User:MargaretRDonald/sandbox

Number of articles in English wikipedia today is  

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Bits & Pieces

 * Papers about Lantana in wikidata
 * Kelly Tall's github stuff
 * Kigelia africana
 * Problems landing in WLE Australia
 * Takaka marble
 * Other talk proposals

Korean articles

 * User:MargaretRDonald/sandbox/Korean articles
 * Query for sinologists
 * Google doc for 18 Noveember

Things to be written

 * User:MargaretRDonald/sandbox/Volker W. Framenau

Experiments (Web2Cit)

 * Velleia Sm. APNI
 * Acacia kingiana (SPRAT) (Not possible: no citoid version)
 * Beroe cucumis Fabricius, 1780 AFD
 * Cuphonotus andreanus Acacia aculeatissima PLantNET
 * Maireana cheelii (VicFlora - still citoid)
 * Xanthoria elegans (Link) Th.Fr. Australian lichens
 * Acanthothecis aquilonia Index Fungorum
 * Abroma molle ATRF Abroma molle (QLD biota) complete failure
 * Cuphonotus andraenus (AVH - incomplete)
 * Acacia pulchella Acacia Mill. Acacia abrupta FloraBase
 * Acacia acinacea another Acacia PlantNET
 * author (from Annie)
 * a book (Annie)
 * an award (Annie)
 * AFD ref with compiler still not right Aegiochus piihuka
 * AFD Natatolana albicaudata Natatolana brucei
 * Acacia baileyana (Ausweeds) No citoid form
 * prime ministerial diary Crikey.com (citoid already good enough)
 * Aatolana springthorpei SeaLifeBase. Acropora arabensis
 * 109 Edward street Queensland Heritage Register
 * Ciini paper

Scholia for other uses

 * Topic: seed dispersal
 * Topic: wildfires
 * Topic: apomixis
 * taxon: Phragmites australis
 * software: ImageJ

Other things

 * *Youngjin:Global Account
 * AlphaLemur:Global Account
 * Jjw:Global Account
 * Oronsay:Global Account
 * EmpAhmadK:Global Account
 * Ambrosia 10:Global Account
 * JarrahTree:Global Account
 * Jellomister:Global Account
 * Bracteantha:Global Account
 * Elliottbledsoe:Global Account
 * AmandaSLawrence:Global Account
 * Bahnfrend:Global Account
 * Doctor 17 :Global Account
 * DrThneed:Global Account
 * Calistemon:Global Account
 * Teckez:Global Account
 * Elintripido:Global Account
 * RowanEisner2:Global Account
 * Rowaneisner:Global Account
 * Loqiical:Global Account
 * NimAryan:Global Account
 * Srsbb:Global Account
 * Hakea 68:Global Account
 * Webpaige02:Global Account

Algae December 19,2020 Note reference 21 has links to three authors Laura Wegener Parfrey, David Joseph Patterson and Laura A. Katz Reversion of the cite Q edit produced: December 222, 2020 with no author links. It would be courteous to maintain these author links rather than to destroy them by a simple "revert edit". The article of 19 December links primary authors of subject matter to the subject and these links should be maintained with subsequent edits. MargaretRDonald (talk) 00:30, 23 December 2020 (UTC)
 * Ban: copyright violation
 * User:MargaretRDonald/sandbox/New Guinea annexation
 * User:MargaretRDonald/sandbox/Shane T. Ahyong
 * User:MargaretRDonald/sandbox/Paruku indigenous Protected Area
 * User:MargaretRDonald/sandbox/Powerhouse
 * User:MargaretRDonald/sandbox/Thoughts on WLE 2021 In Australia
 * User:MargaretRDonald/sandbox/Thoughts on WLE 2021 In AustraliaV2
 * User:MargaretRDonald/sandbox/Volker W. Framenau
 * User:MargaretRDonald/sandbox/Chris Watts
 * User:MargaretRDonald/sandbox/Håvard Rue
 * User:MargaretRDonald/sandbox/Nick Reid
 * User:MargaretRDonald/sandbox/Amyema gaudichaudi
 * User:MargaretRDonald/sandbox/Beel
 * User:MargaretRDonald/sandbox/Arafura Marine Park
 * User:MargaretRDonald/sandbox/Colonial exhibitions
 * User:MargaretRDonald/sandbox/WLE Banner mockup
 * User:MargaretRDonald/sandbox/Elja Arjas
 * User:MargaretRDonald/sandbox/WLE 2022 Prizes
 * User:MargaretRDonald/sandbox/Daniel McAlpine
 * User:MargaretRDonald/sandbox/Levinson
 * User:MargaretRDonald/sandbox/FRV Kapala
 * User:MargaretRDonald/sandbox/Don Francois

