Pre-workshop

Pre-workshop instructions for participants.

R and RStudio

R is software for statistical analyses. R-studio is software to help a user use the R (i.e. integrated development environment; IDE).

There are many guides on how to obtain and/or update R and RStudio, for example:

• R Basics for Paleoecologists by C.A. Kiahtipes, a previous part of the APD series of workshops.
• Install or Update R tutorial by Jennifer Huck

Packages

Packages are tools that contain a series of functions for a specific need. We need to make sure that all packages used throughout the workshop are installed on everyone’s computer.

Install packages

Make a list of packages needed from CRAN

package_list <-
  c(
    "tidyverse", # general data wrangling and visualisation
    "pander", # nice tables
    "Bchron", # age-depth modelling
    "janitor", # string cleaning
    "remotes", # installing packages from GitHub
    "neotoma2" # access to the Neotoma database
  )

Install all packages from CRAN

lapply(
  package_list, utils::install.packages
)

Install packages from GitHub

# Install R-Ratepol
remotes::install_github("HOPE-UIB-BIO/R-Ratepol-package")

Test if everything is set-up

The following code should produce "Everything is good to go", not error ("All required packages are not installed").

if (
  isTRUE(
    all(
      c(package_list, "RRatepol") %in%
        as.data.frame(
          utils::installed.packages()
        )[, 1]
    )
  )
) {
  cat("Everything is good to go")
} else {
  warning("All required packages are not installed")
}