diff --git a/NEWS.md b/NEWS.md index a8e2890c..39f3880e 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,6 +1,10 @@ # development +* Add Barreto et al 2023 (based on PALEO-PGEM, covering the last 5 M years), +and all the WorldClim data (present, and future projections with multiple models +and emission scenarios). * Improve `get_ice_mask()`, `get_land_mask()`, and `distance_from_sea()` to work on series rather than just on slices. +* Speed up `region_*()` functions when subsetting the extent/cropping. # pastclim 1.2.4 * Updates on how time is handled to stay in sync with changes in `terra`. diff --git a/README.md b/README.md index d0e7f867..bfcc25f4 100644 --- a/README.md +++ b/README.md @@ -12,7 +12,8 @@ dev](https://img.shields.io/github/checks-status/EvolEcolGroup/pastclim/dev?labe This `R` library is designed to provide an easy way to extract and manipulate palaeoclimate reconstructions for ecological and -anthropological analyses. +anthropological analyses. It is also able to handle timeseries of future +reconstructions. The functionalities of `pastclim` are described in [Leonardi et al. (2023)](https://doi.org/10.1111/ecog.06481). Please cite it if you use @@ -54,10 +55,12 @@ 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 +Pastclim currently includes data from Beyer et al 2020 (a reconstruction +of climate based on the HadCM3 model for the last 120k years), Krapp +et al 2021 (which covers the last 800k years with a statistical emulator of HadCM3), +Barreto et al 2023 (covering the last 5M years using hte PALEO-PGEM emulator), +and the WorldClim data (present, and future projections with a number of models and +emission scenarios). More details on each of these datasets can be found [here](https://evolecolgroup.github.io/pastclim/articles/a1_available_datasets.html). There are also instructions on how to build and use [custom diff --git a/vignettes/a0_pastclim_overview.Rmd b/vignettes/a0_pastclim_overview.Rmd index 2b61820b..2cc863ef 100644 --- a/vignettes/a0_pastclim_overview.Rmd +++ b/vignettes/a0_pastclim_overview.Rmd @@ -64,40 +64,26 @@ vignette("pastclim_overview", package = "pastclim") Depending on the operating system you use, you might need additional packages to build a vignette. ------------------------------------------------------------------------- - -NOTE: `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" -``` - -being reported. 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 -[stack**overflow**](https://stackoverflow.com/questions/61598340/why-does-rastertopoints-generate-an-error-on-first-call-but-not-second) - # Download the data You will need to download climatic reconstructions before being able to -do any real work with `pastclim`. Currently the library contains two -datasets: *Beyer2020* which covers the last 120k years; and, for project -that go further back in time, *Krapp2021* which goes back to 800kya. It -is possible to add additional, custom datasets, but you will need some -familiarity with handling `netcdf` files (see the vignette on 'custom -dataset'). - -```{r eval=FALSE} -vignette("custom_datasets", package = "pastclim") -``` +do any real work with `pastclim`. +Pastclim currently includes data from Beyer et al 2020 (*Beyer2020*, a reconstruction +of climate based on the HadCM3 model for the last 120k years), Krapp +et al 2021 (*Krapp2021*, which covers the last 800k years with a statistical emulator of HadCM3), +Barreto et al 2023 (*Barreto2023*), covering the last 5M years using hte PALEO-PGEM emulator), +and the WorldClim data ("WorldClim_2.1_*", present, and future projections with a number of models and +emission scenarios). More information on each of these +datasets can be found +[here](https://evolecolgroup.github.io/pastclim/articles/a1_available_datasets.html). +For detailed instructions on how to use the WorldClim dataset, can be found in [this article](https://evolecolgroup.github.io/pastclim/articles/a3_pastclim_present_and_future.html) +There are also instructions on how to build and use [custom +datasets](https://evolecolgroup.github.io/pastclim/articles/a2_custom_datasets.html), +but you will need some +familiarity with handling `netcdf` files. A list of all datasets available can be obtained by typing -```{r eval=FALSE} -vignette("available_datasets", package = "pastclim") -``` - Please be aware that using any dataset made available to `pastclim` will require to cite both `pastclim` as well as the original publication presenting the dataset. The reference to cite for `pastclim` can be