From af09ce0c55953ba9273a8c346beea9658523bd6a Mon Sep 17 00:00:00 2001 From: "Luna L. Sanchez Reyes" Date: Mon, 10 Apr 2023 18:09:11 -0700 Subject: [PATCH] update schedule and exercises --- lectures/lecture-reusable-code-2.md | 4 +-- readings/before-opentree.md | 18 ---------- readings/before-reusable-code-loops.md | 2 +- readings/before-tree-thinking.md | 2 +- readings/before-trees-and-tables.md | 15 ++++---- readings/before-trees-opentree.md | 36 +++++++++++++++++++ ...g-trees.md => before-trees-visualizing.md} | 16 +++++---- schedule.md | 2 +- 8 files changed, 58 insertions(+), 37 deletions(-) delete mode 100644 readings/before-opentree.md create mode 100644 readings/before-trees-opentree.md rename readings/{before-visualizing-trees.md => before-trees-visualizing.md} (72%) diff --git a/lectures/lecture-reusable-code-2.md b/lectures/lecture-reusable-code-2.md index 43d3e33..7500e76 100644 --- a/lectures/lecture-reusable-code-2.md +++ b/lectures/lecture-reusable-code-2.md @@ -122,7 +122,7 @@ 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) @@ -130,7 +130,7 @@ my_results 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) diff --git a/readings/before-opentree.md b/readings/before-opentree.md deleted file mode 100644 index 6e34a46..0000000 --- a/readings/before-opentree.md +++ /dev/null @@ -1,18 +0,0 @@ ---- -layout: page -element: reading -title: 'Getting phylogenetic trees' -language: R -pagetype: 'before class' -symbol: -week: "Apr 20" ---- - - -## Publications - - -## Public data stores - - -### Open Tree of Life diff --git a/readings/before-reusable-code-loops.md b/readings/before-reusable-code-loops.md index e75514f..8b770fd 100644 --- 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: -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 index a02c82f..50d8770 100644 --- a/readings/before-tree-thinking.md +++ b/readings/before-tree-thinking.md @@ -8,6 +8,6 @@ symbol: 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 index 2b90800..df38569 100644 --- 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: -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 - + --> diff --git a/readings/before-trees-opentree.md b/readings/before-trees-opentree.md new file mode 100644 index 0000000..a6b23de --- /dev/null +++ b/readings/before-trees-opentree.md @@ -0,0 +1,36 @@ +--- +layout: page +element: reading +title: 'Getting phylogenetic trees' +language: R +pagetype: 'before class' +symbol: +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. + + + + + + diff --git a/readings/before-visualizing-trees.md b/readings/before-trees-visualizing.md similarity index 72% rename from readings/before-visualizing-trees.md rename to readings/before-trees-visualizing.md index 6af8294..25d7c26 100644 --- a/readings/before-visualizing-trees.md +++ b/readings/before-trees-visualizing.md @@ -5,25 +5,29 @@ title: 'Visualizing trees' language: R pagetype: 'before class' symbol: -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 + diff --git a/schedule.md b/schedule.md index b879b66..07b8146 100644 --- 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',