updated traits tutorials

Author: dlebauer

index.Rmd

@@ -9,4 +9,8 @@ output:
   bookdown::pdf_book: default
 ---
 
-# Preamble
+# Preamble
+
+```{r}
+knitr::opts_chunk$set(echo = FALSE, cache = TRUE)
+```

sensors/05-command-line-hyperspectral-workflow.Rmd

@@ -1,5 +1,5 @@
 # Command Line Hyperspectral Workflow
 
 ```{r}
-include_url("https://docs.google.com/document/d/1QWBUHsRql_c_q15WoFrUGRMGk0gZQ-y85y6tpd9pdNM/pub")
+knitr::include_url("https://docs.google.com/document/d/1QWBUHsRql_c_q15WoFrUGRMGk0gZQ-y85y6tpd9pdNM/pub")
 ```

traits/00-BETYdb-getting-started.Rmd

@@ -127,32 +127,42 @@ writeLines('9999999999999999999999999999999999999999',
            con = '~/.betykey_public')
 ```
 ```{r traits}
-terraref_test_url <- "https://terraref.ncsa.illinois.edu/bety-test/"
-
-betykey <- readLines('~/.betykey_public', warn = FALSE)
+terraref_test_url <- 
+public_betykey <- 
 
 ```
 
+### Our first Query 
+
 ```{r simulated-LAI}
 sorghum_lai <- betydb_query(table = 'search',
                             trait = "LAI",
                             api_version = 'beta',
                             limit = 5000,
-                            betyurl = terraref_test_url, 
-                            key = betykey)
+                            betyurl = "https://terraref.ncsa.illinois.edu/bety-test/", 
+                            key = readLines('~/.betykey_public', warn = FALSE))
 
-#traits <- betydb_query(table = "traits",
-#              api_version = 'beta',
-#              limit = 5000,
-#              betyurl = terraref_test_url, 
-#              key = betykey)
+```
 
+Notice all of the arguments? We can change this by setting the default options 
 
 
+```{r}
+options(betydb_key = readLines('~/.betykey_public', warn = FALSE),
+        betydb_url = "https://terraref.ncsa.illinois.edu/bety-test/",
+        betydb_api_version = 'beta')
 ```
 
-```{r}
+Now the same query can be reduced to:
 
+```{r eval=FALSE}
+sorghum_lai <- betydb_query(table = 'search',
+                            trait = "LAI",
+                            limit = 5000)
+```
+
+
+```{r}
 ggplot(data = sorghum_lai) +
   geom_smooth(aes(x = lubridate::yday(lubridate::ymd_hms(raw_date)), y = mean, color = as.factor(lubridate::year(lubridate::ymd_hms(raw_date)))), span = 0.5) +
 #  scale_x_datetime(date_breaks = '6 months', date_labels = "%b %Y") +

traits/01-simulated-sorghum.Rmd

@@ -140,17 +140,13 @@ The virtual crop is encoded as a set of associated species and prior estimates o
 
 
 ```{r}
-terraref_test_url <- "https://terraref.ncsa.illinois.edu/bety-test/"
-## note that this key accesses public data. In part 2 you will use your own key to access the actual data
 
-public_key <- "9999999999999999999999999999999999999999"
+options(betydb_key = readLines('~/.betykey_public', warn = FALSE),
+        betydb_url = "https://terraref.ncsa.illinois.edu/bety-test/",
+        betydb_api_version = 'beta')
 
-
-SLA <- (betydb_search(query = "SLA", 
-                      betyurl = terraref_test_url, 
-                      key = public_key, 
-                      api_version = "beta")
-  %>% filter(scientificname == 'Sorghum bicolor'))
+sorghum_lai <- betydb_query(trait = "LAI",
+                            api_version = 'beta')
 
 ```
 
@@ -159,7 +155,7 @@ Now we have queried all of the Specific Leaf Area records, we can see that these
 
 
 ```{r sla-fig, fig.height=2, fig.width=6}
-ggplot(SLA) + 
+ggplot(sorghum_lai) + 
   geom_histogram(aes(mean), binwidth = 1)
 ```