Tag: taxon panel
It’s been a while since the last blog post. We’ve been busy getting v3.0 out there and fixing anything that’s been cropping up, and many have now upgraded, or plan to upgrade in the near future.
One of the small but important changes in v3.0 was the addition of an occurrence type for “Transported” specimens, being those that are reworked environmentally but not stratigraphically. As well as this, we combined the “Caved” attribute into the same occurrence type, making them mutually exclusive, and thereby forming a hierarchy of “levels of displacement”, which begins with “In-situ” and ends with “Caved”, as illustrated on the new Picklist:
Since this introduction, we’ve had some feedback on whether we should also add a further level, of “Contaminated” occurrences. This would sit below Caved in the hierarchy. These can be specimens from modern contaminants, the lab, or drilling mud itself, none of which implicate caving of the borehole, but would be useful to be able to exclude from certain displays and operations.
We could add this new type as a further option in the v3.0 list. It would not require any changes to existing v3.0 databases, but an application update would be required for v3.0 (and v2.1) to be able to handle any data set which uses the new attribute.
Any comments on this proposal, positive or negative, would be welcome.
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.
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…
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…