Project title: Finding Heat tolerant corals for selective breeding
Description of project goals: Characterize reef environments, calculate survival for larvae and juveniles from heat stress experiments, create BRTs to predict environments for high, heritable survival, map them to GBR locations
Notes: All required packages and the versions (especially for BRT section in Script 3) are listed.
#Script 1 "eReefs extract_Githubtidy_Final.Rmd"
Files: #Temperature data-- eReefs2014_2020_AGFReefs.csv #too large for Github, email me or download yourself directly from the "eReefs extractor tool" (https://extraction.ereefs.aims.gov.au/) for these reefs listed in map file available from Script 2 GBRONLYSSTAExport_Output_csv.csv Export_OutputDHW.txt #this is also too large for Github. You can download directly from cortad via ftp (link in script). ARCGIS_KQuigley_Satdata_AGF18sites_CSVlatlong.csv
#Relative Importance-- RelativeImportance_summaryAGF18.csv
#Find the reefs-- #in zipped folder together "DRT and TS files zipped all GBR Github.zip" #Alternatively, they can all be extracted using the "eReefs extractor tool" (https://extraction.ereefs.aims.gov.au/) for all reefs across hourly or daily intervals
2006.8591169-collected.csv 2006.db53de4-collected.csv 2005.5e5e11c-collected.csv 2005.380fbd9-collected.csv
#Script 2 "AGF2018_larval_heatstress_Githubtidy_Final.R"
Files: AGF18.Sites_Github.csv larvaldataAGF2018_Github.csv AGF_yr2_Juvs_cur.singles_aliveatT1.csv #only single juveniles, clumps of juveniles removed larv_juv_comparision_combo.csv
#Sections include: map, larval survival, juvenile survival, juvenile survival by symbiont, Supp figures
#Script 3 "Prediction_AGF18_githubtidy_NatCommschecks_v2_Final.R"
Files: larv6.csv #Download the larval data with satellite data attached appended---- juv6.6_subset.zip #unzip for csv
Supplementary Material
#Best to follow the original script https://github.com/LaserKate/MontiSymTransgen with full annotation but the version used for this analysis can be found in the script above
#Script 4 ITS2_test_analysis_KQ_AGFJuveniles2018_Githubtidy.Rmd
Files: adaptors.fasta arif_ITS2_DB_mod.fasta Juveniles_AGF18_Phyloseq_Metadata.csv ITS2_AGF18_Ariftax_Edit.csv
Source files can be requested as well but are too large for Github to host. However, all raw data is available on Github. save30.11.21.Rdata (zip file) - 691.MB retesting_BRTs_April2021.RData (zip file) - 78.6 MB