Merge pull request #2 from ocean-tracking-network/cb-ghpages-setup

initial setup from checklist - ghpages
ocean-tracking-network · Jan 24, 2024 · 5364636 · 5364636
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diff --git a/README.md b/README.md
@@ -1,45 +1,3 @@
-# OTN's Workshop Curriculum Base
-Telemetry workshop materials created by OTN, to be curated and taught to future groups.
-
-## Cloning/Remixing OTN Workshop Base
-
-First, you will need to create a copy of the repository. We do this by forking the repository. 
-
-**How to fork a repo:**
-
-1. Go to the otn-workshop-base repository homepage
-
-2. In the top right-hand of the page (just under the profile picture), click the 'Fork' button (between "Unwatch" and "Star").
-
-3. Make sure the 'Owner' is set to 'ocean-tracking-network.'
-
-4. Give the repo a meaningful name. Typical format is yyyy-organization-subject-workshop, where yyyy is the year the workshop is taking place, organization is the audience to whom we're giving it, and subject is the course material we're teaching.
-
-5. Provide a useful description.
-
-6. Click Create Fork.
-
-Once the fork is created, you will need to follow a few short steps to get the site up and running.
-
-**How to stand up the website:**
-
-1. In your new fork's repo site, go to the "Settings" tab (it's just under the 'Unwatch' button next to the 'Fork' button).
-
-2. In the left sidebar of that page, click the 'Pages' tab.
-
-3. Under the 'Source' section, set the source branch to gh-pages (the folder will default to /(root), this is fine). Click 'Save'. This step will happen automatically when you push a commit to gh-pages, but it's fine to do it manually too.
-
-4. The site will now be published at the link on this page (in the highlighted box at the top of the settings). Note that it may take a while for the site to be visible, depending on your caching settings. Give it about 15 minutes.
-
-If something goes wrong with the site build, you’ll receive an e-mail at the address associated with the GitHub account that owns the new repository. In this case, contact a developer to see that the error gets fixed. 
-
-From here there are two branches with which you need to be concerned if you are building a workshop: `master` and `gh-pages`. ‘Master’ contains all of the R code for the lessons. If you want to make changes to the code, work with master as your base. Gh-pages is the branch that controls the display of the workshop website. If you want to change lesson content, work with gh-pages as your base. 
-
-Note that while master contains the code itself, lessons in gh-pages contain references to, and snippets of, the code. Gh-pages will NOT be updated if you update the code in master- it is your responsibility to make sure that any changes you make to the code in master are reflected in gh-pages’ lesson text. 
-
-You are also free to add or delete lessons from your branch as befits the workshop you are giving; however, note that if you do this, you WILL need to renumber the remaining lessons so that their titles feature sequential numbers. If you do not do this, the links between lessons will be broken. 
-
-Lessons are written in Markdown so be sure that your formatting is correct. Additional Markdown guidance can be found [here](https://www.markdownguide.org/cheat-sheet/). 
-
-You can find these instructions and more at the [OTW Wiki page](https://github.com/ocean-tracking-network/otn-workshop-base/wiki).
+# 2024 Dalhousie Biologging course Intro to R
+Telemetry workshop materials created by OTN, to be curated and taught to Dal's undergraduate biologging course in winter 2024.
 
diff --git a/Resources/800px-LA2-Europe-UTM-zones.png b/Resources/800px-LA2-Europe-UTM-zones.png
diff --git a/Resources/Bangley ACT BRT Analysis.pdf b/Resources/Bangley ACT BRT Analysis.pdf
diff --git a/Resources/Bangley ACT BRT Analysis.pptx b/Resources/Bangley ACT BRT Analysis.pptx
diff --git a/Resources/Bangley OTN Workshop.pptx b/Resources/Bangley OTN Workshop.pptx
diff --git a/Resources/ErieBubblePlot.png b/Resources/ErieBubblePlot.png
diff --git a/Resources/GAMs.pptx b/Resources/GAMs.pptx
diff --git a/Resources/YAPS.pptx b/Resources/YAPS.pptx
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diff --git a/Resources/actel_introduction.ppsx b/Resources/actel_introduction.ppsx
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diff --git a/Resources/actel_paper_published_version.pdf b/Resources/actel_paper_published_version.pdf
diff --git a/Resources/actel_spatial_challenge.png b/Resources/actel_spatial_challenge.png
diff --git a/Resources/actel_spatial_txt.png b/Resources/actel_spatial_txt.png
diff --git a/Resources/actel_study_sections.png b/Resources/actel_study_sections.png
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diff --git a/Resources/install_instructions.docx b/Resources/install_instructions.docx
diff --git a/Resources/maslow's.png b/Resources/maslow's.png
diff --git a/Resources/whoriskey_telemstats101.pptx b/Resources/whoriskey_telemstats101.pptx
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diff --git a/_config.yml b/_config.yml
@@ -10,7 +10,7 @@
 carpentry: "swc"
 
