brew install cdoPrerequisites
Prerequisites
Our course is not intended for absolute beginners in R. While participants don’t need to be highly proficient, a basic understanding of R and programming syntax is required. For example, participants should know how to create an R project and open a script, read in data using commands, make basic plots using base R, and write for loops. A basic understanding of the shell/command line is advantageous, but not required. Further, previous experience using the terra package and working with netCDF files is a plus, but again, not required.
In addition to having R and RStudio already installed, you will need to install (i) CDO, (ii) NCO, (iii) wget, (iv) Panoply and (v) a suite of R packages.
Important
We strongly recommend using a macOS laptop for the workshop. We’ve found that Windows users can run into issues with installing and using CDO, which is required for the workshop (see below).
To see if you may have software issues during our workshop, install the prerequisites below, download this folder here, and run the runme.R script. If you don’t run into any errors, great! If you do, you will need to do some troubleshooting before the workshop.
CDO
You will need CDO (Climate Data Operators) installed prior to the workshop. CDO comprises a suite of over 600 operators for standard (and speedy) processing of climate and forecast model outputs. More information on CDO found here.
MacOS
The simplest way to install CDO is via Homebrew. If you haven’t already installed Homebrew, do so here. Then, open terminal and run the following code:
More information available on the CDO MacOS website.
Windows
CDO is meant for use on POSIX-compatible operating systems (e.g., like Linux and MacOS), so downloading on Windows requires some extra steps.
Recent versions of Windows (>=10) includes an Ubuntu embedded Linux, offering the opportunity to install CDO via Ubuntu’s native package manager. First, install the Ubuntu app from the Microsoft Store application. Then open the Ubuntu terminal and type:
sudo apt-get upgrade
sudo apt-get install cdo #write your password, if promptedMore information available on the CDO Windows website.
NCO
Similar to CDO, we will install NCO (netCDF operators), which are a suite of operators that take netCDF file formats and facilitate file manipulation.
Mac
brew install ncoWindows
Installing NCO on windows can be tricky. Here is a discussion forum.
wget
wget is a bash command used for downloading files from the internet. We will use this to download our ESMs via wget scripts from the ESGF website.
macOS
Run the following in terminal:
brew install wgetWindows
Check out the link here. You may need to do some extra fiddling - see here or check out Youtube for further help.
Panoply
Panoply is a data viewer for netCDF, HDF and GRIB data arrays, administered by NASA Goddard Space Flight Center. Panoply requires that your computer has a compatible Java 11 (or later version) JRE or JDK installed.
Download Panoply here.
R Packages
Ensure you have the following R packages installed, listed below.
#Install pacman
if (!require("pacman")) install.packages("pacman")
# Install packages, if not already installed
pacman::p_load(tidyverse, # Working with 'tidy' data
furrr, parallelly, purrr, # Run functions in parallel
tictoc, beepr, # Understand code execution time
ncdf4, raster, terra, # For working with netCDFs
tmap, # Map visualization
plotrix, # Taylor Diagrams
RCurl, xml2, rvest, # Downloading files
zoo) Changing your path
Lastly, once you have downloaded the repository, you will need to open __scripts/helpers.R, and change your pth object to suit your machine (see Line 7). I’ve set mine as "/Users/admin/Documents/GitHub/esmRworkshop_rladies26"; change yours to reflect where this folder is located on your machine.
Below are the dependencies and package versions the instructors will use for the workshop.
