minor changes to enable book to compile

Author: dlebauer

_bookdown.yml

@@ -1,6 +1,7 @@
 book_filename: "terraref-tutorials"
-output_dir: "book-output"
+output_dir: "docs"
 language:
   ui:
     chapter_name: "Chapter "
-rmd_files: ["index.Rmd", "traits/00-BETYdb-getting-started.Rmd", "traits/01-simulated-sorghum.Rmd", "sensors/05-command-line-hyperspectral-workflow.Rmd"]
+rmd_files: ["index.Rmd", "traits/00-BETYdb-getting-started.Rmd", "traits/01-simulated-sorghum.Rmd", "traits/02-danforth-phenotyping-facility.Rmd",
+            "traits/03-maricopa-field-scanner.Rmd","traits/04-agronomic-metadata.Rmd"]#, "sensors/05-command-line-hyperspectral-workflow.Rmd"]

sensors/01-meteorological-data.Rmd

@@ -3,7 +3,7 @@ title: "01-meteorological-data.Rmd"
 output: html_document
 ---
 
-```{r setup, include=FALSE}
+```{r met-setup, include=FALSE}
 knitr::opts_chunk$set(echo = FALSE, cache = TRUE)
 
 api_url <- "https://terraref.ncsa.illinois.edu/clowder/api"

sensors/02-sensor-metadata.Rmd

@@ -6,7 +6,7 @@ date: "`r Sys.Date()`"
 output: html_document
 ---
 
-```{r setup, include=FALSE}
+```{r sensor-metadata-setup, include=FALSE}
 knitr::opts_chunk$set(echo = TRUE, cache = TRUE)
 library(jsonlite)
 library(dplyr)
@@ -43,7 +43,7 @@ knitr::kable(par_metadata$content$rsr)
 ```
 #### PAR sensor RSR curve 
 
-```{r rsr-curve}
+```{r par-rsr-curve}
 par_rsr <- data.frame(wavelength = unlist(par_metadata$content$rsr$wavelength),
                       response = unlist(par_metadata$content$rsr$response))
 

sensors/03-laser-scanner-3D.Rmd

@@ -7,17 +7,17 @@ output: md_document
 
 ```{r setup, include=FALSE}
 knitr::opts_chunk$set(echo = TRUE, warning = FALSE, cache = TRUE)
-```
-
-
-Based on documentation for the `readLiDAR` package
-
-```{r}
 library(rLiDAR) 
 library(ggplot2)
 library(dplyr)
 library(rgl)
 theme_set(theme_bw())
+```
+
+
+Based on documentation for the `readLiDAR` package
+
+```{r import-las}
 # Importing LAS file:
 
 lasfile <- "~/terraref/documentation/tutorials/data/51458297-0d25-416a-91a5-a2f0ae1a1083__Top-heading-east_0.las"
@@ -26,14 +26,22 @@ LAS <- readLAS(lasfile) %>%
   as_data_frame %>% 
   mutate(Z = (Z - min(Z)))
 
+```
+
+```{r downsample-las}
 LAS_sample <- LAS %>% 
   filter(Z>200) %>% 
   sample_frac(size = 0.01)
+```
 
+```{r lidar-cluster}
 xyz <- LAS_sample[,1:3]
 # Getting LiDAR clusters
 set.seed(1)
 clLAS <- kmeans(xyz, 32)
+```
+
+```{r lidar-visualization}
 # Set the points id
 id <- as.factor(clLAS$cluster)
 

traits/01-simulated-sorghum.Rmd

@@ -198,7 +198,7 @@ knitr::kable(variables %>%
                select(name, description, units))
 ```
 
-```{r all_sorghum}
+```{r all_sorghum, cache=TRUE}
 
 
 site_id <- betydb_query(table = 'sites', sitename = "Central IL Plot D")$id

traits/02-danforth-phenotyping-facility.Rmd

@@ -73,7 +73,7 @@ Which columns do we want?
 
 
 
-```{r}
+```{r danforth-sorghum-cleanup}
 danforth_sorghum <- danforth_sorghum %>% 
   dplyr::select(date, scientificname, cultivar, entity, trait, mean, units) %>% 
   mutate(label = paste0(trait, ifelse(units == '', '', paste0(' (', units, ')'))), date = lubridate::ymd(date), genotype = cultivar)