Fix EDA temporal plots that had NA values plotted

R/30_eda.R

@@ -54,6 +54,8 @@ eda_temporal <- function(data) {
       nest_by(Initial_quarter, .keep = TRUE) |>
       mutate(Plot = list({
         data |>
+          filter(!is.na(Values)) |>
+          droplevels() |> 
                 ggplot(aes(y = Site, x = Acquire_date_time)) +
                 geom_line() +
                 geom_point(aes(colour = Baseline)) +
@@ -99,6 +101,8 @@ eda_type_temporal <- function(data) {
       nest_by(ZoneName, Type, .keep = TRUE) |>
       mutate(Plot = list({
         data |>
+          filter(!is.na(Values)) |>
+          droplevels() |> 
           ggplot(aes(y = Site, x = Acquire_date_time)) +
           ## geom_line(color = "gray50") +
           geom_point(aes(colour = Baseline), fill = NA, shape = 16) +

deploy.bat

@@ -7,7 +7,7 @@ set image=ghcr.io/open-aims/dh_sediment_monitoring:main
 :: A port for the docker container
 set container_port=3838
 :: The location to mount the input data folder in the containter
-set input_mount=/home/project/input
+set input_mount=/home/project
 
 
 :: === CHECK DOCKER IS INSTALLED ===

docs/manual.qmd

@@ -248,6 +248,19 @@ are excel files that adhere to the structure outlined in
 
 ## Data {#sec-data}
 
-<span class="fas fa-circle-check"></span>
+### Raw data panel
+
+{{< include ../md/data_raw_instructions.md >}}
+
+
+### Processed data panel
+
+::: {.callout-note}
+This panel will not become active until the completion of Stage 3.
+:::
+
+
+{{< include ../md/processed_data_instructions.md >}}
+
 
 {{< fa thumbs-up >}}