At 14cdf06 the website displays using the old theme when running blogdown::serve_site():

https://github.com/ArminderD/Data_management

This exercise was developed for the Australian Field Epidemiology Training Program, The Masters of Philosophy (Applied Epidemiology) offered through the Australian National University. This exercise provides an introduction to the RStudio environment including basic commands and the generation of basic graphs. The exercise also serves as an introduction to data management in epidemiology introducing the concepts of data checking, data cleaning, and manipulation of variables.

In the lecture outbreak stats primer
See
For Thibaut.pdf

contrib by C Donnelly

There have been a lot of problems with math rendering on this site. It looks to be because we started with a blogdown framework, but then moved away from it for some reason.

At the moment, we are being bitten by support (or lack thereof) for mathjax on this platform. There is likely a way around this through hugo, but honestly, I'm not sure what it is and it is super frustrating.

https://github.com/ArminderD/Case_control

This case study was developed for the Australian Field Epidemiology Training Program, The Masters of Philosophy (Applied Epidemiology) offered through the Australian National University. In this exercise we will use a case control for an outbreak of Shiga toxin producing E. coli infection to conduct a simple descriptive analysis, and estimate measures of association. The study will allow us to interpret findings of a case control study that employs frequency matching of controls. We will also analyse the data employing pair matching of cases and controls.

Remove the section beginning:
Now that you know how to parametrise a discretised Gamma distribution matching

The current instructions for rendering documents are without a lot of caveats that I've encountered:

1. Figures get placed into the content/post/<postname>_files/figure_<something> directory by default and require the contributor to manually move them to static/post/<postname>_files/figure_<something>

2. Pandoc 2.x (shipped with the preview version of Rstudio) has deprecated markdown_github and now uses gfm for rendering. I've fixed this in 61ac7b7 for the render_new_rmds_to_md(), but it currently means that we can't put the rendering information in the header and expect it to work for everyone.

3. Due to Hugo, relative paths for figure references will not work, resulting in an error if the document is rendered by clicking the "knit" button. I believe this can be circumvented by using knitr::include_graphics() with here() (i.e. https://github.com/zkamvar/dissertation/blob/master/chapters/00-introduction.Rmd#L157).

4. I've found myself using the following command a lot:

unlink("content/post/practical-stegen.md"); learn::render_new_rmds_to_md()

• Should twittername become "RECONEPI"?

• There's no dedicated email address for RECON, right?

Here are the various things which would be good to improve on or add to the website:

• a search engine which can be used to find documents by category (e.g. lecture, practical) and tags (i.e. any keyword relating to content)

• other pages (e.g. "about") linked from the landing page, and instructions on how to add and link new pages

• a ribbons system indicating the category of documents on the post images of the landing page

• record license as part of the yaml header of posts, handled as category and tags, and displayed alongside ribbons

• an option to specify how many posts to display on the landing page, with the rest of the content displayed by following a link 'next'

• add Disqus support

• add a post on how to contribute material to the website // unsure about this, to discuss

Some of the packages used in the Ebola practicals part 1 and 2 have changed. It would be good to recompile these practicals, and maybe update a couple of practices illustrated in them. This issue concerns part 1 only.

Links

• part 1:
  https://www.reconlearn.org/post/simulated-evd-early.html

• part 2, though not for this issue):
  https://www.reconlearn.org/post/practical-ebola-reconstruction.html

I will PR changes in the coming days.

@zkamvar @maelle @stephlocke
Right, so I start to have a better idea of what is happening on this.

Context

I am using this kind of buttons in a new case study:
https://www.w3schools.com/bootstrap/tryit.asp?filename=trybs_collapsible&stacked=h

The issue

They work well when using rmarkdown::render("foo_Rmd"), but not when rendered on the website; I have added the headers of the example above to layout/partials/head.html, so the issue doesn't seem to come from there. If we look at the source file content/post/test-buttons.Rmd:

---
title: "Test collapse button"
author: "Thibaut Jombart"
authors: "Thibaut Jombart"
date: 2018-10-24
licenses: CC-BY
categories: "case study"
slug: button-test
image: img/highres/graduation-1965.jpg
showonlyimage: true
---


Here is an attempt at collapse button, taken from:
https://www.w3schools.com/bootstrap/tryit.asp?filename=trybs_collapsible&stacked=h


<div class="container">
  <h2>Simple Collapsible</h2>
  <p>Click on the button to toggle between showing and hiding content.</p>
  <button type="button" class="btn btn-info" data-toggle="collapse" data-target="#demo">Simple collapsible</button>
  <div id="demo" class="collapse">
    Lorem ipsum dolor sit amet, consectetur adipisicing elit,
    sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam,
    quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat.
  </div>
</div>

After using learn::render_new_rmds_to_md(), the file content/post/test-buttons.md looks like:

Here is an attempt at collapse button, taken from: <https://www.w3schools.com/bootstrap/tryit.asp?filename=trybs_collapsible&stacked=h>

<h2>
Simple Collapsible
</h2>
<p>
Click on the button to toggle between showing and hiding content.
</p>
<button type="button" class="btn btn-info" data-toggle="collapse" data-target="#demo">
Simple collapsible
</button>
    Lorem ipsum dolor sit amet, consectetur adipisicing elit,
    sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam,
    quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat.

