Pushing up Ostracode work to move it back to Neotoma.

Author: SimonGoring

…pport/EANOD published data June 2024.csv …e_support/EANODpublisheddataJune2024.csvProposals/ostracode_support/EANOD published data June 2024.csv renamed to Proposals/ostracode_support/EANODpublisheddataJune2024.csv Proposals/ostracode_support/EANOD published data June 2024.csv renamed to Proposals/ostracode_support/EANODpublisheddataJune2024.csv

@@ -0,0 +1,148 @@
+"","x"
+"1","container"
+"2","pond"
+"3","lake"
+"4","cave"
+"5","supralittoral"
+"6","rice field"
+"7","ditch"
+"8","intertidal"
+"9","ditch, concrete"
+"10","gutter, concrete"
+"11","container, concrete"
+"12","well"
+"13","puddle"
+"14","spring"
+"15","field"
+"16","pool"
+"17","stream"
+"18","lake, beach"
+"19","rice field, but see comments"
+"20","marsh"
+"21","river mouth"
+"22","river"
+"23","river, mouth"
+"24","swamp"
+"25","stream, mouth"
+"26","seep"
+"27","lake, oxbow"
+"28","spring runoff"
+"29","lake, thermal"
+"30","wet leaf litter by small stream feeding pond"
+"31","soil by small stream feeding pond"
+"32","soil approx. 15 cm from small stream feeding pond"
+"33","wet leaf approx. 15 cm from small stream feeding pond"
+"34","channel, artificial"
+"35","marsh, lower part of marsh, ‘old stream’"
+"36","marsh, lower part of marsh"
+"37","rock pool at coast"
+"38","pool fed by seep, at coast"
+"39","rock pool, brackish"
+"40","other"
+"41","spring, crack in rock containing tiny trickle"
+"42","muddy area below steep slope and small waterfall"
+"43","reservior"
+"44","lake, shore"
+"45","lake beach"
+"46","wetland"
+"47","waterfall"
+"48","river, gravel bank"
+"49","river, sand bank"
+"50","pond fed by spring"
+"51","lake, littoral edge of lake, in lotus patch"
+"52","lake, littoral edge of lake, floating blanket weed"
+"53","channel"
+"54","lotus field"
+"55","estuary (detritus)"
+"56","estuary, brackish"
+"57","estuary"
+"58","canal"
+"59","marsh, reed marsh"
+"60","spring, trickle on rock face"
+"61","rockpool"
+"62","rock pool"
+"63","sandpit, flooded"
+"64","cave, lake in limestone cave system"
+"65","marsh, salt"
+"66","pond, irrigation"
+"67","cave, artificial, puddle"
+"68","water fall"
+"69","river, lower reaches"
+"70","river, riverside, lower reaches"
+"71","seep in dried streamlet"
+"72","marsh (pond)"
+"73","spring at coast"
+"74","cave, natural cave"
+"75","marsh, coastal marsh, reeds"
+"76","lake, artificial"
+"77","river, dead arm"
+"78","puddle, small"
+"79","pond, small"
+"80","creek"
+"81","groundwater, well"
+"82","lake estuary"
+"83","estuary-like"
+"84","lake, lagoon"
+"85","river, mangrove forest"
+"86","stream in urban area. Host Procambarus clarkii"
+"87","bog"
+"88","pond, probably a temporary livestock pond"
+"89","pool under a waterfall"
+"90","bog/ditch"
+"91","pond and trickle"
+"92","container, plastic, with mud and rice plants."
+"93","mangrove forest"
+"94","pool, spring fed"
+"95","river - brackish"
+"96","river - tidal"
+"97","stream - interstitial"
+"98","rice field - abandoned"
+"99","creek, brackish"
+"100","river, tidal"
+"101","river, interstitial"
+"102","pool below waterfall"
+"103","stream, mountain stream"
+"104","swamp at lake shore"
+"105","swamp, artificial"
+"106","pond, artificial"
+"107","lake (oxbow lake)"
+"108","oxbow lake"
+"109","creek, small creek in river bed"
+"110","pond, mud of dried artificial pond"
+"111","puddle, small puddle on limestone cliff, 10m above sea level"
+"112","LAKE"
+"113","PEAT_BOG"
+"114","SEEPAGE"
+"115","POND"
+"116","SPRING"
+"117","STREAM"
+"118","CAVE"
+"119","RIVER"
+"120","SHALLOW_LAKE"
+"121","FRESHWATER_MARSH"
+"122","SHALLOW-LAKE"
+"123","WET_MEADOW"
+"124","ROCK_POOL"
+"125","SALT_LAKE"
+"126","OTHER"
+"127","COASTAL_LAGOON"
+"128","INTERSTITIAL"
+"129","SALT_MARSH"
+"130","DELTA"
+"131","GROUNDWATER"
+"132","PUDDLE"
+"133","CHANNEL"
+"134","RICEFIELD"
+"135","DITCH"
+"136","FLOODED_QUARRY"
+"137","WELL"
+"138","FARM_POND"
+"139","RESERVOIR"
+"140","TROUGH"
+"141","CANAL"
+"142","SALTPANS"
+"143","LAB_CULTURE"
+"144","FISH_POND"
+"145","RESERVOIRS"
+"146","SALTPAN"
+"147","IRRIGATED_LAND"

