Merge pull request #1 from reefgenomics/main

update README

CBASSED50_demo.qmd

@@ -1,13 +1,13 @@
 ---
 title: "CBASSED50 Demo"
-author: "Yulia Iakovleva, Christian Voolstra"
+author: "Yulia Iakovleva, Christian R Voolstra"
 format: html
 editor: visual
 ---
 
 # About CBASSED50
 
-CBASSED50 allows you to process CBASS data. To learn more about CBASSED50 see <https://onlinelibrary.wiley.com/doi/10.1111/gcb.15148>.
+CBASSED50 allows you to process CBASS data. To learn more about CBASSED50 see <https://aslopubs.onlinelibrary.wiley.com/doi/10.1002/lom3.10555>.
 
 # Get Started
 
@@ -37,6 +37,8 @@ library(CBASSED50)
 
 # Define Data Source
 
+Here you can choose to either run a provided "Internal Dataset" or your own "Custom Dataset". To become familar with the input file format and check that everything is running smoothly, we suggest to run the "Internal Dataset" first (see below).
+
 ## Internal Dataset
 
 The first time you may want to run the whole code with the data set that is already provided with the `CBASSED50` package.
@@ -72,7 +74,7 @@ mandatory_columns()
 
 Your data shouldn't contain any missing data, otherwise the row with missing values will be discarded.
 
-### Specify Project Directory and Working Environment
+### Specify Project Directory and Working Environment for Custom Data
 
 If you want to load and analyze your data, run the following chunk of the code.
 

README.md

@@ -1,6 +1,8 @@
 # CBASSED50
 
-The CBASSED50 R package to process CBASS data.
+The CBASSED50 R package to process CBASS-derived PAM data. Minimal requirements are PAM data (or data from any other continous variable that decreases with temperature, e.g. relative bleaching scores) from 4 fragments subjected to 4 temperature profiles of at least 2 colonies from 1 coral species from 1 site. Please refer to the [CBASS method paper](https://aslopubs.onlinelibrary.wiley.com/doi/10.1002/lom3.10555) for in-depth information regarding CBASS acute thermal stress assays, ED50 thermal thresholds, etc. 
+
+Evensen, N. R., Parker, K. E., Oliver, T. A., Palumbi, S. R., Logan, C. A., Ryan, J. S., Klepac, C. N., Perna, G., Warner, M. E., Voolstra, C. R., & Barshis, D. J. (2023). The Coral Bleaching Automated Stress System (CBASS): A low‐cost, portable system for standardized empirical assessments of coral thermal limits. Limnology and Oceanography, Methods / ASLO, 21(7), 421–434. https://doi.org/10.1002/lom3.10555 
 
 # Get Started