produces in Styphelia stomarrhena, listing three authors, none of whom currently (2020-12-26) has an enwiki article. But the moment an article appears for any one of these authors, this Cite Q template will link to that author. This capacity to produce links long after one has finished with an article, is an essential difference from the one by one referencing (with its multiple capacity for all problems of referencing) espoused by many who have contributed to the discussion.

Note that I can change to produce:. In other words, one can write names any which way. Thus it is always possible to write name that satisfy the criticism above. One simply uses the parameters available in

Problems with NZPCN identifier
Carmichaelia appressa has the NZPCN id 407 in the taxonbar which leads (after much button pressing and a lot of determination) to the wayback record for C. appressa. Is a New Zealander interested in proposing a new identifier (NZPCN2) which leads directly to the NZPCN current entry.

Wikidata proposal, February 2022
As you know I have been working hard to get the Australian Faunal Directory up to wikidata. Toby Hudson constructed a mix'n.match for it and now 130,000+ of 170,000 items are up on wikidata. The remaining 40,000 did not find a match and that is largely for the reason that there is no match. This reflects the fact that tiny animals, unicellular animals, small animals of the sea floor, and so on, are neither in the databases nor in wikidata. Databases differ in their naming of authorities, differ in the names they consider accepted, and databases are not up to date.

I note that Curtis magazine (september 2021) described seven new (Australian) species of Nicotiana. These are all now in APNI (though not yet plants of the world). I am concerned about how often the various biota mix'n'match catalogues are updated. Thus, I would expect that every year the majority of the databases for which there are mix'n'match catalogues change. Are we capturing the change. For example I would expect that now we are in the process of getting AFD up to wikidata, there are many items in a GBIF mix'n'match catalogue which would now find a preliminary match. FishBase is said to be 100% matched, but scientists do not stop finding new species and reclassifying the old. I believe it is an active database and not static. We need a plan and a set of timings for updating most biota mix'n'match catalogues.

The 40000 unmatched AFD entries are indeed largely unmatched  so far. This points to 1. a lack of data in the various fauna databases, 2 the mismatch and disagreements between taxonomists. For this reason I think it is a matter of some urgency to work systematically to get GBIF, EOL, ALA,  BioLib, iNaturalist and other databases fully up to wikidata. In many cases this may mean updating the mix'n'match catalogues. While this may seem outside wikimedia Australia's ambit, I don't think it is, as we always need confirmation about accepted species and synonyms.

We also desperately need a mix'n'match for SPRAT (I have not so far found one). Currently the identifier occurs in the taxonbar and signals that a taxon (usually species / subspecies) is threatened. An official mentor for a defined period would help me resolve many of these issues.

Toby has told me: ""Reloading data from an external catalogue is fairly easy (or even scheduled) if it was scraped in the first place. (but be careful about doing it often or on big sets, because it can impose heavy server load) For example, go to https://mix-n-match.toolforge.org/#/jobs/238 and press "autoscrape". It will take at least a few hours, so don't press twice!

I didn't scrape AFD, I downloaded each letter's search csv individually, then combined them. That was laborious, and I won't do it again for the next year or two.

