hroughout this course, we will be using R and RStudio during tutorials and demonstrations around best practices in reproducibility, productivity, and data management. To facilitate these tutorials, and to avoid major headaches down the road, it is *essential* that participants/students are working with common tools. So, **please ensure that you have the most recent versions of R and RStudio installed** (or as recent as your operating system will allow). Please also **install the packages listed below**, which we will be using throughout the course. #### **Current versions** - **R** is currently on version 4.1.0 ("Camp Pontanezen") - **RStudio** is currently on version 4.1.1717\ \ #### **Check which versions you're running** To check which version of RStudio you have: - Open RStudio - In the toolbar, select **RStudio \> About RStudio** - you should have RStudio version 1.4 or higher To check which version of R you have: - Open RStudio - See the first line of the welcome message in your **console**, or run the command sessionInfo() - You should have R version 4.0 or higher\ \ #### **Installing R and RStudio** If you don't already have R and RStudio installed, or don't have the most recent versions, you can download them from: - [Download RLinks to an external site.](https://utstat.toronto.edu/cran/) - [Download RStudioLinks to an external site.](https://rstudio.com/products/rstudio/download/#download) Be sure to read the relevant download and installation instructions for your operating system (Windows, Mac OS, Linux) **N.B.** Downloading RStudio **does not** download R. You will need to install both. We recommend installing R first, then RStudio. **Mac users**: R recently underwent a major update (from version 3.6 to version 4.0), which may cause compatibility issues with older version of Mac OS (\< version 10.12). If you cannot install the most recent version of R on your machine, we recommend using [rstudio.cloud Links to an external site.](https://rstudio.cloud/)(**free** up to 15 hours per month; *preferred*) or installing an older version (R version 3.6.3).\ \ #### **Packages to install** We will be using the following R packages throughout the course. Please be sure to install them before the first class. You can find a refresher on installing (and maintaining) packages [here Links to an external site.](http://www.sthda.com/english/wiki/installing-and-using-r-packages). (Reminder: you can use install.packages() or the point-and-click user interface in RStudio.) **Packages**: - tidyverse [info Links to an external site.](https://www.tidyverse.org/packages/)\ This is actually a suite of cooperating packages, which can be installed together using install.packages("tidyverse"). Packages and dependencies from the tidyverse that we'll be making use of during the course include: readr, tidyr, dplyr, and lubridate (these don't need to be installed separately!) - assertr [infoLinks to an external site.](https://github.com/ropensci/assertr) - taxize [infoLinks to an external site.](https://github.com/ropensci/taxize) - myTAI [infoLinks to an external site.](https://github.com/drostlab/myTAI) #### **R / RStudio help** [Getting help with RLinks to an external site.](https://www.r-project.org/help.html) **Installing/updating R and RStudio** More resources to come, but for now, see this for help installing R and RStudio: [https://datacarpentry.org/r-socialsci/setup.htmlLinks to an external site.](https://datacarpentry.org/r-socialsci/setup.html) **Updates R and keeping old versions** - **Windows**: for Windows users, new versions get installed in their own directory, adding to old versions. You can then select which version you wish to use in RStudio (though the latest version is used by default).\ - See this [support pageLinks to an external site.](https://support.rstudio.com/hc/en-us/articles/200486138-Changing-R-versions-for-RStudio-desktop) - **Mac OS**: for Mac users, instructions regarding multiple installations can be found [here Links to an external site.](https://jacobrprice.github.io/2019/09/19/Installing-multiple-parallel-R-versions.html). You will be able to switch between R versions by installing the [RSwitch tool Links to an external site.](https://rud.is/rswitch/). Specifically, before open RStudio, you can run **RSwitch** (find it in Spotlight search on Mac), and select which version of R you wish to run. **R Basics** If you have never used R/RStudio before, we recommend going through a brief tutorial to get a feel for how R and RStudio work. There are *many* options for learning R. One which we recommend is [Data Carpentry's R for Ecologists Links to an external site.](https://datacarpentry.org/R-ecology-lesson/)lessons. If you are new to R, please complete this before the first day of class. **Having Problems?** One of the postdocs (Ellen Bledsoe) will be holding office hours on **Friday, Sept. 2 from 8-10 am PDT / 9-11 am CST / 11am-1pm EDT**at [this Zoom link Links to an external site.](https://uregina-ca.zoom.us/j/7428820473). If you can't make these office hours, please email Ellen ([ellen.bledsoe\@uregina.ca](mailto:ellen.bledsoe@uregina.ca)).