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Module 1 Script

Module 1 introduces the Commonwealth Blue Charter and its Action Groups focused on sustainable ocean development, emphasizing the importance of ocean data and observation technologies. It outlines various ocean sampling technologies and their applications in addressing ocean-related research questions. The module also highlights the use of R software for data analysis, its benefits, and the setup process for the workshop.

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jude
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4 views

Module 1 Script

Module 1 introduces the Commonwealth Blue Charter and its Action Groups focused on sustainable ocean development, emphasizing the importance of ocean data and observation technologies. It outlines various ocean sampling technologies and their applications in addressing ocean-related research questions. The module also highlights the use of R software for data analysis, its benefits, and the setup process for the workshop.

Uploaded by

jude
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
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Module 1 Script

Module 1: Introduction to Using R


Module 1 Overview
Slide 1: Title Slide
In this section, you will learn about:

§ The Commonwealth and its Action Groups;


§ Different types of oceanographic instruments;
§ The importance of turning ocean measurements into ocean information; and, lastly
§ R, and why we choose to use R.

M1 Lesson 1: The Commonwealth Blue Charter


Slide 1: Title Slide
Slide 2: Commonwealth Blue Charter
The Commonwealth Blue Charter is an agreement by all Commonwealth countries to actively
cooperate in addressing ocean-related issues and meet commitments for sustainable ocean
development.

Implementation of the Commonwealth Blue Charter is through ‘Action Groups’. These are member-
driven, and led by ‘Champion’ countries. Action Groups unlock the power of 56 nations and guide the
development of tools and training.

There are 10 action groups, each dedicated to addressing specific ocean issues.

Slide 3: Ocean Observation Action Group


Canada is proud to be Champion of the Commonwealth Blue Charter on Ocean Observation. The
Action Group is working to advance :

§ Opportunities to increase the innovation, development and deployment of ocean


observational technologies, including in Small Island Developing States;
§ The accessibility to, and sharing of, ocean observational data, knowledge and best practices;
§ The breaking down barriers to better integrate ocean observational data, information and
knowledge into decisions, products, and services; and
§ Inclusivity within the context of ocean science.

Slide 4: End of Lesson


Module 1 Script

M1 Lesson 2: Ocean Data


Slide 1: Title Slide
Slide 2: Ocean Sampling Technologies
Many technologies exist to generate ocean data that can be used to expand our knowledge of the state
of the ocean. This figure shows a number of ocean sampling technologies that can be used to answer a
number of research questions.

Slide 3: Question
Small drones can be used to answer: ‘Is the abundance of keystone species changing?’

Slide 4: Question
Buoys and other moorings can be used to answer: ‘Is the sea elevation changing?’ and ‘What was
the path of a certain storm?’
Slide 5: Question
Aerial surveys can be used to answer: ‘Are species migrating as a result of global warming?’ and ‘Is the
land changing over time?’

Slide 6: Question
Satellites can be used to answer: ‘Is sea surface temperature changing?’, ‘Is the surface oxygen content
changing?’, and ‘Are there changes in sea ice?’

Slide 7: Question
Observers can be used to answer: ‘Have whale sightings changes in the last year?’ and ‘Has there been
a change in sea birds?’

Slide 8: Question
SCUBA divers can be used to answer: ‘What is the animal behaviour in a certain area?’ and ‘What is the
abundance of delicate organisms?’

Slide 9: Question
Sonar can be used to answer: ‘Where are zooplankton located in your research study?’ and ‘What are
the internal waves like in your research area?’

Slide 10: Question


Trawl nets can be used to answer: ‘What are the species abundance in a given area?’

Slide 11: Question


Satellite tagging can be used to answer: ‘Are species migrating as a result of global warming?
Module 1 Script

Slide 12: Question


Plankton net tows can be used to answer: ‘What is the abundance of zooplankton and phytoplankton?’
and ‘Do we see aggregation on right whales in a certain area?’

Slide 13: Question


Rosettes or CTDs can be used to answer: ‘Is the ocean warming near you?’, ‘Is the ocean becoming
more acidic?’, ‘Are the oceans becoming more anoxic?’, ‘What are the currents like in a specific area?’,
‘What is the structure of the water column, such as stratification?’, and ‘What is the phytoplankton
abundance?’

