Read me 1.
*****************************************************DATA CREATORS*****************************************************

CREATORS:		Matthew Clements
CONTRIBUTORS:	Matthew Clements and Maria Byrne
CONTACT:		Matthew.clements@sydney.edu.au

********************************************************DATA FILES*********************************************************

FILE NAMES:	Clements & Byrne 2026.xlsx & Clements & Byrne 2026.Rmd

****************************************************DATA DEFINITIONS****************************************************

Xlsx Sheet: Breakpoint analyses & SPCs
Contains larval salinity tolerance data used for breakpoint regression analyses.

Variable
Description
Units
Pre-settlement assay salinity exposure duration (days)
Duration larvae were exposed to experimental salinity
days
Salinity_Treatment
Experimental salinity level
PSU
Startin n
Number of larvae at start of assay
count
Normal
Number of larvae with normal morphology
count
Survival
Number of larvae surviving assay
count
Normal (%)
Percentage normal morphology
%
Survival (%)
Percentage survival
%


Sheet: Larval settlement assays (long)
* Low salinity exposure duration (d) = duration of larval low-salinity exposure
* Duration in settlement assay = time spent in settlement assay
* Salinity = larval salinity treatment group
* Metamorphic response = categorical metamorphic outcome
* Value (%) = percentage value for the recorded response

Sheet: Juvenile abundance
* Rep ID = replicate ID
* Pre-settlement assay salinity exposure duration (days) = duration of low-salinity exposure before settlement
* Duration in settlement assay (days) = number of days in settlement assay
* Larval Salinity Group = salinity treatment group
* Handpicked larvae (#normal competent larvae placed in settlement assay) = number of competent larvae used in the assay
* Juveniles = number of juveniles produced

Sheet: Juvenile production & size
* Pre-settlement assay salinity exposure duration (days) = pre-settlement exposure duration
* Elapsed time to become a juvenile (duration in settlement assay (days)) = time taken to reach juvenile stage
* Larval Salinity Group = salinity treatment group
* Rep unique code = replicate code
* Handpicked = number of larvae used
* Days since settlement = juvenile age after settlement
* Area (10^5 um^2) = juvenile area


***************************************************Experimental design***************************************************
Codes
* Salinity treatment values appear as numeric salinities, including 17, 19, 22, 25, 30, and 34
* Exposure durations are coded as 2, 4, 7 or 2d, 4d, 7d
* Juvenile age is coded using text values such as 1 day old and 5 day old
Units
* Salinity: PSU
* Exposure duration: days
* Settlement assay duration: days
* Juvenile area: 10^5 µm^2
* Counts: number of individuals
* Percentages: %



**********************************************TECHNICAL REQUIREMENTS**********************************************

SOFTWARE:	R; RStudio

Technical requirements
Hardware
Not specified in the uploaded files.
Software
The R Markdown file indicates analysis in R using these packages:
* segmented
* broom
* brglm2
* MASS
* visreg
* ResourceSelection
* readxl
* dplyr
* strucchange
* car
* emmeans
* knitr
* ggplot2
* gridExtra
* grid
* cowplot
* lme4
* MuMIn
The analyses were written for rendering as an html_document.
File formats
* .xlsx = raw/structured data workbook
* .Rmd = analysis and reporting script
* rendered output expected as .html

Analytical scope of the R Markdown file
The uploaded R Markdown file contains analyses for:
1. Breakpoint analyses of larval normal morphology and survival under low salinity
2. Larval settlement assays
3. Juvenile success analyses using GLMMs
4. Juvenile production and juvenile size analyses
It uses the Excel workbook as the primary data source and subsets sheets by treatment duration, salinity group, settlement duration, and juvenile age.
If you want, I can next turn this into a polished manuscript-style Data availability and code availability section.

*********************************************************Notes****************************************************************

Re: Read me 1. The dataset and associated R Markdown workflow document experimental analyses of Crown-of-Thorns Starfish (COTS) larval and juvenile responses to low-salinity exposure. Laboratory assays tested the effects of pre-settlement salinity treatments (17Ð34 PSU) applied for 2, 4, or 7 days on larval morphology, survival, settlement success, and juvenile performance. The Excel workbook (Clements & Byrne 2026.xlsx) contains four structured datasets covering breakpoint analyses of larval tolerance, larval settlement outcomes, juvenile abundance, and juvenile production and size, while the accompanying R Markdown file (Clements and Byrne 2026.Rmd) provides the full analytical workflow used to process and analyse these data. Statistical analyses include binomial GLMs, segmented breakpoint regressions, generalized linear mixed models, and post-hoc comparisons, implemented in R using packages such as segmented, brglm2, lme4, emmeans, and ggplot2. Together, the files provide a reproducible framework for quantifying how short-term low-salinity exposure during the larval stage influences subsequent settlement success and juvenile development in COTS.



Read me 2.
*****************************************************DATA CREATORS*****************************************************

CREATORS:		Matthew Clements
CONTRIBUTORS:	Matthew Clements and Maria Byrne
CONTACT:		Matthew.clements@sydney.edu.au

********************************************************DATA FILES*********************************************************

FILE NAMES:	eReefs timeseries data extraction summaries.Rmd

ACRONYMS/CODES:	PSU Ð Practical Salinity Units; eReefs Ð Environmental Reef modelling system; GBR Ð Great Barrier Reef

*****************************************************DATA SOURCES*****************************************************

WHERE: 	eReefs data was collected from their THREDDS server and data extraction tool (https://extraction.ereefs.aims.gov.au/extract-data) 

****************************************************DATA DEFINITIONS****************************************************

VARIABLES:		
Variable
Description
Units
salinity
Surface salinity
PSU
latitude
Grid latitude
degrees
longitude
Grid longitude
degrees
time
Model timestep
Date

**********************************************TECHNICAL REQUIREMENTS**********************************************

SOFTWARE:	R; RStudio; NetCDF tools

*********************************************************Notes****************************************************************

Read me 2 describes the R code for reproducing the eReefs salinity plume analyses associated with major freshwater flood events affecting the Great Barrier Reef reported in Clements & Byrne 2026 Ð Carry-over effects of decreased salinity on. Larval metamorphosis and the early juvenile in context with eReefs hydrodynamic models. The code shown represents an example workflow for analysing the entire suit of the modelled series. The same approach can be applied to all plume dates associated with the 2011, 2019, and 2023 events. The full code and data used in the manuscript is extensive and so full code can be recreated by copy and pasting the example provided or via the above email. 
Document Title (adjust in Document Properties)

Gene Melzack	21 September 2018	Page 2


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