Merge pull request #107 from James-Thorson/development

Adding V4.4.0 with new simulate feature
James-Thorson-NOAA · Jun 29, 2018 · 94f412c · 94f412c
2 parents e4c819b + f820a06
commit 94f412c
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Showing 7 changed files with 1,226 additions and 6 deletions.
diff --git a/R/Build_TMB_Fn.R b/R/Build_TMB_Fn.R
@@ -106,7 +106,7 @@ function( TmbData, Version, Q_Config=TRUE, CovConfig=TRUE,
   Obj$control <- list(parscale=1, REPORT=1, reltol=1e-12, maxit=100)
 
   # Add normalization in
-  if(Version %in% c("VAST_v4_3_0","VAST_v4_2_0","VAST_v4_1_0") & TmbData$Options['normalize_GMRF_in_CPP']==FALSE ){
+  if(Version %in% c("VAST_v4_4_0","VAST_v4_3_0","VAST_v4_2_0","VAST_v4_1_0") & TmbData$Options['normalize_GMRF_in_CPP']==FALSE ){
     message("Normalizing GMRF in R using `TMB::normalize` feature")
     Obj = TMB::normalize(Obj, flag="include_data", value=FALSE)
   }

diff --git a/R/Data_Fn.R b/R/Data_Fn.R
@@ -262,7 +262,7 @@ function( Version, FieldConfig, OverdispersionConfig=c("eta1"=0,"eta2"=0), ObsMo
   if(Version%in%c("VAST_v4_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_e"=n_e, "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_ez"=ObsModel_ez, "Options"=Options2use, "yearbounds_zz"=yearbounds_zz, "b_i"=b_i, "a_i"=a_i, "c_iz"=c_iz, "e_i"=e_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$M2 )
   }
-  if(Version%in%c("VAST_v4_3_0","VAST_v4_2_0","VAST_v4_1_0")){
+  if(Version%in%c("VAST_v4_4_0","VAST_v4_3_0","VAST_v4_2_0","VAST_v4_1_0")){
     Return = list( "n_i"=n_i, "n_s"=c(MeshList$anisotropic_spde$n.spde,n_x)[Options_vec['Method']+1], "n_x"=n_x, "n_t"=n_t, "n_c"=n_c, "n_e"=n_e, "n_p"=n_p, "n_v"=n_v, "n_l"=n_l, "n_m"=ncol(Z_xm), "Options_vec"=Options_vec, "FieldConfig"=FieldConfig_input, "OverdispersionConfig"=OverdispersionConfig_input, "ObsModel_ez"=ObsModel_ez, "include_data"=TRUE, "Options"=Options2use, "yearbounds_zz"=yearbounds_zz, "b_i"=b_i, "a_i"=a_i, "c_iz"=c_iz, "e_i"=e_i, "s_i"=s_i, "t_iz"=t_iz-min(t_iz,na.rm=TRUE), "v_i"=match(v_i,sort(unique(v_i)))-1, "PredTF_i"=PredTF_i, "a_xl"=a_xl, "X_xj"=X_xj, "X_xtp"=X_xtp, "Q_ik"=Q_ik, "t_yz"=t_yz, "Z_xm"=Z_xm, "spde"=list(), "spde_aniso"=list(), "M0"=GridList$M0, "M1"=GridList$M1, "M2"=GridList$M2 )
   }
   if( "spde" %in% names(Return) ) Return[['spde']] = MeshList$isotropic_spde$param.inla[c("M0","M1","M2")]

