update reference page

nicholasjclark · Nov 15, 2024 · f32fd6e · f32fd6e
1 parent 0220dea
commit f32fd6e
Show file tree

Hide file tree

Showing 62 changed files with 439 additions and 476 deletions.
diff --git a/R/forecast.mvgam.R b/R/forecast.mvgam.R
@@ -34,7 +34,8 @@ forecast <- function(object, ...){
 #'             trend_model = AR(),
 #'             noncentred = TRUE,
 #'             data = simdat$data_train,
-#'             chains = 2)
+#'             chains = 2,
+#'             silent = 2)
 #'
 #' # Hindcasts on response scale
 #' hc <- hindcast(mod)
@@ -864,7 +865,8 @@ forecast_draws = function(object,
                    'linkfun',
                    'forecast_trend',
                    'extract_series_trend_pars',
-                   'mvgam_predict')
+                   'mvgam_predict',
+                   'prep_varma_params')
     attr(funs_list, 'envir') <- as.environment(asNamespace("mvgam"))
     attr(funs_list, 'mode') <- 'function'
 

diff --git a/R/lfo_cv.mvgam.R b/R/lfo_cv.mvgam.R
@@ -70,7 +70,8 @@
 #'                newdata = dat$data_test,
 #'                burnin = 300,
 #'                samples = 300,
-#'                chains = 2)
+#'                chains = 2,
+#'                silent = 2)
 #'
 #'# Fit a less appropriate model
 #'mod_rw <- mvgam(y ~ s(season, bs = 'cc', k = 6),
@@ -80,7 +81,8 @@
 #'               newdata = dat$data_test,
 #'               burnin = 300,
 #'               samples = 300,
-#'               chains = 2)
+#'               chains = 2,
+#'               silent = 2)
 #'
 #'# Compare Discrete Ranked Probability Scores for the testing period
 #'fc_ar2 <- forecast(mod_ar2)
@@ -96,10 +98,12 @@
 #'# for estimating model parameters
 #'lfo_ar2 <- lfo_cv(mod_ar2,
 #'                  min_t = 40,
-#'                  fc_horizon = 3)
+#'                  fc_horizon = 3,
+#'                  silent = 2)
 #'lfo_rw <- lfo_cv(mod_rw,
 #'                 min_t = 40,
-#'                 fc_horizon = 3)
+#'                 fc_horizon = 3,
+#'                 silent = 2)
 #'
 #'# Plot Pareto-K values and ELPD estimates
 #'plot(lfo_ar2)

diff --git a/R/loo.mvgam.R b/R/loo.mvgam.R
@@ -52,7 +52,8 @@
 #'              data = rbind(simdat$data_train,
 #'              simdat$data_test),
 #'              family = gaussian(),
-#'              chains = 2)
+#'              chains = 2,
+#'              silent = 2)
 #'
 #'# Inspect the model and calculate LOO
 #'conditional_effects(mod1)
@@ -65,14 +66,16 @@
 #'               formula = y ~ s(season, bs = 'cc', k = 6) +
 #'               s(season, series, bs = 'fs',
 #'               xt = list(bs = 'cc'), k = 4),
-#'               chains = 2)
+#'               chains = 2,
+#'               silent = 2)
 #'conditional_effects(mod2)
 #'loo(mod2)
 #'
 #'# Now add AR1 dynamic errors to mod2
 #'mod3 <- update(mod2,
 #'               trend_model = AR(),
-#'               chains = 2)
+#'               chains = 2,
+#'               silent = 2)
 #'conditional_effects(mod3)
 #'plot(mod3, type = 'trend')
 #'loo(mod3)

diff --git a/docs/reference/forecast.mvgam-1.png b/docs/reference/forecast.mvgam-1.png
diff --git a/docs/reference/forecast.mvgam-10.png b/docs/reference/forecast.mvgam-10.png
diff --git a/docs/reference/forecast.mvgam-11.png b/docs/reference/forecast.mvgam-11.png
diff --git a/docs/reference/forecast.mvgam-12.png b/docs/reference/forecast.mvgam-12.png
diff --git a/docs/reference/forecast.mvgam-2.png b/docs/reference/forecast.mvgam-2.png
diff --git a/docs/reference/forecast.mvgam-3.png b/docs/reference/forecast.mvgam-3.png
diff --git a/docs/reference/forecast.mvgam-4.png b/docs/reference/forecast.mvgam-4.png
diff --git a/docs/reference/forecast.mvgam-5.png b/docs/reference/forecast.mvgam-5.png
diff --git a/docs/reference/forecast.mvgam-6.png b/docs/reference/forecast.mvgam-6.png
diff --git a/docs/reference/forecast.mvgam-7.png b/docs/reference/forecast.mvgam-7.png
diff --git a/docs/reference/forecast.mvgam-8.png b/docs/reference/forecast.mvgam-8.png
diff --git a/docs/reference/forecast.mvgam-9.png b/docs/reference/forecast.mvgam-9.png
diff --git a/docs/reference/forecast.mvgam.html b/docs/reference/forecast.mvgam.html
diff --git a/docs/reference/lfo_cv.mvgam.html b/docs/reference/lfo_cv.mvgam.html
diff --git a/docs/reference/loo.mvgam-1.png b/docs/reference/loo.mvgam-1.png
diff --git a/docs/reference/loo.mvgam-2.png b/docs/reference/loo.mvgam-2.png
diff --git a/docs/reference/loo.mvgam-3.png b/docs/reference/loo.mvgam-3.png
diff --git a/docs/reference/loo.mvgam-4.png b/docs/reference/loo.mvgam-4.png
diff --git a/docs/reference/loo.mvgam-5.png b/docs/reference/loo.mvgam-5.png
diff --git a/docs/reference/loo.mvgam-6.png b/docs/reference/loo.mvgam-6.png
diff --git a/docs/reference/loo.mvgam-7.png b/docs/reference/loo.mvgam-7.png