Collaborative R Notes

This set of notes is for students at Chico State to help build a reference for themselves and future users on how to do tasks in R.

General resources

• https://norcalbiostat.github.io/MATH130/faq.html
• https://datacarpentry.org/R-genomics/index.html

Script Files

• A script file with a .R file type is mainly R, all discussion/comments need to be in #comment form
• An Rmarkdown (.Rmd) file is like a lab notebook where you can write R code,
  • See Math 130 Week 1 lesson 03 or the RStudio tutorial page for an overview.
  • A Quarto (.qmd) file is the new generation of Rmarkdown files. See Hello Quarto tutorial to get started

Packages / Libraries

A package is a collection of functions that can be used to do things like create graphics or run advanced models. To get access to these functions you have to load the package by typing

library(packagename)

where packagename is the name of the package you are trying to load. Examples include tidyverse, here and janitor.

Import and preprocessing

• External data files are often saved as text files (.txt), comma separated values (.csv) or as Excel files (.xlsx)

Import Data into R

If my data set is named AddHealth_Wave_IV.csv and it is located in my data folder, then it can be read into R using the read_csv function.

raw <- read_csv(here("data", "AddHealth_Wave_IV.csv"))

Here I am assigning the data set to the name raw.

Only read in selected variables

mydata <- raw %>%
  select(BIO_SEX, H4TO1, H4TO2)

check the data type

class(mydata$H4TO1)

Export R formatted data

save(mydata, here("data", "addhealth_clean.Rdata"))

Nice settings for your rendered document

At the top of your qmd file, in the YAML header add the following

title: "Describing Relationships between variables"
date: "2022-09-19"
author: "Robin Donatello"
format: 
    pdf
execute:
  echo: true

Hide warning messages

For a single code chunk:

Inside the code chunk, at the top, use the hash-pipe to set code chunk options

execute:
  echo: true
  warning: false
  message: false

For the entire document:

At the top of your qmd file, in the YAML header under execute add lines to disable warning and message.

|# message: false
table(mpg$class)

Applying labels to levels of categorical variable

depress$marital <- factor(depress$marital, 
                          labels = c("Never Married", "Married", 
                          "Divorced", "Separated", "Widowed"))

Force a page break

Add \newpage to a blank line.

---

Data Exploration and Vizualization

Side by side plots

This uses div tags. Copy it exactly, then insert your own code chunks.

:::: {.columns}

::: {.column width="50%"}
code chunk to create plot 1
:::

::: {.column width="50%"}
code chunk to create plot 2
:::

::::

Expand the y axis so that your numbers can be seen

Expand the y-axis to a number a little larger than your max value using ylim(lower, upper)

plot_frq(mpg$class) + ylim(c(0,100))