Avoid/Silence immaterial warnings/messages in vignettes

Author: lcbrooks

vignettes/archive.Rmd

@@ -30,6 +30,8 @@ library(epidatr)
 library(epiprocess)
 library(data.table)
 library(dplyr)
+library(purrr)
+library(ggplot2)
 
 dv <- covidcast(
   data_source = "doctor-visits",
@@ -48,6 +50,8 @@ library(epidatr)
 library(epiprocess)
 library(data.table)
 library(dplyr)
+library(purrr)
+library(ggplot2)
 ```
 
 ## Getting data into `epi_archive` format
@@ -189,8 +193,6 @@ marked by dotted vertical lines, and draw the latest curve in black (from the
 latest snapshot `x_latest` that the archive can provide).
 
 ```{r, fig.width = 8, fig.height = 7}
-library(purrr)
-library(ggplot2)
 theme_set(theme_bw())
 
 self_max = max(x$DT$version)
@@ -203,15 +205,15 @@ snapshots <- map_dfr(versions, function(v) {
 
 ggplot(snapshots %>% filter(!latest),
             aes(x = time_value, y = percent_cli)) +  
-  geom_line(aes(color = factor(version))) + 
+  geom_line(aes(color = factor(version)), na.rm=TRUE) + 
   geom_vline(aes(color = factor(version), xintercept = version), lty = 2) +
   facet_wrap(~ geo_value, scales = "free_y", ncol = 1) +
   scale_x_date(minor_breaks = "month", date_labels = "%b %y") +
   labs(x = "Date", y = "% of doctor's visits with CLI") + 
   theme(legend.position = "none") +
   geom_line(data = snapshots %>% filter(latest),
                aes(x = time_value, y = percent_cli), 
-               inherit.aes = FALSE, color = "black")
+            inherit.aes = FALSE, color = "black", na.rm=TRUE)
 ```
 
 We can see some interesting and highly nontrivial revision behavior: at some

vignettes/compactify.Rmd

@@ -28,7 +28,7 @@ For this example, we have one chart using LOCF values, while another doesn't
 use them to illustrate LOCF. Notice how the head of the first dataset differs
 from the second from the third value included.
 
-```{r}
+```{r, message=FALSE}
 library(epiprocess)
 library(dplyr)