Closed wwieder closed 4 years ago
wwieder
commented
4 years ago @piersond It looks like there are NEON data in the tarball, but these also aren't coming up on the bivariate plots (e.g. looking at soil texture, silt below, on the maps NEON sites show up), but these aren't coming into the x-y plots? Also, @srearl current NEON data are missing location_name, at least through shiny?
srearl
commented
4 years ago The Shiny app in its currents state throws an error, at least for me, when plotting NEON sites. This does not seem to be the case, though, if I use a more recent tarball, e.g., below.
For NEON locations, I think that also was addressed with the more recent tarball, e.g., image above, and note that the content of location and site names differs, e.g., below.
| network | location_name | site_code |
|---|---|---|
| DIRT | H.J. Andrews | AND |
| LTER | H.J. Andrews Reference | HJA |
| LTER | Cascade Head | HJA |
| LTER | Metolius Research Natural Area | HJA |
| LTER | Pringle Falls Research Natural Area | HJA |
| LTER | White River | HJA |
| LTER | Nisqually R. | HJA |
| LTER | Ohanapecosh R. | HJA |
| LTER | Carbon R. | HJA |
| LTER | T. T. Munger Research Natural Area | HJA |
| LTER | S. Fork Hoh R. | HJA |
| LTER | Quinault RNA | HJA |
| LTER | Twin Creeks RNA | HJA |
| LTER | Thermokarst Gradient, Toolik | ARC |
| LTER | SnowShrub, Toolik | ARC |
| CZO | Gordon Gulch | BcCZO |
| LTER | NA | BES |
| LTER | Murphy Dome | BNZ |
| LTER | Eight Mile Lake, Thaw Gradient | BNZ |
| LTER | Varies | BNZ |
| LTER | Carbon in Permafrost Experimental Heating Research (CiPEHR) | BNZ |
| DIRT | Bousson Environmental Research Reserve | BOU |
| CZO | Calhoun CZO | CCZO |
| LTER | greater Phoenix metropolitan area | CAP |
| LTER | Cedar Creek BioCON | CDR |
| LTER | Cedar Creek Fire Frequency Experiment | CDR |
| LTER | Coweeta basin | CWT |
| CZO | Angelo Reserve South Meadow, CA | Eel |
| LTER | Harvard Forest | HFR |
| LTER | Harvard Forest | HRF |
| LTER | Prospect Hill | HRF |
| LTER | Watershed 1 | HBR |
| LTER | Watershed 5 | HBR |
| LTER | Watershed 6 | HBR |
| LTER | Jornada | JRN |
| LTER | W.K. Kellogg Biological Station | KBS |
| LTER | Konza Prairie Biological Station | KNZ |
| LTER | Bisley Experimental Watersheds | LUQ |
| LTER | East Peak elevation gradient | LUQ |
| NEON | BART_megapit_roots | BART |
| NEON | HARV_megapit_roots | HARV |
| NEON | RMNP_megapit_roots | RMNP |
| NEON | CPER_megapit_roots | CPER |
| NEON | STER_megapit_roots | STER |
| NEON | CLBJ_megapit_roots | CLBJ |
| NEON | OAES_megapit_roots | OAES |
| NEON | YELL_megapit_roots | YELL |
| NEON | MOAB_megapit_roots | MOAB |
| NEON | NIWO_megapit_roots | NIWO |
| NEON | JORN_megapit_roots | JORN |
| NEON | ONAQ_megapit_roots | ONAQ |
| NEON | BLAN_megapit_roots | BLAN |
| NEON | SCBI_megapit_roots | SCBI |
| NEON | SERC_megapit_roots | SERC |
| NEON | DSNY_megapit_roots | DSNY |
| NEON | JERC_megapit_roots | JERC |
| NEON | OSBS_megapit_roots | OSBS |
| NEON | GUAN_megapit_roots | GUAN |
| NEON | LAJA_megapit_roots | LAJA |
| NEON | UNDE_megapit_roots | UNDE |
| NEON | KONZ_megapit_roots | KONZ |
| NEON | UKFS_megapit_roots | UKFS |