…code_support/NODE database 22May2024.csv …racode_support/NODEdatabase22May2024.csvProposals/ostracode_support/NODE database 22May2024.csv renamed to Proposals/ostracode_support/NODEdatabase22May2024.csv Proposals/ostracode_support/NODE database 22May2024.csv renamed to Proposals/ostracode_support/NODEdatabase22May2024.csv

@@ -0,0 +1,37 @@
+Benzie, J.A.H. 1989. The distribution and habitat preference of ostracods (Crustacea: Ostracoda) in a coastal sand-dune lake, Loch of Stra thbeg, north-east Scotland. Freshwater Biology, 22, 309-321.
+Beyer, G., Meisch, C. & Wouters, K. 1997. New records of freshwater Ostracoda (Crustacea) from La Gomera, El Hierro, Fuerteventura and Tenerife (Canary islands). Bull. Soc. Nat. luxemb., 98, 239-259.
+Boomer, I., Horne, D. J. & Smith, R. J. 2006. Freshwater Ostracoda (Crustacea) from the Assynt region, NW Scotland: new Scottish records and a checklist of Scottish freshwater species. Bulletin de L'Institut Royal des Sciences Naturelles de Belgique, Biologie, 76, 111-123.
+Danielopol, D.L. 1991. Spatial distribution and dispersal of interstitial Crustacea in alluvial sediments of a backwater of the Danube at Vienna. Stygologia, 6 (2), 97-110.
+Danielopol, D.L., Horne, D.J. & Wood, R.N. 1996. Notes on the ecology of Metacypris cordata (Ostracoda, Timiriaseviinae); why does it not colonise groundwater habitats? In: Keen, M.C. (ed.), Proceedings of 2nd European Ostracodologists' Meeting, Glasgow 1993, 175-180, British Micropalaeontological Society, London.
+Drost, R. 1925. Zur Entomostraken-Fauna des Seeburger Sees. Zeitschrift fur Morphologie und Okologie der Tiere, Bd.4, 1/2 Heft, 1-87. 
+Fryer, G. 1993. The freshwater Crustacea of Yorkshire. Yorkshire Naturalists’ Union and Leeds Philosophical and Literary Society; 312 pp. Titus Wilson & Son, Kendal.
+Fryer, G. & Forshaw, O. 1979. The freshwater Crustacea of Rhum (Inner Hebrides) - a faunistic and ecological survey. Biological Journal of the Linnean Society, 11, 333-367.
+Gonzalez Mozo, M. E., Martens, K. & Baltanas, A. 1996. A taxonomic revision of European Herpetocypris Brady & Norman, 1889 (Crustacea, Ostracoda). Bulletin de L'Institut Royal des Sciences naturelles de Belgique, Biologie, 66, 93-132.
+Griffiths, H. I & Evans, J. G. 1992. Potamocypris arcuata (Sars, 1903) new to Britain. Crustaceana, 62, 110-112.
+Griffiths, H.I., Martin, D.S., Shine, A.J. & Evans, J.G. 1993. The ostracod fauna (Crustacea, Ostracda) od the profundal benthos of Loch Ness. Hydrobiologia, 254, 111-117.
+Gulen, D. 1985. Bisexual Ostracoda (Crustacea) populations in Anatolia. Istanbul Univ. Fen Fak. Mec. Seri B, 50, 81-86.
+Henderson, P.A. & Bamber, R.N. 1988. The rediscovery and redescription of the freshwater ostracod Candonopsis scourfieldi Brady, 1910 (Ostracoda: Podocopida). Journal of Natural History, 22, 465-471.
+Holmes, P.F. 1937. Ostracoda of Lake Ohrid. Sonder-Abdruck aus dem Archiv fur Hydrobiologie, 31, 484-500.
+Janz, H. 1983. Die Ostracoden (Crustacea) des Schoenbuchs bei Tubingen. Jh.Ges.Naturkde. Wurttenberg, 138, 245-259.
+Jungwirth, M.  1979. Limnocythere inopinata (Baird) (Cytheridae, Ostracoda): its distribution pattern and relation to the superficial sediments of Neusiedlersee. In: Loffler, H. (Ed.), Neusiedlersee: the limnology of a shallow lake in central Europe.  385-388. Dr W.Junk.
