11th October 2021
Things have been changing on here. Much of that has been behind the scenes with a move to a new VPS for extra speed and all the upheaval that brings. It also gained me a better system for less money than the old upgrade path was costing me and everything feels more responsive as well. Extra work has gone into securing the website as well and I have learned a lot as that has progressed. New lessons were added to older, and sometimes forgotten, ones.
The more obvious change for those who have been here before is that the visual appearance has been refreshed. A new theme has been applied with a multitude of tweaks to make it feel unique and to iron out any rough edges that there may be. This remains a WordPress-based website and new theme is a variant of the Appointee subtheme of the Appointment theme. WordPress does only supports child theming but not grandchild theming so I had to make a copy of Appointee of my own so I could modify things as I see fit.
To my eyes, things do look cleaner, crisper and brighter so I hope that it feels the same to you. Like so many designs these days, the basis is the Bootstrap framework and that is no bad thing in my mind though the standardisation may be too much for some tastes. What has become challenging is that it is getter harder to find new spins on more traditional layouts with everything going for a more magazine-like appearance and summaries being shown on the front page instead of complete articles. That probably reflects how things are going for websites these days so it may be that the next refresh could be more home grown and that is a while away yet.
As the website heads towards its sixteenth year, there is bound to be continuing change. In some ways, I prefer that some things remain unchanged so I use the classic editor instead of Gutenburg because that works best for me. Block-based editing is not for me since I prefer to tinker with code anyway. Still, not all of its influences can be avoided and I have needed to figure out the new widgets interface. It did not feel that intuitive but I suppose that I will grow accustomed to it.
My interest in technology continues even if it saddens me at time and some things do not impress me; the Windows 11 taskbar is one of those so I will not be in any hurry to move away from Windows 10. Still, the pandemic has offered its own learning with virtual conferencing allowing one to lurk and learn new things. For me, this has included R, Python, Julia and DevOps among other things. That proved worthwhile during a time with many restrictions. All that could yield more content yet and some already is on the way.
As ever, it is my own direct working with technology that yields some real niche ideas that others have not covered. With so many technology blogs out there, they may be getting less and less easy to find but everyone has their own journey so I hope to encounter more of them. There remain times when doing precedes telling and that is how it is on here. It is not all about appearances since content matters as much as it ever did.
11th September 2021
The thrust of an exhortation from a computing handbook publisher comes to mind here: don’t just look things up on Google, read a book so you really understand what you are doing. Something like those words was used to sell an eBook on Github but the same sentiment applies to R or any other computing language. Using a search engine will get you going or add to existing knowledge but only a book or a training course will help to embed real competence.
In the case of R, there is a myriad of blogs out there that can be consulted as well as function and package documentation on RDocumentation or rrdr.io. For the former, R-bloggers or R Weekly can make good places to start while ones like Stats and R, Statistics Globe, STHDA, PSI’s VIS-SIG and anything from Posit (including their main blog as well as their AI one) can be worth consulting. Additionally, there is also RStudio Education and the NHS-R Community, which also have a Github repository together with a YouTube channel. Many packages have dedicated websites as well so there is no lack of documentation with all of these so here is a selection:
Distill for R Markdown
Databases using R
COVID-19 Data Hub
To come to the real subject of this post, R is unusual in that books that you can buy also have companions websites that contain the same content with the same structure. Whatever funds this approach (and some appear to be supported by RStudio itself by the looks of things), there certainly are a lot of books available freely online in HTML as you will see from the list below while a few do not have a print counterpart as far as I know:
Big Book of R
R Programming for Data Science
Hands-On Programming with R
Cookbook for R
R Graphics Cookbook
R Markdown: The Definitive Guide
R Markdown Cookbook
RMarkdown for Scientists
bookdown: Authoring Books and Technical Documents with R Markdown
blogdown: Creating Websites with R Markdown
pagedown: Create Paged HTML Documents for Printing from R Markdown
Dynamic Documents with R and knitr
Engineering Production-Grade Shiny Apps
Outstanding User Interfaces with Shiny
Mastering Spark with R
Happy Git and GitHub for the useR
HTTP Testing in R
Outstanding User Interfaces with Shiny
Engineering Production-Grade Shiny Apps
The Shiny AWS Book
Many of the above have counterparts published by O’Reilly or Chapman & Hall, to name the two publishers that I have found so far. Aside from sharing these with you, there is also the personal motivation of having the collection of links somewhere so I can close tabs in my Firefox session. There are other web articles open in other tabs that I need to retain and share but these will need to do for now and I hope that you find them as useful as I do.
