| title | author | date | output | ||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
A Simple Workflow |
Simon Goring, Socorro Dominguez Vidaña |
2022-09-20 |
|
This document is intended to act as a primer for the use of the new Neotoma R package, neotoma2. The neotoma2 package is available from GitHub and can be installed in R using the devtools package by using:
devtools::install_github('NeotomaDB/neotoma2')
library(neotoma2)In this tutorial you will learn how to:
- Search for sites using site names and geographic parameters
- Filter results using temporal and spatial parameters
- Obtain sample information for the selected datasets
- Perform basic analysis including the use of climate data from rasters
For this workbook we use several packages, including leaflet, sf and others. We load the packages using the pacman package, which will automatically install the packages if they do not currently exist in your set of packages.
options(warn = -1)
pacman::p_load(neotoma2, dplyr, ggplot2, sf, geojsonsf, leaflet, raster, DT)Note that R is sensitive to the order in which packages are loaded. Using neotoma2:: tells R explicitly that you want to use the neotoma2 package to run a particular function. So, for a function like filter(), which exists in other packages such as dplyr, you may see an error that looks like:
Error in UseMethod("filter") :
no applicable method for 'filter' applied to an object of class "sites"In that case it's likely that the wrong package is trying to run filter(), and so explicitly adding dplyr:: or neotoma2:: in front of the function name (i.e., neotoma2::filter())is good practice.
If you're planning on working with Neotoma, please join us on Slack where we manage a channel specifically for questions about the R package. You may also wish to join our Google Groups mailing list, please contact us to be added.
There are several ways to find sites in neotoma2, but we think of sites as being spatial objects primarily. They have names, locations, and are found within the context of geopolitical units, but within the API and the package, the site itself does not have associated information about taxa, dataset types or ages. It is simply the container into which we add that information. So, when we search for sites we can search by:
- siteid
- sitename
- location
- altitude (maximum and minimum)
- geopolitical unit
We may know exactly what site we're looking for ("Lac Mouton"), or have an approximate guess for the site name (for example, we know it's something like "Lait Lake", or "Lac du Lait", but we're not sure how it was entered specifically).
We use the general format: get_sites(sitename="XXXXX") for searching by name.
PostgreSQL (and the API) uses the percent sign as a wildcard. So "%Lait%" would pick up "Lac du Lait" for us (and would pick up "Lake Lait" and "This Old Laity Hei-dee-ho Bog" if they existed). Note that the search query is also case insensitive, so you could simply write "%lait%".
spo_sites <- neotoma2::get_sites(sitename = "%Lait%")
plotLeaflet(spo_sites)<div id="htmlwidget-c479bdd89c96fc5b1760" style="width:672px;height:480px;" class="leaflet html-widget"></div>