+Kaufmann A. 1900. Cypriden und Darwinuliden der Schweiz. Revue suisse de Zoologie 8: 209–423.
+Kosmal A. 1968. On the distribution of Ostracoda in the littoral of lake Kisajno (Masurian Lake District). Polskie Archiwum Hydrobiologii 15 (28): 87-102 Warszawa
+Latour J., Garczynski R., Sywula T. 1966. Badania nad solniskami srodladowymi Polski (Investigation into inland saline areas of Poland). Badania Fizjograficzne nad Polska Zachodnia, 18: 7-65, Poznan
+Lerner-Seggev, R. 1968. The fauna of Ostracoda in Lake Tiberias.  Israel Journal of Zoology, 17, 117-143.
+Loffler, H. 1979. The crustacean fauna of the Phragmites belt (Neusiedlersee). in: Loffler, H. (Ed.), Neusiedlersee: the limnology of a shallow lake in central Europe.  385-388. Dr W.Junk.
+Lowndes, A.G. 1930. Some rare and little-known British freshwater ostracods.  Report of the Marlborough College Natural History Society, No. 79, 82-112.
+Lowndes, A.G., 1932. Herpetocypris palpiger, a new species of freshwater Ostracod. Annals and Magazine of Natural History, 9 (50), 155-157.
+Martens, K. & Dumont, H.J. 1984. The ostracod fauna (Crustacea, Ostracoda) of Lake Donk (Flanders): a comparison between two surveys 20 years 
+Mbahinzireki, G., F. Uiblein & H. Winkler (1991): Microhabitat selection of ostracods in relation to predation and food.- Hydrobiologia 222: 115-119.
+Meisch, C. 1990. Ostracodes et ecologie de deux etangs de gravieres d'Alsace et du Luxembourg (Crustacea, Ostracoda). Bull. Soc. Nat. luxemb., 90, 183-197.
+Petkovski, T. 1958b. Zwei neue Ostracoden aus dem Dojransee. - Bioloski Glasnik 11 (114): 27-34.
+Petkovski, T. K. 1969b. Zwei neue Limnocythere-arten aus Mazedinien (Crustacea - Ostracoda). Acta Musei Macedonici scientarum naturalium, 12 (1), 1-18.
+Petkovski, T. K. 1977. Ostracodenfauna des Mindelsees (S.W. Deutschland). Acta Musei Macedonici scientarum naturalium, 15 (3), 49-94.
+Ponyi, J.E. 1992. Studies on the Crustacean fauna of a Hungarian hot spring (Heviz Spa). Zool.Jb.Syst., 119, 397-404.
+Scharf, B.W. 1982. Muschelkrebse aus dem Murnauer Moos (Crustacea, Ostracoda). Entomofauna, Suppl.1, 119-124. 
+Scharf, B.W. 1984. Lebende und fossile Muschelkrebse (Crustacea, Ostracoda) im Meerfelder Maar. Cour. Forsch. Inst. Senckenberg, 65, 81-86. 
+Usskilat, F. 1957. Untersuchungen am Oligohalinikum der Schlei. II. Uber die Ostracodengemeinschaften des Haddebyer und Selker Moores. Kieler Meeresforsch., Bd.31, Heft 2, 151-178. 
+Wagenleitner, H. 1990. Morphology and evolution of Cypria cavernae n.sp. (Ostracoda, Crustacea). Bull.Soc.Nat.luxemb., 90, 199-226.
+Wendling, K. & Scharf, B.W. 1992. Macrozoobenthos including Ostracoda (Crustacea). in: Scharf, B.W. & Bjork, S. (Eds), Limnology of the Eifel maar lakes. Ergebnisse der Limnologie, 38, 239-262.
+Wouters, K. 1983. Contributions to the study of Belgian Ostracoda. 1. The Ostracoda from the environs of Buzenol (gaume District, Belgium).  Bull. Inst. r. Sci. nat. Belg., 55, Biologie, (4), 1-9, pl. 1.
+Wouters, K. 1984. Contributions to the study of Belgian Ostracoda. 2. Cypria subsalsa Redeke, 1936, in Belgium, with a redescription of the species.  Bull. Inst. r. Sci. nat. Belg., 55, Biologie, (10), 1-7, pls 1-2.