29th April 2010
Last weekend, I ended up doing a spot of file structure reorganisation on the web server for www.johnhennessy.co.uk and needed to correct some file pointers in entries on my outdoors blog. Rather than grabbing a plugin from somewhere, I decided to edit the posts table directly. First, I needed to select the affected observations and this is where I needed to pick out the affected rows and edit them in MySQL Query Browser. To do that, I needed basic string searching so I opened up my MySQL eBook from Apress and constructed something like the following:
select * from posts_table where post_text like ‘%some_text%’;
The % wildcard characters are needed to pick out a search string in any part of a piece of text. There may be more sophisticated method but this did what I needed in a quick and dirty manner without further ado. Well, it was what I needed.
19th April 2010
My trying out WordPress 3.0 in advance of its final release has brought me errors on the links management page. After a spot of poking around the TRAC, I found that the bug already has been reported and that the cause is an extraneous column in the *_links table called link_category. The change in taxonomy handling over the years seems to have made it redundant so I removed the said column from the database using a command like the following from both the MySQL command line and MySQL Query Browser:
alter table wordpress.wp_links drop link_category;
That seems to have made those errors go away and I hop that their upgrade code takes care of this before WordPress 3.0 is let loose of the general blogging public. Taking out the coding brittleness would do too.
10th January 2010
Admittedly, I have been keeping away from Twitter and its kind for a while now but the current run of cold weather in the Britain and Ireland has alerted me to its usefulness and I have given the thing a go. With public transport operator website heaving over the last week, the advantages of microblogging became more than apparent, thanks in no small part to the efforts of Centrebus, National Rail Enquiries and the U.K. Met Office. The pithy nature of any messages saves the effort needed to compile a longer blog post and to read it afterwards. This aspect makes it invaluable for those times when all that needs to be communicated is short and sweet. Anything that cuts down on the information tide that hits all of us every day cam only be a good thing.
Along with Twitter, there is a whole suite of tools available for various bits and pieces. First off, there’s integration with WordPress courtesy of plugins like Alex King’s Twitter Tools. After that, there are numerous web applications for taming the beast. Though I only can say that I scratched the surface of what’s available, I have come accross HootSuite and Twitterfeed. The former is a console for managing more than one Twitter account at once while also offering the facility to do the same for Facebook, LinkedIn, WordPress.com and others too. Twitterfeed may be more limited in scope with offering to turn RSS feeds into tweets but it has its place too. HootSuite might have something similar for WordPress but Twitterfeed is a good more universal in its sweep. Naturally, there’s more out there than these two but I am not trying to be exhaustive here. If I make use of any other such services, I even might get inspired to mention them on here.
6th November 2009
There is a place on WordPress.com where I share various odds and ends about public transport in the U.K. It’s called On Trains and Buses and I try not to go tinkering with the design side of things too much. You only have the ability to change the CSS and my previous experience of doing that with this edifice while it lived on there taught me not to expect too much even if there are sandbox themes for anyone to turn into something presentable, not that I really would want to go doing that in full view of everyone (doing if offline first and copying the CSS afterwards when it’s done is my preferred way of going about it). Besides, I wanted to see how WordPress.com fares these days anyway.
While my public transport blog just been around for a little over a year, it’s worn a few themes over that time, ranging from the minimalist The Journalist v1.9 and Vigilance through to Spring Reloaded. After the last of these, I am back to minimalist again with DePo Masthead, albeit with a spot of my own colouring to soften its feel a little. I must admit growing to like it but it came to my attention that it was a bespoke design from Derek Powazek that Automattic’s Noel Jackson turned into reality. The result would appear that you cannot get it anywhere but from the WordPress.com Subversion theme repository. For those not versed in the little bit of Subversion action that is needed to get it, I did it for you and put it all into a zip file without making any changes to the original, hoping that it might make life easier for someone.
Download DePo Masthead
7th October 2009
One of the things that I do out of curiosity and self-interest is to keep tabs on what is happening with development versions of software that I use. It is for this reason that I always have a development version of WordPress on the go so as to ensure that the next stable version doesn’t bring my blog to its knees. There have been contributions from my own self to the development effort, mainly in the form of bug reports with the occasional bug fix too.
