList$n_p)), "lambda2_k"=rep(0,DataList$n_k), "L2_z"=NA, "L_omega2_z"=NA, "L_epsilon2_z"=NA, "logkappa2"=log(0.9), "Beta_mean2"=0, "logsigmaB2"=log(1), "Beta_rho2"=0, "Epsilon_rho2"=0, "logSigmaM"=rep(1,DataList$n_c)%o%c(log(5),log(2),log(5)), "eta2_vf"=NA, "Omegainput2_sf"=NA, "Epsiloninput2_sft"=NA )
}
if(Version%in%c("VAST_v2_6_0","VAST_v2_5_0","VAST_v2_4_0","VAST_v2_3_0","VAST_v2_2_0","VAST_v2_1_0","VAST_v2_0_0")){
if(Version%in%c("VAST_v2_7_0","VAST_v2_6_0","VAST_v2_5_0","VAST_v2_4_0","VAST_v2_3_0","VAST_v2_2_0","VAST_v2_1_0","VAST_v2_0_0")){
Return = list("ln_H_input"=c(0,0), "beta1_ct"=NA, "gamma1_j"=rep(0,DataList$n_j), "gamma1_ctp"=array(0,dim=c(DataList$n_c,DataList$n_t,DataList$n_p)), "lambda1_k"=rep(0,DataList$n_k), "L1_z"=NA, "L_omega1_z"=NA, "L_epsilon1_z"=NA, "logkappa1"=log(0.9), "Beta_mean1"=0, "logsigmaB1"=log(1), "Beta_rho1"=0, "Epsilon_rho1"=0, "log_sigmaratio1_z"=rep(0,ncol(DataList$t_iz)), "eta1_vf"=NA, "Omegainput1_sf"=NA, "Epsiloninput1_sft"=NA, "beta2_ct"=NA, "gamma2_j"=rep(0,DataList$n_j), "gamma2_ctp"=array(0,dim=c(DataList$n_c,DataList$n_t,DataList$n_p)), "lambda2_k"=rep(0,DataList$n_k), "L2_z"=NA, "L_omega2_z"=NA, "L_epsilon2_z"=NA, "logkappa2"=log(0.9), "Beta_mean2"=0, "logsigmaB2"=log(1), "Beta_rho2"=0, "Epsilon_rho2"=0, "log_sigmaratio2_z"=rep(0,ncol(DataList$t_iz)), "logSigmaM"=rep(1,DataList$n_c)%o%c(log(5),log(2),log(5)), "eta2_vf"=NA, "Omegainput2_sf"=NA, "Epsiloninput2_sft"=NA )
}
# Overdispersion
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