The

Should include:

• slide on sampling and random variables
• slide on confidence interval
• slide on variability and credibility interval
• some illustrations of bad practices / good practices

@AmmerB @zkamvar I am using this issue to discuss work on the Stegen case study. Plan is:

• take down the current version, which nobody probably used; it is still present on the website but not linked from any page

• make a new draft of the case study in a new branch, with rough narrative and all the analyses // Thibaut

• solve technical issues (see below) // Zhian and Thibaut

• polish narrative // Amrish

• review code // Zhian

• once we have the final post, generate files to distribute to Malta's participants (folder containing data, adapted scripts, Rmd, etc.) // Zhian

Use readxl instead of xlsx to avoid Java dependencies

https://github.com/ArminderD/ReCon_Rcourse

This case study was developed for the Australian Field Epidemiology Training Program, The Masters of Philosophy (Applied Epidemiology) offered through the Australian National University. The case study is based on cross-sectional survey data looking at risk factors for acute respiratory infection in Australia. The case study provides basic principles for understanding logistic regression, demonstrate how to perform a simple multivariable analysis in R, check model fit, and interpret results.

there appear to be stale practicals in the static/solutions directory: https://github.com/reconhub/learn/tree/master/static/solutions

It might be a good idea to clean these up or create a new learn:: function that will auto-generate these solution practicals. in the future.

worth noting in stegen that there are other packages with a "here" function.
E.g. people later loaded dplyr and lubridate after here, so then couldnt use here::here.
Maybe worth adding a note on semicolon use.... ?

https://github.com/ArminderD/Count_data

This exercise was developed for the Australian Field Epidemiology Training Program, The Masters of Philosophy (Applied Epidemiology) offered through the Australian National University. This exercise provides an introduction to analysing count data in R, including understanding distribution patters of count and rate data and performing appropriate analysis of count data.

For instance at:
https://reconlearn-ld.netlify.com/post/simulated-evd-early.html

after the command line plot(x, node_shape = "sex", shapes = c(male = "male", female = "female"), selector = FALSE) the plot should be a htmlwidget, not a png.

See https://reconlearn.netlify.com/post/simulated-evd-early/ for the corresponding version on the old site.

Somehow, the mathjax is not being processed. For example this line (https://github.com/reconhub/learn/blame/master/content/post/practical-ebola-response.md#L276) turns into this:

https://github.com/ArminderD/Regression_practical

This case study was developed for the Australian Field Epidemiology Training Program, The Masters of Philosophy (Applied Epidemiology) offered through the Australian National University. The case study steps through how to adjust for potential confounders using the example from a study on blood lead levels and IQ. The case study provides basic principles for understanding logistic regression, demonstrate how to perform a simple multivariable analysis in R, check model fit, and interpret results.

Some of the packages used in the Ebola practicals part 1 and 2 have changed. It would be good to recompile these practicals, and maybe update a couple of practices illustrated in them. This issue concerns part 2 only.

Links

• part 2:
  https://www.reconlearn.org/post/practical-ebola-reconstruction.html

• part 1 (though not for this issue):
  https://www.reconlearn.org/post/simulated-evd-early.html

In the into to R practical, the link to the linelist incorrectly downloads the contacts file instead.

