Inferring marine migration from otolith biogeochemical signatures of a wide-ranging fish

Requirements

Otolith data

Assumed path to data:

data/ototlith_sst.csv

OISST data

NOAA High Resolution SST data provided by the NOAA/OAR/ESRL PSL, Boulder, Colorado, USA, from their Web site at https://psl.noaa.gov/data/gridded/data.noaa.oisst.v2.highres.html

Need the files

sst.day.mean.2007.nc
sst.day.mean.2008.nc
sst.day.mean.2009.nc
sst.day.mean.2010.nc
lsmask.oisst.v2.nc

For the model need to combine all sst data into one file with NCO software available here: http://nco.sourceforge.net/#Binaries

Ubuntu / debian use command

ncrcat sst.day.mean.20??.nc sst.day.mean.nc

Also need NetCDF installation for RNetCDF library

Assumed paths to data:

data/sst.day.mean.nc
data/lsmask.oisst.v2.nc

R LIBRARIES

Rcpp
RNetCDF 
progress
tidyverse
lubridate
mapdata
gganimate
patchwork

Usage

Run scripts in order.

• Run 00_simulate_migration.R with both the north and west configuration.
• 01_wrangle_data.R expects simulation files from these simulations to piece together with the observed data.
• 02_hmm.R Runs the HMM on the specified time series
• 03_summarise.R Generate combined files from specified HMM outputs to support visualisation.
• o4_manuscript_plots.R Generate plots associated with the manuscript