update schedule and exercises

LunaSare · Apr 11, 2023 · af09ce0 · af09ce0
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diff --git a/lectures/lecture-reusable-code-2.md b/lectures/lecture-reusable-code-2.md
@@ -122,15 +122,15 @@ my_results
 
 ### Looping using functions
 
-#### Exercise 2: [Mass of dinosaurs with loops]({{ site.baseurl }}/exercises/Loops-size-estimates-by-name-loop-R) (30 min)
+#### Exercise 6: [Mass of dinosaurs with loops]({{ site.baseurl }}/exercises/Loops-size-estimates-by-name-loop-R) (30 min)
 
 <!-- https://datacarpentry.org/semester-biology/exercises/Loops-size-estimates-by-name-loop-R/ -->
 
 ### Looping over files
 
 Practical uses of `for` loops
 
-#### Exercise 3: [Automatic analysis of muliple files]({{ site.baseurl }}/exercises/Loops-multi-file-analysis-R) (30 min)
+#### Exercise 7: [Automatic analysis of muliple files]({{ site.baseurl }}/exercises/Loops-multi-file-analysis-R) (30 min)
 
 <!-- https://datacarpentry.org/semester-biology/exercises/Loops-multi-file-analysis-R/ -->
 

diff --git a/readings/before-opentree.md b/readings/before-opentree.md
diff --git a/readings/before-reusable-code-loops.md b/readings/before-reusable-code-loops.md
@@ -5,7 +5,7 @@ title: 'Reusing code - Loops'
 language: R
 pagetype: 'before class'
 symbol: <i class="fa fa-book fa-lg"></i>
-week: "Apr 6"
+week: "Apr 6, 11"
 ---
 
 ## A) Prepare for in-class exercises

diff --git a/readings/before-tree-thinking.md b/readings/before-tree-thinking.md
@@ -8,6 +8,6 @@ symbol: <i class="fa fa-book fa-lg"></i>
 week: "Apr 25, 27"
 ---
 
-## A) Models and phylogenetic correlation
+## Models and phylogenetic correlation
 
 - [How to measure and test phylogenetic signal](https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/j.2041-210X.2012.00196.x)
diff --git a/readings/before-trees-and-tables.md b/readings/before-trees-and-tables.md
@@ -5,21 +5,20 @@ title: 'Joining trees and tables'
 language: R
 pagetype: 'before class'
 symbol: <i class="fa fa-book fa-lg"></i>
-week: "Apr 13, 18"
+week: "Apr 20"
 ---
 
-**Day 1**
-
-## A) Joining trees to data tables
+Complete the following readings:
 
 - [What is phylogenetic analysis?](https://www.news-medical.net/health/What-is-Phylogenetic-Analysis.aspx)
 - Read [Reading a Phylogenetic Tree: The Meaning of Monophyletic Groups](https://www.nature.com/scitable/topicpage/reading-a-phylogenetic-tree-the-meaning-of-41956/#:~:text=Phylogenies%20are%20useful%20for%20organizing,events%20that%20occurred%20during%20evolution).
 
-**Day 2**
 
-## B) Plotting data from tables on trees
 
 
-<!-- ## Day 4: Phylogenetic correlation
+<!--
+## A) Joining trees to data tables
+
+## B) Plotting data from tables on trees
 
-- [How to measure and test phylogenetic signal](https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/j.2041-210X.2012.00196.x) -->
+ -->
diff --git a/readings/before-trees-opentree.md b/readings/before-trees-opentree.md
@@ -0,0 +1,36 @@
+---
+layout: page
+element: reading
+title: 'Getting phylogenetic trees'
+language: R
+pagetype: 'before class'
+symbol: <i class="fa fa-book fa-lg"></i>
+week: "Apr 18"
+---
+
+- Follow the tutorial [Module 24: An Intro to Phylogenetic Tree Construction in R](https://fuzzyatelin.github.io/bioanth-stats/module-24/module-24.html).
+
+- In a new Rmd document, try to complete as many of the steps from the tutorial as you can.
+
+- Document the parts that are hardest to complete, and how much time it took you to figure out each one.
+
+- If you can't make all parts of the tutorial run, it is ok.
+
+- I just want to see that you tried to run most of them, and if you succed that is great! If not, that is ok too.
+
+
+
+
+
+<!--
+Lecture:
+
+## Publications
+
+
+## Public data stores
+
+
+### Open Tree of Life
+
+ -->
diff --git a/readings/before-visualizing-trees.md → readings/before-trees-visualizing.md b/readings/before-visualizing-trees.md → readings/before-trees-visualizing.md
@@ -5,25 +5,29 @@ title: 'Visualizing trees'
 language: R
 pagetype: 'before class'
 symbol: <i class="fa fa-book fa-lg"></i>
-week: "Apr 11"
+week: "Apr 13"
 ---
 
-## A) Reading and plotting phylogenies
+## Reading and plotting phylogenies in base R
 
 - Complete [introduction-to-phylogenetics](https://www.ebi.ac.uk/training/online/courses/introduction-to-phylogenetics/)
 - Read [The Newick tree format](https://evolution.genetics.washington.edu/phylip/newicktree.html).
-- Watch [Introduction to CRAN and Bioconductor](https://www.youtube.com/watch?v=qAvJ92qCGqE).
 
 
-## B) Joining phylogenies to data tables
+<!--
+https://www.google.com/search?q=INTRO+TO+PHYLOGENETIC+TREES+IN+R&oq=INTRO+TO+PHYLOGENETIC+TREES+IN+R&aqs=chrome..69i57j33i160l3j33i15i22i29i30j33i22i29i30l5.5425j0j4&sourceid=chrome&ie=UTF-8
+
+
+## Day 2 Joining phylogenies to data tables
 
 - [What is phylogenetic analysis?](https://www.news-medical.net/health/What-is-Phylogenetic-Analysis.aspx)
 - Read [Reading a Phylogenetic Tree: The Meaning of Monophyletic Groups](https://www.nature.com/scitable/topicpage/reading-a-phylogenetic-tree-the-meaning-of-41956/#:~:text=Phylogenies%20are%20useful%20for%20organizing,events%20that%20occurred%20during%20evolution).
 
+- Watch [Introduction to CRAN and Bioconductor](https://www.youtube.com/watch?v=qAvJ92qCGqE).
 
-## C) Plotting data on Phylogenies
+## Day 3 Plotting data on Phylogenies
 
 
-<!-- ## Day 4: Phylogenetic correlation
+## Day 4: Phylogenetic correlation
 
 - [How to measure and test phylogenetic signal](https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/j.2041-210X.2012.00196.x) -->
diff --git a/schedule.md b/schedule.md
@@ -13,8 +13,8 @@ assignments: ['The Data Life Cycle', # the importance of programming for data sc
 'Reusing code - Apply functions',
 'Reusing code - Loops',
 'Visualizing trees',
-'Joining trees and tables',
 'Getting phylogenetic trees',
+'Joining trees and tables',
 'Tree thinking',
 # 'Public Data Stores',
 'Review Week',