RStudio | Thought splinters

Images in Different File Formats

Fri, 14 May 2021 00:00:00 +0000

I have investigated the different methods for inserting images into various file formats and conversion procedures.

Image handling in .Rmd, .md and .Rmarkdown files

At first I looked on the various options for handling of images in .Rmd files.
Then – as a contrast program – I tested the outcomes of image handling procedures in .md files.
And finally I investigated the image procedures in.Rmarkdown files.

Observed results

The situation is complex and not easy to grasp. But on a meta-level, the case is pretty straightforward: The decision for a file format is much more important than the details in image handling.

.Rmd: The window provided via Visual R Markdown provides all its great features only in .Rmd files. With the new page bundle feature in Hugo some disadvantages of .Rmd file disappear: As every file is in its own folder the several files produced by the conversion process do not hamper anymore. But .Rmd files loose some of the nice features of the Academic theme, e.g., the table of contents on the ride side. Also the chunk option fig.align does not work with the Academic theme. To date I could not find & solve the annoying problem.
.Rmarkdown: It turns out that .Rmarkdown files have the greatest advantages. They have now almost the same features of R Markdown (writing and applying R code, using references and bibliography), but provides also the benefits of the (Academic) theme via the Goldmark renderer. Yes, you can’t use the full functionality of the Visual R Markdown window for including images but you could use instead the Hugo figure shortcode.¹

So the situation is pretty straightforward: The Hugo figure shortcode is for all different file formats a good solution. In the case of .Rmd files they have to be embedded in an HTML-chunk as demonstrated in the .Rmd post.

Additional tip

RStudio markdown snippet do not work in .md files. I do not understand why not. Ok, there is no R programming code but it coud be used for other (text) snippets. RStudio markdown snippet do work with .Rmarkdown files. So I have prepared an snippet to include the Hugo figure shortcode syntax and saved under ‘ff’. So I just need to type ff + SHIFT-Tab to get a template with all the parameters .

At the moment I do not know if using the figure shortcode results in some processing penalties. At least I read and experienced it myself that with many images the standard time-out parameter for Netlify has to be set much higher than the standard 10 seconds. ↩︎

Announcing the R package coinsR

Fri, 02 Aug 2019 00:00:00 +0000

Update 2021-05-21: Because of some breaking changes in the Hugo site structure and management in the last three years, coinsR works at the moment only with individual pages.

This blog entry announces the R program coinsR to produce bibliographic metadata automatically for websites within the Hugo framework. The dominant use case at the moment is with the blogdown package.

In a previous blog entry I wrote about the advantages of providing bibliographic metadata for your web pages producing COinS. COinS is the abbreviation of Context Objects in Spans. It refers to a microformat standard to embed bibliographic metadata as HTML.

A COinS string includes HTML code for all the information necessary to cite a publication correctly. It works for every type of writing (books, papers, web pages). COinS embedded in your HTML pages help your blog readers or website visitors to cite your posts and pages correctly.

I wrote also a detailed tuorial how to produce COinS with the help of the free bibliographical research tool Zotero. But this is a quite complicated procedure with several steps. Besides, it works only for every page individually and not automatically for all blog entries of your website.

To produce COinS for every web page quickly was my motivation to write the R package coinsR.

Use cases of `coinsR` and its limitations

The package requires:

Hugo with the R package blogdown
Config file in the TOML format (config.toml)
Blog entries with YAML frontmatter

I plan for a future version to loosen the last two limitations and allow config.yaml and TOML frontmatter (but not for .json).

Update 2021-05-21: This plan is still relevant: I would like to loosen some restrictions and improve the user interface.

You can call coinsR via an RStudio Addin for every page individually. But you can also produce COinS automatically for all files under a specific directory.

Where to find `coinsR` and how to install it?

You can download the package from Github with

remotes::install_github('petzi53/coinsR', build_vignettes = TRUE)

I am trying to prepare coinsR as an R package distributed via the CRAN repository. But as I am still not very experienced in R programming, I am not sure if I will succeed.

You will find a detailed description in the help file and the vignette description of how to invoke the two functions coins_this() and coins_all().

