Dataset from: High consistency and repeatability in the breeding migrations of a benthic shark

Dataset and scripts used for manuscript: High consistency and repeatability in the breeding migrations of a benthic shark. 

Project title: High consistency and repeatability in the breeding migrations of a benthic sharkDate:23/04/2024

Folders:- 1_Raw_data    - Perpendicular_Point_068151, Sanctuary_Point_068088, SST raw data, sst_nc_files, IMOS_animal_measurements, IMOS_detections, PS&Syd&JB tags, rainfall_raw, sample_size, Point_Perpendicular_2013_2019, Sanctuary_Point_2013_2019, EAC_transport- 2_Processed_data    - SST (anomaly, historic_sst, mean_sst_31_years, week_1992_sst:week_2022_sst including week_2019_complete_sst)    - Rain (weekly_rain, weekly_rainfall_completed)    - Clean (clean, cleaned_data, cleaned_gam, cleaned_pj_data)- 3_Script_processing_data     - Plots(dual_axis_plot (Fig. 1 & Fig. 4).R, period_plot (Fig. 2).R, sd_plot (Fig. 5).R, sex_plot (Fig. 3).R     - cleaned_data.R, cleaned_data_gam.R, weekly_rainfall_completed.R, descriptive_stats.R, sst.R, sst_2019b.R, sst_anomaly.R- 4_Script_analyses    - gam.R, gam_eac.R, glm.R, lme.R, Repeatability.R- 5_Output_doc    - Plots (arrival_dual_plot_with_anomaly (Fig. 1).png, period_plot (Fig.2).png, sex_arrival_departure (Fig. 3).png, departure_dual_plot_with_anomaly (Fig. 4).png, standard deviation plot (Fig. 5).png)    - Tables (gam_arrival_eac_selection_table.csv (Table S2), gam_departure_eac_selection_table (Table S5), gam_arrival_selection_table (Table. S3), gam_departure_selection_table (Table. S6), glm_arrival_selection_table, glm_departure_selection_table, lme_arrival_anova_table, lme_arrival_selection_table (Table S4), lme_departure_anova_table, lme_departure_selection_table (Table. S8))

  Descriptions of scripts and files used:- cleaned_data.R: script to extract detections of sharks at Jervis Bay. Calculate arrival and departure dates over the seven breeding seasons. Add sex and length for each individual. Extract moon phase (numerical value) and period of the day from arrival and departure times.  - IMOS_detections.csv: raw data file with detections of Port Jackson sharks over different sites in Australia.  - IMOS_animal_measurements.csv: raw data file with morphological data of Port Jackson sharks  - PS&Syd&JB tags: file with measurements and sex identification of sharks (different from IMOS, it was used to complete missing sex and length).  - cleaned_data.csv: file with arrival and departure dates of the final sample size of sharks (N=49) with missing sex and length for some individuals.  - clean.csv: completed file using PS&Syd&JB tags, note: tag ID 117393679 was wrongly identified as a male in IMOS and correctly identified as a female in PS&Syd&JB tags     file as indicated by its large size.  - cleaned_pj_data: Final data file with arrival and departure dates, sex, length, moon phase (numerical) and period of the day.

- weekly_rainfall_completed.R: script to calculate average weekly rainfall and correlation between the two weather stations used (Point perpendicular and Sanctuary point).  - weekly_rain.csv: file with the corresponding week number (1-28) for each date (01-06-2013 to 13-12-2019)  - weekly_rainfall_completed.csv: file with week number (1-28), year (2013-2019) and weekly rainfall average completed with Sanctuary Point for week 2 of 2017  - Point_Perpendicular_2013_2019: Rainfall (mm) from 01-01-2013 to 31-12-2020 at the Point Perpendicular weather station  - Sanctuary_Point_2013_2019:  Rainfall (mm) from 01-01-2013 to 31-12-2020 at the Sanctuary Point weather station  - IDCJAC0009_068088_2017_Data.csv: Rainfall (mm) from 01-01-2017 to 31-12-2017 at the Sanctuary Point weather station (to fill in missing value for average rainfall of week 2 of 2017)

- cleaned_data_gam.R: script to calculate weekly counts of sharks to run gam models and add weekly averages of rainfall and sst anomaly  - cleaned_pj_data.csv  - anomaly.csv: weekly (1-28) average sst anomalies for Jervis Bay (2013-2019)  - weekly_rainfall_completed.csv: weekly (1-28) average rainfall for Jervis Bay (2013-2019_  - sample_size.csv: file with the number of sharks tagged (13-49) for each year (2013-2019)

- sst.R: script to extract daily and weekly sst from IMOS nc files from 01-05 until 31-12 for the following years: 1992:2022 for Jervis Bay  - sst_raw_data: folder with all the raw weekly (1:28) csv files for each year (1992:2022) to fill in with sst data using the sst script  - sst_nc_files: folder with all the nc files downloaded from IMOS from the last 31 years (1992-2022) at the sensor (IMOS - SRS - SST - L3S-Single Sensor - 1 day - night time – Australia).  - SST: folder with the average weekly (1-28) sst data extracted from the nc files using the sst script for each of the 31 years (to calculate temperature anomaly).

- sst_2019b.R: script to extract daily and weekly sst from IMOS nc file for 2019 (missing value for week 19) for Jervis Bay  - week_2019_sst: weekly average sst 2019 with a missing value for week 19  - week_2019b_sst: sst data from 2019 with another sensor (IMOS – SRS – MODIS - 01 day - Ocean Colour-SST) to fill in the gap of week 19  - week_2019_complete_sst: completed average weekly sst data from the year 2019 for weeks 1-28.

- sst_anomaly.R: script to calculate mean weekly sst anomaly for the study period (2013-2019) using mean historic weekly sst (1992-2022)   - historic_sst.csv: mean weekly (1-28) and yearly (1992-2022) sst for Jervis Bay  - mean_sst_31_years.csv: mean weekly (1-28) sst across all years (1992-2022) for Jervis Bay  - anomaly.csv: mean weekly and yearly sst anomalies for the study period (2013-2019)

- Descriptive_stats.R: script to calculate minimum and maximum length of sharks, mean Julian arrival and departure dates per individual per year, mean Julian arrival and departure dates per year for all sharks (Table. S10), summary of standard deviation of julian arrival dates (Table. S9)   - cleaned_pj_data.csv

- gam.R: script used to run the Generalized additive model for rainfall and sea surface temperature  - cleaned_gam.csv

- glm.R: script used to run the Generalized linear mixed models for the period of the day and moon phase  - cleaned_pj_data.csv  - sample_size.csv

- lme.R: script used to run the Linear mixed model for sex and size  - cleaned_pj_data.csv

- Repeatability.R: script used to run the Repeatability for Julian arrival and Julian departure dates   - cleaned_pj_data.csv