<script type="application/json" data-for="htmlwidget-c479bdd89c96fc5b1760">{"x":{"options":{"crs":{"crsClass":"L.CRS.EPSG3857","code":null,"proj4def":null,"projectedBounds":null,"options":{}}},"calls":[{"method":"addProviderTiles","args":["Stamen.TerrainBackground",null,null,{"errorTileUrl":"","noWrap":false,"detectRetina":false}]},{"method":"addTiles","args":["https://{s}.tile.openstreetmap.org/{z}/{x}/{y}.png",null,null,{"minZoom":0,"maxZoom":18,"tileSize":256,"subdomains":"abc","errorTileUrl":"","tms":false,"noWrap":false,"zoomOffset":0,"zoomReverse":false,"opacity":1,"zIndex":1,"detectRetina":false,"attribution":"© <a href=\"https://openstreetmap.org\">OpenStreetMap<\/a> contributors, <a href=\"https://creativecommons.org/licenses/by-sa/2.0/\">CC-BY-SA<\/a>"}]},{"method":"addCircleMarkers","args":[45.31417,6.81528,10,null,null,{"interactive":true,"draggable":false,"keyboard":true,"title":"","alt":"","zIndexOffset":0,"opacity":1,"riseOnHover":true,"riseOffset":250,"stroke":true,"color":"#03F","weight":5,"opacity.1":0.5,"fill":true,"fillColor":"#03F","fillOpacity":0.2},{"showCoverageOnHover":true,"zoomToBoundsOnClick":true,"spiderfyOnMaxZoom":true,"removeOutsideVisibleBounds":true,"spiderLegPolylineOptions":{"weight":1.5,"color":"#222","opacity":0.5},"freezeAtZoom":false},null,"<b>Lac du Lait<\/b><br><b>Description:<\/b> Lake almost filled. Physiography: depression in mountain. Surrouding vegetation: pasture with rare uncinata.<br><a href=http://apps.neotomadb.org/explorer/?siteids=3220>Explorer Link<\/a>",null,null,{"interactive":false,"permanent":false,"direction":"auto","opacity":1,"offset":[0,0],"textsize":"10px","textOnly":false,"className":"","sticky":true},null]}],"limits":{"lat":[45.31417,45.31417],"lng":[6.81528,6.81528]}},"evals":[],"jsHooks":[]}</script>
The neotoma package used a bounding box for locations, structured as a vector of latitude and longitude values: c(xmin, ymin, xmax, ymax). The neotoma2 R package supports both this simple bounding box, but also more complex spatial objects, using the sf package. Using the sf package allows us to more easily work with raster and polygon data in R, and to select sites from more complex spatial objects. The loc parameter works with the simple vector, WKT, geoJSON objects and native sf objects in R. Note however that the neotoma2 package is a wrapper for a simple API call using a URL (api.neotomadb.org), and URL strings can only be 1028 characters long, so the API cannot accept very long/complex spatial objects.
Looking for sites using a location. We're putting three representations of the Czech Republic here as part of a list with three elements, a geoJSON, WKT and bounding box representation. We've also transformed the cz$geoJSON element to an object for the sf package. Any of these four spatial representations work with the neotoma2 package.
cz <- list(geoJSON = '{"type": "Polygon",
"coordinates": [[
[12.40, 50.14],
[14.10, 48.64],
[16.95, 48.66],
[18.91, 49.61],
[15.24, 50.99],
[12.40, 50.14]]]}',
WKT = 'POLYGON ((12.4 50.14,
14.1 48.64,
16.95 48.66,
18.91 49.61,
15.24 50.99,
12.4 50.14))',
bbox = c(12.4, 48.64, 18.91, 50.99))
cz$sf <- geojsonsf::geojson_sf(cz$geoJSON)[[1]]
cz_sites <- neotoma2::get_sites(loc = cz$geoJSON, all_data = TRUE)## Your search returned 89 objects.
You can always simply plot() the sites objects, but you will lose some of the geographic context. The plotLeaflet() function returns a leaflet() map, and allows you to further customize it, or add additional spatial data (like our original bounding polygon, cz$sf, which works directly with the R leaflet package):
neotoma2::plotLeaflet(cz_sites) %>%
leaflet::addPolygons(map = .,
data = cz$sf,
color = "green")<div id="htmlwidget-6ab42737af1853d2db8a" style="width:672px;height:480px;" class="leaflet html-widget"></div>
