Ecoinformatics Redmine: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362008-11-19T22:03:14ZEcoinformatics Redmine
Redmine InfoVeg - Bug #3681 (New): Add 'Original Label Taxon' field to the specimen recordhttps://projects.ecoinformatics.org/ecoinfo/issues/36812008-11-19T22:03:14ZRobert Peetpeet@unc.edu
<p>When I look at a specimen on the SE Atlas such as NCU-75254 and it gives<br />the name as Magnolia virginiana, that is simply how we track the current best name. Then there are two determiniations (Meyer 1990 and Tober 1992), and they are shown in full. The collector was Ashe in 1897 and he probably did assign a name and it is not shown. Specify stores this as 'original label taxon' and we need to add that field to the other fields shown in the label display, perhaps immediately below collectors.</p> InfoVeg - Bug #3617 (New): Add directions for citation to homepagehttps://projects.ecoinformatics.org/ecoinfo/issues/36172008-11-10T17:33:41ZRobert Peetpeet@unc.edu
<p>Liu, X, R.K. Peet and A.S. Weakley. Atlas of the Flora of the Southeastern United States. University of North Carolina Herbarium (NCU), University of North Carolina, Chapel Hill, NC. <a class="external" href="http://www.herbarium.unc.edu/seflora/">http://www.herbarium.unc.edu/seflora/</a>. Observed [Month, Day, Year].</p> InfoVeg - Bug #3612 (New): Citation instructionshttps://projects.ecoinformatics.org/ecoinfo/issues/36122008-11-08T23:29:06ZRobert Peetpeet@unc.edu
<p>We need to place explanation for citation of teh Atlaas on the hoempage.</p>
<p>Might I suggest:<br />Liu, X, R.K. Peet and A.S. Weakley. Atlas of the Flora of the Southeastern<br />United States. University of North Carolina Herbarium (NCU), University of<br />North Carolina, Chapel Hill, NC. <a class="external" href="http://www.herbarium.unc.edu/seflora/">http://www.herbarium.unc.edu/seflora/</a>.<br />Observed [Month, Day, Year].</p> InfoVeg - Bug #3411 (New): Site records and plot records (BLUE RECORDS)https://projects.ecoinformatics.org/ecoinfo/issues/34112008-06-22T22:53:19ZRobert Peetpeet@unc.edu
<p>Bruce Sorrie just sent a long list of county site records, but we have no way to add these as blue recordes other than to pretend they are plots and give Bruce his own corner of the CVS dataset. We need a new blue category for site records contributed by individuals.</p>
<p>We also lack a way to see details of plots, such as geocoordinates, placenames, dates, observer, and co-occurring species. This suggests the need for a new tab for site records, similar to the tab for specimens.</p> InfoVeg - Bug #3410 (New): Literature record option does not workhttps://projects.ecoinformatics.org/ecoinfo/issues/34102008-06-22T22:45:36ZRobert Peetpeet@unc.edu
<p>I went into the admin page and added a (fictional) record for literature for Aristida stricta for Orange Co NC based on Peet 1993. It does not show up on the map. I do not see a place to turn on and off literature records. How do we see these?</p> InfoVeg - Bug #3305 (New): handle specimens from small or fragmentary collectionshttps://projects.ecoinformatics.org/ecoinfo/issues/33052008-05-20T21:44:11ZRobert Peetpeet@unc.edu
<p>Carol Ann wrote:</p>
<blockquote>
<p>I have just databased some specimens from GMUF (herbarium of George Mason<br />University) and put them under SERIES = X-GMUF (we are series NCU; State is<br />series State-NCSC).</p>
<p>The ATLAS pulls the data just fine, but the GMUF specimens do NOT appear in<br />red on the map. This is for Pseudotaenidia montana, by the way.</p>
<p>We are also going to be databasing DOOK specimens of Marshallia obovata and<br />TENN specimens of Marshallia grandiflora, and would want these to map in RED<br />, just as specimens from NCSC and WEWO do now.</p>
</blockquote>