Refreshing the automatches (e.g. GBIF now finding matches created by the AFD) is also pretty easy. E.g. go to https://mix-n-match.toolforge.org/#/jobs/3296 and click "automatch by search". (But it looks like that particular GBIF set may only be a subset of the entire GBIF?)""

However, I was not able to use the help above

(I am very proud that all 130,000+ AFD id'ed taxa have parents which means that we can find all AFD fishes, frogs, reptiles, cnidarians.... that are up.  This is not the case for many other taxa which means for example that hunting for all fungi on wikidata misses many taxa that are fungi (the parents die out before reaching P171* fungi)

AFD
The first priority is to get up species and subspecies from AFD: these are the things which scientists describe. These are the things which have matching museum specimens.

All of these wikidata items must have the following properties: P31, P171, P105, P225, P6039.The property of AFD id (P6039) has several queries which permit the cleaning up of its misuse in wikidata. Other queries: has this Qitem a parent, is it an instance of a taxon? need also to be run. (This person managed to put up many fungi duplicates because the simple query: "list all taxa which are fungi" fails to list all fungi on wikidata, since many fungi taxa fail to have parents.)

Taxonomy
Most Australian biota databases follow key Australian resources. Thus, ALA, and SPRAT follow APNI and AFD. However, to illustrate some of the difficulties, consider Psopheticus accepted by AFD, WorMS (with a different year from AFD), and doubtful for GBIF which  has a different author and year, yet still describes a crab genus. It is important, given the many disagreements with respect to acceptance and author name that other (non-Australian) databases be brought into a more complete state. So that the some 40,000 new taxa find their counterparts in GBIF, EOL and insects of the world, etc. Updating of these databases mix'n'match so that new preliminarily matched taxa can easily be seen in wikidata is paramount. It means that anyone working on a wikidata item may easily see that GBIF (for example) has a corresponding identifier. In other words, just as when we work on a wikidata item for a person, we see many identifiers which may belong to that person, and we click on those that match. Currently there seems to be no preliminary matching for any of our approximately 40,000 new wikidata items.

I am hoping that the mentoring part of this program will give me the skills to make the addition of other wikidata identifiers easier than doing searches for a taxon name on the corresponding databases. I envisage this as learning more about updating mix'n'match effectively.

Other Australian biota tasks

 * 1) Species Profile and Threats Database: Fauna and Species Profile and Threats Database: Flora (SPRAT) with the wikidata property P2455 needs to be fully uploaded to wikidata
 * 2) Endangered communities are also listed by SPRAT. Thus the communities listed in List of endangered ecological communities in NSW have SPRAT ids.  The community SPRAT id has not yet been proposed as a property but needs to be and needs to be fully populated in wikidata (a small and easily completed task). (The current full list can be downloaded as a file and contains 94 communities. This list does not contain the urls and potential ids for communities.) The critically endangered community, Natural Temperate Grassland of the South Eastern Highlands, would have the id 152. This id should form part of the authority control bar for pages describing Australian endangered communities.

Expected outcomes

 * 1) All genera, species and subspecies of AFD to be in wikidata by December 2022. (But not  tribes, subtribes, subfamilies and subgenera. These may come later. )
 * 2) SPRAT ids for fauna and flora to be complete in wikidata.
 * 3) A mastery (?) of the many and varied ways of updating mix'n'match catalogs: to extend my skills (and those of anyone else wishing to join the mentoring sessions) and to allow the easier matching of eg. GBIF data. (Widening the audience base will expand the much needed wikidata skills of others who wish to contribute in wikidata)

Other desired outcomes
Australian Flora have a multiplicity of ids, most of which are informative about the taxonomy and many which give excellent descriptions. However, algae, fungi and fauna are less well served.


 * 1) Easier updating of the EOL id, GBIF id, BioLib id, Index Fungorum id, MycoBank id, NCBI id, iNaturalist id to match Australian fungi, lichens and fauna already uploaded to wikidata.