RStudio Snippets for Markdown

Wed, 12 Jun 2019 00:00:00 +0000

Tutorial for RStudio code snippets

Code snippets are text macros which you can insert into your programs. They are used for repetitive tasks and can boost your productivity tremendously. Here I am not going to explain how to use it. There are already several good tutorials around:

The official RStudio tutorial on code snippets
A Blog entry by Jake Daniels: How RStudio Snippets Improve My Productivity
A Blog entry by Jozef Hajnala: 4 ways to be more efficient using RStudio’s Code Snippets, with 11 ready to use examples
A Video by Sharon Machlis: R tip: Save time with RStudio code snippets (part of her video channel Do more with R)

Eight useful reminders

In this post, I want to summarize some important details, which I learned laboriously after time-consuming trials:

The Markdown section in the snippet editor works only with .Rmd and .Rmarkdown files. – So if you are going to write just text (e.g., a blog entry) and you want use RStudio snippets to insert shortcodes than you have to write into .Rmd / .Rmarkdown files.
The snippets in the R section of the snippet editor are for code chunks whereas the snippets in the Markdown section work only in markdown text of .Rmd / .Rmarkdown files.
To insert snippets in the Markdown part of .Rmd / .Rmarkdown files, you have to use SHIFT-TAB (and not just TAB as for R snippets in the code chunks).
To write your snippets, you have to use the TAB key for indenting. 4 Spaces do not work!
It is legitimate to write huge snippets for large code junks. For instance, you can write complex ggplot2 snippets as a kind of a template you are going to use frequently.
For large code chunks, it may be preferable to write the snippets with the RStudio code pane. You can load the snippet files under ~/.R/r.snippets respectively ~.R/markdown.snippets into RStudio.
You can share you snippets sending these files to your colleagues and collaborators.
Do not use names, which are difficult to type to call your snippets. For instance, to insert the markdown syntax for an image do not name it “![” but “ii” for example.

RStudio installieren (Deutsch)

Wed, 03 Jan 2018 00:00:00 +0000

Installation von RStudio

Bedienung dieser Diashow

Steuerungselemente: Pfeile rechts unten
Achtung: Manchmal gibt es außer vor und zurück auch hinauf und hinunter
Folienstruktur-Überblick: ESC-Taste
Zoomen: ALT + (STRG für LINUX) KLICK in das Objekt. Noch ein Klick: Herauszoomen.
Beenden: Mit dem Browser zurück gehen

Voraussetzungen

Bevor wir komfortabel mit R arbeiten können, müssen wir einige Programme installieren

Die aktuelle Version von R
Die aktuelle Version der Entwicklungsumgebung RStudio
Die aktuelle Version von LaTeX

Alle Programme sind Open Source: Sowohl Quellcode als auch Programme sind frei und kostenlos erhältlich.

Installation von RStudio

R noch nicht installiert? Beginnen Sie mit diesem Link
Ansonsten rufen Sie die RStudio-Downloadseite auf

Wählen Sie Mac oder Windows-Downlaod

Speichern Sie Ihre Programm-Version

Klicken Sie auf den Download-Link
Speichern Sie die Installationsdatei
Entpacken Sie RStudio
Rufen Sie RStudio dann auf

Es erscheint nun die Entwicklungsumgebung
Klicken Sie in die obere Leiste, damit Sie alle 4 Fensterbereiche sehen

Erkunden Sie Fenster und Reiter von RStudio

Hilfreich ist auch diesen Video
Mehr zu Entwicklungsumgebung dann, wenn wir mit R zu arbeiten beginnen

Zusammenfassung

Es gibt auch YouTube-Videos zum Ansehen
Die Schritte für Mac und Windows sind ähnlich:
z.B. für Mac hier und hier
und für Windows hier und hier
Ein Link, der nochmals alle Schritte zusammenfasst
Sie sollten jetzt R und RStudio installiert haben

Präsentation beenden

Sie beenden nun diese Präsentation mit (Browser Pfeil rückwärts)
ACHTUNG: Browser rückwärts – und nicht Folien Pfeil links!

RStudio | Thought splinters

Images in Different File Formats

Image handling in .Rmd, .md and .Rmarkdown files

Observed results

Additional tip

Announcing the R package coinsR

Use cases of coinsR and its limitations

Where to find coinsR and how to install it?

RStudio Snippets for Markdown

Tutorial for RStudio code snippets

Eight useful reminders

RStudio installieren (Deutsch)

Installation von RStudio

Voraussetzungen

Installation von RStudio

Wählen Sie Mac oder Windows-Downlaod

Speichern Sie Ihre Programm-Version

Zusammenfassung

Präsentation beenden

Use cases of `coinsR` and its limitations

Where to find `coinsR` and how to install it?