Dispersal in the global coastal ocean
Would you, without running your own regional numerical ocean
circulation model or downloading terrabytes of numerical ocean
circulation model output, like to:
- See where all particles that left a place in the global coastal
ocean (say Portsmouth NH) and drift at the surface (or some other depth)
for 30 days go?
- Do you want to know where all particles that left from within some
distance of the coast and ended up at Portsmouth NH started?
- Do you want to know if larvae were released at Portsmouth NH, and
allowed to settle in coastal habitat for 5 generations, where would they
end up? Where would their density be greatest?
- IMPORTANT: At least at first, a limited number of
release depths, and vertical behaviors will be included. Currently,
initial depths of 1, 10, 20 and 40 meters and advection by only
horizontal or by horizontal and vertical currents is available for North
and South America. Globally, all these depths and vertical behaviors
will be added during 2023. The current status of available starting
depths and behaviors can be found at https://github.com/JamiePringle/EZfate.
All this can be done in R with pre-computed particle tracks
calculated from currents from the Mercator 1/12th of degree global ocean
model described in in
this data sheet. The particle tracking was made with oceanParcels, a
python package described in at oceanparcels.org. For details of
dates included, depths released and depth behaviors simulated, see the
current github repository at https://github.com/JamiePringle/EZfate.
NOTE WELL: if you have trouble downloading data, update to the latest
version of this code from GitHub. If I ever have to change where or how
I store the data, the updated code will be modified to access the
data.
To quickly see what you need to do generate these figures, and to
adapt this resource to your needs, the following R notebooks are
provided. If you want to get a quick glimpse of the capabilities of this
code, you can skip ahead to notebook 04 and the following notebooks. But
if you want to use this code, please go through them carefully and in
order through at least notebook 4.
- 02_whatYouNeedToHave:
Describes what needs to be configured in R before using this code.
- 03_getData_Subset_and_Combine:
How to retrive the dispersal data you need, and subsetted by space,
relese time, and time drifting with the currents as appropiate to your
project.
- 04_dataStructure_and_basicPlotting:
A description of how the connectivity data is stored in R, and how to
make simple plots of the dispersal data. At the end of this, you will be
able to plot where particles released at a single point go, and where
all the particles from an arbitrary region go.
- 05_connectivityModeling:
The particle fate data obtained above can be used to model the dispersal
of particles over multiple releases in a defined habitat. This can be
used to model connectivity of marine populations. How to define a
habitat and model dispersal is described here for a simple 1 species
model with no density dependence.
- 06_backwardsInTimeModeling:
Often it will be important to understand where particles which have
arrived at a specific place came from. This describes how to start doing
this.
To download the code to run it locally, go to the gitHub directiory and
look at the right-hand side toolbar for the “Releases” tab and click on
the green “latest” button, or go to this
page.
There are some other R notebooks you might find helpful.
In the next section, you will learn what R packages must be
installed to use EZfate.