<script type="application/json" data-for="htmlwidget-6ab42737af1853d2db8a">{"x":{"options":{"crs":{"crsClass":"L.CRS.EPSG3857","code":null,"proj4def":null,"projectedBounds":null,"options":{}}},"calls":[{"method":"addProviderTiles","args":["Stamen.TerrainBackground",null,null,{"errorTileUrl":"","noWrap":false,"detectRetina":false}]},{"method":"addTiles","args":["https://{s}.tile.openstreetmap.org/{z}/{x}/{y}.png",null,null,{"minZoom":0,"maxZoom":18,"tileSize":256,"subdomains":"abc","errorTileUrl":"","tms":false,"noWrap":false,"zoomOffset":0,"zoomReverse":false,"opacity":1,"zIndex":1,"detectRetina":false,"attribution":"© <a href=\"https://openstreetmap.org\">OpenStreetMap<\/a> contributors, <a href=\"https://creativecommons.org/licenses/by-sa/2.0/\">CC-BY-SA<\/a>"}]},{"method":"addCircleMarkers","args":[[49.726332,49.04174,49.76853,48.776394,49.75811,48.985354,48.77444,48.86363,49.232262,48.955424,48.942402,49.143988,50.601566,49.324306,49.69159,49.001672,49.02481,48.988224,49.68134,49.22716,49.250916,48.943358,50.604486,48.981118,48.977644,49.65,49.073406,50.38667,50.37944,50.23694,50.12944,50.58861,50.585,48.912768,48.86687,48.902724,48.922278,50.660758,48.936984,49.4925,50.04739,50.078526,49.52056,50.084794,50.198894,50.25,50.604006,50.59666,50.58407,50.5942,50.61135,50.58548,50.602896,50.5544,50.53615,50.52961,50.5651,50.660422,50.74655,50.736004,50.762596,50.76618,50.21592,50.29944,50.259284,50.198036,50.131382,50.143812,50.06635,50.1125,49.38333,50.09072,49.37639,48.728684,49.06961,48.85583,49.382508,49.233718,49.21306,49.131188,49.027572,49.22278,49.19194,49.14056,49.13722,49.70826,48.86351,48.85754,49.639158],[15.970602,15.19097,15.372874,16.4207,15.35538,14.708586,14.927156,14.79583,14.621568,14.804076,14.807094,14.703396,14.609992,15.532934,15.45905,14.777506,14.76891,16.392582,15.47796,15.372418,14.087762,17.068908,16.213004,16.663514,17.199456,15.41667,14.346472,14.13056,14.11556,14.53278,13.92972,16.1175,16.13167,13.813122,13.876662,13.837848,13.821796,15.752374,16.972656,18.55083,17.22029,13.213992,18.63083,17.217524,15.96132,16.45,16.12701,16.10404,16.1524,16.11156,16.20246,16.18415,16.242544,16.30578,16.34791,16.31002,16.27412,15.852968,15.6871,15.70752,15.551962,15.541672,14.831158,14.57833,14.573476,14.66948,13.723426,13.82766,14.23871,14.39167,17.95,14.40639,14.02583,16.90096,17.45758,14.91667,15.412416,15.42525,15.31472,15.241478,15.295758,13.79528,13.80139,13.79028,13.83,18.21357,17.32711,17.28043,15.87283],10,null,null,{"interactive":true,"draggable":false,"keyboard":true,"title":"","alt":"","zIndexOffset":0,"opacity":1,"riseOnHover":true,"riseOffset":250,"stroke":true,"color":"#03F","weight":5,"opacity.1":0.5,"fill":true,"fillColor":"#03F","fillOpacity":0.2},{"showCoverageOnHover":true,"zoomToBoundsOnClick":true,"spiderfyOnMaxZoom":true,"removeOutsideVisibleBounds":true,"spiderLegPolylineOptions":{"weight":1.5,"color":"#222","opacity":0.5},"freezeAtZoom":false},null,["<b>Kameničky<\/b><br><b>Description:<\/b> Drained sloping spring mire. Physiography: Kameničská kotlina Basin at its N margin. Surrounding vegetation: Alder carr.<br><a href=http://apps.neotomadb.org/explorer/?siteids=1399>Explorer Link<\/a>","<b>Bláto<\/b><br><b>Description:<\/b> After deep drainage quite mineral peat. Physiography: broad flat closure of a brook valley. Surrounding vegetation: present: secondary spruce plantations.<br><a href=http://apps.neotomadb.org/explorer/?siteids=3021>Explorer Link<\/a>","<b>Chraňbož<\/b><br><b>Description:<\/b> Small mire. Surrounding vegetation: fagion, Luzulo-Fagion.<br><a href=http://apps.neotomadb.org/explorer/?siteids=3052>Explorer Link<\/a>","<b>Dvůr Anšov<\/b><br><b>Description:<\/b> Fen. Physiography: dyje river alluvium. Surrounding vegetation: carpinion.