separate oue first code steps so set wd can be set to eval=FALSE

tutorials/R/AOP/Hyperspectral/Work-With-Hyperspectral-Data-In-R/Work-With-Hyperspectral-Data-In-R.Rmd

@@ -143,22 +143,28 @@ Please be sure that you have *at least* version 2.10 of `rhdf5` installed. Use:
 # Load `terra` and `rhdf5` packages to read NIS data into R
 library(terra)
 library(rhdf5)
+```
+
+<div id="ds-dataTip" markdown="1">
+
+<i class="fa fa-star"></i> **Data Tip:** To update all packages installed in 
+R, use `update.packages()`.
+
+</div>
 
+```{r set-wd, eval=FALSE, results="hide" }
 # set working directory to ensure R can find the file we wish to import and where
 # we want to save our files. Be sure to move the download into your working directory!
 wd <- "~/data/" #This will depend on your local environment
 setwd(wd)
+```
 
-# Define the file name to be opened
+```{r define-h5, results="hide" }
+# Define the h5 file name to be opened
 f <- paste0(wd,"NEON_hyperspectral_tutorial_example_subset.h5")
 ```
 
-<div id="ds-dataTip" markdown="1">
-
-<i class="fa fa-star"></i> **Data Tip:** To update all packages installed in 
-R, use `update.packages()`.
-
-</div>
+You can use `h5ls` and/or `View(h5ls(...))` to look at the contents of the hdf5 file, as follows:
 
 ```{r view-file-strux, eval=FALSE, comment=NA}
 # look at the HDF5 file structure 

tutorials/R/AOP/Hyperspectral/Work-With-Hyperspectral-Data-In-R/Work-With-Hyperspectral-Data-In-R.html

@@ -176,10 +176,12 @@ <h2 id="read-hdf5-data-into-r">Read HDF5 data into R</h2>
 library(terra)
 
 library(rhdf5)
-
-
-
-# set working directory to ensure R can find the file we wish to import and where
+</code></pre>
+<div id="ds-dataTip" markdown="1">
+<p><i class="fa fa-star"></i> <strong>Data Tip:</strong> To update all packages installed in
+R, use <code>update.packages()</code>.</p>
+</div>
+<pre><code># set working directory to ensure R can find the file we wish to import and where
 
 # we want to save our files. Be sure to move the download into your working directory!
 
@@ -188,15 +190,11 @@ <h2 id="read-hdf5-data-into-r">Read HDF5 data into R</h2>
 setwd(wd)
 
 
-
-# Define the file name to be opened
+# Define the h5 file name to be opened
 
 f &lt;- paste0(wd,&quot;NEON_hyperspectral_tutorial_example_subset.h5&quot;)
 </code></pre>
-<div id="ds-dataTip" markdown="1">
-<p><i class="fa fa-star"></i> <strong>Data Tip:</strong> To update all packages installed in
-R, use <code>update.packages()</code>.</p>
-</div>
+<p>You can use <code>h5ls</code> and/or <code>View(h5ls(...))</code> to look at the contents of the hdf5 file, as follows:</p>
 <pre><code># look at the HDF5 file structure 
 
 View(h5ls(f,all=T))

tutorials/R/AOP/Hyperspectral/Work-With-Hyperspectral-Data-In-R/Work-With-Hyperspectral-Data-In-R.md

@@ -145,7 +145,13 @@ Please be sure that you have *at least* version 2.10 of `rhdf5` installed. Use:
 
     library(rhdf5)
 
-
+<div id="ds-dataTip" markdown="1">
+
+<i class="fa fa-star"></i> **Data Tip:** To update all packages installed in 
+R, use `update.packages()`.
+
+</div>
+
 
     # set working directory to ensure R can find the file we wish to import and where
 
@@ -155,18 +161,12 @@ Please be sure that you have *at least* version 2.10 of `rhdf5` installed. Use:
 
     setwd(wd)
 
-
 
-    # Define the file name to be opened
+    # Define the h5 file name to be opened
 
     f <- paste0(wd,"NEON_hyperspectral_tutorial_example_subset.h5")
 
-<div id="ds-dataTip" markdown="1">
-
-<i class="fa fa-star"></i> **Data Tip:** To update all packages installed in 
-R, use `update.packages()`.
-
-</div>
+You can use `h5ls` and/or `View(h5ls(...))` to look at the contents of the hdf5 file, as follows:
 
 
     # look at the HDF5 file structure