add the overview. firm-up the workshop instructions and corrections t…

…he prepare

core/week-11/overview.qmd

@@ -9,27 +9,27 @@ xxxxx
 
 ### Learning objectives
 
--   dd
--   dd.
--   dd
--   d
+The successful student will be able to:
+
+-   explain what a research compendium is and describe its components
+-   relate the content and concepts in Core 1 and Core 2 to the
+    research compendium
+-   Create a quarto document and:
+    -   appreciate the role of the YAML header 
+    -   format text as bold, italics, headings etc
+    -   add citations and a bibliography
+    -   create automatically numbered figures and tables with cross references in text
+    -   set default code chunk behaviour and those for individual chunks 
+    -   use inline code to report results
+    -   insert special characters and mathematical expressions with LaTeX
+
 
 ### Instructions
 
 1.  [Prepare](study_before_workshop.qmd)
 
-    i.  📖 Read 
 
 2.  [Workshop](workshop.qmd)
 
-    i.  💻 dd.
-
-    ii. 💻 ddd
-
-    iii. 💻 ddd
-
-3.  [Consolidate](study_after_workshop.qmd)
 
-    i.  💻 dd
 
-    ii. 💻 dd

core/week-11/study_before_workshop.qmd

@@ -19,7 +19,7 @@ editor:
 
 This module is assessed by:
 
-::: incremental
+
 -   Oral presentation 30%
 
 -   Project Report and Research Compendium 70% of which
@@ -28,12 +28,14 @@ This module is assessed by:
     -   30% compendium (*i.e.*, 21% of the total mark)
 
 These slides are a guide to Research compendium.
-:::
+
 
 ## What is a Research Compendium?
 
 **Overview of assessment**
 
+::: {style="font-size: 60%;"}
+
 *Stage 3 Integrated Masters students are expected to submit a Research
 Compendium that is a documented collection of all the digital parts of
 the research project including data (or access to data), code and
@@ -49,10 +51,14 @@ of the results which is covered in the report. There is no word or size
 limit for any part of the compendium but its contents should be concise
 and minimal. Extraneous text, code or files will be penalised.*
 
+:::
+
 ## What is a Research Compendium?
 
 **Overview of assessment**
 
+::: {style="font-size: 60%;"}
+
 *Stage 3 Integrated Masters students are expected to submit a Research
 Compendium that is a **documented collection of all the digital parts of
 the research project** including data (or access to data), code and
@@ -70,17 +76,22 @@ no word or size limit for any part of the compendium but its contents
 should be concise and minimal. Extraneous text, code or files will be
 penalised.*
 
+:::
+
 ## What is a Research Compendium?
 
+::: {style="font-size: 80%;"}
+
 ::: incremental
--   Zipped folder containing all data, code, and text associated with a
+-   Zipped folder containing all data, code and text associated with a
     research project organised and documented clearly. Any unscripted
     processing should be described.
 
--   Everything needed to reproduce the results, and no more. The
-    compendium should not be a dumping ground for data files and
-    scripts. It needs to be curated. You may generate files that are not
-    needed to reproduce your work and these should be removed.
+-   Everything needed to understand what the project is and reproduce 
+    the results, and no more. The compendium should not be a dumping 
+    ground for data files and scripts. It needs to be curated. You 
+    may generate files that are not needed to reproduce your work and 
+    these should be removed.
 
 -   Your compendium might be a single Quarto/RStudio Project, or it
     might be folder including an RStudio Project and some additional
@@ -89,15 +100,17 @@ penalised.*
 -   Ideally uses literate programming to create submitted report
 :::
 
+:::
+
 ## Use guidelines from Core 1 and 2
 
 -   follow the guidance in [Core
     1](https://3mmarand.github.io/BIO00088H-data/core/week-1/overview.html)
-    on organisation, naming things, and documentation
+    on organisation, naming things and documentation
 
 -   follow the guidance in [Core
     2](https://3mmarand.github.io/BIO00088H-data/core/week-2/overview.html)
-    well-formatted code, consistency, modularisation and documentation
+    on well-formatted code, consistency, modularisation and documentation
 
 ## Project level documentation
 
@@ -106,8 +119,8 @@ penalised.*
 
 -   primarily in the README file but some details may be in scripts
 
--   title, concise description of the work, date, overview of compendium
-    contents
+-   title, concise description of the work, author exam number, date, overview 
+    of compendium contents
 