 # Overall title for pages.
-title: "OTN's Telemetry Workshop Curriculum Base"
+title: "BIOL/MARI 4323 - Introduction to R"
 
 # Life cycle stage of the lesson
 # possible values: "pre-alpha", "alpha", "beta", "stable"

diff --git a/_episodes/00-otn-update.md b/_episodes/00-otn-update.md
@@ -18,7 +18,7 @@ Please contact **[email protected]** if you are interested in connecting with your re
 
 ##  Intended Audience
 
-This set of workshop material is directed at researchers who are ready to begin the work of acoustic telemetry data analysis. The first few lessons will begin with introductory R - no previous coding experince required. The workshop material progresses into more advanced techniques as we move along, beginning around lesson 8 "Introduction to Glatos". 
+This set of workshop material is directed at researchers who are ready to begin the work of acoustic telemetry data analysis. The first few lessons will begin with introductory R - no previous coding experince required.
 
 If you'd like to refresh your R coding skills outside of this workshop curriculum, we recommend [Data Analysis and Visualization in R for Ecologists](https://datacarpentry.org/R-ecology-lesson/ "Website for R ecology lesson") as a good starting point. Much of this content is included in the first two lessons of this workshop.
 
@@ -32,41 +32,3 @@ OTN-affiliated telemetry networks all provide researchers with pre-formatted dat
 
 Before diving in to a lot of analysis, it is important to take the time to clean and sort your dataset, taking the pre-formatted files and combining them in different ways, allowing you to analyse the data with different questions in mind.
 
-There are multiple R packages necessary for efficient and thorough telemetry data analysis.  General packages that allow for data cleaning and arrangement, dataset manipulation and visualization, pairing with oceanographic data and temporo-spatial locating are used in conjuction with the telemetry analysis tool packages `remora`, `actel` and `glatos`. 
-
-There are many more useful packages covered in this workshop, but here are some highlights:
-
-
-####  Intro to the `glatos` Package
-
-`glatos` is an R package with functions useful to members of the Great Lakes Acoustic Telemetry Observation System (http://glatos.glos.us). Developed by Chris Holbrook of GLATOS, OTN helps to maintain and keep relevant. Functions may be generally useful for processing, analyzing, simulating, and visualizing acoustic telemetry data, but are not strictly limited to acoustic telemetry applications.  Tools included in this package facilitate false filtering of detections due to time between pings and disstance between pings.  There are tools to summarise and plot, including mapping of animal movement. Learn more [here](https://github.com/ocean-tracking-network/glatos/).
-
-Maintainer: Dr. Chris Holbrook, ( [email protected] )
-
-
-####  Intro to the `actel` Package
-
-This package is designed for studies where animals tagged with acoustic tags are expected to move through receiver arrays. `actel` combines the advantages of automatic sorting and checking of animal movements with the possibility for user intervention on tags that deviate from expected behaviour. The three analysis functions: explore, migration and residency, allow the users to analyse their data in a systematic way, making it easy to compare results from different studies.
-
-Author: Dr. Hugo Flavio, ( [email protected] )
-
-
-####  Intro to the `remora` Package
-
-This package is designed for the Rapid Extraction of Marine Observations for Roving Animals (`remora`). This is [an R package](https://github.com/IMOS-AnimalTracking/remora) that enables the integration of animal acoustic telemetry data with oceanographic observations collected by ocean observing programs. It includes functions for:
-
-- Interactively exploring animal movements in space and time from acoustic telemetry data
-- Performing robust quality-control of acoustic telemetry data as described in Hoenner et al. 2018
-- Identifying available satellite-derived and sub-surface in situ oceanographic datasets coincident and collocated with the animal movement data, based on regional Ocean Observing Systems
-- Extracting and appending these environmental data to animal movement data
-
-Whilst the functions in `remora` were primarily developed to work with acoustic telemetry data, the environmental data extraction and integration functionalities will work with other spatio-temporal ecological datasets (eg. satellite telemetry, species sightings records, fisheries catch records).
-
-Maintainer: Created by a team from [IMOS Animal Tracking Facility](https://imos.org.au/facilities/animaltracking), adapted to work on OTN-formatted data by Bruce Delo ( [email protected] )
-
-
-#### Intro to the `pathroutr` Package
-
-The goal of `pathroutr` is to provide functions for re-routing paths that cross land around barrier polygons. The use-case in mind is movement paths derived from location estimates of marine animals. Due to error associated with these locations it is not uncommon for these tracks to cross land. The `pathroutr` package aims to provide a pragmatic and fast solution for re-routing these paths around land and along an efficient path. You can learn more [here](https://github.com/jmlondon/pathroutr)
-
-Author: Dr. Josh M London ( [email protected] )