<br><a href=http://apps.neotomadb.org/explorer/?siteids=3090>Explorer Link<\/a>","<b>Hroznotín<\/b><br><b>Description:<\/b> Small mire. Surrounding vegetation: fagion, Luzulo-Fagion.<br><a href=http://apps.neotomadb.org/explorer/?siteids=3152>Explorer Link<\/a>","<b>Spolí<\/b><br><b>Description:<\/b> NA<br><a href=http://apps.neotomadb.org/explorer/?siteids=3168>Explorer Link<\/a>","<b>Velanská cesta<\/b><br><b>Description:<\/b> NA<br><a href=http://apps.neotomadb.org/explorer/?siteids=3169>Explorer Link<\/a>","<b>Červené blato<\/b><br><b>Description:<\/b> NA<br><a href=http://apps.neotomadb.org/explorer/?siteids=3170>Explorer Link<\/a>","<b>Borkovická blata<\/b><br><b>Description:<\/b> Peat sediment complex undergoing peat excavation.<br><a href=http://apps.neotomadb.org/explorer/?siteids=3171>Explorer Link<\/a>","<b>Branná<\/b><br><b>Description:<\/b> NA<br><a href=http://apps.neotomadb.org/explorer/?siteids=3172>Explorer Link<\/a>","<b>Barbora<\/b><br><b>Description:<\/b> NA<br><a href=http://apps.neotomadb.org/explorer/?siteids=3173>Explorer Link<\/a>","<b>Švarcenberk<\/b><br><b>Description:<\/b> Lakes area. Physiography: Basin in plain. Surrounding vegetation: Cultivated fields and forest.<br><a href=http://apps.neotomadb.org/explorer/?siteids=3174>Explorer Link<\/a>","<b>Jestřebské blato<\/b><br><b>Description:<\/b> Vast swamps. Surrounding vegetation: pino-Quercetum.<br><a href=http://apps.neotomadb.org/explorer/?siteids=3175>Explorer Link<\/a>","<b>Loučky<\/b><br><b>Description:<\/b> Sloping spring fen. Physiography: a closure of broad flat brook valley. Surrounding vegetation: pine and spruce plantations.<br><a href=http://apps.neotomadb.org/explorer/?siteids=3254>Explorer Link<\/a>","<b>Malčín<\/b><br><b>Description:<\/b> Broad alluvium of a stream. Surrounding vegetation: quercion robori-petraeae.<br><a href=http://apps.neotomadb.org/explorer/?siteids=3269>Explorer Link<\/a>","<b>Mokré louky (South)<\/b><br><b>Description:<\/b> Cultural meadow. Surrounding vegetation: quercion robori-petraeae.<br><a href=http://apps.neotomadb.org/explorer/?siteids=3289>Explorer Link<\/a>","<b>Mokré louky (North)<\/b><br><b>Description:<\/b> NA<br><a href=http://apps.neotomadb.org/explorer/?siteids=3290>Explorer Link<\/a>","<b>Olbramovice<\/b><br><b>Description:<\/b> Spring peat bog. Surrounding vegetation: alnenion glutinoso-incanae.<br><a href=http://apps.neotomadb.org/explorer/?siteids=3327>Explorer Link<\/a>","<b>Palašiny<\/b><br><b>Description:<\/b> Broad alluvium of a stream. Surrounding vegetation: quercion robori-petraeae.<br><a href=http://apps.neotomadb.org/explorer/?siteids=3341>Explorer Link<\/a>","<b>Řásná<\/b><br><b>Description:<\/b> Artificial lake with neighbouring fen. Physiography: valley mire. Surrounding vegetation: spruce plantation.<br><a href=http://apps.neotomadb.org/explorer/?siteids=3371>Explorer Link<\/a>","<b>Řežabinec<\/b><br><b>Description:<\/b> Artificial fish pond with marginal fen. Physiography: slightly undulated landscape. Surrounding vegetation: meadows, fields, alder carr.<br><a href=http://apps.neotomadb.org/explorer/?siteids=3377>Explorer Link<\/a>","<b>Svatobořice-Mistřín<\/b><br><b>Description:<\/b> Peat bog. Surrounding vegetation: quercetea robori-petraeae.<br><a href=http://apps.neotomadb.org/explorer/?siteids=3452>Explorer Link<\/a>","<b>Vernéřovice<\/b><br><b>Description:<\/b> Flat valley. Physiography: valley fen, slightly sloping. Surrounding vegetation: cultivated fields, meadow, spruce.