Introduction update

_quarto.yml

@@ -20,6 +20,7 @@ book:
     - ch1.qmd
     - ch2.qmd
     - ch3.qmd
+    - ch4.qmd
 
 format:
   html:

ch1.qmd

@@ -1,23 +1,29 @@
 ---
 title-block-banner: true
 ---
+
 # Operators and data types
 
 ## Basic operators
 
-In this section, we will learn about some basic R operators that are used to perform operations on values and variables. Some most commonly used operators are shown in the table below.
+In this section, we will learn about some basic R operators that are used to perform operations on variables. Some most commonly used operators are shown in the table below.
 
 <center>![](images/Basic_operators.png){width="70%"}</center>
 
+> R follows the conventional order (sequence) to solve mathematical operations, abbreviated as BODMAS: Brackets, Orders (exponents), Division, Multiplication, Addition, and Subtraction
+
 ```{r Chapter 1, message = FALSE, warning = FALSE}
-2+4+7 # Sum 
+2+4+7 # Sum
+4-5   # Subtraction
+2*3   # Multiplication
+1/2   # Division
 
 # Order of operation
 1/2*3+4-5
 1/2*(3+4-5)
 1/(2*(3+4-5))
 1/(2*3+4-5) 
-## Notice how output changes with the placement of operators
+# Notice how output changes with the placement of operators
 
 # Other operators:
 2^3
@@ -26,7 +32,7 @@ sqrt(4)
 pi
 
 # Clear the Environment
-rm(list=ls())
+rm(list=ls()) # rm is for remove,ls is short for list. The empty parenthesis i.e. () signifies all content. 
 ```
 
 ## Basic data operations
@@ -36,8 +42,8 @@ In this section, we will create some vector data and apply built-in operations t
 ```{r Basic data operation, message = FALSE, warning = FALSE}
 # The "is equal to" or "assignment operator in R is "<-" or "=" 
 
-# Generate sample data
-data<-c(1,4,2,3,9)
+# Generate sample data. Remember "c" comes from for "concatenate". 
+data<-c(1,4,2,3,9)    # Try data = c(1,4,2,3,9). Is there any difference in data in both cases?
 
 # rbind combines data by rows, and hence "r"bind
 # cbind combines data by columns, and hence "c"bind
@@ -74,16 +80,20 @@ sd(data)         # Standard deviation
 var(data)        # Variance
 
 # Text data
-data=c("TAMU","GEOS","BAEN","WMHS") 
+data=c("LSU","SPESS","AgCenter","Tigers") 
 data             # View
 data[1]
 
 # Mixed data
-data=c(1,"GEOS",10,"WMHS") # All data is treated as text if one value is text
-data[3]                    # Note how output is in quotes i.e. "10"
+data=c(1,"LSU",10,"AgCenter") # All data is treated as text if one value is text
+data[3]                       # Note how output is in quotes i.e. "10"
 
 ```
 
+
+> *For help with a function in R, just type ? followed by the function to display information in the help menu. Try pasting `?sd` in the console.*
+
+
 ## Data types
 
 In R, data is stored as an "array", which can be 1-dimensional or 2-dimensional. A 1-D array is called a "vector" and a 2-D array is a "matrix". A table in R is called a "data frame" and a "list" is a container to hold a variety of data types. In this section, we will learn how to create matrices, lists and data frames in R.

