In recent weeks we’ve been busy enhancing the stratigraphic range chart plot to display abundance events. Many thanks to Martin Pearce at Evolution Applied for working through this with us.
The stratigraphic range panel is designed as an alternative type of view on a composite standard (event scheme). It shows the ranges of events in time.
A note on terminology: the ‘range chart’ I will be referring to is different from a ‘species distribution chart’ showing abundance variations in a well section – which I do often hear referred to as a ‘range chart’. The range chart in question is concerned with time.
A simple range chart showing a few species might look like this:
Events relating to the same species are grouped together. In this case there are three events for Palynodinium grallator – a total species range, plus two abundance event ranges.
At the moment there is no formal way to link these abundance events (denoted by the [A] and [SA]) to an abundance scheme which defines them. A simple workaround is to create an abundance scheme with exactly the same name as the composite standard. The stratigraphic range panel will pick this up and use it to identify abundance events. Any term abbreviation from the abundance scheme which appears in the event name surrounded by brackets (you may use parentheses, square or angled brackets) will be interpreted as an abundance event. Go to the full post…
Over the past few weeks we’ve been polishing a new feature for “overplotting” biozone panels. This feature gives you more flexibility over which biozone schemes you can include in the same columns. It was something we allowed for in the v2.1 data model but hadn’t got around to implementing yet. And yes, I am aware that “overplot” isn’t officially part of the English language, but it does describe the concept quite succinctly!
Hopefully you are already aware that:
- Biozone intervals are always linked to a scheme.
- Biozone schemes are linked to a discipline.
- There are four panel types for biozones: one for to each discipline.
- A biozone panel in a block template has a scheme attribute. When you add a panel template to a block template, you can either:
- Choose one scheme belonging to the panel’s discipline, or
- choose no scheme (“<panel per scheme>”), in which case you will see all of the intervals linked to schemes with the panel’s discipline, either merged into one column or as separate, automatically generated panels.
In short, this means you could either select all the schemes for a discipline, or one scheme only.
Adding the overplot function makes things much more flexible, giving you complete control over which intervals will appear in which columns, and even allowing you to mix disciplines. It is a simple technique (on your side anyway!) which tells one panel to draw on top of the previous panel. Go to the full post…
You get a shiny new computer with a nice high resolution screen but when you start up StrataBugs, the text font looks too small so you can hardly read it, and some windows are clipped so you can’t see everything that’s supposed to be there without enlarging it. Moreover, every time you get a simple dialog box pop-up, the icon, instead of looking like this:
is clipped, like this:
So, what’s going on? Well, it’s possible in Windows to set your display preferences so that text fonts and other windows components are made larger and more readable, without sacrificing the overall number of pixels available on screen (unlike, say, lowering the overall screen resolution, which doesn’t look good on modern flat screen monitors). As higher resolution monitors have become the norm, the default settings on a new Windows installation is actually for this preference to be set to 125%, so you might already have enlarged text without realising it. The problem is that a lot of software, and this includes the Java library code that StrataBugs uses, doesn’t respond in a uniform way to the font size change, resulting in the general loss of beauty described above.
In general, if you’re running a recent update of StrataBugs, you will have seen that the text is reduced in size compared to the general Windows font sizes, so that the text and other components fit into the StrataBugs windows as they are designed. Older builds (including v2.0), will have parts of some of the dialogs missing, where the window is too small to accommodate the enlarged controls. We’ve been tweaking things again recently, to get around the tiny menu font sizes and the clipping you see above, which makes life a bit easier on the eyes.
We would also recommend that you don’t opt for the ultra high resolution 4K screens for Windows, as the application will look tiny, however this doesn’t affect the Mac community, as the scaling for their Retina displays is already built into the libraries. We’ve always bemoaned the lack of pixels available on standard issue laptops with a resolution of 1366 x 768, which is the bare minimum of space you need. More pixels are definitely better, as long as you can still read it.
The best solution, for now, is to right-click on your desktop background, select Display Preferences and reset the size to 100% ….
You might find this a bit tricky to start with, but you might also like the extra screen “real estate” that this gives you. If after a while you still find yourself squinting at the screen, try moving your chair closer, or visit an optician and invest in a new pair of glasses!
A couple of people have stumbled over this one in recent weeks. No “bug bounties” I’m afraid folks – this behaviour is intentional. Honestly, it’s not a bug, it’s a feature!
In a high precision study, you may have analysed many samples within a small depth range. If the occurrence data were plotted at the exact analysis depth, then all the histograms and labels would plot on top of each other.