Proposals/ostracode_support/habitat_equiv.csv

@@ -0,0 +1,64 @@
+---
+title: "Managing Ostracode Elements"
+format: html
+---
+
+```{r read_tables, echo = FALSE}
+library(readr)
+library(dplyr)
+library(httr)
+library(jsonlite)
+
+node <- readr::read_csv('NODEdatabase22May2024.csv')
+eanode <- readr::read_csv('EANODpublisheddataJune2024.csv')
+```
+
+## Table Additions
+
+The following tables need new information to manage the data:
+
+* `ndb.publications` (Publication data)
+* `ndb.depenvttypes` (New depositional environments)
+* `ndb.lakeparametertypes` (Add lake water type/quality)
+
+## Publications
+
+For publications we will search all publications using CrossRef, and add them if we can find them. Otherwise, we will simply add the citation string.
+
+```{r extract_publications}
+unique_pubs <- eanode$bibliographicCitation |> unique()
+node_pubs <- c(readr::read_lines('node_publications.txt') |> unique(), unique_pubs)
+new_pubs = list()
+
+fetch_url = "https://api.crossref.org/works"
+for (i in unique_pubs) {
+    cross_result <- httr::GET(url = fetch_url, query=list(query=i), 
+        httr::add_headers(`User-Agent`="NeotomaDataScraper;mailto:goring@wisc.edu"))
+    data <- content(cross_result)['message'][[1]]
+    scores <- sapply(data$items, function(j){j$score})
+    if (diff(scores)[1] < diff(scores)[2] * 10) {
+        ref = data$items[1]
+        new_pubs[[length(new_pubs) + 1]] <- list(citation = i,
+                                                 json = toJSON(ref[[1]]),
+                                                 doi = ref[[1]]$DOI)
+        cat("Positive hit for pub.\n")
+    } else {
+        new_pubs[[length(new_pubs) + 1]] <- list(citation = i,
+                                                 json = NA)
+    }
+}
+
+```
+
+## Lake Parameters
+
+We need to add the following critical `lakeparametertypes` to Neotoma. We need to account for the values "Lentic", "lotic", Subterranean", and "estuarine".
+
+```{sql}
+INSERT INTO ndb.lakeparametertypes (lakeparametershortname, lakeparameter)
+VALUES('AquaticSystem', 'Aquatic System');
+
+```
+
+## Depositional Environments
+