Data Carpentry’s aim is to teach researchers basic concepts, skills, and tools for working with data so that they can get more done in less time, and with less pain. The lessons below were designed for those interested in working with ecology data in R.
This is an introduction to R designed for participants with no programming experience. These lessons can be taught in a day (~ 6 hours). They start with some basic information about R syntax, the RStudio interface, and move through how to import CSV files, the structure of data frames, how to deal with factors, how to add/remove rows and columns, how to calculate summary statistics from a data frame, and a brief introduction to plotting. The last lesson demonstrates how to work with databases directly from R.
Data Carpentry’s teaching is hands-on, so participants are encouraged to use their own computers to ensure the proper setup of tools for an efficient workflow. These lessons assume no prior knowledge of the skills or tools, but working through this lesson requires working copies of the software described below. To most effectively use these materials, please make sure to download the data and install everything before working through this lesson.
Data files for the lesson are available and can be downloaded manually here: https://doi.org/10.6084/m9.figshare.1314459
However, we will download them directly from R during the lessons when we need them.
R and RStudio are separate
downloads and installations. R is the underlying statistical computing
environment, but using R alone is no fun. RStudio is a graphical
integrated development environment (IDE) that makes using R much easier
and more interactive. You need to install R before you install RStudio.
After installing both programs, you will need to install the
tidyverse package from within RStudio.
Follow the instructions below for your operating system, and then follow
the instructions to install
sessionInfo(), which will also display which version of R you are running. Go on the CRAN website and check whether a more recent version is available. If so, please download and install it. You can check here for more information on how to remove old versions from your system if you wish to do so.
.exefile that was just downloaded
sessionInfo(), which will also display which version of R you are running. Go on the CRAN website and check whether a more recent version is available. If so, please download and install it.
.pkgfile for the latest R version
sudo apt-get install r-base, and for Fedora
sudo yum install R), but we don’t recommend this approach as the versions provided by this are usually out of date. In any case, make sure you have at least R 3.3.1.
sudo dpkg -i rstudio-x.yy.zzz-amd64.debat the terminal).
If you had R installed before, please execute the next instruction in the R Console:
This should return an R version newer than 4.2. For instance:
 "R version 4.2.1 (2022-06-23)"
If you have an older version of R, you will need to install a newer version before proceeding.
After installing R and RStudio, you need to install the
After starting RStudio, at the console type:
install.packages(c("tidyverse", "patchwork", "hexbin"))
You can also do this by going to Tools -> Install Packages and typing the names of the packages separated by a comma.
After installing tidyverse, execute the following instructions in the R Console by typing them and pressing Return/Enter.
library(patchwork) library(hexbin) library(tidyverse)
and if the output is similar to:
── Attaching packages ───────────────────────────────────────── tidyverse 1.3.2 ── ✔ ggplot2 3.3.6 ✔ purrr 0.3.5 ✔ tibble 3.1.8 ✔ dplyr 1.0.10 ✔ tidyr 1.2.1 ✔ stringr 1.4.1 ✔ readr 2.1.3 ✔ forcats 0.5.2 ── Conflicts ──────────────────────────────────────────── tidyverse_conflicts() ── ✖ dplyr::filter() masks stats::filter() ✖ dplyr::lag() masks stats::lag()
you are all set and ready to start.
If instead, any of the following error messages is displayed:
Error in library(hexbin) : there is no package called ‘hexbin’ Error in library(patchwork) : there is no package called ‘patchwork’ Error in library(tidyverse) : there is no package called ‘tidyverse’
You will need to repeat the installation command above and troubleshoot the installation in case any error is displayed. Searching for the exact error in your favourite search engine can be helpful, otherwise please request help to the course instructors or your local IT support team.
The list of contributors to this lesson is available here.
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