It has long been possible to use StrataBugs to create ‘closure’ diagrams, showing the relative abundance of different groups of species. I use the term ‘groups’ rather than ‘Groups’ intentionally, since the ‘groups’ may also be ‘categories’. A recent change has made this feature a little more flexible.
The new feature in brief
Let’s say a palynologist wants a quick overview of the relative abundance of marine vs terrestrial species. In practice this is achieved by comparing the abundance of dinocysts (category DC) with the abundance of pollen and spores (cateogry SP). Since all species belong to a category already, it’s simply a case of creating a panel which is grouped by category, and displayed as a relative stacked sawtooth plot. The only problem was that all the other palynology categories which happened to show up in the data would also be included in the plot (the left-hand panel in the image below). In the data below, the DA category represents the number of dinocysts in the first 100 specimens, so that’s what I want to compare to the SP count (N.B. your counting method might be different!).
We have now made it possible to ‘filter’ the panel by more than one category, which allows you to create the right-hand panel below comparing just DC and SP. Species not belonging to the filter categories are excluded from the data.
To make use of this setting, you need to select the ‘Outer’ panel properties tab, and choose ‘Restrict data to’. Here you can choose from a list of categories. To select more than one category, hold down CTRL while you select from the list.
A recap on groups and categories
All genera (and therefore species) must belong to one (and only one) category. This is a convenient way of, well, categorising taxa. Most StrataBugs users will not need to modify the standard list of categories – it would make exchanging data between databases more difficult.
Groups, on the other hand, are entirely under your control, and one species can belong to any number of groups. Groups can be attached to projects.
Both are useful for creating charts. You can find our more in the help.
More about closure diagrams
The inner panels above are created with the following options:
- ‘Group data by’ is set to ‘categories’ – this means that counts of species from the same category will be aggregated. You could also use groups here, in which case either the outer or inner panel must be filtered to a group set (which defines the selection of groups).
- ‘Plot type’ is set to ‘stacked curves’ – rather than showing the different categories in individual columns.
- ‘Calculation style’ is set to ‘relative (inner)’ which means that instead of showing the absolute count for each category, we’re showing the count as a percentage of the total for the inner panel. In this case you could also select ‘relative (outer)’ (i.e. the count is relative to the outer panel), because the inner and outer panels are showing the same data (more in this previous post).
You can find out more about the biostratigraphy panel options here.
Amongst the many voices of approval from those that have got to grips with the templated charts in v2.1 there are always a few folks who are permanently wedded to the idea of “one well, one chart”, and don’t want to work in a templated view of the world. They also prefer a WYSIWIG panel property editor, so they can make individual panel changes as required for the well they’re working on. For them, getting to know the options available on the standard chart is where they need to start.
The Standard chart tab in the Samples & Interpretations module is always present, and contains a panel for all the data types that are present in the well. You can customise the standard chart by clicking in the chart properties icon in the toolbar: and using the panel list to add/edit and delete panels. Right clicking on any panel in the chart will bring up the option to edit the panel’s properties.
In this way you can create the chart you want. When you’re done, you can then use the rightmost button to save the chart as a template.
At this point you can name your template for use in the next well. Any panels that have different properties to the default will be saved in the new template.
In your second well, use the penultimate button on the toolbar to load the template you previously made into the standard chart…
Now, make any changes you like to the panel properties. When you’re done, pres the last button again to save the template.At this stage you have a choice: if you update the existing template, then this will also apply to your first well and any others that happen to be using this template. This may or may not be what you want. To keep things simple, you can select New Template, and the template name will be suffixed by the well name, and thereafter opened in a new tab bearing the template name.
When you next open your wells, the template tabs will reopen in the same state they were saved in, while the standard chart will reset to the default layout. To make changes, see above (load your template into the standard chart ….)
Lots more information on the charts tab, as always, in the help here.
We try to make it as easy and ‘safe’ as possible for you to explore StrataBugs without inadvertantly corrupting your data. That’s why we always ask you to confirm before deleting something. Last week we were clicking about in this way (exploring), trying to think through an idea, when we stumbled upon a feature that we’d completely forgotten was there.
A helpful user had made a great suggestion. In their own words:
Being able to add interpretations (e.g. chronostrat) via the charts in the Samples & Interpretations module would be a very useful addition, rather than having to keep switching tabs back and forth.
The thought process on our side goes something like this: Well, yes, that would be good! How would that work? Double-click somewhere? There’s already some double-click action in the zones panel (*try double-clicking in a zones panel*) – you can edit existing zones by double-clicking on them. So, maybe double-click where there isn’t a zone? (*double-click where there’s no zone*) Hey, look, it brings up the interval dialog! So we already implemented this! (*try the same on another panel*) Oh dear, doesn’t seem to work in this panel, why’s that?
There are, literally, millions of lines of code in StrataBugs. It’s not surprising that we forget about some of them.
Go to the full post…
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…
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.
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!
Expect the blog to feature many, many posts about the biostratigraphy panels. There are so many combinations of panel options that I shouldn’t think anybody is au fait with all of them – probably not even me! I want to start with something relatively (excuse the pun) simple. I’m also choosing this because it’s something that wasn’t possible before the new charts module was released.
My examples use data from our demo dataset. My template starts out as a simple ‘group by category’ palynology panel – that is, I’ve kept all the basic options except changing “group data by” to “category”. In the real world this would be better as groups, for which you will also need to restrict the outer panel to a group set.
Everybody should be familiar with the “relative (inner)” calculation style – it’s been in StrataBugs since the year dot. It would transform a simple absolute-abundance style plot like this:
Into a relative-abundance plot like this:
Each column shows its count relative to the total count for the analysis across the whole panel. Each row adds up to 100%. Well, OK, nearly 100% – since you asked, we’re rounding up to integer values except where we have less than 1%. Go to the full post…
A previous comment on this blog noted “I still forget that changing something on the template I’m working on changes all the previously made charts.” I promised to address the subject of decoupled panels. I don’t want to call this a “solution” because that would imply that templated panels are a problem! It is really useful to template panels, in the right context (more on that below).
Decoupled panels have their place too. Sometimes you will want to make modifications to a panel which are very specific to one block template, project or well. Not only are you sure that you won’t need the panel elsewhere, you also want to protect it from out-of-context modification in the future.
You could “copy” an existing panel template and work with your copy. You would still need to remember not to modify it later, and it would still be clutter in your panel templates list.
Decoupling is the process of making the copied panel template “local” or “private” to a block template. The panel is no longer associated with its original template; it is not named, it will not appear in the tree and cannot be used in other blocks. If the block template is read-only then this panel cannot be edited. Its settings will be lost if the block template is deleted. Underneath, it’s still using a panel template, but for all practical purposes the panel properties become part of the block template.