rebuild jsdgam example

nicholasjclark · Dec 19, 2024 · bd20133 · bd20133
1 parent 32b5803
commit bd20133
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Showing 75 changed files with 641 additions and 437 deletions.
diff --git a/R/jsdgam.R b/R/jsdgam.R
@@ -195,7 +195,7 @@
 #'   geom_histogram() +
 #'   facet_wrap(~ species, scales = 'free')
 #'
-#' ggplot(dat, aes(x = lat, y = lon, col = log(count + 1))) +
+#' ggplot(dat, aes(x = lon, y = lat, col = log(count + 1))) +
 #'   geom_point(size = 2.25) +
 #'   facet_wrap(~ species, scales = 'free') +
 #'   scale_color_viridis_c() +
@@ -209,7 +209,7 @@
 #'
 #'                           # Each factor estimates a different nonlinear spatial process, using
 #'                           # 'by = trend' as in other mvgam State-Space models
-#'                           factor_formula = ~ gp(lat, lon, k = 6, by = trend) - 1,
+#'                           factor_formula = ~ gp(lon, lat, k = 6, by = trend) - 1,
 #'                           n_lv = 3,
 #'
 #'                           # The data and grouping variables
@@ -230,19 +230,19 @@
 #'
 #'               # Each factor estimates a different nonlinear spatial process, using
 #'               # 'by = trend' as in other mvgam State-Space models
-#'               factor_formula = ~ gp(lat, lon, k = 6, by = trend) - 1,
+#'               factor_formula = ~ gp(lon, lat, k = 6, by = trend) - 1,
 #'               n_lv = 3,
 #'
 #'               # Change default priors for fixed random effect variances and
 #'               # factor P marginal deviations to standard normal
 #'               priors = c(prior(std_normal(),
 #'                                class = sigma_raw),
 #'                          prior(std_normal(),
-#'                                class = `alpha_gp_trend(lat, lon):trendtrend1`),
+#'                                class = `alpha_gp_trend(lon, lat):trendtrend1`),
 #'                          prior(std_normal(),
-#'                                class = `alpha_gp_trend(lat, lon):trendtrend2`),
+#'                                class = `alpha_gp_trend(lon, lat):trendtrend2`),
 #'                          prior(std_normal(),
-#'                                class = `alpha_gp_trend(lat, lon):trendtrend3`)),
+#'                                class = `alpha_gp_trend(lon, lat):trendtrend3`)),
 #'
 #'               # The data and the grouping variables
 #'               data = dat,
@@ -303,7 +303,7 @@
 #'
 #' # Plot the median log(count) predictions on a grid
 #' newdata$log_count <- preds[,1]
-#' ggplot(newdata, aes(x = lat, y = lon, col = log_count)) +
+#' ggplot(newdata, aes(x = lon, y = lat, col = log_count)) +
 #'   geom_point(size = 1.5) +
 #'   facet_wrap(~ species, scales = 'free') +
 #'   scale_color_viridis_c() +

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