Pre publication

.gitignore

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 # Other folders
 /supplement
 /figures
-/results/*
+/results/*
+
+docs_raw/
+others/

README.md

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+
+
+<!-- README.md is generated from README.qmd. Please edit that file -->
+
+# <img src="logo.jpg" align="right" width="240" /> Modeling the Species Distribution of Sea Urchins in the Western Atlantic
+
+## Introduction
+
+This project assessed how climate change will impact the distribution of
+three key species of sea urchins in the Western Atlantic. This was done
+through SDMs produced using LGCP models under a Bayesian framework. For
+more details, reader is referred to the publication “A thorny future for
+sea urchins in the Tropical Western Atlantic” (under review). All codes
+and data used in the study are available in this folder, except original
+climatic layers, which are available online.
+
+## Interactive results
+
+An interactive version of the results of this work is availabe at
+[silasprincipe.github.io/herbinv](http://silasprincipe.github.io/herbinv)
+
+## Files included
+
+**data**: all data used in the study  
+– **env**: environmental data  
+– **lyva**: *Lytechinus variegatus* data  
+– **eclu**: *Echinometra lucunter* data  
+– **trve**: *Tripneustes ventricosus* data  
+– **sst_limits**: SST data for the thermal limits part **codes**: all
+codes used in the study  
+**functions**: all functions that were used either directly or as
+support in the study **gis**: shapefiles
+
+### Codes
+
+- data\_\*: data download and preparing  
+- prep\_\*: prepare data (environmental variables)  
+- lgcp_prepare_data: prepare all data necessary for fitting the LGCP
+  model through INLA  
+- lgcp_model\_\*: models for each species
+- plot\_\*: produce figures
+- sst\_\*: codes used for producing the mechanistic model or for
+  estimating thermal limits  
+- supp\_\*: supplementary analysis
+
+## Related repositories
+
+- Species Distribution Modeling of reef building coral species of the
+  Western Atlantic:
+  [silasprincipe/reefbuilders](https://github.com/silasprincipe/reefbuilders)
+
+------------------------------------------------------------------------
+
+Please, contact us if you have any questions on how to use the codes.

README.qmd

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+---
+format: gfm
+---
+
+<!-- README.md is generated from README.qmd. Please edit that file -->
+
+```{r, echo = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>",
+  fig.path = "figures/"
+)
+```
+
+# <img src="logo.jpg" align="right" width="240" /> Modeling the Species Distribution of Sea Urchins in the Western Atlantic  
+
+
+## Introduction
+
+This project assessed how climate change will impact the distribution of three key species of sea urchins in the Western Atlantic. This was done through SDMs produced using LGCP models under a Bayesian framework. For more details, reader is referred to the publication "A thorny future for sea urchins in the Tropical Western Atlantic" (under review). All codes and data used in the study are available in this folder, except original climatic layers, which are available online. 
+
+## Interactive results
+
+An interactive version of the results of this work is availabe at [silasprincipe.github.io/herbinv](http://silasprincipe.github.io/herbinv)  
+
+## Files included
+
+**data**: all data used in the study  
+-- **env**: environmental data  
+-- **lyva**: _Lytechinus variegatus_ data  
+-- **eclu**: _Echinometra lucunter_ data  
+-- **trve**: _Tripneustes ventricosus_ data  
+-- **sst_limits**: SST data for the thermal limits part 
+**codes**: all codes used in the study  
+**functions**: all functions that were used either directly or as support in the study
+**gis**: shapefiles
+
+### Codes
+
+- data_*: data download and preparing  
+- prep_*: prepare data (environmental variables)  
+- lgcp_prepare_data: prepare all data necessary for fitting the LGCP model through INLA   
+- lgcp_model_*: models for each species
+- plot_*: produce figures
+- sst_*: codes used for producing the mechanistic model or for estimating thermal limits  
+- supp_*: supplementary analysis
+
+## Related repositories
+
+- Species Distribution Modeling of reef building coral species of the Western Atlantic: [silasprincipe/reefbuilders](https://github.com/silasprincipe/reefbuilders)
+
+---
+
+Please, contact us if you have any questions on how to use the codes.