Fixed miscellaneous plot warnings (#78)

Fixes legends for figures 1 and 5

analysis/paper/hubEnsembles_manuscript.qmd

@@ -149,7 +149,7 @@ hubExamples::forecast_outputs |>
   ) |>
   dplyr::mutate(value=round(value, 2), 
                 model_id = "model-X") |>
-  dplyr::select(abbr_fc_col) |>
+  dplyr::select(all_of(abbr_fc_col)) |>
   dplyr::arrange(horizon) |>
   knitr::kable(col.names = formatted_fc_col)
 ```
@@ -176,7 +176,7 @@ hubExamples::scenario_outputs |>
     horizon == "26", 
     output_type_id %in% c(0.25, 0.5, 0.75)
   ) |>
-  dplyr::select(abbr_scn_col) |>
+  dplyr::select(all_of(abbr_scn_col)) |>
   dplyr::mutate(model_id = "model-Y", 
                 scenario_id = substr(scenario_id,1,1)) |>
   knitr::kable(col.names = formatted_scn_col)
@@ -505,16 +505,16 @@ pc_fin <- cowplot::ggdraw(pc + theme(legend.position = "none")) +
   )
 
 # combine into final figure
-l <- cowplot::get_legend(pa)
-l2 <- cowplot::get_legend(pc)
+l <- cowplot::get_plot_component(pa, "guide-box", return_all = TRUE)[[3]]
+l2 <- cowplot::get_plot_component(pc, "guide-box", return_all = TRUE)[[3]]
 
 cowplot::plot_grid(
   cowplot::plot_grid(
     pa + theme(legend.position = "none"), pb_fin, pc_fin,
     labels = LETTERS[1:3], nrow = 1, rel_widths = c(0.34, 0.33, 0.33)
   ),
   cowplot::plot_grid(
-    "", l, l2, "",
+    NULL, l, l2, NULL,
     nrow = 1, rel_widths = c(0.175, 0.325, 0.325, 0.175)
   ),
   ncol = 1, rel_heights = c(0.95, 0.05)
@@ -887,7 +887,10 @@ model_output_plot <- dplyr::bind_rows(mean_ens, model_output_plot) |>
     output_type %in% c("median", "mean", "quantile"),
     reference_date == "2022-12-17"
   ) |>
-  dplyr::mutate(target_date = reference_date + horizon)
+  dplyr::mutate(
+    target_date = reference_date + horizon, 
+    output_type_id = as.numeric(output_type_id)
+  )
 target_data_plot <- hubExamples::forecast_target_ts |>
   dplyr::filter(
     location == "25", 
@@ -911,7 +914,7 @@ p2 <-
   labs(y = "incident hospitalizations")
 
 # Pull legend
-l <- cowplot::get_legend(p1)
+l <- cowplot::get_plot_component(p1, "guide-box", return_all = TRUE)[[3]]
 
 # Assemble plots
 cowplot::plot_grid(
@@ -970,7 +973,7 @@ flu_forecasts_raw |>
     target == "1 wk ahead inc flu hosp",
     quantile %in% c(0.025, 0.1, 0.25, 0.75, 0.9, 0.975)
   ) |>
-  dplyr::select(zoltar_col) |>
+  dplyr::select(all_of(zoltar_col)) |>
   knitr::kable(col.names = formatted_zoltar_col)
 ```