<p>My response:<br />It becomes awkward to have each collection fragment have its own checkbox,<br />and also somewhat misleading in that we will only have a small fragment of<br />the much large collection of specimens. Alan and I agreed that we <br />probably should simply change the WEWO box on the maps to 'Other' and have<br />all the odd lots dumped into that single pile for mapping purposes. When <br />you look at the record for the collection, you will see where it lives. <br />This will probably be a pretty simple fix. This does not preclude adding<br />other large collections with their own checkboxes if they someday become<br />available.</p> InfoVeg - Bug #3301 (New): Annotate incorrectly identified recordshttps://projects.ecoinformatics.org/ecoinfo/issues/33012008-05-19T02:33:42ZRobert Peetpeet@unc.edu
<p>Just as we can flag cultivated records, we should have a way to flag widely published buyt incorrectly identified records. Consider Baptisia cinerea reported in USDA and teh GA atlas from Wheeler Co, GA, which has subsequently been reidentified as B. lanceolata. This should probably get a special color (that agets covered over by even a site record) on the map indicating a record that is incorrect. The correction mechanism should be in the admin functions, just like tagging cultivated observations.</p> InfoVeg - Bug #3041 (New): inferring relationships of higher order nodes based on geographic rangehttps://projects.ecoinformatics.org/ecoinfo/issues/30412007-12-23T19:15:36ZRobert Peetpeet@unc.edu
<p>If one looks at the relationship of Acer negundo (a higher order node with relationships inferred from lower order relationships) one finds<br />1. Acer negundo (W) < Acer negundo (G&C 1991)<br />2. Acer negundo (W) > Acer negundo var. texanum (G&C 1991)<br />and no other G&C relationships</p>
<p>Relationship 1 is in error because because Weakley recognized that G&C includes vars from outside the range of Weakley, but the relationship should be equal because we now define relationships based on common range coverage; ie we have contingent relationships. This needs to be descroibed for a possible TDWG revision. Also, we need to screen the other relationships for this problem.</p>
<p>Also we are missing a relationship:<br />Acer negundo (W) > Acer negundo var negundo (G&C 1991)</p>
<p>Perhaps this is missing because it needs to be inferred from:<br />Acer negundo var negundo (W) < Acer negundo var negundo (G&C 1991)<br />Acer negundo var violaceaum (W) < Acer negundo var negundo (G&C 1991)</p>
<p>I am not sure what would happen if we corrected 1 above to be =.<br />Would this allow the missing relationship to be inferred? If not,<br />this suggests a need to rework the inference rules.<br />to accommodate the situation of unequal ranges of authorities.</p> InfoVeg - Bug #2944 (New): Allow multiple concept sources in CVS datahttps://projects.ecoinformatics.org/ecoinfo/issues/29442007-09-08T21:13:12ZRobert Peetpeet@unc.edu
<p>We currently assign all CVS data to Weakley concepts. We will shortly revise the CVS list and replace the records in the database with new ones. Most will still be to Weakley concepts, but some will be to other concepts (primarily RAB). We need to be sure the database system can handle this. Please report what can now be done and what options might be available.</p> InfoVeg - Bug #2943 (New): Implement new color scheme to help color-blind usershttps://projects.ecoinformatics.org/ecoinfo/issues/29432007-09-08T21:01:55ZRobert Peetpeet@unc.edu
<p>The color scheme we use for maps is not very user-friendly for color-blind users. We need to study options for alternate color schemes. Bob needs to assign to someone to study.</p>
<p><a class="external" href="http://www.stcsig.org/usability/topics/colorblind.html">http://www.stcsig.org/usability/topics/colorblind.html</a><br /><a class="external" href="http://trace.wisc.edu/world/web/">http://trace.wisc.edu/world/web/</a><br /><a class="external" href="http://usability.about.com/od/websiteaudiences/a/colorblind.htm">http://usability.about.com/od/websiteaudiences/a/colorblind.htm</a></p> InfoVeg - Bug #2752 (New): commit atlas to cvshttps://projects.ecoinformatics.org/ecoinfo/issues/27522007-01-26T22:04:25ZRobert Peetpeet@unc.edu
