Save missing figure with fmd outbraks for the article.

README.Rmd

@@ -41,24 +41,7 @@ loadd(
 
 ```{r cases-and-risk, fig.width = 3}
 # tmap_mode(mode = "plot")
-tm_shape(st_as_sf(FA)) +
-  tm_fill(
-    "Exposition",
-    title = "Risk level",
-    labels = risk_labs,
-    palette = viridisLite::inferno(4, begin = 0.1, end = 0.9),
-    legend.reverse = TRUE
-  ) +
-  tm_bubbles(
-    title.size = "Nmbr. outbr.",
-    size = "m",
-    alpha = .4,
-    col = "white"
-  ) +
-tm_shape(st_as_sf(TN)) +
-  tm_borders() +
-  tm_compass() +
-  tm_scale_bar()
+readd("fig_fmd_outbreaks")
 ```
 ```{r freq-expo, fig.width = 7}
 fig_freq_expositions

src/plan.R

@@ -7,6 +7,8 @@
 
 paper_figs_data = tribble(
   ~basename, ~obj, ~w, ~h, ~dev,
+  "Figure1", "fig_fmd_outbreaks", 7, 7, "pdf",
+  "Figure1", "fig_fmd_outbreaks", 7, 7, "png",
   "Figure2", "fig_risks_intro_expo", 7, 7, "pdf",
   "Figure2", "fig_risks_intro_expo", 7, 7, "png",
   "Figure3", "fig_freq_expositions", 7, 5, "pdf",
@@ -108,7 +110,7 @@ plan <- drake_plan(
   
   ## Readme
   readme = rmarkdown::render(
-    knitr_in(here("README.Rmd")),
+    knitr_in(!!here("README.Rmd")),
     quiet = FALSE
   ),
   
@@ -187,6 +189,26 @@ plan <- drake_plan(
     ungroup(),
   
   risk_labs = c("Negligible", "Low", "High", "Very high"),
+
+  fig_fmd_outbreaks = tm_shape(st_as_sf(FA)) +
+    tm_fill(
+      "Exposition",
+      title = "Risk level",
+      labels = risk_labs,
+      palette = viridisLite::inferno(4, begin = 0.1, end = 0.9),
+      legend.reverse = TRUE
+    ) +
+    tm_bubbles(
+      title.size = "Nmbr. outbr.",
+      size = "m",
+      alpha = .4,
+      col = "white"
+    ) +
+    tm_shape(st_as_sf(TN)) +
+    tm_borders() +
+    tm_compass() +
+    tm_scale_bar()
+  ,
   
   fig_freq_expositions = plot_freq_expositions(
     myData, TAB, FA,