Posts | Thi Hao Pham

How to create a website by using R blogdown and hugo theme

Sat, 08 Apr 2023 00:00:00 +0000

In this post, I want to share with you how to create a website for free by using R blogdown.

If you are totally new with R studio, github, git,…let’s get started by installing somethings.

1. Install things

Install R studio
Create Github account (free)
Install git
Download blogdown package, and devtools (if needed)
Download hugo package

2. Set up your pre-born website

You go to your Github account: in the overview tab, click “New” to create a new repository that will store all content of your R documents related to your website. After you click “Create repository”, you will see that repository apprears as one of the project in you Github page, you click to “Code” and copy the url link.
You go to R: File -> New project -> Version control -> Git -> paste the link that you’ve just copied. Then a (semi-)empty project is created.
In the console, you check the version of hugo by type: hugo_version() -> enter. It’s very important, you will know why later.
Go to themes.gohugo.io to choose the theme that you like. Clicking to the link will lead you to that theme page. If you see the buttom “Homepage” click to it. If you don’t, search google: “[name_of_your_chosen_theme] github”. Then go to its Github repository. Copy the whole name of the theme (line on the top which includes author’s name/theme’s name)
Go to R studio. In the console, you type blogdown::new_site(theme = “it-gro/hugo-theme-w3css-basic”. Remove exceeded spaces. Then press enter. When it finish, you have a webpage built in your local computer.
Tell R/Git who you are: Go to Tools -> Shell. If you don’t find “shell” in tools, no worries, just go to terminal (the tab next to console). You type: git config –global user.name “put_your_Github_username”. Then hit enter
You type: git config –global user.email “put_your_email_you_used_for_github”. Then hit enter
Now you commit everything you’ve just added to github. STill in the terminal, you type: git add -A.
On the Git window, you see all boxes are checked. Click “commit”, type comments, click “commit”. when it’s done, close that small window. Then click “push”

3. Set up your website in Netlify:

On your account page, click tab “Sites” -> “add new site” -> “import an existing project” -> “github” -> choose your github project
Click “show advance” -> click “new variable”. In the “key” box, you type: “HUGO_VERSION”. In the “Value” box, you paste the version of hugo.
Click “deploy”. When a new page appears, you click to “deploy new site”. Then you’re almost done.
If you want to change domain, go to deploy setting, change the domain.
If links in your website don’t appear in the way the should, go back to R studio, look for config.toml file. The first line (commonly), replace the baseurl link by your actual web link, save it, and commit it. Your’re done.

That’s it. Let try it and good luck!

Note: If you have any questions along the way, just google and seek for answers in Github. I think ChatGPT may not be very helpful in this case.

Additional materials:

Summarized Zotero hacks

Fri, 07 Apr 2023 00:00:00 +0000

In this post, I want to share with you how to use Zotero effectively for organizing your references. Additionally, if you use R markdown for writing reports/ manuscripts, using Zotero is a must for citing references quickly and easily.

First of all you need to

Install Zotero: https://www.zotero.org/
Install Zotero connector (with the brower you use): https://www.zotero.org/download/
Install useful plugins (Zotfile, Better BibTeX): https://www.zotero.org/support/plugins

2. Organize your Zotero

I highly recommend you to set-up your Zotero before you start adding references.

Creating groups in your Zotero library according to your projects.
Set location of pdf files and their (new) names: This step is very important. When Zotero download pdf files, it will store those files in separate folders (one article in one folder) in the C:\User\admin\Zotero with random & non-sense names. However, I’m sure that you want to locate all those pdf files in folders where you can easily find and work with. You click Tools -> Zotfile References…, then:
- In the General settings tab, the lower part (Location of file), choose “Custom Location”, then choose where you want to keep your pdf file. I highly recommend you choose an online path (Google drive/ OneDrive), so you can access to your pdf files anywhere.
- Then check the underneath line “Use subfolder defined by:…”. This is to organize your pdf files into different folders. In the box next to it you can indicate how you want to name your subfolder: %y: by year; %w: by journal; and importantly %c: by name of your Zotero group. Before % sign, you need to put \ (for Window) or / (for Mac). For example, I use Window so I would add: \%c
- In Renaming rules (will automatically remain the pdf file according to the rule you set): set the rule as you like
- Other tabs: you can check if you want to change anything. Otherwise, we’re fine as it is now.

