Workshop at CSEE 2023: developing a reproducible workflow in R using functions, {targets} and {renv}
Developed and delivered by:
Projects
Short break
Functions
Lunch break
{targets}
Short break
{renv} + {conflicted}
Overall
Section 1: Projects
Section 2: Functions
Section 3: {targets}
Section 4: {renv} + {conflicted}
This workshop is aimed at improving our ability to use and create reproducible workflows. All the materials should be accessible from the side bar (slides, exercises, resources for further reading, and the link to the GitHub repository can be accessed by clicking on the GitHub icon).
We don't have any strict dependencies on specific versions of R or R packages, but it would be good to have at least R version 4.0 and a recent version of RStudio.
We are using Quarto to build the workshop's website and exercises, so it could be helpful for you to install it too. If you don't have time to, you can always complete exercises in an R script - so no pressure.
Install first the Quarto CLI from the here then the package with the command at the bottom.
Please install the following packages (after updating R):
pkgs <- c(
'targets',
'igraph',
'data.table',
'dplyr',
'ggplot2',
'testthat',
'janitor',
'renv',
'rlang',
'conflicted',
'palmerpenguins',
'visNetwork',
'quarto',
'xml2',
'downlit',
'usethis'
)
install.packages(pkgs)
To download the workshop materials for a participant, use this command:
library(usethis)
# (Set your own destination directory)
use_course(
'https://github.com/robitalec/2023-CSEE-reproducible-workflows-workshop/archive/refs/heads/participant.zip',
destdir = '~/Documents')
Or by downloading and unziping the ZIP file at this link: https://github.com/robitalec/2023-CSEE-reproducible-workflows-workshop/archive/refs/heads/participant.zip.
Then open up the RStudio project.
Example data for this workshop is borrowed from the Palmer Long-Term Ecological Research (LTER). Here is the study description from the Palmer LTER site:
The Palmer Long-Term Ecological Research (LTER) study area is located to the west of the Antarctic Peninsula extending South and North of the Palmer Basin from onshore to several hundred kilometers off shore. Palmer Station is one of the three United States research stations located in Antarctica. It is on Anvers Island midway down the Antarctic Peninsula at latitude 64.7 South, longitude 64.0 West.
The Palmer LTER studies a polar marine biome with research focused on the Antarctic pelagic marine ecosystem, including sea ice habitats, regional oceanography and terrestrial nesting sites of seabird predators. The Palmer LTER is one of more than 26 LTER research sites located throughout the United States, Puerto Rico and Tahiti; each focused on a specific ecosystem, that together constitute the LTER Network.
We gratefully acknowledge the Palmer LTER for releasing data freely and openly for diverse uses - in our case for training analytical skills of researchers in ecology.
The first dataset is already available in R through the palmerpenguins R package. There is a raw version and a cleaned version. They contain data for 344 penguins, with the following variables (cleaned version):
The following datasets are available directly from the Palmer LTER Data Catalog. To download the data to the raw-data/ directory, run the function download_example_data() (R/download_example_data.R).
This second dataset contains monthly averaged weather timeseries from Palmer Station, Antarctica, with the following variables:
Link to data (CSV):
The third dataset contains monthly sea ice area from the region around the Palmer Station, Antarctica, with the following variables:
Note: this data is formatted with months as columns, years as rows, and cells filled with the corresponding area.
Link to data (TXT):
The fourth dataset contains Adelie penguin adult and chick counts
Link to data (CSV):
This project is released under the GNU General Public License v3.0. Read it here.