Handbook v2.5 en #410

nsbatra · 2024-10-14T07:16:11Z

Creating the PR to allow easier comparison (e.g. file filter)
I am now reviewing Arran's edits and may edit further as necessary.
Then the plan is to:

Merge
Change name of repo to epirhandbook
Change name of folder away from "new_pages"
Make final revision to any URLs in book to account for the above two points
Release a new version
Cascade changes to other languages based on files changed, not commits.

…s and grammar issues.

…dated. Should have a discussion on twitter links and non-English learning materials

git status git status @ :

…handbook_eng into handbook_v2.5_en

…github

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nsbatra · 2024-10-14T07:54:33Z

new_pages/basics.qmd

@@ -364,7 +360,7 @@ age_pyramid(linelist, "age_cat5", "gender")
 **A more complex `age_pyramid()` command might include the *optional* arguments to:**

 -   Show proportions instead of counts (set `proportional = TRUE` when the default is `FALSE`)\
-   Specify the two colors to use (`pal =` is short for "palette" and is supplied with a vector of two color names. See the [objects](#objectstructure) page for how the function `c()` makes a vector)
+-   Specify the two colors to use (`pal =` is short for "palette" and is supplied with a vector of two color names. See the [objects](https://epirhandbook.com/new_pages/basics.html#objects) page for how the function `c()` makes a vector)


@arranhamlet is there a reason this link was hard-coded to URL instead of to the page's tag?

Missed this in my update of file paths. Updated now.

nsbatra · 2024-10-14T08:00:24Z

new_pages/basics.qmd

@@ -483,7 +480,7 @@ In summary: to use the functions available in an R package, 2 steps must be impl

 #### Your library {.unnumbered}

-Your "library" is actually a folder on your computer, containing a folder for each package that has been installed. Find out where R is installed in your computer, and look for a folder called "win-library". For example: `R\win-library\4.0` (the 4.0 is the R version - you'll have a different library for each R version you've downloaded).
+Your "library" is actually a folder on your computer, containing a folder for each package that has been installed. Find out where R is installed in your computer, and look for a folder called "win-library". For example: `R\win-library\4.4.1` (the 4.4.1 is the R version - you'll have a different library for each R version you've downloaded).


@arranhamlet can you check if "win-library" is still relevant and change this if necessary? In my R install now, the folder to the library is "R/R-4.4.1/library"

Updated, the library location has changed.

nsbatra · 2024-10-14T08:02:03Z

new_pages/basics.qmd


 **Install from Github**

-Sometimes, you need to install a package that is not yet available from CRAN. Or perhaps the package is available on CRAN but you want the *development version* with new features not yet offered in the more stable published CRAN version. These are often hosted on the website [github.com](https://github.com/) in a free, public-facing code "repository". Read more about Github in the handbook page on [Version control and collaboration with Git and Github].
+Sometimes, you need to install a package that is not yet available from CRAN. Or perhaps the package is available on CRAN but you want the *development version* with new features not yet offered in the more stable published CRAN version. These are often hosted on the website [github.com](https://github.com/) in a free, public-facing code "repository". Read more about Github in the handbook page on [Version control and collaboration with Git and Github](https://epirhandbook.com/new_pages/collaboration.html).


Can this go directly to the # tag for the page instead of the URL?

@arranhamlet

nsbatra

@arranhamlet thanks for all this work.
Let's connect to discuss a few parts, and whether you have time for small corrections or not.

nsbatra · 2024-10-14T08:02:38Z

new_pages/basics.qmd


 **Install from Github**

-Sometimes, you need to install a package that is not yet available from CRAN. Or perhaps the package is available on CRAN but you want the *development version* with new features not yet offered in the more stable published CRAN version. These are often hosted on the website [github.com](https://github.com/) in a free, public-facing code "repository". Read more about Github in the handbook page on [Version control and collaboration with Git and Github].
+Sometimes, you need to install a package that is not yet available from CRAN. Or perhaps the package is available on CRAN but you want the *development version* with new features not yet offered in the more stable published CRAN version. These are often hosted on the website [github.com](https://github.com/) in a free, public-facing code "repository". Read more about Github in the handbook page on [Version control and collaboration with Git and Github](https://epirhandbook.com/new_pages/collaboration.html).


@arranhamlet

nsbatra · 2024-10-14T08:22:43Z

new_pages/basics.qmd

@@ -922,7 +932,7 @@ gen_out_table

 **Columns**

-Columns in a dataset are also objects and can be defined, over-written, and created as described below in the section on Columns.
+Columns in a dataset are also objects and can be defined, over-written, and created as described below in the section on [Columns](https://epirhandbook.com/new_pages/basics.html#columnsvariables).


@arranhamlet can this also just be the # tag so that if the URL shifts it will still work?