> devtools::session_info()
─ Session info ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.4.1 (2024-06-14)
os macOS Sonoma 14.5
system aarch64, darwin20
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/Los_Angeles
date 2026-02-04
rstudio 2024.04.2+764 Chocolate Cosmos (desktop)
pandoc NA
quarto 1.5.55 @ /usr/local/bin/quarto
─ Packages ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
abind 1.4-5 2016-07-21 [1] CRAN (R 4.4.0)
audio 0.1-11 2023-08-18 [1] CRAN (R 4.4.0)
base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.4.0)
beepr * 2.0 2024-07-06 [1] CRAN (R 4.4.0)
bitops 1.0-8 2024-07-29 [1] CRAN (R 4.4.0)
cachem 1.1.0 2024-05-16 [1] CRAN (R 4.4.0)
chromote 0.5.1 2025-04-24 [1] CRAN (R 4.4.1)
class 7.3-22 2023-05-03 [1] CRAN (R 4.4.1)
classInt 0.4-11 2025-01-08 [1] CRAN (R 4.4.1)
cli 3.6.5 2025-04-23 [1] CRAN (R 4.4.1)
codetools 0.2-20 2024-03-31 [1] CRAN (R 4.4.1)
colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.4.0)
cols4all 0.8 2024-10-16 [1] CRAN (R 4.4.1)
crosstalk 1.2.1 2023-11-23 [1] CRAN (R 4.4.0)
data.table 1.16.4 2024-12-06 [1] CRAN (R 4.4.1)
DBI 1.2.3 2024-06-02 [1] CRAN (R 4.4.0)
devtools 2.4.5 2022-10-11 [1] CRAN (R 4.4.0)
dichromat 2.0-0.1 2022-05-02 [1] CRAN (R 4.4.0)
digest 0.6.37 2024-08-19 [1] CRAN (R 4.4.1)
dplyr * 1.1.4 2023-11-17 [1] CRAN (R 4.4.0)
e1071 1.7-16 2024-09-16 [1] CRAN (R 4.4.1)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.4.0)
farver 2.1.2 2024-05-13 [1] CRAN (R 4.4.0)
fastmap 1.2.0 2024-05-15 [1] CRAN (R 4.4.0)
forcats * 1.0.0 2023-01-29 [1] CRAN (R 4.4.0)
fs 1.6.6 2025-04-12 [1] CRAN (R 4.4.1)
furrr * 0.3.1 2022-08-15 [1] CRAN (R 4.4.0)
future * 1.67.0 2025-07-29 [1] CRAN (R 4.4.1)
generics 0.1.3 2022-07-05 [1] CRAN (R 4.4.0)
ggplot2 * 4.0.0 2025-09-11 [1] CRAN (R 4.4.1)
globals 0.18.0 2025-05-08 [1] CRAN (R 4.4.1)
glue 1.8.0 2024-09-30 [1] CRAN (R 4.4.1)
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.4.0)
gtable 0.3.6 2024-10-25 [1] CRAN (R 4.4.1)
hms 1.1.3 2023-03-21 [1] CRAN (R 4.4.0)
htmltools 0.5.8.1 2024-04-04 [1] CRAN (R 4.4.0)
htmlwidgets 1.6.4 2023-12-06 [1] CRAN (R 4.4.0)
httpuv 1.6.16 2025-04-16 [1] CRAN (R 4.4.1)
httr 1.4.7 2023-08-15 [1] CRAN (R 4.4.0)
jsonlite 2.0.0 2025-03-27 [1] CRAN (R 4.4.1)
KernSmooth 2.23-24 2024-05-17 [1] CRAN (R 4.4.1)
later 1.4.2 2025-04-08 [1] CRAN (R 4.4.1)
lattice 0.22-6 2024-03-20 [1] CRAN (R 4.4.0)
leafem 0.2.4 2025-05-01 [1] CRAN (R 4.4.1)
leaflegend 1.2.1 2024-05-09 [1] CRAN (R 4.4.0)
leaflet 2.2.2 2024-03-26 [1] CRAN (R 4.4.0)
leaflet.providers 2.0.0 2023-10-17 [1] CRAN (R 4.4.0)
leafsync 0.1.0 2019-03-05 [1] CRAN (R 4.4.0)
lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.4.0)
listenv 0.9.1 2024-01-29 [1] CRAN (R 4.4.0)
lubridate * 1.9.3 2023-09-27 [1] CRAN (R 4.4.0)
lwgeom 0.2-14 2024-02-21 [1] CRAN (R 4.4.0)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.4.0)
maps 3.4.2 2023-12-15 [1] CRAN (R 4.4.0)
maptiles 0.10.0 2025-05-07 [1] CRAN (R 4.4.1)
