XID vs. Lucid Comparison for a Search Example - - PDF of this page.
This page last modified on 25 July, 2008
Abstract
In a companion article Taxonomic Databases for Naive Users we recommend a three-step strategy, and a Multiple-Entry key/database designed to match that strategy, for an inexperienced user seeking to identify an unknown species.
In this article we provide illustrated examples from searches using the XID and Lucid systems for the same database and for the same species. A reader will probably conclude with us that the inexperienced user seeking to use our search strategy will reach the identification goal more quickly, and with fewer steps, using XID rather than Lucid. There are other uses of Multiple-Entry keys and for those Lucid may be more successful than XID, but we are not familiar and experienced with those and will not comment on them further.
Introduction
The wildflower specimen used in most of the examples in this article is one of the 25 illustrated with closeup thumbnail photographs shown in Figure 1:
Figure 1. Unidentified wildflowers from Test Key/Database
The specimen used in most of this article is To Be Identified #5 shown at top right of this matrix. Full screen photographs of this plant are available at http://www.kenbowles.net/sdwildflowers at a location that will become apparent in one of the XID screenshots. Like all of the nearly 500 species shown on that website, details needed for identification are shown in a series of photographs for each species.
Stage 2.
In the XID key, 3 menu/attribute selections lead to 12 species in the Species Remaining list. The XID screen with the Gallery displayed (second search stage) is shown in Figure 2.
Figure 2. XID search Stage 2 with Gallery displayed.
The Lucid search reaching the Stage 2 Gallery is show in Figure 3.
Figure 3. Lucid search Stage 2 with Gallery displayed.
As may be seen, Lucid shows the Attributes (Feature States) that have been selected, and replaces the Species Remaining and Species Discarded lists with the Gallery, i.e. the Images of the Species Remaining.
In both XID and Lucid Stage 2 is concluded when we observe that the left-most photo in the second row, matching Fagonia laevis, matches our specimen. This makes Fagonia laevis the most likely solution to the search. But to make sure, we must go to Stage 3 and check that most of the marked Attributes of Fagonia laevis actually match the specimen.
Stage 3.
The most efficient way to check whether the marked Attributes of Fagonia laevis actually match the specimen is to display a list showing which Attributes have been marked for the Species. In XID, this process is very simple: One clicks the Species name in the Remaining list to display the Species Description in the right pane. Since the list is long, only a portion is shown in a single display screen, and vertical scrolling is required to see desired portions of the list, as in Figure 4.
Figure 4. Portion of XID Description showing Marked Attributes in Blue.
The latest version of XID uses a different color scheme for this list of marked Attributes in context of their associated Menu names, but the principle is the same as shown here.
In our Test Key, the low-probability Notable Recognition Clues (i.e. the Differentiating Attributes), in menus with names starting with "nrc$", are shown before the First Stage Menus. They are the attributes that botanists often use in their conventional keys to differentiate the Species or Genus from others in the key. Most or all of these "nrc$" attributes should match your specimen.
Since the Lucid Player lacks any operation that produces a similar list of Marked Attributes for Stage 3 review, we have built a companion program that produces such a Species Profile list using the .CSV file Exported by the Lucid Builder. An example for Fagonia laevis is shown in Figure 5.
Figure 5. Portion of Lucid Profile showing Marked Attributes in Italics.
The numbers in brackets show the number of species Key-wide that are marked for the same Attribute in the same Menu.
To display the separate Profile window, one needs to click the document icon next to the Species name in the Entities Remaining list. Figure 6 illustrates for the Fagonia laevis example. The Lucid Factsheet Viewer window that pops up to display the Profile is non-modal, meaning that one can continue making selections in the Player window. But the Factsheet Viewer is displayed over the Player window, and must be moved off-screen at least far enough to uncover the Player portions you need to use.
Figure 6. Search example showing Profile icon for Fagonia laevis.
There is a method in Lucid for producing a list similar to the Profile if the result of Stage 3 is a single Remaining Species. See Figure 15, and related discussion, at the end of this article for an example. That method does not work if the Profile is needed to complete the search near the end of Stage 3 for help in resolving differences among a few remaining Species.
Alternate completion of Stage 3.
