changed chunk parameters and commented out sections that were not running correctly (HTTP 504)

Author: kimberlyh66

traits/05-maricopa-field-scanner.Rmd

@@ -23,7 +23,7 @@ options(betydb_key = readLines('.betykey', warn = FALSE),
 
 First, query the plots for Season 2. The simple way to use this is based on the fact that the plot names at Maricopa contain the season. 
 
-```{r traits-05-query-mac-sites}
+```{r traits-05-query-mac-sites, echo = TRUE}
 sites <- betydb_query(
 	table = "sites",
 	city = "Maricopa", sitename = "~Season 2 range", limit = "none")
@@ -33,10 +33,10 @@ A more robust (but complicated way) would be to query the experiments and experi
 
 ### Plot Season 2 plots
 
-```{r traits-05-map-mac-polygons}
+```{r traits-05-map-mac-polygons, echo = TRUE}
 site_bounds <- (sites
-	%>% rowwise()
-	%>% do(boundaries = readWKT(text = .$geometry, id = .$id)))
+  %>% rowwise()
+  %>% do(boundaries = readWKT(text = .$geometry, id = .$id)))
 
 site_bounds <- do.call('rbind', site_bounds$boundaries)
 #names(site_bounds) <- sites$sitename
@@ -53,35 +53,46 @@ leaflet() %>%
   addPolygons(data=site_bounds, popup = sites$sitename)
 ```
 
+```{r}
 ## Cultivars
 
+```
 
 ```{r traits-05-mac-cultivars}
-cultivars <- betydb_query(
-  table = "cultivars", limit = "none") %>% 
-  rename(cultivar_id = id)
-
-traits <- traits <- betydb_search(
-  Season = "~Season 4", 
-  include_unchecked = 'true',
-  limit = "none") %>% 
-  rename(trait_id = id)
+#cultivars <- betydb_query(
+#  table = "cultivars", limit = "none") %>% 
+#  rename(cultivar_id = id)
+
+
+# getting HTTP 504 - Gateway timeout
+# comment this chunk out
+#traits <- traits <- betydb_search(
+#  Season = "~Season 4", 
+#  include_unchecked = 'true',
+#  limit = "none") %>% 
+#  rename(trait_id = id)
 ```
 
-
+```{r}
 ## Time series of canopy cover, height, NDVI
 
-First look up variables by name. Let's look for measurements related to canopy size:
+#First look up variables by name. Let's look for measurements related to canopy size:
+
+```
 
 ```{r traits-05-height-cover-ndvi}
-variables <- betydb_query(
-		table = "variables", name = "~^(NDVI|canopy_height|canopy_cover|)$")
+#variables <- betydb_query(
+#		table = "variables", name = "~^(NDVI|canopy_height|canopy_cover|)$")
 
-variables %>% 
-  select(id, name, units, n_records = `number of associated traits`)
+#variables %>% 
+#  select(id, name, units, n_records = `number of associated traits`)
 ```
 
-Exercise: Why are there two variables named canopy_height, and what database fields should you examine to decide which one you want?
+```{r}
+
+#Exercise: Why are there two variables named canopy_height, and what database fields should you examine to decide which one you want?
+
+```
 
 ```{r traits-05-get-variables-comment}