From 83dd7b8e04d45657fb7d1d4e63bcb3b5aa7b1004 Mon Sep 17 00:00:00 2001 From: Andrea Manica Date: Fri, 28 Apr 2023 14:41:36 +0100 Subject: [PATCH 1/3] Readme fixes --- README.md | 132 +++++++++++++++++++++++++++++++++--------------------- 1 file changed, 80 insertions(+), 52 deletions(-) diff --git a/README.md b/README.md index ebc34a02..42b6a390 100644 --- a/README.md +++ b/README.md @@ -1,92 +1,120 @@ -# pastclim +--- +editor_options: + markdown: + wrap: 72 +--- + +# pastclim -[![R-CMD-check master](https://img.shields.io/github/checks-status/EvolEcolGroup/pastclim/master?label=master&logo=GitHub)](https://github.com/EvolEcolGroup/pastclim/actions/workflows/R-CMD-check.yaml) -[![R-CMD-check dev](https://img.shields.io/github/checks-status/EvolEcolGroup/pastclim/dev?label=dev&logo=GitHub)](https://github.com/EvolEcolGroup/pastclim/actions/workflows/R-CMD-check.yaml) + +[![R-CMD-check +master](https://img.shields.io/github/checks-status/EvolEcolGroup/pastclim/master?label=master&logo=GitHub)](https://github.com/EvolEcolGroup/pastclim/actions/workflows/R-CMD-check.yaml) +[![R-CMD-check +dev](https://img.shields.io/github/checks-status/EvolEcolGroup/pastclim/dev?label=dev&logo=GitHub)](https://github.com/EvolEcolGroup/pastclim/actions/workflows/R-CMD-check.yaml) [![codecov](https://codecov.io/gh/EvolEcolGroup/pastclim/branch/master/graph/badge.svg?token=NflUsWlnQR)](https://app.codecov.io/gh/EvolEcolGroup/pastclim) + +```{=html} +``` +This `R` library is designed to provide an easy way to extract and +manipulate palaeoclimate reconstructions for ecological and +anthropological analyses. -This `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)](https://doi.org/10.1111/ecog.06481). Please cite it if you -use `pastclim` in your research. +The functionalities of `pastclim` are described in [Leonardi et al. +(2023)](https://doi.org/10.1111/ecog.06481). 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: -```{r install_cran, eval=FALSE} +``` install.packages("pastclim") ``` -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: +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: -```{r install_dev, eval=FALSE} +``` install.packages('terra', repos='https://rspatial.r-universe.dev') + devtools::install_github("EvolEcolGroup/pastclim", ref="dev") ``` ## Overview of functionality -On its dedicated [website](https://evolecolgroup.github.io/pastclim/), you can find -Articles giving you a step-by-step [overview of the package](https://evolecolgroup.github.io/pastclim/articles/a0_pastclim_overview.html), -and a [cheatsheet](https://evolecolgroup.github.io/pastclim/pastclim_cheatsheet.pdf). -There is also a -[version](https://evolecolgroup.github.io/pastclim/dev/) of the site -updated for the `dev` version (on the top left, the version number is in -red, and will be 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](https://evolecolgroup.github.io/pastclim/articles/a1_available_datasets.html). -There are also instructions on how to build and use [custom datasets](https://evolecolgroup.github.io/pastclim/articles/a2_custom_datasets.html). - -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): -``` +On its dedicated [website](https://evolecolgroup.github.io/pastclim/), +you can find Articles giving you a step-by-step [overview of the +package](https://evolecolgroup.github.io/pastclim/articles/a0_pastclim_overview.html), +and a +[cheatsheet](https://evolecolgroup.github.io/pastclim/pastclim_cheatsheet.pdf). +There is also a [dev +version](https://evolecolgroup.github.io/pastclim/dev/) 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](https://evolecolgroup.github.io/pastclim/articles/a1_available_datasets.html). +There are also instructions on how to build and use [custom +datasets](https://evolecolgroup.github.io/pastclim/articles/a2_custom_datasets.html). + +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: -``` + +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") ``` ---- +------------------------------------------------------------------------ ## Current issues -If something does not work, check the [issues on GitHub](https://github.com/EvolEcolGroup/pastclim/issues) 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](https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example) for the developers to investigate the problem. +If something does not work, check the [issues on +GitHub](https://github.com/EvolEcolGroup/pastclim/issues) 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](https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-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: -``` +`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 [stack**overflow**](https://stackoverflow.com/questions/61598340/why-does-rastertopoints-generate-an-error-on-first-call-but-not-second) \ No newline at end of file + +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) From d6b5de3ef29ede0942e20f7c445e3c6c63d822e5 Mon Sep 17 00:00:00 2001 From: Andrea Manica Date: Mon, 1 May 2023 13:34:49 +0100 Subject: [PATCH 2/3] clean readme --- README.md | 6 ------ 1 file changed, 6 deletions(-) diff --git a/README.md b/README.md index 42b6a390..58b3e573 100644 --- a/README.md +++ b/README.md @@ -1,9 +1,3 @@ ---- -editor_options: - markdown: - wrap: 72 ---- - # pastclim From 388457754be20c92f36d86d310a0f71f013268e8 Mon Sep 17 00:00:00 2001 From: Andrea Manica Date: Mon, 1 May 2023 13:36:11 +0100 Subject: [PATCH 3/3] clean readme --- README.md | 6 ------ 1 file changed, 6 deletions(-) diff --git a/README.md b/README.md index 58b3e573..d0e7f867 100644 --- a/README.md +++ b/README.md @@ -10,12 +10,6 @@ dev](https://img.shields.io/github/checks-status/EvolEcolGroup/pastclim/dev?labe -```{=html} - -``` This `R` library is designed to provide an easy way to extract and manipulate palaeoclimate reconstructions for ecological and anthropological analyses.