Adds Tweedie closes #43

R/VAST_spp.R

@@ -85,7 +85,7 @@
 #' }
 #'
 VAST_spp <- function(dir, species,
-  dist = c("lognormal", "gamma")) {
+  dist = c("lognormal", "gamma", "tweedie")) {
 
   #### Get species, survey, and strata info
   info <- nwfscSurvey::GetSpp.fn(species)
@@ -107,7 +107,8 @@ VAST_spp <- function(dir, species,
   for (obs in dist) {
     obs_model <- switch(obs,
       lognormal = c(1, 0),
-      gamma = c(2, 0)
+      gamma = c(2, 0),
+      tweedie = c(10, 2)
     )
     modeldir <- file.path(sppdir, paste(survey, obs, sep = "_"))
     settings <- list(

R/get_settings.R

@@ -69,6 +69,11 @@ get_settings <- function(settings = NULL, verbose = FALSE) {
     default = c(Beta1 = 0, Beta2 = 0, Epsilon1 = 0, Epsilon2 = 0))
   Settings_all$FieldConfig <- get_settings_single(Settings_all$field,
     default = c(Omega1 = 1, Epsilon1 = 1, Omega2 = 1, Epsilon2 = 1))
+  if (Settings_all[["ObsModelcondition"]][1] == 10) {
+    # Following items are specific to the Tweedie distribution #43
+    Settings_all[["FieldConfig"]][c("Omega1", "Epsilon1")] <- 0
+    Settings_all[["RhoConfig"]][c("Beta1")] <- 3
+  }
 
   # Overdispersion
   if (is.null(Settings_all[["overdispersion"]])) {

R/plot_qq.R

@@ -42,6 +42,10 @@ plot_qq <- function(outdir, model) {
             ),
           MoreArgs = list(shape = 1 / (sigmaM^2))))
   }
+  if (model[["data_list"]][["ObsModel_ez"]][1] == 10) {
+    message("QQ plot is not yet implemented for the Tweedie distribution. See #45.")
+    return(invisible())
+  }
 
   grDevices::png(file.path(outdir, "VASTWestCoast_QQ.png"), height = 18, width = 18, units = "cm",
     res = 300)

R/summary_nwfsc.R

@@ -42,7 +42,9 @@ summary_nwfsc <- function(obj, parameter_estimates, savedir = NULL) {
     "Poisson-link", 
     switch(as.character(obj$env$data$ObsModel[1]),
       "1" = "Lognormal",
-      "2" = "Gamma")))
+      "2" = "Gamma",
+      "10" = "Tweedie"))
+  )
   TableA[6, ] <- c("Spatial effect for encounter probability", 
     ifelse(obj$env$data$FieldConfig[1, 2] < 0, "No", "Yes"))
   TableA[7, ] <- c("Spatio-temporal effect for encounter probability",