| NEON | MLBS_megapit_roots | MLBS |
| NEON | ORNL_megapit_roots | ORNL |
| NEON | DELA_megapit_roots | DELA |
| NEON | DCFS_megapit_roots | DCFS |
| NEON | NOGP_megapit_roots | NOGP |
| NEON | WOOD_megapit_roots | WOOD |
| NEON | STEI_megapit_roots | STEI |
| NEON | TREE_megapit_roots | TREE |
| NEON | GRSM_megapit_roots | GRSM |
| NEON | LENO_megapit_roots | LENO |
| NEON | TALL_megapit_roots | TALL |
| NEON | SRER_megapit_roots | SRER |
| NEON | ABBY_megapit_roots | ABBY |
| NEON | WREF_megapit_roots | WREF |
| NEON | SJER_megapit_roots | SJER |
| NEON | SOAP_megapit_roots | SOAP |
| NEON | TEAK_megapit_roots | TEAK |
| NEON | BARR_megapit_roots | BARR |
| NEON | BONA_megapit_roots | BONA |
| NEON | DEJU_megapit_roots | DEJU |
| NEON | HEAL_megapit_roots | HEAL |
| NEON | BART_megapit_soil | BART |
| NEON | HARV_megapit_soil | HARV |
| NEON | RMNP_megapit_soil | RMNP |
| NEON | CPER_megapit_soil | CPER |
| NEON | STER_megapit_soil | STER |
| NEON | CLBJ_megapit_soil | CLBJ |
| NEON | OAES_megapit_soil | OAES |
| NEON | YELL_megapit_soil | YELL |
| NEON | MOAB_megapit_soil | MOAB |
| NEON | NIWO_megapit_soil | NIWO |
| NEON | JORN_megapit_soil | JORN |
| NEON | ONAQ_megapit_soil | ONAQ |
| NEON | BLAN_megapit_soil | BLAN |
| NEON | SCBI_megapit_soil | SCBI |
| NEON | SERC_megapit_soil | SERC |
| NEON | DSNY_megapit_soil | DSNY |
| NEON | JERC_megapit_soil | JERC |
| NEON | OSBS_megapit_soil | OSBS |
| NEON | GUAN_megapit_soil | GUAN |
| NEON | LAJA_megapit_soil | LAJA |
| NEON | UNDE_megapit_soil | UNDE |
| NEON | KONA_megapit_soil | KONA |
| NEON | KONZ_megapit_soil | KONZ |
| NEON | UKFS_megapit_soil | UKFS |
| NEON | MLBS_megapit_soil | MLBS |
| NEON | ORNL_megapit_soil | ORNL |
| NEON | DELA_megapit_soil | DELA |
| NEON | DCFS_megapit_soil | DCFS |
| NEON | NOGP_megapit_soil | NOGP |
| NEON | WOOD_megapit_soil | WOOD |
| NEON | STEI_megapit_soil | STEI |
| NEON | TREE_megapit_soil | TREE |
| NEON | GRSM_megapit_soil | GRSM |
| NEON | LENO_megapit_soil | LENO |
| NEON | TALL_megapit_soil | TALL |
| NEON | SRER_megapit_soil | SRER |
| NEON | ABBY_megapit_soil | ABBY |
| NEON | WREF_megapit_soil | WREF |
| NEON | SJER_megapit_soil | SJER |
| NEON | SOAP_megapit_soil | SOAP |
| NEON | TEAK_megapit_soil | TEAK |
| NEON | BARR_megapit_soil | BARR |
| NEON | TOOL_megapit_soil | TOOL |
| NEON | BONA_megapit_soil | BONA |
| NEON | DEJU_megapit_soil | DEJU |
| NEON | HEAL_megapit_soil | HEAL |
| NEON | PUUM_megapit_soil | PUUM |
| NEON | BART_periodicRoots | BART |
| NEON | DEJU_periodicRoots | DEJU |
| NEON | DSNY_periodicRoots | DSNY |
| NEON | GUAN_periodicRoots | GUAN |
| NEON | HARV_periodicRoots | HARV |
| NEON | JORN_periodicRoots | JORN |
| NEON | KONZ_periodicRoots | KONZ |
| NEON | LENO_periodicRoots | LENO |
| NEON | MLBS_periodicRoots | MLBS |
| NEON | MOAB_periodicRoots | MOAB |
| NEON | OAES_periodicRoots | OAES |
| NEON | ONAQ_periodicRoots | ONAQ |
| NEON | ORNL_periodicRoots | ORNL |
| NEON | PUUM_periodicRoots | PUUM |
| NEON | SCBI_periodicRoots | SCBI |
| NEON | SJER_periodicRoots | SJER |
| NEON | SOAP_periodicRoots | SOAP |
| NEON | STEI_periodicRoots | STEI |