Or like this: dates as I saw done below. Whatever the proper syntax is for quarto

nsbatra · 2024-10-14T08:37:07Z

new_pages/characters_strings.qmd

-    * Detect and locate - `str_detect()`, `str_subset()`, `str_match()`, `str_extract()`  
-    * Modify and replace - `str_sub()`, `str_replace_all()`  
-7. Regular expressions ("regex")
+1. Combine, order, split, arrange - `str_c()`, `str_glue()`, `str_order()`, `str_split()`.


@arranhamlet flagging these periods for review

nsbatra · 2024-10-14T08:38:24Z

new_pages/characters_strings.qmd

-1) the character vector(s)  
-2) start position  
-3) end position  
+1) the character vector(s).  


Flagging these periods for review

nsbatra · 2024-10-14T08:38:58Z

new_pages/characters_strings.qmd

-2) Meta characters  
-3) Quantifiers  
-4) Groups  
+1) Character sets.  


Flagging these periods for review as not complete sentences

nsbatra · 2024-10-14T10:14:10Z

new_pages/quarto.qmd

+
+Quarto provides the flexibility and automation that R Markdown pioneered, with a more powerful underlying flexibility that streamlines a lot of the sharing and publishing processes of your work! While R Markdown is tied to R, Quarto documents allow you to use a number of different programming languages such as R, Python, Javascript and Julia. This means that if you are working with people writing in several different coding languages, they can all use the same document to carry out their analysis.
+
+Even if you are only working in R, Quarto has several advantages. Rather than relying on individual packages to create different outputs, Quarto handles this all internally. To produce a website, PowerPoint slides, or a html report, rather than using external packages, Quarto has this functionality inbuilt. This means you have fewer packages to update, and if one of the packages is no longer maintained, you don't need to change your approach to maintain the same output.


Not clear waht other packages would be involvced in Rmd?
Can't Rmd also use chunks of other programming languages? It's just more clunky?

As is my understanding, R Markdown outputs are generated through a number of different packages (i.e. slides through xaringan (https://bookdown.org/yihui/rmarkdown/xaringan.html), isoslides (https://bookdown.org/yihui/rmarkdown/ioslides-presentation.html), revaljs (https://bookdown.org/yihui/rmarkdown/revealjs.html).

Quarto appears to handle this within itself, https://quarto.org/docs/faq/rmarkdown.html.

I had no idea Rmarkdown could use other languages, but yes it appears it can (https://bookdown.org/yihui/rmarkdown/language-engines.html). I'll update this section to mention this.

nsbatra · 2024-10-14T10:15:40Z

new_pages/quarto.qmd

+knitr::include_graphics(here::here("images", "quarto/5_quarto_report.png"))
+```
+
+## Moving beyond simple reports


What to do about the issues Chris Jarvis raised about objects in the environment not being found, and issues changing the saving location?

This is included in the section ### Limitations of Quarto {.unnumbered}

nsbatra · 2024-10-14T13:59:38Z

new_pages/rmarkdown.qmd

-4) Process data  
-5) Produce outputs (tables, plots, etc.)  
-6) Save outputs, if applicable (.csv, .png, etc.)  
+1) Set global **knitr** options.  


periods need to be reviewed

nsbatra · 2024-10-14T16:30:01Z

old_bookdown/new_pages/heatmaps.Rmd

@@ -469,9 +469,16 @@ Now use a column from the above data frame (`facility_order$location_name`) to b
 pacman::p_load(forcats)

 # create factor and define levels manually
+numerical_order <- gsub("Facility ","",


This file that was edited seems to be not the current one - see how it is in the "old_bookdown folder. Can you bring the edits over to the actual Qmd?

nsbatra · 2024-10-14T16:32:19Z

old_bookdown/new_pages/collaboration.Rmd

@@ -671,7 +671,7 @@ you were working on.
 *PULL* - First, click the "Pull" icon (downward arrow) which fetches and
 pulls at the same time.

-*PUSH* - Clicking the green "Pull" icon (upward arrow). You may be asked
+*PUSH* - Clicking the green "Push" icon (upward arrow). You may be asked


This file that was edited seems to be not the current one - see how it is in the "old_bookdown folder. Can you bring the edits over to the actual Qmd?

aran can you get rid of these changes in your branch pls as we have removed old_bookdown from this repo

…handbook_eng into handbook_v2.5_en

aspina7 · 2024-11-01T15:31:13Z

link to list of changes
https://docs.google.com/document/d/1BL0ShICZHfEycfxfiXGgjG1HpXokUWeuRV_yNv87rAo/edit?tab=t.0

aspina7 · 2024-11-05T09:36:48Z

new_pages/phylogenetic_trees.qmd

@@ -23,17 +23,17 @@ sample_data <- read.csv(here::here("data","phylo", "sample_data_Shigella_tree.cs


 ggtree(tree, layout="circular", branch.length='none') %<+% sample_data + # the %<+% is used to add your dataframe with sample data to the tree


so ggtree and treeio arent on cran and chuck an error @arranhamlet

seems they need to be installed with {BiocManager} from bioconductor

Yes, I updated the quarto document with this, lines 47-62. Is it still throwing an error?