diff --git a/R/Param_Fn.R b/R/Param_Fn.R
@@ -95,7 +95,7 @@ function( Version, DataList, RhoConfig=c("Beta1"=0,"Beta2"=0,"Epsilon1"=0,"Epsil
   if(Version%in%c("VAST_v2_8_0")){
     Return = list("ln_H_input"=c(0,0), "beta1_ct"=NA, "gamma1_j"=rep(0,ncol(DataList$X_xj)), "gamma1_ctp"=array(0,dim=c(DataList$n_c,DataList$n_t,DataList$n_p)), "lambda1_k"=rep(0,ncol(DataList$Q_ik)), "L1_z"=NA, "L_omega1_z"=NA, "L_epsilon1_z"=NA, "logkappa1"=log(0.9), "Beta_mean1"=0, "logsigmaB1"=log(1), "Beta_rho1"=0, "Epsilon_rho1"=0, "log_sigmaratio1_z"=rep(0,ncol(DataList$t_iz)), "eta1_vf"=NA, "Omegainput1_sf"=NA, "Epsiloninput1_sft"=NA, "beta2_ct"=NA, "gamma2_j"=rep(0,ncol(DataList$X_xj)), "gamma2_ctp"=array(0,dim=c(DataList$n_c,DataList$n_t,DataList$n_p)), "lambda2_k"=rep(0,ncol(DataList$Q_ik)), "L2_z"=NA, "L_omega2_z"=NA, "L_epsilon2_z"=NA, "logkappa2"=log(0.9), "Beta_mean2"=0, "logsigmaB2"=log(1), "Beta_rho2"=0, "Epsilon_rho2"=0, "log_sigmaratio2_z"=rep(0,ncol(DataList$t_iz)), "logSigmaM"=rep(1,DataList$n_c)%o%c(log(5),log(2),log(1)), "delta_i"=rnorm(n=ifelse(any(DataList$ObsModel_ez[,1]%in%c(11,14)),DataList$n_i,1),sd=0.1), "eta2_vf"=NA, "Omegainput2_sf"=NA, "Epsiloninput2_sft"=NA )
   }
-  if(Version%in%c("VAST_v4_3_0","VAST_v4_2_0","VAST_v4_1_0","VAST_v4_0_0","VAST_v3_0_0")){
+  if(Version%in%c("VAST_v4_4_0","VAST_v4_3_0","VAST_v4_2_0","VAST_v4_1_0","VAST_v4_0_0","VAST_v3_0_0")){
     Return = list("ln_H_input"=c(0,0), "beta1_ct"=NA, "gamma1_j"=rep(0,ncol(DataList$X_xj)), "gamma1_ctp"=array(0,dim=c(DataList$n_c,DataList$n_t,DataList$n_p)), "lambda1_k"=rep(0,ncol(DataList$Q_ik)), "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$t_iz)), "eta1_vf"=NA, "Omegainput1_sf"=NA, "Epsiloninput1_sft"=NA, "beta2_ct"=NA, "gamma2_j"=rep(0,ncol(DataList$X_xj)), "gamma2_ctp"=array(0,dim=c(DataList$n_c,DataList$n_t,DataList$n_p)), "lambda2_k"=rep(0,ncol(DataList$Q_ik)), "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_e)%o%c(log(5),log(2),log(1)), "delta_i"=rnorm(n=ifelse(any(DataList$ObsModel_ez[,1]%in%c(11,14)),DataList$n_i,1),sd=0.1), "eta2_vf"=NA, "Omegainput2_sf"=NA, "Epsiloninput2_sft"=NA )
   }
   # Overdispersion

diff --git a/examples/VAST--multispecies_example.Rmd b/examples/VAST--multispecies_example.Rmd
@@ -2,7 +2,7 @@
 title: Example script for VAST for spatio-temporal analysis of multispecies catch-rate
   data
 author: "James Thorson"
-date: "October 26, 2016"
+date: "`r Sys.Date()`"
 output:
   pdf_document:
     fig_caption: yes

diff --git a/examples/VAST--single-species_example.Rmd b/examples/VAST--single-species_example.Rmd
@@ -2,7 +2,7 @@
 title: Example script for VAST for spatio-temporal analysis of single-species catch-rate
   data
 author: "James Thorson"
-date: "October 10, 2016"
+date: "`r Sys.Date()`"
 output:
   pdf_document:
     fig_caption: yes