In the same vein, I have had a development version of Ubuntu installed in a VirtualBox virtual machine. There have been breakages and reinstallations along the way when an update results in disruption but it is intriguing too to see how a Linux distribution comes to fruition. In the early days of Karmic Koala (9.10), everything was thrown together more loosely and advances looked less obvious. It is true to say the ext4 file systems support was already in place but the interface looked like a tweaked version of the standard GNOME desktop. Over time, the desktop has been customised and boot messages hidden out of sight. Eye candy like new icons and backgrounds have begun to entice while other features such as an encrypted home folder, Software Store and Ubuntu One came into place. Installation screens became slicker and boot times reduced. All of this may seem incremental but revolutions can break things and you only have to look at the stuttering progress of Windows to see that. Even with all of these previews, I still plan to do a test run of the final revision of 9.10 before committing to putting it in place on my main home PC. Bearing the scars of misadventures over the years has taught me well.
Windows development is a less open process but I have been partial fo development versions there too. In fact, beta and release candidate installations of Windows 7 have convinced me to upgrade from Windows XP for those times when a Windows VM needs to fired up in anger. A special offer has had me ordering in advance and sitting back and waiting. With my Windows needs being secondary to my Linux activities, I am not so fussed about taking my time and I have no intention of binning Windows XP just yet anyway.
The trouble with all of this previewing is that you get buffeted by the ongoing development. That is very true of Ubuntu 9.10 and has been very much part and parcel of the heave that brought WordPress 2.7 into being last year. Things get added and then removed as development tries to fins that sweet spot or a crash results and you need to rebuild things. It is small wonder that you are told not to put unfinished software on a production system. Another consequence might be that you really question why you are watching all of this and come to decide that what you already have is a place of safety in comparison to what’s coming. So far, that has never turned out to be true but there’s no harm in looking before you leap either.
18th September 2009
Being a user of Textpattern, I should have a vested interested in any developments in that venerable web platform. However, the latest release came out at the end of August unbeknownst to me and that’s with an entry on the Dev Blog. Those blog entries come irregularly so that might have been how I missed it but there were other things going on in my life like the installation of new windows in my house and weekends spent in Scotland and Ireland.
Still, the whole release was more low key than, say, a new version of WordPress where many would be shouting how important the upgrade would be and with messages turning up on blog administration screens too. There may be good reason for this given the recent problems experienced by those who fail to keep up with progress. Of course, WordPress is a major target for unwanted attention so it’s best to keep your wits about you. The low key nature of Textpattern might be an asset when it comes to warding off miscreants and its greater compatibility with more technically minded folk may help security too. Saying all of that may be pure speculation but you only have to look at the world of operating systems to see how the idea came into my mind.
A later posting on the Txp blog tells you about the new goodies available in release 4.2.0 but here’s a short selection to whet your appetite: themes for the administration area, multiple sites and new tags. Upgrading proved painless though I did try it out on an offline version of the microsite where I use Textpattern before making a move on its online counterpart. All went smoothly but it’s alway best to look before you leap or a site rebuild might be in order and no one needs that.
16th July 2009
I was perusing a recent copy of Linux Format and encounter a feature describing a self-hosted alternative to the likes of Flickr: Gallery. From my quick look, it looks fully featured, offering themes and even shopping cart facilities for those who want to sell their wares. The screenshots on the the open source project’s website look promising but, for a fuller appraisal, I would need to spend some time trying to bend it to my will. Before anyone mentions it, I am aware that WordPress can be used for photoblogging but this tool seems to take things a bit further. It’s the sort of thing about which I might have wondered given the pervasiveness of content management systems these days. My own custom built photo gallery is devoid of a slick back end, hence why Gallery caught my eye, but I’ll continue with it and may even get to adding the needful myself.
9th March 2009
With the profusion of Content Management Systems out there, open source and otherwise, my curiosity has been aroused for a while now. In fact, Automattic’s aspirations for WordPress (the engine powering this blog) now seem to go beyond blogging and include wider CMS-style usage. Some may even have put the thing to those kinds of uses but I am of the opinion that it has a way to go yet before it can put itself on a par with the likes of Drupal and Joomla!.
Speaking of Drupal, I decided to give it a go a while back and came away with the impression that it’s a platform for an entire website. At the time, I was attracted by the idea of having one part of a website on Drupal and another using WordPress but the complexity of the CSS in the Drupal template thwarted my efforts and I desisted. The heavy connection between template and back end cut down on the level of flexibility too. That mix of different platforms might seem odd in architectural terms but my main website also had a custom PHP/MySQL driven photo gallery too and migrating everything into Drupal wasn’t going to be something that I was planning. In hindsight, I might have been trying to get Drupal to perform a role for which it was never meant so I am not holding its non-fulfillment of my requirements against it. Drupal may have changed since I last looked at it but I decided to give an alternative a go regardless.