| NEON | STER_periodicRoots | STER |
| NEON | TALL_periodicRoots | TALL |
| NEON | TOOL_periodicRoots | TOOL |
| NEON | UKFS_periodicRoots | UKFS |
| NEON | UNDE_periodicRoots | UNDE |
| NEON | WOOD_periodicRoots | WOOD |
| NA | New England Pasture | NA |
| NutNet | Abiskojaure | NA |
| NutNet | American Camp | NA |
| NutNet | Antisana | NA |
| NutNet | Archbold Biological Station | NA |
| NutNet | Azi | NA |
| NutNet | Azi Two | NA |
| NutNet | Bad Lauchstaedt | NA |
| NutNet | Fort�n Chacabuco | NA |
| NutNet | Barta Brothers | NA |
| NutNet | Bayreuth | NA |
| NutNet | Boulder South Campus | NA |
| NutNet | Benedictine Bottoms | NA |
| NutNet | Bunchgrass (Andrews LTER) | NA |
| NutNet | Bogong | NA |
| NutNet | Buttercup (Andrews LTER) | NA |
| NutNet | Bunya Mountains | NA |
| NutNet | Burrawan | NA |
| NutNet | Slieve Carran | NA |
| NutNet | Chichaqua Bottoms | NA |
| NutNet | Cedar Creek LTER | NA |
| NutNet | Cedar Point Biological Station | NA |
| NutNet | CEREEP - Ecotron IDF | NA |
| NutNet | Las Chilcas | NA |
| NutNet | Companhia das Lezirias | NA |
| NutNet | Cowichan | NA |
| NutNet | Derrimut | NA |
| NutNet | Doane College Spring Creek Prairie | NA |
| NutNet | Elkhorn | NA |
| NutNet | Elliott Chaparral | NA |
| NutNet | Elva | NA |
| NutNet | Ethabuka (Main Camp) | NA |
| NutNet | Ethabuka (South Site) | NA |
| NutNet | Finley NWR | NA |
| NutNet | Fruebuel | NA |
| NutNet | Galleno | NA |
| NutNet | Mt Gilboa | NA |
| NutNet | Glacial Heritage | NA |
| NutNet | Glacier Creek Preserve | NA |
| NutNet | Hall’s Prairie | NA |
| NutNet | Hart Mountain | NA |
| NutNet | Hastings UCNRS | NA |
| NutNet | Heronsbrook (Silwood Park) | NA |
| NutNet | Hanover | NA |
| NutNet | Hog Island Site 1 | NA |
| NutNet | Hog Island Site 2 | NA |
| NutNet | Hopland REC | NA |
| NutNet | Jasper Ridge Biological Preserve | NA |
| NutNet | JeNut | NA |
| NutNet | Jornada LTER | NA |
| NutNet | Karkevagge | NA |
| NutNet | Kellogg Biological Station LTER | NA |
| NutNet | Kibber (Spiti) | NA |
| NutNet | Kidman Springs | NA |
| NutNet | Kilpisj�rvi | NA |
| NutNet | Kinypanial | NA |
| NutNet | Kirikukyla | NA |
| NutNet | Koffler Scientific Reserve at Joker’s Hill | NA |
| NutNet | Konza LTER | NA |
| NutNet | KonzaN1B | NA |
| NutNet | Tres Lagoas | NA |
| NutNet | Lakeside Laboratory | NA |
| NutNet | Laktajakka | NA |
| NutNet | Lancaster | NA |
| NutNet | Leadbetter Point | NA |
| NutNet | Lookout (Andrews LTER) | NA |
| NutNet | Lubbock (Texas Tech Univ) | NA |
| NutNet | Mar Chiquita | NA |
| NutNet | Mclaughlin UCNRS | NA |
| NutNet | Metompkin | NA |
| NutNet | Mitchell grassland | NA |
| NutNet | Missoula | NA |
| NutNet | Minnesota State University Moorehead | NA |
| NutNet | Mt. Caroline | NA |
| NutNet | Nillahcootie | NA |
| NutNet | Veluwe | NA |
| NutNet | Niwot Ridge LTER | NA |
| NutNet | Papenburg | NA |
| NutNet | Pichincha | NA |
| NutNet | Pingelly Paddock | NA |
| NutNet | Pinjarra Hills | NA |
| NutNet | Podocarpus | NA |
| NutNet | Potrok Aike | NA |
| NutNet | Rookery (Silwood Park) | NA |
| NutNet | Saana | NA |
| NutNet | Sagehen Creek UCNRS | NA |