 -   all the software information including versions
 

core/week-11/workshop.qmd

@@ -35,18 +35,27 @@ library(tidyverse)
 
 In this workshop we will go through an example quarto document. You will learn:
 
+-   what the YAML header is 
 -   formatting (bold, italics, headings)
--   chunk options to control whether code and output are in the rendered document
--   adding citations
--   figures and tables with cross referencing and autonumberiung
--   inline coding to report results
--   special characters and equations
+-   to control default and individual chunk options 
+-   how to add citations
+-   figures and tables with cross referencing and automatic numbering
+-   how to use inline coding to report results
+-   how to insert special characters and equations
 
 # Exercise
 
-🎬 make a start on your compendium
+🎬 The example RStudio project containing this code here: [chaffinch](https://github.com/3mmaRand/chaffinch). You can download the project as a zip file from there but there is some code that will do that automatically for you. Since this is an RStudio Project, do not run the code from inside a project. You may want to navigate to a particular directory or edit the `destdir`:
 
-🎬 make a start on a quarto doc
+```r
+usethis::use_course(url = "3mmaRand/chaffinch", destdir = ".")
+
+```
+You can agree to deleting the zip. You should find RStudio restarts and you have a new project called chaffinch-xxxxxx. The xxxxxx is a commit reference - you do not need to worry about that, it is just a way to tell you which version of the repo you downloaded. You can now run the code in the project.
+
+🎬 Make an outline of your compendium. This could be a sketch on paper or slide or from the mindmap software you usually use. Or it could be a skeleton of folders and files on your computer.
+
+🎬 Make a start on a quarto doc. 
 
 
 

images/images.qmd

@@ -121,12 +121,12 @@ tracking <- tracking |>
 
 You now have a dataframe with all the tracking data which is relatively easy to summarise and plot using tools you know.
 
-There is an example RStudio project containing this code here: [tips](https://github.com/3mmaRand/tips). You can also download the project as a zip file from there but there is some code that will do that automatically for you. Since this is an RStudio Project, do not run the code from inside a project:
+There is an example RStudio project containing this code here: [tips](https://github.com/3mmaRand/tips). You can also download the project as a zip file from there but there is some code that will do that automatically for you. Since this is an RStudio Project, do not run the code from inside a project. You may want to navigate to a particular directory or edit the `destdir`:
 
 ```{r}
 #| eval: false
-usethis::use_course(url = "3mmaRand/tips")
+usethis::use_course(url = "3mmaRand/tips", destdir = ".")
 ```
 
-You can agree to deleting the zip. You should find RStudio restarts and you have a new project called tips-xxxxxx. The xxxxxx is a commit reference - you do not need to worry about that, it is just a way to tell you which version of the repro you downloaded.
+You can agree to deleting the zip. You should find RStudio restarts and you have a new project called tips-xxxxxx. The xxxxxx is a commit reference - you do not need to worry about that, it is just a way to tell you which version of the repo you downloaded.
 You can now run the code in the project.

structures/structures.qmd

@@ -65,11 +65,11 @@ You can then install the gemmi package again.
 
 I think that's it! You can now download the RStudio project and run each chunk in the quarto document.
 
-There is an example RStudio project here: [structure-analysis](https://github.com/3mmaRand/structure-analysis). You can also download the project as a zip file from there but there is some code that will do that automatically for you. Since this is an RStudio Project, do not run the code from inside a project:
+There is an example RStudio project here: [structure-analysis](https://github.com/3mmaRand/structure-analysis). You can also download the project as a zip file from there but there is some code that will do that automatically for you. Since this is an RStudio Project, do not run the code from inside a project. You may want to navigate to a particular directory or edit the `destdir`:
 
 ```{r}
 #| eval: false
-usethis::use_course(url = "3mmaRand/structure-analysis")
+usethis::use_course(url = "3mmaRand/structure-analysis", destdir = ".")
 ```
 
 You can agree to deleting the zip. You should find RStudio restarts and you have a new project called structure-analysis-xxxxxx. The xxxxxx is a commit reference - you do not need to worry about that, it is just a way to tell you which version of the repo you downloaded.