title | date |
---|---|
Reproducible Methods in Research and Teaching |
September 16, 2019 |
We highly recommend following this tutorial to adequately prepare for the workshop. Before or during the workshop, it will not be possible to provide any assistance in installing either base software or needed packages. If you do not have necessary software or lack basic skills in using it (See the section on Required Basic Proficiency below), you will not be able to work through this workshop. We apologize in advance for being blunt on this matter and hope to provide an optimal learning experience.
Every operating system is different and so is the environment it provides in order for software to run without issue. For this reason, it is important that you have full privileges for running and modifying the software on your computer. Please ensure that you have administrative privileges. If you are using an institution owned laptop and your IT is reluctant to give you admin control, then please seriously consider bringing a laptop that you own.
The entire workshop and its documentation will be posted at github.com/wyoibc/rdar. To avoid paper waste, we will not be printing copies and we urge you to not do so as well.
- Follow the link to your operating system and install the latest version CRAN Mirror at UC Berkeley unless you already have it. As of this writing, the latest version was
3.6.1
nicknamedAction of the Toes
.
Is graphical front-end for the R programming language - one that we will use during the workshop. Download the Desktop version here.
If you have a favorite text editor (Notepad doesn't count, though Notepad++ does), then you are all set. Otherwise, we highly recommend Vim
.
-
On Mac OSX, the best way to install Vim is through the Homebrew Package Manager. Install both commandline
vim
and GUImacvim
. -
For Windows, access download link on this page.
-
Alternatively, on Windows you may also use Notepad++
- On Mac OSX, Git is available by default. Try
git --version
in a terminal session. It should spit out something like the following:
git --version
git version 2.20.1 (Apple Git-117)
- For Windows, obtain Git from this link
Pandoc is a versatile document converter which we will need during the second half of our workshop. Installation links are avilable on this page.
The base version of the R programming language installs basic packages for statistical analysis. In addition, you will need several other packages. For the purposes of this workshop, getting the Tidyverse group of packages should be sufficient. If we need additional packages during the workshop, we can install those on the fly.
In either R-Studio or in R terminal session, simply type the following to install the tidyverse group:
install.packages("tidyverse")
Alternatively, you can get them from GitHub:
require(devtools)
devtools::install_github('hadley/tidyverse')
This will install the following packages:
- ggplot2
- dplyr
- tidyr
- readr
- purrr
- tibble
- stringr
- forcats
We will interact with GitHub throughout the workshop so you will need a free account with this service. Sign up for a new account on this page.
Because this is not a beginner workshop, we will not have time to cover any introductory lessons in using R. Certain amount of proficiency is expected in R, RStudio and text editing. Below, we provide some examples of the tasks we expect you to be able to do comfortably when you attend the workshop.
-
Basic Operations: R-Studio interface and what each window within the GUI is showing you
-
Package Management: Ability to install packages from repositories such as
-
The Comprehensive R Archive Network (CRAN)
-
GitHub source code repositories
-
Bioconductor packages
-
-
File Management: Opening flat text data files in various formats such as tab-delimited (
.txt
) or comma-delimited (.csv
) and storing them as objects in R's memory. Saving data frames to hard disk as plain text files. -
Data Wrangling: Various methods of interfacing with your data objects
-
The
object[1:10,1:5]
coordinate system of accessing specific positions within data -
The
object$colname
operator -
Basic math operators such as
mean
,min
,max
,summary
etc.
-
-
Graphics: Basic skills in plotting
- Histograms, scatterplots and basic plotting functions (see
?plot()
for details)
- Histograms, scatterplots and basic plotting functions (see
-
Finding Help:
- R has comprehensive help documentation which can, in most cases be accessed with
?function_name
.
- R has comprehensive help documentation which can, in most cases be accessed with
-
Opening new or existing files, editing, saving and closing them
-
Perform search and replace functions on the entire file
-
Package-specific help forums
-
R-Users Official mailing lists