Towards the end of last year, I began to look at Textpattern (otherwise known as Txp) in the same vein and it worked well enough after a little effort that I was able to replace what was once a visitor dossier with a set of travel jottings. In some respects, Textpattern might feel less polished when you start to compare it with alternatives like WordPress or Drupal but the inherent flexibility of its design leaves a positive impression. In short, I was happy to see that it allowed me to achieve what I wanted to do.
If I remember correctly, Textpattern’s default configuration is that of a blog and it can be used for that purpose. So, I got in some content and started to morph the thing into what I had in mind. My ideas weren’t entirely developed so some of that was going on while I went about bending Txp to my will. Most of that involved tinkering in the Presentation part of the Txp interface though. It differs from WordPress in that the design information like (X)HTML templates and CSS are stored in the database rather than in the file system à la WP. Txp also has its own tag language called Textile and, though it contains conditional tags, I find that encasing PHP in <txp:php></txp:php> tags is a more succinct way of doing things; only pure PHP code can be used in this way and not a mixture of such in <?php ?> tags and (X)HTML. A look at the tool’s documentation together with perusal of Apress’ Textpattern Solutions got me going in this new world (it was thus for me, anyway). The mainstay of the template system is the Page and each Section can use a different Page. Each Page can share components and, in Txp, these get called Forms. These are included in a Page using Textile tags of the form <txp:output_form form=”form1″ />. Style information is edited in another section and you can have several style sheets too.
The Txp Presentation system is made up of Sections, Pages, Forms and Styles. The first of these might appear in the wrong place when being under the Content tab would seem more appropriate but the ability to attach different page templates to different sections places their configuration where you find it in Textpattern and the ability to show or hide sections might have something to do with it too. As it happens, I have used the same template for all bar the front page of the site and got it to display single or multiple articles as appropriate using the Category system. It may be a hack but it appears to work well in practice. Being able to make a page template work in the way that you require really offers a great amount of flexibility and I have gone with one sidebar rather than two as found in the default set up.
Txp also has facility to add plugins (look in the Admin section of the UI) and this is very different from WordPress in that installation involves the loading of an encoded text file, probably for sake of maintaining the security and integrity of your installation. I added the navigation facility for my sidebar and breadcrumb links in this manner and back end stuff like Tiny MCE editor and Akismet came as plugins too. There may not be as many of these for Textpattern but the ones that I found were enough to fulfill my needs. If there are plugin configuration pages in the administration interface, you will find these under the Extensions tab.
To get the content in, I went with the more laborious copy, paste and amend route. Given that I was coming from the plain PHP/XHTML way of doing things, the import functionality was never going to do much for me with its focus on Movable Type, WordPress, Blogger and b2. The fact that you only import content into a particular section may displease some too. Peculiarly, there is no easy facility for Textpattern to Textpattern apart from doing a MySQL database copy. Some alternatives to this were suggested but none seemed to work as well as the basic MySQL route. Tiny MCE made editing easier once I went and turned off Textile processing of the article text. This was done on a case by case basis because I didn’t want to have to deal with any unintended consequences arising from turning it off at a global level.
While on the subject of content, this is also the part of the interface where you manage files and graphics along with administering things like comments, categories and links (think blogroll from WordPress). Of these, it is the comment or link facilities that I don’t use and even have turned comments off in the Txp preferences. I use categories to bundle together similar articles for appearance on the same page and am getting to use the image and file management side of things as time goes on.
All in all, it seems to work well even if I wouldn’t recommend it to many to whom WordPress might be geared. My reason for saying that is because it is a technical tool and is used best if you are prepared to your hands dirtier from code cutting than other alternatives. I, for one, don’t mind that at all because working in that manner might actually suit me. Nevertheless, not all users of the system need to have the same level of knowledge or access and it is possible to set up users with different permissions to limit their exposure to the innards of the administration. In line with Textpattern’s being a publishing tool, you get roles such as Publisher (administrator in other platforms), Managing Editor, Copy Editor, Staff Writer, Freelancer, Designer and None. Those names may mean more to others but I have yet to check out what those access levels entail because I use it on a single user basis.
There may be omissions from Txp like graphical presentation of visitor statistics in place of the listings that are there now and the administration interface might do with a little polish but it does what I want from it and that makes those other considerations less important. That more cut down feel makes it that little more useful in my view and the fact that I have created A Wanderer’s Miscellany may help to prove the point. You might even care to take a look at it to see what can be done and I am sure that it isn’t even close to exhausting the talents of Textpattern. I can only hope that I have done justice to it in this post.