This can make it difficult to see the finer detail. In order to get around this problem, we ‘distribute’ the analyses into the surrounding empty space, such that each data point is readable.
Possibly the most frequently asked question we are asked is “why do my samples show with different numbers of decimal places?”, or “where are the decimal places on my cuttings?”. StrataBugs charts have always displayed the different sample types with precision which reflects the nature of the sampling. Cuttings samples show to the nearest whole metre (or foot) because it would be misleading to suggest the depth was any more precise than that.
Here’s the full information for all sample types:
|CU||cutting||nearest whole metre or foot|
|SC||sidewall core||1 decimal place|
|CO||core||2 decimal places|
|OC||outcrop||2 decimal places|
|LOG||log pick||1, 2 or 3dp – configurable by super-user (Control Panel > Config > Default samples depths)|
This affects the charts and wherever samples are displayed along with their type and label in the data tables. The position of samples is still determined by the depth you give them (and which, in the case of cores (and optionally cuttings) may be affected by core shifting).
These levels of precision follow an industry convention used since version 1.0 of StrataBugs. One drawback is sometimes where you have a well originally drilled in feet and now dislayed in metres, where you would like to show the cuttings depths to 2 decimal places to reflect the converted number. You can do this in the Samples panel by checking off the “Display symbols” option in the panel propeties.
Within the database itself, all sample depths are stored in metres to at least three decimal places (dependent on the database type).
Analyses may be ‘prepared’ (yet to be analysed), ‘analysed’ (contains occurrences), or ‘barren‘ – indicating that they have been analysed but found to contain no taxa.
When we reviewed and tightened up all aspects of the way the biostrat data were stored in v2.0, it seemed sensible to enforce that analyses marked as barren did not contain occurrences of microfossils. Therefore the only option when clicking the barren flag was to clear all the occurrences. It’s been pointed out to us since that analyses can contain accessory minerals or perhaps caved taxa, while still technically being barren of microfossils.
The most recent test update will allow you to have your cake and eat it – you still get the option to clear the occurrence list, but you can have some analysed data while the analysis is marked as barren. This doesn’t require a change to the underlying data model, and any data files exported will reflect what you have on screen. The only caveat is that if somebody without the update imports the file, their analysis will not be barren.
In this second post about giving your database a spring spruce-up, I’m going to outline some tips for cleaning up your list of schemes.
You are mostly going to be working in the Schemes & Interpretations module. Select Schemes > Strataigraphic schemes to bring up the Schemes window.
Spring is in the air here in the UK and I for one have forgotten my new year’s resolutions. Blow away the cobwebs and embrace the new season feeling virtuous by spending a little time spring-cleaning your StrataBugs database. All databases need ongoing tidying up, organising and pruning. It need not be a huge job – a little dusting here and there to keep things in shape will go a long way if performed frequently. Perhaps get into the habit of performing these tasks at the end of each project.
Go to the full post…
A useful addition to StrataBugs 2.1 is the ability to include entire genera in groups. Previously if you wanted to do this, you would have had to find all the taxa from the genus (probably via a taxon search) and add them to the group. If you or a colleague added another species to the genus, you’d have to remember to add it to the group. The new system saves you this hassle and guarantees that the group stays up-to-date.
You should be familiar with the Taxon Database’s ‘Taxa’ window – this is your working list of taxa. Let me introduce you to its sister, the ‘Genus’ window. Open by choosing from the menu Taxa > Genera.
You can populate it with genera by hitting the search icon, or by dragging onto it species from any tables or lists in StrataBugs. Drag a genus from here onto the Taxa window to populate it with the member species. You can also drag the genera directly into your taxon groups. Go to the full post…
Did we mention that the charts are interactive?! You’ll get a lot more out of them if you are familiar with these keyboard shortcuts.
- Use your mouse wheel to move up and down…
- … and hold down SHIFT with the mouse wheel to go left-right.
- Hold down CTRL with the mouse wheel to zoom in and out.
- CTRL and +/- also zoom in and out.
- CTRL and 1 zooms to the normal scale.
- CTRL and 0 (zero) zooms out so that the whole chart fits on your screen.
- Hold down ALT and draw a box to zoom to that area:
- Hold down the q key to toggle on the magnifer:
Undo and Redo
- Use CTRL+Z to undo or CTRL+SHIFT+Z to redo.
Note – these are for undoing changes you have made to data via the chart – e.g. by dragging a node on the depth/age panel, or dragging an interval boundary. They won’t undo anything you have done via a dialog, including changing the chart properties!