Questions / difficulties

 * 1) How do I know (find out) if the GBIF mix'n'match uses the entire catalogue?
 * 2) I have updated the AFD catalog many times and have has a result corrected various incorrect double entries, yet these still show as double entries after a "manual sync". I have not yet learned how to make the catalog recognise  that these are now corrected.  See for example, Exoneura rufa, which has just the single AFD-d - Exoneura_(Exoneura)_rufa, but continues to be listed after the manual sync as having a further AFD_id (Exoneura_rufa). This also occurs for Limnodynastes dumerilii where just one AFD-id exists, but two are shown after the manual sync.

Louise Hamby

 * User:MargaretRDonald/sandbox/Louise Hamby
 * User:MargaretRDonald/sandbox/Report for Tom
 * User:MargaretRDonald/sandbox/Savanhdary Vongpoothorn
 * User:MargaretRDonald/sandbox/archive
 * User:MargaretRDonald/sandbox/Gender-age bias
 * User:MargaretRDonald/sandbox/KMN_List
 * User:MargaretRDonald/sandbox/Tweets
 * User:MargaretRDonald/sandbox/Simoselaps
 * User:MargaretRDonald/sandbox/Ilsa Barea
 * User:MargaretRDonald/sandbox/Ladislav Mucina
 * User:MargaretRDonald/sandbox/Thoughts on judging wikilovesearth
 * User:MargaretRDonald/sandbox/Lake
 * User:MargaretRDonald/sandbox/Arve Elvebakk
 * User:MargaretRDonald/sandbox/Greta Stevenson

Celina María Matteri

 * User:MargaretRDonald/sandbox/Celina María Matteri
 * User:MargaretRDonald/sandbox/Montebello Islands Marine Park
 * SPARQL Query for Enwiki articles for taxa authored by Matteri
 * Query for Enwiki articles for taxa authored by Planchon (Planch.)
 * SPARQL Query for Enwiki articles for taxa authored by E.Mey.
 * User:MargaretRDonald/sandbox/Zealandia pustulata
 * User:MargaretRDonald/sandbox/protologue
 * User:MargaretRDonald/sandbox/Zealandia pustulata
 * User:MargaretRDonald/sandbox/protologue

Other things

 * User:MargaretRDonald/Bitching about biodiversity ...
 * User:MargaretRDonald/Sandbox/Marshall Harris Cohen
 * User:MargaretRDonald/Sandbox/bio Wiki Loves Earth
 * User:MargaretRDonald/Sandbox/References for optimal quadrat size

Bloodhound Tracker

 * User:MargaretRDonald/sandbox/Bloodhound Tracker

Chrysocalyx
George Samuel Perrottet and Jean Baptiste Antoine Guillemin when describing a new genus, Chrysocalyx, (not accepted) write: "Le nom de Chrysocalyx est dérivé de chrysos, aureus, et kalyx, calyx, à cause des calices couverts de poils dorés qu'offrent les principales espèces." Note that all usages of chrysocalyx as a species epithet postdate Perrotet's and Guillemin's use of the new word.

Things to do for a Plant project

 * Write articles for Kevin Thiele's photographs
 * Write articles for Jean & Fred Hort's Flickr photos (and in both cases generate reports about usage..)
 * Fragment Flora de l'Egypte engraving images and write articles for them
 * Complete the author/year of pub/reference in wikidata
 * Complete the NT Acacias listed in NT portal
 * Continue the Australian threatened species...