memoise 2.0.1 2021-11-26 [1] CRAN (R 4.4.0)
microbenchmark 1.5.0 2024-09-04 [1] CRAN (R 4.4.1)
mime 0.13 2025-03-17 [1] CRAN (R 4.4.1)
miniUI 0.1.2 2025-04-17 [1] CRAN (R 4.4.1)
ncdf4 * 1.22 2023-11-28 [1] CRAN (R 4.4.0)
pacman * 0.5.1 2019-03-11 [1] CRAN (R 4.4.0)
parallelly * 1.45.1 2025-07-24 [1] CRAN (R 4.4.1)
pillar 1.10.2 2025-04-05 [1] CRAN (R 4.4.1)
pkgbuild 1.4.8 2025-05-26 [1] CRAN (R 4.4.1)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.4.0)
pkgload 1.4.0 2024-06-28 [1] CRAN (R 4.4.0)
plotrix * 3.8-4 2023-11-10 [1] CRAN (R 4.4.0)
png 0.1-8 2022-11-29 [1] CRAN (R 4.4.0)
processx 3.8.6 2025-02-21 [1] CRAN (R 4.4.1)
profvis 0.4.0 2024-09-20 [1] CRAN (R 4.4.1)
promises 1.3.3 2025-05-29 [1] CRAN (R 4.4.1)
proxy 0.4-27 2022-06-09 [1] CRAN (R 4.4.0)
ps 1.9.1 2025-04-12 [1] CRAN (R 4.4.1)
purrr * 1.0.4 2025-02-05 [1] CRAN (R 4.4.1)
R6 2.6.1 2025-02-15 [1] CRAN (R 4.4.1)
raster * 3.6-32 2025-03-28 [1] CRAN (R 4.4.1)
RColorBrewer 1.1-3 2022-04-03 [1] CRAN (R 4.4.0)
Rcpp 1.0.14 2025-01-12 [1] CRAN (R 4.4.1)
RCurl * 1.98-1.16 2024-07-11 [1] CRAN (R 4.4.0)
readr * 2.1.5 2024-01-10 [1] CRAN (R 4.4.0)
remotes 2.5.0 2024-03-17 [1] CRAN (R 4.4.0)
rlang 1.1.6 2025-04-11 [1] CRAN (R 4.4.1)
rstudioapi 0.17.1 2024-10-22 [1] CRAN (R 4.4.1)
rvest * 1.0.4 2024-02-12 [1] CRAN (R 4.4.0)
s2 1.1.9 2025-05-23 [1] CRAN (R 4.4.1)
S7 0.2.0 2024-11-07 [1] CRAN (R 4.4.1)
scales 1.4.0 2025-04-24 [1] CRAN (R 4.4.1)
sessioninfo 1.2.3 2025-02-05 [1] CRAN (R 4.4.1)
sf 1.0-21 2025-05-15 [1] CRAN (R 4.4.1)
shiny 1.11.1 2025-07-03 [1] CRAN (R 4.4.1)
sp * 2.2-0 2025-02-01 [1] CRAN (R 4.4.1)
spacesXYZ 1.3-0 2024-01-23 [1] CRAN (R 4.4.0)
stars 0.6-6 2024-07-16 [1] CRAN (R 4.4.0)
stringi 1.8.7 2025-03-27 [1] CRAN (R 4.4.1)
stringr * 1.5.1 2023-11-14 [1] CRAN (R 4.4.0)
terra * 1.8-54 2025-06-01 [1] CRAN (R 4.4.1)
tibble * 3.3.0 2025-06-08 [1] CRAN (R 4.4.1)
tictoc * 1.2.1 2024-03-18 [1] CRAN (R 4.4.0)
tidyr * 1.3.1 2024-01-24 [1] CRAN (R 4.4.0)
tidyselect 1.2.1 2024-03-11 [1] CRAN (R 4.4.0)
tidyverse * 2.0.0 2023-02-22 [1] CRAN (R 4.4.0)
timechange 0.3.0 2024-01-18 [1] CRAN (R 4.4.0)
tmap * 4.1 2025-05-12 [1] CRAN (R 4.4.1)
tmaptools 3.1-1 2021-01-19 [1] CRAN (R 4.4.0)
tzdb 0.5.0 2025-03-15 [1] CRAN (R 4.4.1)
units 0.8-7 2025-03-11 [1] CRAN (R 4.4.1)
urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.4.0)
usethis 3.1.0 2024-11-26 [1] CRAN (R 4.4.1)
vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.4.0)
viridis 0.6.5 2024-01-29 [1] CRAN (R 4.4.0)
viridisLite 0.4.2 2023-05-02 [1] CRAN (R 4.4.0)
websocket 1.4.4 2025-04-10 [1] CRAN (R 4.4.1)
withr 3.0.2 2024-10-28 [1] CRAN (R 4.4.1)
wk 0.9.4 2024-10-11 [1] CRAN (R 4.4.1)
XML 3.99-0.17 2024-06-25 [1] CRAN (R 4.4.0)
xml2 * 1.4.1 2025-10-27 [1] CRAN (R 4.4.1)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.4.0)
zoo * 1.8-12 2023-04-13 [1] CRAN (R 4.4.0)
[1] /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library