R library is designed to provide an easy way to extract and manipulate palaeoclimate reconstructions for ecological and anthropological analyses.
The functionalities of
pastclim are described in Leonardi et al. (2023). Please cite it if you use
pastclim in your research.
Install the library
pastclim is on CRAN, and the easiest way to install it is with:
The version on CRAN is recommended for every day use. New features and bug fixes appear first on the
dev branch on GitHub, before they make their way to CRAN. If you need to have early access to these new features, you can install
pastclim directly from GitHub. To install from GitHub, you will need to use
devtools; if you haven’t done so already, get it from CRAN with
install.packages("devtools"). Also, note that the
dev version of
pastclim tracks changes in the
dev version of
terra, so you will need to upgrade both libraries with:
install.packages('terra', repos='https://rspatial.r-universe.dev') devtools::install_github("EvolEcolGroup/pastclim", ref="dev")
Overview of functionality
On its dedicated website, you can find Articles giving you a step-by-step overview of the package, and a cheatsheet. There is also a dev version of the site updated for the
dev branch of
pastclim (on the top left of the dev website, the version number is in red and in the format x.x.x.9xxx, indicating it is a development version).
Pastclim currently includes data from Beyer et al 2020, a reconstruction of climate based on the HadCM3 model for the last 120k years, and Krapp et al 2021, which covers the last 800k years. The reconstructions are bias-corrected and downscaled to 0.5 degree. More details on these datasets can be found here. There are also instructions on how to build and use custom datasets.
You can also build the vignettes when installing
pastclim (note that you will need to have the necessary tools to build vignettes already installed; requirements depend on your OS):
devtools::install_github("EvolEcolGroup/pastclim", build_vignette = TRUE)
If you built the vignettes, you can read them directly in R. For example, the overview can be obtained with:
vignette("pastclim_overview", package = "pastclim")
If something does not work, check the issues on GitHub to see whether the problem has already been reported. If not, feel free to create an new issue. Please make sure you have updated to the latest version of
pastclim on CRAN, as well as updating all other packages on your system, and provide a reproducible example for the developers to investigate the problem.
Error in x$.self$finalize()
pastclim relies on
terra to process rasters. There is a known bug in
terra that leads to the occasional message:
"Error in x$.self$finalize() : attempt to apply non-function"
This is an error related to garbage collection, which does not affect the script being correctly executed, so it can be ignored. More discussion of this issue can be found on stackoverflow