ch3.qmd

@@ -1,6 +1,7 @@
 ---
 title-block-banner: true
 ---
+
 # Plotting with ggplot2
 
 ## Import libraries and create sample dataset

ch4.qmd

@@ -0,0 +1,49 @@
+---
+title-block-banner: true
+---
+## EXCERCISE 1
+Retrieving data from USCRN: Extract sample data from a climate reference site in Lafayette, LA, USA for 2021.
+
+```{r}
+#| label: import data
+#| warning: false
+
+# Yearly data from the sample station
+CRNdat = read.csv(url("https://www.ncei.noaa.gov/pub/data/uscrn/products/daily01/2021/CRND0103-2021-LA_Lafayette_13_SE.txt"), header=FALSE,sep="")
+
+# Data headers
+headers=read.csv(url("https://www.ncei.noaa.gov/pub/data/uscrn/products/daily01/headers.txt"), header=FALSE,sep="")
+
+# Column names as headers from the text file
+colnames(CRNdat)=headers[2,1:ncol(CRNdat)]
+
+# Replace fill values with NA
+CRNdat[CRNdat == -9999]=NA
+CRNdat[CRNdat == -99]=NA
+CRNdat[CRNdat == 999]=NA
+
+# View data sample
+library(kableExtra)
+dataTable = kbl(head(CRNdat,3),full_width = F)
+kable_styling(dataTable,bootstrap_options = c("striped", "hover", "condensed", "responsive"))
+
+
+```
+
+```{r}
+#| label: fig-density
+#| fig-cap: "Soil moisture values at USCRN station in Texas"
+#| fig-subcap:
+#|   - "Time series of SM"
+#|   - "SM kernel density"
+#| layout-ncol: 2
+
+# Sample plot for soil moisture
+x=CRNdat$SOIL_MOISTURE_20_DAILY
+
+# Plot time series and density distribution 
+plot(x, type="l", ylab="Soil moisture (v/v)", 
+     col="cyan4", lwd=3)
+plot(density(na.omit(x)), main=" ", xlab="", 
+     col="cyan4", lwd=3)
+```

docs/ch2.html

@@ -175,6 +175,12 @@ <h1 class="title"><span class="chapter-number">3</span>&nbsp; <span class="chapt
   <a href="./ch3.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">Plotting with ggplot2</span></span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./ch4.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">5</span>&nbsp; <span class="chapter-title">EXCERCISE 1</span></span></a>
+  </div>
 </li>
     </ul>
     </div>

docs/ch3.html

@@ -64,6 +64,7 @@
 <script src="site_libs/quarto-search/fuse.min.js"></script>
 <script src="site_libs/quarto-search/quarto-search.js"></script>
 <meta name="quarto:offset" content="./">
+<link href="./ch4.html" rel="next">
 <link href="./ch2.html" rel="prev">
 <script src="site_libs/quarto-html/quarto.js"></script>
 <script src="site_libs/quarto-html/popper.min.js"></script>
@@ -174,6 +175,12 @@ <h1 class="title"><span class="chapter-number">4</span>&nbsp; <span class="chapt
   <a href="./ch3.html" class="sidebar-item-text sidebar-link active">
  <span class="menu-text"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">Plotting with ggplot2</span></span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./ch4.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">5</span>&nbsp; <span class="chapter-title">EXCERCISE 1</span></span></a>
+  </div>
 </li>
     </ul>
     </div>
@@ -291,12 +298,12 @@ <h2 data-number="4.3" class="anchored" data-anchor-id="multivariate-plots"><span
 <pre><code># A tibble: 6 × 4
    Year January Month  Value
   &lt;dbl&gt;   &lt;dbl&gt; &lt;chr&gt;  &lt;dbl&gt;
-1  1913    79.4 Jan    -8.59
-2  1913    79.4 Feb    -7.94
-3  1913    79.4 Mar    -7.35
-4  1914    62.0 Jan    -4.93
-5  1914    62.0 Feb    -7.10
-6  1914    62.0 Mar   -13.1 </code></pre>
+1  1913   19.5  Jan   -11.0 
+2  1913   19.5  Feb    -8.82
+3  1913   19.5  Mar    -2.55
+4  1914    6.44 Jan    -6.10
+5  1914    6.44 Feb    -6.49
+6  1914    6.44 Mar    -5.51</code></pre>
 </div>
 </div>
 <p><strong>Line plot</strong></p>
@@ -615,6 +622,9 @@ <h2 data-number="4.3" class="anchored" data-anchor-id="multivariate-plots"><span
       </a>          
   </div>
   <div class="nav-page nav-page-next">
+      <a href="./ch4.html" class="pagination-link">
+        <span class="nav-page-text"><span class="chapter-number">5</span>&nbsp; <span class="chapter-title">EXCERCISE 1</span></span> <i class="bi bi-arrow-right-short"></i>
+      </a>
   </div>
 </nav>
 </div> <!-- /content -->