New Bits & Pieces

 * Wikicite 2020 (Melbourne)
 * User:MargaretRDonald/sandbox/Wellington/Sydney Report
 * User:MargaretRDonald/sandbox/Plants with SPRAT ids and no article
 * User:MargaretRDonald/sandbox/Tricoryne simplex
 * User:MargaretRDonald/sandbox/Janie Mason
 * Adams, Mary Annie checking the link
 * User:MargaretRDonald/sandbox/Mueller's female collectors
 * User:MargaretRDonald/Sandbox/ReportWOW2019
 * User:MargaretRDonald/Sandbox/Worklist-U3A
 * User:MargaretRDonald/Sandbox/Taxonomy of Newcastelia
 * User:MargaretRDonald/Sandbox/Ephedraceae
 * Python for everybody
 * User:MargaretRDonald/Sandbox/Use of PetScan to generate list of NT acacia articles to be written

Bits and pieces

 * User:MargaretRDonald/sandbox/Prostanthera
 * User:MargaretRDonald/sandbox/Maratus pavonis
 * User:MargaretRDonald/sandbox/Random Breath Testing
 * User:MargaretRDonald/sandbox/Boronia verecunda
 * User:MargaretRDonald/sandbox/Cottesloe Reef Habitat Protection Area
 * User:MargaretRDonald/sandbox/Amar Chaud Joshi
 * User:MargaretRDonald/Sandbox/Worklist-Avalon
 * User:MargaretRDonald/Sandbox/Worklist
 * User:MargaretRDonald/sandbox/WikipediaClassSyllabusU3A
 * User:MargaretRDonald/sandbox/WikipediaClassSyllabus
 * User:MargaretRDonald/sandbox/Miscellaneous
 * User:MargaretRDonald/sandbox/DORCA
 * User:MargaretRDonald/sandbox/List of endangered ecological communities in NSW


 * User:MargaretRDonald/sandbox/Werner von Siemens ring code
 * User:MargaretRDonald/sandbox/References needed


 * User:MargaretRDonald/sandbox/Isopogon pruinosus
 * User:MargaretRDonald/sandbox/Acacia equisetifolia
 * User:MargaretRDonald/sandbox/Indigofera linnaei
 * User:MargaretRDonald/sandbox/Cecarria obtusifolia
 * User:MargaretRDonald/sandbox/Cecarria
 * User:MargaretRDonald/sandbox/Problem with range map
 * User:MargaretRDonald/sandbox/Ficus coronata range
 * User:MargaretRDonald/sandbox/Conostylis bealiana

Stuff
Where species live (Blog) and his article about lizards, and the same type of modelling applied to night-parrots. Both papers used the NicheMapR R-package for the modelling.

K-medoids bootstrap clustering
See K-medoids Distance-Based clustering

How many multiple imputations do you need

 * How many imputations do you need? (Paul von Hippel, October 30, 2019)

Redouté
Pierre-Joseph Redouté (1759-1840). See fr:Pierre-Joseph Redouté Choix des plus belles fleurs, [http://plantillustrations.org/illustration.php?id_illustration=37914 Iris pumila L. var. floribus violaceis. Iris pumila L. var. floribus violaceis. Redouté, P.J., Les Liliacées, vol. 5: t. 261 (1805-1816) (P.J. Redouté)] and at Pierre-Joseph Redouté

Drosera
Carnivorous plants with (Drosera ) glistening, sticky, gland-tipped hairs that bend over entrapped insects or (Aldovandra ) 2-lobed trap-leaves that snap shut on aquatic invertebrates. Flowers small and delicate, in raceme-like cymes (monochasia) that are often coiled (circinate) in bud. Petals 5, free, pink, red or white. Stamens 4 or 5, rarely more. Ovary superior, with several free, feathery styles.

This is a small, cosmopolitan family, richest in Australia. The most widespread genus is Drosera, species of which are commonly called sundews and easily recognised by their glistening, insect-trapping hairs. Various species of Drosera are found almost throughout Australia in nitrogen-poor soils, from swampy peats to seasonally moist sandy soils in heathy vegetation, but never in closed forests. The aquatic genus Aldovandra also occurs in Australia but is rarely encountered.

Stuff on phylogeny and Seine and Barthlott

Diels (1906)

Slide show links

 * Siobhan: VALA2020