it did for me until i installed separately

Ah, it was because they are needed to generate the header image. I've saved this output as a file now rather than re-generating it everytime.

aspina7 · 2024-11-06T15:03:14Z

@arranhamlet - any chance you could update the data import bit of data_table.qmd to match the other chapters please?
It currently reads in linelist_cleaned.xlsx whereas all others read in linelist_cleaned.rds (with echo=FALSE) and then tell the users to import linelist_cleaned.xlsx (with echo=TRUE).
This will make shifting everything over to using {appliedepidata} much easier!

arranhamlet · 2024-11-25T18:50:50Z

@arranhamlet - any chance you could update the data import bit of data_table.qmd to match the other chapters please? It currently reads in linelist_cleaned.xlsx whereas all others read in linelist_cleaned.rds (with echo=FALSE) and then tell the users to import linelist_cleaned.xlsx (with echo=TRUE). This will make shifting everything over to using {appliedepidata} much easier!

Updated!

arranhamlet · 2024-11-25T18:51:12Z

Clicked the wrong button - sorry!

arranhamlet and others added 30 commits July 25, 2024 09:09

Testing

0be7113

Numerous edits to the editorial_style and data_used pages, fixed link…

093f435

…s and grammar issues.

Working through the basics chapter, numerous links that need to be up…

6236817

…dated. Should have a discussion on twitter links and non-English learning materials

Continuing to work through the basics chapter

4a25f73

Fixing the table on object class

77b4ab4

Completed the basics chapter

076e264

Upd to basics

272c4a7

General updates

e50caaf

Importing chapter, minor updates

410659b

Worked through cleaning and dates

c300e6f

Worked through factors

3752295

Updated the iteration chapter

c5f136a

Updated descriptive tables

4d4d472

Updates to regression, standardization, moving averages, data links@

1f2bc63

git status git status @ :

Epidemic and survey analysis done

7a4e68c

Worked through survival analysis

6c9bf82

update list of the lead translator

9e5697b

gis chapter updated

744ef8b

updates to various pages

1e6ac5a

Merge branch 'handbook_v2.5_en' of https://github.com/appliedepi/epiR…

5744ff2

…handbook_eng into handbook_v2.5_en

Epicurve section done

224d203

Large scale updates to numerous chapters filling in issues raised on …

ebfa021

…github

Further changes to chapters

c286b45

Upates to rmarkdown chapter

05f7a6b

Report factor and collaboration chapters reviewed

02d3990

Flexdashboard chapter finished

ca573fc

updated epicurve chapter with incidence2 and completed diagram chapter

e3dbfbe

Updates to epicurve chapter

e548cba

Shiny and time series updated

573cf62

All pages compiling

61d38be

nsbatra commented Oct 14, 2024

View reviewed changes

nsbatra and others added 15 commits October 14, 2024 19:23

small edits after first review of Arran's edits

3eb5e8e

quarto page small edits

a53d14a

Updates to GIS chapter and Quarto

0db3e99

Final update to GIS

fca5341

Updates to make sure github issues have been addressed

259560d

Initial updates following Neale's review

e6a4aa9

update Github Action to show changes in .qmd files only

013d232

Merge branch 'handbook_v2.5_en' of https://github.com/appliedepi/epiR…

0670a27

…handbook_eng into handbook_v2.5_en

Update a brand new PR

69e2f38

compare with master branch instead of main

3427f6c

correctly retrieve only changed .qmd files

be147a8

Don't retrieve files with language extension

6d2c05c

Reformat the PR

93084d2

Final edits flagged

136a8a8

Merge branch 'handbook_v2.5_en' of https://github.com/appliedepi/epiR…

4f0d72c

…handbook_eng into handbook_v2.5_en

Added a book reference to the survey chapter

d04e814

aspina7 reviewed Nov 5, 2024

View reviewed changes

arranhamlet closed this Nov 25, 2024

arranhamlet reopened this Nov 25, 2024

Updates following comments

5ac48f2


		Quarto provides the flexibility and automation that R Markdown pioneered, with a more powerful underlying flexibility that streamlines a lot of the sharing and publishing processes of your work! While R Markdown is tied to R, Quarto documents allow you to use a number of different programming languages such as R, Python, Javascript and Julia. This means that if you are working with people writing in several different coding languages, they can all use the same document to carry out their analysis.

		Even if you are only working in R, Quarto has several advantages. Rather than relying on individual packages to create different outputs, Quarto handles this all internally. To produce a website, PowerPoint slides, or a html report, rather than using external packages, Quarto has this functionality inbuilt. This means you have fewer packages to update, and if one of the packages is no longer maintained, you don't need to change your approach to maintain the same output.

		@@ -23,17 +23,17 @@ sample_data <- read.csv(here::here("data","phylo", "sample_data_Shigella_tree.cs


		ggtree(tree, layout="circular", branch.length='none') %<+% sample_data + # the %<+% is used to add your dataframe with sample data to the tree

Handbook v2.5 en #410

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Handbook v2.5 en #410

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