<p>SEEK policy is to deposit our software in cvs.ecoinformatics.org. Moreover, we are now considering a collaboration with SERNEC where we would share some development activities making it important that they have access to the code so as to have a better idea what we have really been up to.</p> InfoVeg - Bug #2637 (New): RAB records of nominal variety occurrences have incomplete namehttps://projects.ecoinformatics.org/ecoinfo/issues/26372006-11-01T15:09:53ZRobert Peetpeet@unc.edu
<p>Weakley writes:<br />Note all the yellow RAB dots for Ilex longipes, when longipes is unambiguously mapped by RAB as decisua var. longipes. It appears that all decidua dots are being treated as unambiguous.</p>
<p>RKP responds:<br />I think this is a previously undocumented bug. The crux of the problem is<br />that the RAB map label foir the nominal var is Ilex decidua and not Ilex decidua var decidua.</p>
<p>This is probably a widespread problem in the database and we need to <br />systematically search the Radford records for vars and make sure that the<br />records for the nominal varieties are so reported in the database. I <br />think this will be the case for every taxon where there is both the <br />nominal var and a named var. Xianhua should be able to do this rather simply.</p> InfoVeg - Bug #2611 (New): Help function texthttps://projects.ecoinformatics.org/ecoinfo/issues/26112006-10-27T22:56:11ZMichael Leemlee@nceas.ucsb.edu
<p>Peet & Weakley need to add help options</p> InfoVeg - Bug #2609 (New): Erroneous assignment of ambiguous statushttps://projects.ecoinformatics.org/ecoinfo/issues/26092006-10-27T22:53:49ZMichael Leemlee@nceas.ucsb.edu
<p>These last two issues are philosophical ones, rather than anything deriving from errors in the software or problems in the data.</p>
<p>If a user enters a search for an infraspecific taxon that we recognize, a map is displayed with records for that taxon, along with any records determined to the species level for the “parent†species. The species-level records, however, are marked as having an ambiguous identification. This way of distinguishing the species-level records seems valuable and important to me, as long they are to be included in response to an infraspecific taxon search.</p>
<p>In contrast, if a user enters a search for a species which has recognized infraspecific taxa, the software thoughtfully displays a list with the species and the infraspecific taxa, requiring the user to choose among them in order to continue. Should the user select the species, the resulting map shows both species level records and appropriate infraspecific taxon records. The species level records, however, are marked on the map as ambiguous. Displaying the results in this way I think is not consistent with the search the user performed in this case. When the search requested, and the concept illustrated by a map, is a species, it seems most appropriate to me to treat records identified to the species level as not ambiguous, and to display them as not ambiguous. This can be explored by searching on Acer rubrum, and A. rubrum var. rubrum.</p> InfoVeg - Bug #2581 (In Progress): Children should occur in map of parenthttps://projects.ecoinformatics.org/ecoinfo/issues/25812006-10-27T22:31:40ZMichael Leemlee@nceas.ucsb.edu
<p>Mapping of CVS data is not handled consistently for taxa with infraspecific members. For example, a search on Acer rubrum produces a map with CVS data for A. rubrum only, with no var. rubrum or var. trilobum CVS records shown. A search on Acer rubrum var. rubrum yields a map with CVS records for var. rubrum, but no species level A. rubrum CVS data. Mapping is not handled this way for the other data sources. (The same problem does appear to apply to NCNHP data, however. Try mapping Hymenocallis occidentalis compared to H. occidentalis var. occidentalis.)</p>
<p>RKP: A map of Acer rubrum var rubrum shows some counties with CVS records that are not present in the map of Acer rubrum (eg NC Randolph, Davidson, Rowan, Catawba, Alexandar; TN Monroe, Carter). CVS vars should nest up into the parent!! This is an error that needs to be fixed. Perhaps this applies to other data types that conform to Weakley concepts (eg NCNHP)?</p>