In a vanilla session at e726125

> source("R/get_and_update_dependencies.R")
── Attaching packages ─────────────────────────────────────── tidyverse 1.2.1 ──
✔ ggplot2 2.2.1     ✔ purrr   0.2.5
✔ tibble  1.4.2     ✔ dplyr   0.7.5
✔ tidyr   0.8.1     ✔ stringr 1.3.1
✔ readr   1.1.1     ✔ forcats 0.3.0
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
Installing packages into ‘/home/thibaut/R/x86_64-pc-linux-gnu-library/3.5’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
* Adding knitr to Imports
Next: 
Refer to functions with knitr::fun()
* Adding deSolve to Imports
Next: 
Refer to functions with deSolve::fun()
* Adding epicontacts to Imports
Next: 
Refer to functions with epicontacts::fun()
* Adding incidence to Imports
Next: 
Refer to functions with incidence::fun()
* Adding earlyR to Imports
Next: 
Refer to functions with earlyR::fun()
* Adding EpiEstim to Imports
Next: 
Refer to functions with EpiEstim::fun()
* Adding ggplot2 to Imports
Next: 
Refer to functions with ggplot2::fun()
* Adding ape to Imports
Next: 
Refer to functions with ape::fun()
* Adding outbreaks to Imports
Next: 
Refer to functions with outbreaks::fun()
* Adding epitrix to Imports
Next: 
Refer to functions with epitrix::fun()
* Adding outbreaker2 to Imports
Next: 
Refer to functions with outbreaker2::fun()
* Adding visNetwork to Imports
Next: 
Refer to functions with visNetwork::fun()
* Adding projections to Imports
Next: 
Refer to functions with projections::fun()
Error: "tidyverse" must be installed before you can take a dependency on it
In addition: Warning message:
packages ‘"tidyverse"’, ‘"openxlsx"’, ‘"pbapply"’, ‘"mvtnorm"’ are not available (for R version 3.5.0) 

This looks very odd, see screenshot below for p3:

My suspicion is this is because hugo tries to process the folders named ***_files in /content/post/, which are seemingly needed for the html widgets.

Is there a clever way to install all necessary packages to have blogdown compile the learn ressources in one sweep? Spent 30 minutes continously installing additional packages before the thing compiled...

Helloo, I noticed a little error in the case study Stegen on RECONLearn. There's a point at which you make a graph of age distribution by gender under "Graphical exploration", and then under "Going further" in the same section label the y axis "Number of cases". But these are not the cases, this is everyone, including cases and non cases. Looks a bit different for cases and non cases separately. Cheers! Savina

Is "itsalocke" a place-holder?

At 970c33e after removing content/post/lecture-bag-of-slides.md

> learn::render_new_rmds_to_md()


processing file: lecture-bag-of-slides.Rmd
  |......................                                           |  33%
  ordinary text without R code

  |...........................................                      |  67%
label: options (with options) 
List of 1
 $ include: logi FALSE

  |.................................................................| 100%
  ordinary text without R code


output file: lecture-bag-of-slides.knit.md

/usr/bin/pandoc +RTS -K512m -RTS lecture-bag-of-slides.utf8.md --to markdown_github --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output lecture-bag-of-slides.md --standalone 

Output created: lecture-bag-of-slides.md
Error: [ENOENT] Failed to search directory '/home/thibaut/dev/recon/learn/content/post/lecture-bag-of-slides_files/figure-markdown_github': no such file or directory
> 

However it seems the md file has been produced and no temporary files are left in the folder.

Link is broken in the following text:
For a follow-up on this outbreak, have a look at the second part of this simulated response

Currently, there are no solutions hosted. It would be nice to host these.

This was a missed link that needs to be properly referenced:

Thanks to @Imai-N for spotting it

I was re-adding some static images to the README.Rmd (screenshots of PRs), which might help github novices. I am surprised these generate the following error:

> blogdown::serve_site()

Attaching package: ‘testthat’

The following object is masked from ‘package:devtools’:

    setup

Building sites … ERROR 2018/06/06 17:20:45 Failed to read data from img/shot-fork.png/shot-fork.png: Data not supported for extension 'png'
ERROR 2018/06/06 17:20:45 Failed to read data from img/shot-pr-2.png/shot-pr-2.png: Data not supported for extension 'png'
ERROR 2018/06/06 17:20:45 Failed to read data from img/shot-pr.png/shot-pr.png: Data not supported for extension 'png'
Total in 117 ms
Error: Error building site: logged 3 error(s)
To stop the server, run servr::daemon_stop("140025127766648") or restart your R session
Serving the directory /home/thibaut/dev/recon/learn at http://127.0.0.1:3633

I could live without these screenshots, but I'd rather have them there if possible. Any idea what's going on?

Should contain:

• overview of constraints / needs for operational analytics infrastructure
• intro to reportfactory
• intro to linelist
• intro to deployer
• intro to golden rules

in the current version, inline math expressions using $ display normally, but anything with $$ is not rendered; I noticed mathjax.js is not in static/js but not loaded in any of the partials, where it used to be; may that be the origin of the issue? I'm not sure why only some expressions should be rendered though..

The css file for code highlighting is present in static/css/recon.css but I am not sure how this is now supposed to be used / called in the .Rmd files. It would either:

1. be applied automatically to all syntax highlighting in all practicals
2. be applied manually to individual Rmds, e.g. in the yaml header via
   css: path/to/recon.css

My preference goes to 1 (older behaviour) but if only 2 is possible, then it'd be nice to have a working example e.g. on content/post/practical-ebola-response.md
(I can apply changes to other documents)