DONE! Now we are going to ask Zotero to work for us…

3. Make use of Zotero to improve your workflow

3.1. Easily add your references

There are multiple way that you can add your reference to Zotero. Regardless of the way you do, the citation will be added automatically.
Zotero can find PDF files for you if you want and if PDFs are openly available, or you can always add PDF later. This feature is similar to EndNote.

3.1.1. Add individual citation:

Directly from the website: just click to the Zotero add-in icon on the right corner of your webpage. When you only have 1 paper on the webpage, Zotero-add-in icon looks like a paper-icon
Indirectly via identify number (PMID, DOI,…): Click to the icon “Add item(s) by identifier” in the tab-bar of Zotero
Drag and drop the pdf file to Zotero

3.1.2. Add multiple citations:

Directly from the website: Same as above. When you only have 1 paper on the webpage, Zotero-add-in icon looks like a folder-icon. This is super useful when you do a systematic review, you run your search, PubMed or EMBASE returns a list of retrieved papers, you just need to add all of them to Zotero folder :)
Via identify number (PMID, DOI,…): Paste multiple identifiers to the box “Add item(s) by identifier”. Zotero can identify a few hundred of DOIs per time, but much less with PMID.
Drag and drop the pdf files to Zotero. If you want, you can use Zotero to rename (i.e., author_year_title) your pdfs
Import your existing library (BibTeX, RIS, Zotero, Mendeley, or Endnote file): In Zotero, choose File -> Import. If you want to download available pdf: Select all citations (Ctrl A) -> right mouse click -> Find available pdfs.

3.2. Easily fix your previously poor-organized setup

If you have been using Zotero for a while but in an unstructured way, you can still fix it. You can start with setting location for pdf files, then:

Rearrange your Zotero library’s structure: Create (sub)groups. Moving references to the right (sub)groups
Relocate your pdf files: select all citations in your chosen (sub)groups -> right mouse click -> Manage attachments -> rename and move. Zotero (+Zotfile) will rename your pdf files, cut and paste them to the new location that you’ve just set. Amazing!!!

3.3. Deduplication

Zotero can recognize duplicates and merge them when you want. On your left hand side, click “Duplicate items”, click to one of the duplicated items, on your right side, select the item that you want to keep, then click “merge”.

3.4. Edit your references:

3.4.1. Edit the citation

You can change the title to “Title case” or “Sentence case” by selecting the citation -> right click to the title -> choose the option you want
Add note/tag: Choose the action you want on your right hand side. It’s useful when you work in a shared project, you can add your name to the tag to mention you’ve added the ref, or add the status of your work on that reference

3.4.2. Edit the pdf

Highlight: use different color for different purpose. For example: yellow for evidence, blue for refs, …Then you can choose to only show blue or yellow highlighed parts
Export your highlighted parts: Right click to the pdf file (underneath the reference), choose “Add notes from annotations”

3.5. Zotero suggests keywords for your manuscript/report

On the bottom left corner, you see a list of automatic tags in your library. You may want to select some of those for your manuscript :D

3.6. Collaborate with your colleagues in Zotero library

You can share your Zotero library with your colleages easily. Your team members can add/edit references. By adding your/ your colleagues’ name in tags/notes, the team knows who added/edited the refs.

3.6.1 Create a new Zotero group:

You create an account on https://www.zotero.org/
Log in to your account
Click to “Group” tab -> create a new group -> Set a name and choose “public” or “private” as you like.

3.6.2 Move your existing library (folder) from personal library to group library:

Drag and drop your existing folder from personal library to group library. However, doing that way will not move all pdf attachments. That’s why I highly recommend that you organize your group library well at the beginning.

