Growth dynamics of bottlenose dolphins (Tursiops truncatus) at the southern extreme of their range

Version release associated with GitHub repository: https://github.com/leahcrowe-otago/FBD_measurements/tree/main

Workflow:

Identify when in video dolphin surfaces, ID that dolphin

Screen grab the best image of the dolphin above that shows rostrum to tail at/near the surface

used VLC player to go frame by frame

Add screen grab filename to the time and ID from #1

Run "./scripts/Altitudes for snapshots" for each day of droning

this adds a check to make sure GPS of the LiDAR and the metadata from the drone match up

finds altitude for each snapshot

matches up to IDs and outputs file to enter measurements

identifies if altimeter reading meets criteria per Dickson et al. 2020 ("issues" column)

Populate the "altperimage_*" file with measurements (.csvs from Whalelength are later merged in "./scripts/whalength_file_merge.R")

filter by issue == "N"

hide columns C, G, H, and J to AC

Run each resulting image through Whalength

I1P Video stills, -1.5 cm offset

Run "measurements_demo.Rmd" to wrangle data, incorporate life history info ("demo"graphy data), and create some supplementary figures

calls "whalength_file_merge.R"

merges all Whalelength outputs

creates Fig. S4, calibration measurements

Supplementary Figures S5

data output: see data repo for metadata details

individual i measurement data at each capture occasion j for model

individual life history data

Model run in the "./scripts/stan/runstan_allo_mv_t0.R" file: 'run' the 'stan' code of 'allo'metric measurement data in a 'm'ulti'v'ariate model with fixed age at length zero (t0)

data formatting for model

calls the Stan model

main model: "./scripts/stan/vb_mod_all0_t0.stan"

for the supplementary sex/pod effect model: "./scripts/stan/sex_pod_effects.R" runs the model specified in "./scripts/stan/vb_mod_all0_t0_sexpod.stan"

initial values for von Bertalanffy model (init_vb)

fit the model (fit_vb)

save results

"./scripts/Results.R"

read data

summarise results

create table S2

create Figs. 2–4, S6, S7

"Supplementary.qmd" creates the suppmat file

creates supplementary tables

Section 1.3 created from './scripts/Results_age_adjusted.R'

Fig. S1 map created by calling "./scripts/ms_map.R"

Data: "./data/Measurements/Data for review"

Metadata-description.pdf: describes the data in the following files:

ij_1.csv

ij_2.csv

ij_3.csv

ij_ID.csv