updated simulated sorghum and danforth tutorials

Author: dlebauer

README.md

@@ -1,3 +1,4 @@
+
 # Tutorials
 
 ## An introduction to the use of TERRA REF data and software

traits/00-BETYdb-getting-started.Rmd

@@ -5,17 +5,6 @@ date: "`r Sys.Date()`"
 output: html_document
 ---
 
-```{r setup}
-library(traits)
-knitr::opts_chunk$set(echo = FALSE, cache = TRUE)
-library(ggplot2)
-library(ggthemes)
-library(GGally)
-theme_set(theme_bw())
-library(dplyr)
-```
-
-
 ## TERRA Ref Trait Database
 
 The TERRA Ref program uses the BETYdb database and web application software to store plant and plot level trait data. 
@@ -104,21 +93,72 @@ First, lets construct a query by putting together a URL.
 
 What do you see? Do you think that this is all of the records? What happens if you add `&limit=none`? 
 
-### Using the R traits package to query the database
+## Using the R traits package to query the database
 
 The rOpenSci traits package makes it easier to query the TERRA REF trait database, or any database that uses BETYdb software.
 
+First, make sure we have the latest version 
+
+```{r install_traits, echo=FALSE}
+if(packageVersion("traits") == '0.2.0'){
+  devtools::install_github('ropensci/traits')
+}
+```
+
+
+```{r setup}
+library(traits)
+knitr::opts_chunk$set(echo = FALSE, cache = TRUE)
+library(ggplot2)
+library(ggthemes)
+theme_set(theme_bw())
+library(dplyr)
+```
+
+
+
+```{r writing-key}
+# This should be done once with the key sent to you in your email
+# writeLines('abcdefg_rest_of_key_sent_in_email', 
+#            con = '~/.betykey')
+
+# Example with the public key:
+writeLines('9999999999999999999999999999999999999999', 
+           con = '~/.betykey_public')
+```
 ```{r traits}
+terraref_test_url <- "https://terraref.ncsa.illinois.edu/bety-test/"
+
+betykey <- readLines('~/.betykey_public', warn = FALSE)
 
-terraref_betyurl <- "https://terraref.ncsa.illinois.edu/bety/"
-betykey <- readLines('~/.betykey', warn = FALSE)
 ```
 
-```{r}
-sorghum_all <- betydb_search(query = 'Sorghum', 
-                         betyurl = terraref_betyurl, 
-                         key = betykey) 
+```{r simulated-LAI}
+sorghum_lai <- betydb_query(table = 'search',
+                            trait = "LAI",
+                            api_version = 'beta',
+                            limit = 5000,
+                            betyurl = terraref_test_url, 
+                            key = betykey)
+
+#traits <- betydb_query(table = "traits",
+#              api_version = 'beta',
+#              limit = 5000,
+#              betyurl = terraref_test_url, 
+#              key = betykey)
+
+
 
 ```
 
+```{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") +
+  ylim(c(0,6)) + 
+  ylab("Day of Year") + xlab("Leaf Area Index") +  
+  labs(color='Year')
+
+```
 

traits/01-simulated-sorghum.Rmd

@@ -1,16 +1,18 @@
----
+<!---
 title: "Can high throughput phenotyping produce data like this?"
 author: "David LeBauer"
-date: "February 1, 2015"
+date: "`r Sys.Date()`"
 output: html_document
 ---
+-->
+
+# A Simulated Phenotype Dataset
 
-```{r setup}
+```{r}
 library(traits)
 knitr::opts_chunk$set(echo = FALSE, cache = TRUE)
 library(ggplot2)
 library(ggthemes)
-library(GGally)
 theme_set(theme_bw())
 library(dplyr)
 ```
@@ -143,10 +145,11 @@ terraref_test_url <- "https://terraref.ncsa.illinois.edu/bety-test/"
 
 public_key <- "9999999999999999999999999999999999999999"
 
-traits <- c("Vcmax", "c2n_leaf", "cuticular_cond", "SLA", "quantum_efficiency", "leaf_respiration_rate_m2", "stomatal_slope.BB", "Jmax", "chi_leaf", "extinction_coefficient_diffuse")
 
-
-SLA <- (betydb_search(query = "SLA", betyurl = terraref_test_url, key = public_key, api_version = "beta")
+SLA <- (betydb_search(query = "SLA", 
+                      betyurl = terraref_test_url, 
+                      key = public_key, 
+                      api_version = "beta")
   %>% filter(scientificname == 'Sorghum bicolor'))
 
 ```
@@ -165,7 +168,12 @@ ggplot(SLA) +
 ```{r query-traits}
 
 
-traits <- betydb_search("SLA Vcmax",  betyurl = terraref_test_url, key = public_key)
+trait_list <- c("Vcmax", "c2n_leaf", "cuticular_cond", "SLA", "quantum_efficiency", "leaf_respiration_rate_m2", "stomatal_slope.BB", "Jmax", "chi_leaf", "extinction_coefficient_diffuse")
+
+trait_data <- betydb_search(paste(trait_list, collapse = " "),
+                            betyurl = terraref_test_url, 
+                            key = public_key,
+                            limit = 'none')
         
 ```
 
@@ -179,7 +187,7 @@ traits <- betydb_search("SLA Vcmax",  betyurl = terraref_test_url, key = public_
 ```
 
 
-```{r}
+```{r eval=FALSE}
 library(data.table)
 library(dplyr)
 

traits/02-danforth-phenotyping-facility.Rmd

@@ -12,6 +12,11 @@ library(dplyr)
 library(ggplot2)
 library(ggthemes)
 theme_set(theme_bw())
+
+if(packageVersion("traits") == '0.2.0'){
+  devtools::install_github('ropensci/traits')
+}
+
 library(traits)
 ```
 

tutorials.Rproj

@@ -11,3 +11,5 @@ Encoding: UTF-8
 
 RnwWeave: Sweave
 LaTeX: pdfLaTeX
+
+BuildType: Website