minor edits to chunk options and variable names

Author: kimberlyh66

traits/03-access-r-traits.Rmd

@@ -20,7 +20,7 @@ if(packageVersion("traits") == '0.2.0'){
 
 Load other packages that we will need to get started.
 
-```{r 00-setup, message = FALSE, echo = TRUE}
+```{r 00-setup, message = FALSE, echo = TRUE, warning = FALSE}
 library(traits)
 library(ggplot2)
 library(ggthemes)
@@ -83,14 +83,14 @@ sorghum_info <- betydb_query(table = 'species',
 
 Now let's query some trait data.
 ```{r canopy_height, echo = TRUE, message = FALSE}
-sorghum_height <- betydb_query(table     = 'search',
+canopy_height <- betydb_query(table     = 'search',
                                trait     = "canopy_height",
                                sitename  = "~Season 2",
                                limit     = 'none')
 ```
 
 ```{r plot_height}
-ggplot(data = sorghum_height,
+ggplot(data = canopy_height,
        aes(x = lubridate::yday(lubridate::ymd_hms(raw_date)), y = mean)) +
   geom_point(size = 0.5, position = position_jitter(width = 0.1)) +
 # scale_x_datetime(date_breaks = '6 months') +