Then you/your team members can work with the group library in the same way as personal library.

Note: There are thousands of hacks out there so I will update this post every now and then. That’s it for now, I hope that you find this post useful!

Additional materials:

Create a mindmap in a minute using markdown or Rmarkdown

Sun, 26 Mar 2023 00:00:00 +0000

In this post, I want to share with you how to create a mindmap easily using markdown or Rmarkdown.

Using markdown

What you need to do is only inserting a code block markmap (meaning markdown + mindmap) as below:


```markmap
- A tree
  - Branch 1
    - [Leave 1 with a link to a website](https://markmap.js.org/)
    - Leave 2
      which is very long
    - Leave 3 with `a code here`
  - Branch 2
    - Leave a with an equation: $x = {a\over b}$
    - ~~Leave b which is not needed anymore~~
```

Then you will get the mindmap as below:

- A tree
  - Branch 1
    - [Leave 1 with a link to a website](https://markmap.js.org/)
    - Leave 2
      which is very long
    - Leave 3 with `a code here`
  - Branch 2
    - Leave a with an equation: $x = {a\over b}$
    - ~~Leave b which is not needed anymore~~

Please not that Mindmap can be written in markdown, but needs to be supported by a flexible platform, for example Wowchemy hugo template with a webpage output.

Using Rmarkdown

Mindmap feature has not been incoporated into Rmarkdown yet, unfortunately … However, a package named “mindr” can help to convert Markdown (’.md’) or R Markdown (’.Rmd’) texts, R scripts, and directory structures, into mind map widgets or files (’.mm’), and vice versa. You just need to make sure that you choose the output: html_document. How to do so? After installing “mindr” package, you can search “markmap” in Help tab to know how. In summary, there are 2 steps:

Step 1: Create a source text which could be an .Rmd or .md or R script file with the structure below (only text, no YAML):


```
# Branch 1
  ##  Leave 1
  ##  Leave 2
# Branch 2
  ##  Leave a
  ##  Leave b
```

Name the file as you want, for example: “input_text.Rmd” and keep it in the same directory as your second file below.

Step 2: Create a normal .Rmd file with HTML output. Then insert the code below:


```{r} 
input_txt <- readLines("input_text.Rmd", encoding = "UTF-8")
markmap(input_txt, root = "A tree")
```

That’s it. Let try it and good luck!

Additional materials:

My first Shiny Dashboard

Sat, 01 Jan 2022 21:13:14 -0500

Introduction

This Shiny flex dashboard is used to demonstrate how a markov model can be generated using R and how the result can be presented in an interactive way. Users are able to change the input parameters and observe the change of the results immediately.

The example used in this web app is from a publication Briggs et al. (1998). It can be found here: https://pubmed.ncbi.nlm.nih.gov/10178664/

All calculations in this exercise were done by using basic formulas in R. Pre-build R packages for Health Economics were not applied. The results from this web app are comparable with the results drawn using Excel.

Shiny dashboard

Please click to the link below to access to the dashboard. Try it out!

https://e50943-hao-pham.shinyapps.io/1stDashboard_HaoPham/

Posts | Thi Hao Pham

How to create a website by using R blogdown and hugo theme

1. Install things

2. Set up your pre-born website

3. Set up your website in Netlify:

Summarized Zotero hacks

1. Install Zotero and related things

2. Organize your Zotero

3. Make use of Zotero to improve your workflow

3.1. Easily add your references

3.1.1. Add individual citation:

3.1.2. Add multiple citations:

3.2. Easily fix your previously poor-organized setup

3.3. Deduplication

3.4. Edit your references:

3.4.1. Edit the citation

3.4.2. Edit the pdf

3.5. Zotero suggests keywords for your manuscript/report

3.6. Collaborate with your colleagues in Zotero library

3.6.1 Create a new Zotero group:

3.6.2 Move your existing library (folder) from personal library to group library:

Create a mindmap in a minute using markdown or Rmarkdown

Using markdown

Using Rmarkdown

My first Shiny Dashboard

Introduction

Shiny dashboard