update readme with publication

README.Rmd

@@ -16,12 +16,18 @@ knitr::opts_chunk$set(
 
 <!-- badges: start -->
 
-[![Run Tests](https://github.com/BrunaLab/HeliconiaDemography/actions/workflows/run-testthat.yaml/badge.svg)](https://github.com/BrunaLab/HeliconiaDemography/actions/workflows/run-testthat.yaml) [![DOI](https://zenodo.org/badge/289078614.svg)](https://zenodo.org/badge/latestdoi/289078614)
+[![Run Tests](https://github.com/BrunaLab/HeliconiaDemography/actions/workflows/run-testthat.yaml/badge.svg)](https://github.com/BrunaLab/HeliconiaDemography/actions/workflows/run-testthat.yaml) [![Zenodo DOI](https://zenodo.org/badge/289078614.svg)](https://zenodo.org/badge/latestdoi/289078614) [![Paper DOI](https://img.shields.io/badge/DOI-10.1111%2Fgcb.15900-blue)](https://doi.org/10.1111/gcb.15900)
 
 
 <!-- badges: end -->
 
-This repository contains the data and code for a manuscript written for submission to Global Change Biology tentatively titled: "Delayed effects of climate on vital rates leads to demographic divergence in Amazonian forest fragments"
+This repository contains the data and code for:
+
+Scott ER, Uriarte M, Bruna EM (2021) Delayed effects of climate on vital rates lead to demographic divergence in Amazonian forest fragments. Global Change Biology. https://doi.org/10.1111/gcb.15900
+
+## How to cite
+
+If you use the data or code in this repository, please cite the [Zenodo archive](https://zenodo.org/badge/latestdoi/289078614) as well as the Global Change Biology [paper](https://doi.org/10.1111/gcb.15900).
 
 ## How to run
 
@@ -37,18 +43,8 @@ To run the compendium and reproduce all outputs:
 -   Install the [`targets` package](https://docs.ropensci.org/targets/).
 -   Run `targets::tar_make()` or `targets::tar_make_clustermq()` from the R console to run all code and produce all outputs.
 
-**Using HPC**:
-You may need to install packages on the remote HPC if using `tar_make_clustermq()` with the SSH option.  Unfortunately, I'm not sure if there is an easy way to do this using `renv`. You should, however, make sure the same versions of the packages are installed locally and on the HPC, especially `gratia` which I'm using a development version of that has important bugs fixed, but not new bugs introduced.
 
 ## Additional Dependencies
 
 -   Numbering of and in-text references to equations in `paper.Rmd` is handled by [`pandoc-crossref`](https://github.com/lierdakil/pandoc-crossref), which may not be part of the standard RStudio pandoc installation. You might need to install it for the main text to knit correctly to Word.
 
-<!--
-### Licenses
--->
-<!-- **Text and figures :** [CC-BY-4.0](http://creativecommons.org/licenses/by/4.0/) -->
-
-<!-- <!-- **Code :** See the [DESCRIPTION](DESCRIPTION) file -->
-
-<!-- **Data :** [CC-0](http://creativecommons.org/publicdomain/zero/1.0/) attribution requested in reuse -->

README.md

@@ -7,14 +7,24 @@
 
 [![Run
 Tests](https://github.com/BrunaLab/HeliconiaDemography/actions/workflows/run-testthat.yaml/badge.svg)](https://github.com/BrunaLab/HeliconiaDemography/actions/workflows/run-testthat.yaml)
-[![DOI](https://zenodo.org/badge/289078614.svg)](https://zenodo.org/badge/latestdoi/289078614)
+[![Zenodo
+DOI](https://zenodo.org/badge/289078614.svg)](https://zenodo.org/badge/latestdoi/289078614)
+[![Paper
+DOI](https://img.shields.io/badge/DOI-10.1111%2Fgcb.15900-blue)](https://doi.org/10.1111/gcb.15900)
 
 <!-- badges: end -->
 
-This repository contains the data and code for a manuscript written for
-submission to Global Change Biology tentatively titled: “Delayed effects
-of climate on vital rates leads to demographic divergence in Amazonian
-forest fragments”
+This repository contains the data and code for:
+
+Scott ER, Uriarte M, Bruna EM (2021) Delayed effects of climate on vital
+rates lead to demographic divergence in Amazonian forest fragments.
+Global Change Biology. <https://doi.org/10.1111/gcb.15900>
+
+## How to cite
+
+If you use the data or code in this repository, please cite the [Zenodo
+archive](https://zenodo.org/badge/latestdoi/289078614) as well as the
+Global Change Biology [paper](https://doi.org/10.1111/gcb.15900).
 
 ## How to run
 
@@ -39,14 +49,6 @@ To run the compendium and reproduce all outputs:
 -   Run `targets::tar_make()` or `targets::tar_make_clustermq()` from
     the R console to run all code and produce all outputs.
 
-**Using HPC**: You may need to install packages on the remote HPC if
-using `tar_make_clustermq()` with the SSH option. Unfortunately, I’m not
-sure if there is an easy way to do this using `renv`. You should,
-however, make sure the same versions of the packages are installed
-locally and on the HPC, especially `gratia` which I’m using a
-development version of that has important bugs fixed, but not new bugs
-introduced.
-
 ## Additional Dependencies
 
 -   Numbering of and in-text references to equations in `paper.Rmd` is
@@ -55,10 +57,3 @@ introduced.
     which may not be part of the standard RStudio pandoc installation.
     You might need to install it for the main text to knit correctly to
     Word.
-
-<!--
-### Licenses
--->
-<!-- **Text and figures :** [CC-BY-4.0](http://creativecommons.org/licenses/by/4.0/) -->
-<!-- <!-- **Code :** See the [DESCRIPTION](DESCRIPTION) file -->
-<!-- **Data :** [CC-0](http://creativecommons.org/publicdomain/zero/1.0/) attribution requested in reuse -->