Both XID and Lucid provide additional tools intended to help the user to pursue the search to a single Species match. Both provide ways that allow redundant single Species matching, thereby allowing one or more of the Attributes selected to be in error. This forgiveness feature seems to be intended for use in cases where the photographs provided for each Species are not sufficiently detailed, or the Differentiating Attributes are not provided. In those situations it is often necessary to use Middle-Probability attributes that are subject to misinterpretation to help resolve the search to a single Entity match. As will be seen, the XID and Lucid tools for this part of the search are quite different.
XID Stage 3 tools.
The most important of the XID tools is probably the Distinctive Attributes list for a single Species. Figure 7 shows an example for the Fagonia laevis search with 12 Species still in the Remaining list.
Figure 7. Search example showing Distinctive Attributes list for Fagonia laevis.
One displays this list by highlighting the Species name as shown, then right-clicking (with cursor still in the highlighted area) to display the context menu. Select Distinctive Attributes from that menu to display the list shown in the right pane.
The Distinctive Attributes list lines marked "<1>" are those for which the Menu/Attribute combinations shown will result in a single-Species in the Remaining list, and that species will be the highlighted Species. In the example shown, it is not surprising that many of the single-Species items are from the Notable Recognition Clues (i.e. Differentiating Attributes) submenus. Lines marked "<2>" will leave 2 Species in the remaining list, one of them the highlighted Species, and the other chosen from the other still remaining Species. Lines marked "<3>" will leave 2 of the other Species, and so on.
Lucid Stage 3 tools.
The most useful of the Lucid tools with 12 Species still remaining is probably the Differences Tool, which can be invoked from either the Entities menu, or from the corresponding icon near right end of the toolbar. Figure 8 shows an example.
Figure 8. Lucid Differences display with 12 Species Remaining.
This pop-up window is modal, meaning that other Player operations are blocked until the Differences window is closed.
The upper (Different Features) panel is sorted with the menus (i.e. Features) judged to be most advantageous (i.e. with smallest number of multi-species attributes) shown at the top. One needs to review all species to discover how many share the one or more attributes shown for the presumed correct matching species tentatively identified in the Gallery. In the case shown, Solanum parishii also has the Rotate attribute, and it seems that none of the other 10 do. To test whether the result of selecting Rotate will lead to 2 Remaining Species, one must close the Differences window, go to the Flower Appearance - ± Profile View menu, and then select Rotate by checking the little box. But if you review my detailed (website) photos of Fagonia laevis you will not find any photo really good enough to judge whether the profile view of the flowers is truly Rotate shape. Had we been familiar enough with the photos available to have known this, we might have been clever enough to skip directly to the next Different Features alternative.
Going back to the 12 species Differences window, we examine the Inflorescence Arrangement alternative and again find that 2 species including Fagonia laevis share the Solitary Flower or Head attribute. This alternative seems safe to select for the search. When we do so the resulting Different Features alternatives are dramatically easier to compare because only 2 species are shown. One may note that when the Differences window first appears, the lower panel (simply labelled "Differences") is much smaller than the upper panel. To achieve the larger size shown for the lower panel in Figure 8 we had to drag the dividing bar separating the upper/lower panels upward in the window. The Lucid builders have probably implemented the design in this way to discourage use of Differences for more than 2 to 4 remaining species (but no mention of this is made in the Help pages for the Player).
The Lucid Find Best operation (available in the Features menu, or using the equivalent icon in the icons menu bar) is an alternate way to find a suitable menu - - especially once the remaining list has been reduced to just a few species. Find Best has a purpose similar to the Analyze list of XID, but with the companion Next Best operation reports back just one menu at a time. With 10 or more species still in the Remaining list Find Best seems to go through a sequence of menu alternatives similar to the sequence shown in the Differences List. Figure 9 shows how Find Best and Next Best report back the menus that they suggest using.
Figure 9. Find Best suggests next menu to use by expanding that menu.
One would need to refer back to the Differences window (which by now has necessarily been closed) to be reminded which Attribute choice applies to the highlighted species.