Slide 14: Understanding Challenges Facing our Oceans


By answering those scientific questions, we can better understand challenges posed to our oceans and
inform management decisions and policy related to:

§ Ocean warming and marine heatwaves


§ Ocean acidification
§ Ocean hypoxia
§ Algal blooms
§ Ocean events (storm surges, tsunamis)
§ Coastal erosion
§ Changes in biodiversity
§ Boating and swimming safety information
§ Fisheries management
§ Biodiversity conservation
§ Sea level rise
§ Tourism
§ Coastal planning

Slide 15: Data Sources


Because of the changes and challenges that are posed to the ocean, there are a number of
organisations that have made their data public, and the idea is that scientists, or those who are
interested, can use these open-source data to infer and understand some of these challenges. So
there are freely available data through some global initiatives such as: Argo, Biogeochemical (BGC)
Argo, Bermuda Atlantic Time Series (BATS), as well as Ocean Observing Systems and local universities
and government science programmes.

Slide 16: The Process of Generating Information


The idea is that you could follow these steps by answering a research question to make a plan, you then
gather information, analyse data, share your results, inform and advise, and then hopefully answer a
research question,

Slide 17: Turning Ocean Data into Ocean Information


We have identified two barriers that exist when turning ocean data into ocean information. These two
barriers include:
Module 1 Script

1/ The ability to analyse a variety of different data; and

2/ Access to long term large spatial coverage data.

Both barriers will be answered using the platform called R.

Slide 18: End of Lesson

M1 Lesson 3: The R Software


Slide 1: Title Slide
Slide 2: What is R?
So what is R? R is a statistical computing and graphics software and it can run on a wide variety of UNIX
platforms, Windows, and MacOS.

Slide 3: Why R?
The reason we are using R compared to the other coding languages, is, first of all, it is free. Second of
all, it is interactive. It also has easy linkage with other languages for speed, meaning if you are used to
Python, excel, etc., you can easily transfer that over into the R language. It also has a suite of statistical
functions which we will be learning and using later today, such as linear regression, and it also has
extensive testing for the Comprehensive R Archive Network (otherwise known as CRAN). So CRAN is a
place that when a coding package is created, CRAN is a place where that package becomes published
to. The benefit to CRAN is that in order for a package to get on to CRAN, they must first go through a
suite of testing in order to get on to it. So what this means is that if a user is using a package that is on
CRAN, you can assume that it is a reliable package. Now that doesn't mean that you're not going to
identify bugs in a certain package, but it means for the most part the functionality of the package will be
appropriate. And then lastly we are using R because it contains informative help pages, which we’ll make
use of throughout this workshop.

Slide 4: Setup Demonstration


Before starting this workshop, you should have received a document that has all of the required steps
for this workshop. That will look something like this, where you see that in order to complete this
workshop, there are a number of previous steps that you should do. The first step is to download R with
the link provided. Secondly, download RStudio with the link provided. You are then required to run the
following code in RStudio to install the required packages. In order to do this, you can simply copy and
paste this code from the document and then paste it into your RStudio. Next, you are also provided with
a link to a folder named workshop_material. When you click on this, you'll see that you’re provided with
all of the required files for this workshop. To download this onto you own device, you simply click the
little arrow here and then click download. Step five says to move this folder out of your downloads to the
desired location on your device. To do this, go over to downloads until you see a file named
workshop_material. You should then move this to wherever you want it to be stored on your device.
Step six is to set your working directory in RStudio to be wherever you store the workshop_material
folder. In order to do that, go to your RStudio -you can see I am in the directory where I stored this file –
Module 1 Script

and click inside of that workshop_material, and then click this little gear, and click “set as working
directory”. Any steps that I just mentioned there for setting the directory are exemplified with
screenshots that show the exact same thing. For the second part of the setup, all you have to do is to
copy and paste this code and directly put it into RStudio. This code is for the second part of this
workshop, when we are dealing with Argo floats data, and when we get to that part of the workshop we’ll
explain what it is happening in each line of this code.

Slide 5: End of Lesson

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