| NutNet | Saline Experimental Range | NA |
| NutNet | Savannah River | NA |
| NutNet | Sedgwick Reserve UCNRS | NA |
| NutNet | Serengeti | NA |
| NutNet | Sevilleta LTER | NA |
| NutNet | Shortgrass Steppe LTER | NA |
| NutNet | Sheep Experimental Station | NA |
| NutNet | Sierra Foothills REC | NA |
| NutNet | Smith Prairie | NA |
| NutNet | Spindletop | NA |
| NutNet | San Pablo de Vald�s | NA |
| NutNet | Summerveld | NA |
| NutNet | Petuniabukta | NA |
| NutNet | Temple | NA |
| NutNet | Trelease | NA |
| NutNet | Tyson | NA |
| NutNet | University of California - Santa Cruz | NA |
| NutNet | UF Range Cattle REC | NA |
| NutNet | Ukulinga | NA |
| NutNet | Duke Forest | NA |
| NutNet | UWO Observatory | NA |
| NutNet | Val Mustair | NA |
| NutNet | Vassijaure | NA |
| NutNet | Yarramundi | NA |
| LTER | Green Lakes Valley | NWT |
| LTER | Saddle snow fence | NWT |
| LTER | Saddle | NWT |
| CZO | Redondo Peak catchments | JRB-CZO |
| CZO | Marshall Gulch | SCM-CZO |
| LTER | PJ Girdled | SEV |
| LTER | JSAV | SEV |
| LTER | PJ Control | SEV |
| LTER | Shrub | SEV |
| LTER | PJC | SEV |
| LTER | Burned Grass | SEV |
| LTER | Unburned Grass | SEV |
| LTER | MCON | SEV |
| LTER | Ppine | SEV |
| LTER | The Fertilizer Study | SEV |
| CZO | Shale Hills Catchment | SSHCZO |
| LTER | SGS-LTER Ecosystem Stress Area | SGS |
| LTER | Earthwatch Project | SGS |
| DIRT | Síkfokút Experimental Forest, Hungary | SIK |
| CZO | Providence creek | SSCZO |
| CZO | Bull Creek | SSCZO |
| CZO | NA | SSCZO |
| CZO | Providence Creek | SSCZO |
| DIRT | University of Michigan Biological Station | UMBS |
wwieder
commented
4 years ago It seems like rows need a site_code (and maybe also a location_name) for all plotting features to work in shiny? This seems like something all sites should have anyway? Maybe we need a check for this in the homog script @srearl? Also, maybe need to see where this is not true in the tarball?
srearl
commented
4 years ago @wwieder yeah, even if location and site were nothing more than duplicates, having content in both vars could be helpful at various points. Have a look at the table in the earlier comment of this issue, that is every unique combination of location, site for a fairly recent tarball. I see a missing location for one of the SSCZO and BES LTER but otherwise it looks like mostly just NutNet.
piersond
commented
4 years ago @wwieder done with this one?
wwieder
commented
4 years ago I hope so, but haven't check much. probably OK to close.
On Fri, Sep 27, 2019 at 10:23 AM Derek Pierson notifications@github.com wrote:
@wwieder https://github.com/wwieder done with this one?
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/lter/lterwg-som-shiny/issues/3?email_source=notifications&email_token=AB5IWJEY3HKU7VJ4W24T7VTQLYXRDA5CNFSM4ITUUOJKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7ZNH7Y#issuecomment-536007679, or mute the thread https://github.com/notifications/unsubscribe-auth/AB5IWJE7J7TNEVUJVIPNDFTQLYXRDANCNFSM4ITUUOJA .
-- Will Wieder Project Scientist CGD, NCAR 303-497-1352
Check to make sure shiny isn't inadvertently missing data for some reason (e.g. where are NutNet data)?