R Script for 3D scatterplot in RMarkdown (main heading)

This script displays key features of a basic R script in the form of an RMarkdown file which integrates text and R code in code chunks.

Text/comments - only needs to be “commented” when in code chunks
Code - in special “code chunks”
Hashtags in main text: RMarkdown formatting
Text formatting options: headings, bulletted lists, bold, italics, and more.

Key thing to know (sub0heading)

At the top of .RMD files is a YAML header (not shown in rendered documents).

YAML is a markup language for formatting documents (“Yet Another Markup Language” some call it).

In RStudio, .Rmd files can be run in “notebook mode” with some output produced BELOW the code chunk. This is the default, and I usually turn it off.

Load package

Code chunks start with 3 ticks and r in brackets.

Comments can be included in chunks.

Click on the right-pointing triangle to run it (among other ways).

NOTE:

This 1st line of code runs install.packages() to download the R library called “scatterplot3d” from a website. You usually only have to run install.packages() once a semester to download the library for either the first time or to get the most recent version.

Uncomment the line of code if you have never downloaded the package before.

#code chunk starts here

## download from website
# install.packages("scatterplot3d")

## load package into memory
library(scatterplot3d)

## Warning: package 'scatterplot3d' was built under R version 4.2.1

# code chunk ends here

Code chunks start with 3 ticks.

Data

Create individual vectors (sub-sub heading)

# code chunk starts

stem_density   <- c(483, 521, 531, 451, 513, 547,
                    500, 561, 478, 634, 582, 531, 532, 554, 549)
basal_area     <- c(32.6,41.5,44.2,37.6,42.1,34.0,
                    27.7,34.2,30.2,28.7,34.0,34.6,30.9,27.5,27.4)
tree_height_m  <- c(47.6,42.6,43.2,47.9,48.0,33.6,
                    33.2,32.6,31.9,37.5,35.1,38.2,32.5,35.8,35.8)
altitude       <- c(237,246,360,392,396,528,567,580,
                    605,627,650,668,721,850,909)

# code chunk ends

Create dataframe

df <- data.frame(stem_density,
                 basal_area, 
                 tree_height_m, 
                 altitude)

Look at dataframe

If you are in notebook mode while in RStudio, the code below will show the output below the code chunk; otherwise it will show up in the RStudio console. It will always be printed out when the document is rendered.

head(df)

##   stem_density basal_area tree_height_m altitude
## 1          483       32.6          47.6      237
## 2          521       41.5          42.6      246
## 3          531       44.2          43.2      360
## 4          451       37.6          47.9      392
## 5          513       42.1          48.0      396
## 6          547       34.0          33.6      528

Make plot

Again, if you are in notebook mode, this plot will show the output below the code chunk; otherwise it will show up in the RStudio console.

scatterplot3d(x = df$stem_density,
              y = df$basal_area,
              z = df$tree_height_m,
              cex.symbols = 1, 
              type = "h")

Rendering RMarkdown files to documents

RMarkdown is a markup language, so RMarkdown files can be converted to several forms as long as you have the proper tools installed on your computer. This is called rendering. Types of output include

Word documents
PDF (requires “LaTex”)
RPubs websites (RStudio’s quasi-blogging platform)
HTML
PowerPoint (requires additional packages and markup)
…and more

Challenges

Easy

Change the color, shape of the points, and point size.
Delete type = “h” and see what happens
Change one of the axes to altitude
Make labels for the axes

Hard

Consult the help file using ?scatterplot3d and change the viewing angle of the plot.

CODE CHECKPOINT - Rendering an RMarkdown file to Word

2022-10-03