Now we are ready to start coding. There are three ways of doing this: by OTUs (Fig. 20), by characters (Fig. 21) or by viewing the whole matrix (grid coding, Figs 1 & 22).
To code a specific OTU for all characters you click (code) to the right of this OTU in the matrix OTU view (Fig. 18). This will take you to the one-click coding view (Fig. 20) where you simply click on the appropriate character state in the list. This will immediately take you to the next character. If you need more information about any character you can open a new window showing the character description (see Fig. 11) by clicking the id no. next to the character name. Note: both this and the following type of one-click coding do not clear any previous codings. You can, however, see if there are any such previous codings by noting if any state has the Tag link after it. Only actual codings can be tagged and are therefore the only ones with the Tag link.
Coding all OTUs for a specific character works in the same way as coding by OTU. Click (code) next to the character name in the matrix character view (Fig. 19) to get to the one-click coding by character (Fig. 21). When you click a state you are taken to the next OTU. The only difference from OTU coding in the example is that only one of them is showing a character with illustrated states. Note also that you can only assign a single state this way. If you need to enter multiple states you need to use the following, third alternative.
Grid coding is accessed through the top left menu. There are two views: the actual grid (Fig. 1) and the coding (Fig. 22). You will notice, in the former, that any OTU or character matrix name provides a link to more information about the item. Also, positioning the mouse cursor over any cell will show you the corresponding OTU, character and coding in clear text immediately above the grid (see Fig. 1). The latter view (Fig. 22), is what you see whenever you click on a cell in the matrix. Here is where you change the coding by checking the appropriate boxes and hitting submit, but potentially also by adding a Tag to an already existing coding.
Tags can be used throught MX to attach notes and comments to various data. Here, we use tags specifically in order to differentiate between different kinds of missing data. This is the reason why every character has an unassigned state. Tags can only be added to existing codings. Note that only state unassigned has a Tag link next to it in Figs 22 & 23 and is also the only state with its box checked.
How to deal with uncoded, uncertain or polymorphic characters is upto the the user. The Chalcidoid project makes the following distinctions:
- UNCODED simply means any untouched cell. These are symbolized by a long dash in the grid view.
- UNASSIGNED is a general term to denote any of the three following until explicitly specified.
- INAPPLICABLE means that the character does not apply for this taxon, like features of veins of apterous insects. This, and unknown, is coded by a short dash.
- UNKNOWN means there is no information available, but at least someone had a look at it.This and inapplicable are coded by a short dash.
- UNDECIDED means someone had a look but cannot decide for a coding. This could, at least in theory, be indicated by checking ALL states of the character for this taxon (except unassigned).
- UNCERTAIN is when two or more states are checked because the person that did the coding couldn’t decide. Undecided could therefore be viewed as a special case of uncertain.
- POLYMORPHIC is when two or more states are checked because all these states apply to the taxon (e.g. in different forms such as sexual and parthenogenetic generation females).
- Unknown and inapplicable both need a tag to be distinguishable. The same is true for uncertain and polymorphic with the difference that you will have to arbitrarily choose one of the coded states to attach the tag to. Undecided, too, needs a tag in order to be unambiguously coded and not construed as fully polymorphic.
When you click Tag you get a pop-up window (Fig. 23), from the first box of which you pick the desired keyword. Proceed to click create unless you want to add something into the Notes field. The resulting tagged coding will look like in figure 22.
In order to quickly find out which codings have a tag associated with them you choose the grid tags view (Fig. 24). A highlighted cell with a T indicates a tag, and clicking it will take you to the full view of that coding (Fig. 22 again).