Lucid also has a Shortcut Features operation (Features menu or equivalent menu bar icon) which vaguely resembles the XID Distinctive Attributes operation. In the Lucid version, the Shortcut Features list includes menus corresponding to the "<1>" items of XID, but for all Remaining Species!! Figure 10 shows an example that applies when there are 12 Species in the Remaining list. Lucid offers no clue as to which Species correspond to each suggested menu item in the Shortcut list.
Figure 10. Lucid Shortcut Features list with 12 Species still in the Remaining list.
It's a roulette game to find out which of the suggested Features (i.e. menu/attribute combinations) apply to the Species tentatively found in the Gallery. However the Shortcut list does have a useful function which we will demonstrate at the end of this article.
Forgiveness provisions
In XID one can set a Forgiveness Level of 0, 1, 2, or 3 using the Options menu. For example, when the Level is 1, then one of the Attributes selected so far can be wrong (i.e. fails to match the Attribute value marked in the database) while the Species will still be shown in the Species Remaining list. To illustrate, we start with Figure 11 showing only Fagonia laevis matching:
Figure 11. Fagonia laevis selected with the 5 Attributes in the right panel.
Notice that the Forgiveness Level is set to the default value of 0, as shown in the lower right portion of the Status Bar.
Next, we set Forgiveness Level to 1 with no change in selected Attributes, as seen in Figure 12.
Figure 12. Forgiveness Level now set to -1.
The Distinctive Attributes panel for Fagonia laevis, now seen on the right, shows a long list of Attribute selections that would again reduce the Species Remaining list to just 1. The content of this list does not change when we raise the Forgiveness Level to a higher (i.e. more negative) value. Notice that all of the Notable Recognition Clues ("nrc$") Attributes are included among the Distinctive Attributes marked "<1>".
From the length of this list, it is apparent that we could raise the Forgiveness Level to -3 by assuring that at least 4 Attributes match Fagonia laevis in addition to the initial set of Attributes we used to reduce the Species list to 4 Species.
Use of the Forgiveness feature of XID in this manner is a way to raise the probability that a correct Species ID has been reached, but checking the full list of Attributes marked in the XID Species Description panel (equivalent to the add-on Profile we had to provide for working with Lucid) is a much better way to do this!!
In Lucid the equivalent of Forgiveness is provided using the Ranked Sorting Mode of the Entities menu. This is shown in Figure 13 for the same Attribute selection set used in the XID example above.
Figure 13. Ranked Species list of Lucid in the right panel.
Important! Notice that the right panel is in the Lists tab - - i.e. not the Trees tab used in many of our earlier Lucid illustrations. If you try to switch from Filtered Sorting Mode (Entities menu) to Ranked Sorting Mode while the right panel is set to the Trees tab, the Player will no longer respond to any commands and will have to be terminated.
When the Player starts up it is set by default to the Trees tab. This shows the Species list in the same order (both Remaining and Discarded sub-panels) as in the Lists panel. In our Test Key we have not used the nested Trees format for the Remaining and Discarded lists (e.g. for nesting Species within Families which Lucid would permit) because it does not exist in our XID master for this key.
In the Ranked list of Figure 13, Species marked 80% correspond to Forgiveness -1 since 80 percent of the 5 marked Attributes are matched for those Species. Those marked 60% correspond to Forgiveness -2.
In Lucid the 5 selected Attributes of Figure 13 lead to turning on the "nrc$ Petals (all others) Individually" Feature (menu), and we know from the Profile page for Fagonia laevis that Petal Base a Narrow "Claw" applies in that menu. Using this changes the percentages in the Lucid Ranked Species list as seen in Figure 14.
Figure 14. Ranked Species list with 6 Attributes selected.
In Lucid there is a simple equivalent of the XID method for selecting redundant matching attributes such as we illustrated earlier in this section using the Distinctive Attributes list of Figure 12. With just a single Species selected, invoke Shortcuts in the Features menu or the equivalent icon in the taskbar of icons. Figure 15 shows the result with Fagonia laevis selected.
Figure 15. Shortcut list with single Species Fagonia laevis selected.
This list is equivalent to our Profile listing for this Species. However, there is no tool directly available in Lucid to permit selecting a single Species directly without knowing a combination of Attributes that will select that Species. In our XID Test Database, the Family and Genus menus would be a start, but we have not implemented similar Species and SubSpecies menus to extend the idea.