<br><a href=http://apps.neotomadb.org/explorer/?siteids=3492>Explorer Link<\/a>","<b>Velké Němčice<\/b><br><b>Description:<\/b> Svratka river bank. Surrounding vegetation: carpinion.<br><a href=http://apps.neotomadb.org/explorer/?siteids=3497>Explorer Link<\/a>","<b>Vracov<\/b><br><b>Description:<\/b> Artificial lake after peat exploitation. Physiography: flat valley. Surrounding vegetation: pine plantations and fields.<br><a href=http://apps.neotomadb.org/explorer/?siteids=3502>Explorer Link<\/a>","<b>Závidkovice<\/b><br><b>Description:<\/b> Organic sediment in narrow alluvium. Surrounding vegetation: quercion robori-petraeae.<br><a href=http://apps.neotomadb.org/explorer/?siteids=3518>Explorer Link<\/a>","<b>Zbudovská blata<\/b><br><b>Description:<\/b> Burried peat. Physiography: broad floodplain. Surrounding vegetation: meadows, fields.<br><a href=http://apps.neotomadb.org/explorer/?siteids=3519>Explorer Link<\/a>","<b>Vrbka<\/b><br><b>Description:<\/b> Peat in edge of Ohre valley. The local egetation of a once-active fen is today heavily tansformed by peat extraction. Physiography: Filled depression of artesian area. Surrounding vegetation: Agricultural area.<br><a href=http://apps.neotomadb.org/explorer/?siteids=13450>Explorer Link<\/a>","<b>Zahájí<\/b><br><b>Description:<\/b> Medium-size spring mire. Physiography: Brook valley. Surrounding vegetation: Cultivated fields.<br><a href=http://apps.neotomadb.org/explorer/?siteids=13451>Explorer Link<\/a>","<b>Tišice<\/b><br><b>Description:<\/b> Filled-in oxbow lake in the river. Physiography: Floodplain, terrace gravel. Surrounding vegetation: Cultivated fields.<br><a href=http://apps.neotomadb.org/explorer/?siteids=13452>Explorer Link<\/a>","<b>Rynholec<\/b><br><b>Description:<\/b> Palustrine. Physiography: Plain. Surrounding vegetation: Cultivated fields.<br><a href=http://apps.neotomadb.org/explorer/?siteids=13468>Explorer Link<\/a>","<b>Anenské údolí<\/b><br><b>Description:<\/b> Peat bog in a sandstone valley. Physiography: Valley. Surrounding vegetation: Spruce forest.<br><a href=http://apps.neotomadb.org/explorer/?siteids=14264>Explorer Link<\/a>","<b>Teplické údolí<\/b><br><b>Description:<\/b> Peat bog. Physiography: Sand stone valley. Surrounding vegetation: Spruce forest.<br><a href=http://apps.neotomadb.org/explorer/?siteids=14266>Explorer Link<\/a>","<b>Malá niva<\/b><br><b>Description:<\/b> Large ombrotrophic mire. Physiography: Valley of Teplá Vltava River. Surrounding vegetation: Beech forests.<br><a href=http://apps.neotomadb.org/explorer/?siteids=14272>Explorer Link<\/a>","<b>Mrtvý luh<\/b><br><b>Description:<\/b> Raised bog. Physiography: Glacial mountain lake, Sumava mountains. Surrounding vegetation: Forests and fields.<br><a href=http://apps.neotomadb.org/explorer/?siteids=14275>Explorer Link<\/a>","<b>Soumarské rašeliniště<\/b><br><b>Description:<\/b> Large ombrotrophic mire. Physiography: Open valley in Sumava Mountains.<br><a href=http://apps.neotomadb.org/explorer/?siteids=14277>Explorer Link<\/a>","<b>Velká niva<\/b><br><b>Description:<\/b> Large ombrotrophic mire. Physiography: Open valley in Sumava Mountains.<br><a href=http://apps.neotomadb.org/explorer/?siteids=14278>Explorer Link<\/a>","<b>Černohorské rašeliniště<\/b><br><b>Description:<\/b> Bog. Physiography: Mountain ombrotrophic peat bog. Surrounding vegetation: Picea forest with Sorbus a.& Vaccinum m.<br><a href=http://apps.neotomadb.org/explorer/?siteids=14282>Explorer Link<\/a>","<b>Čejčské jezero<\/b><br><b>Description:<\/b> Drained lake. Physiography: Valley in southern Moravian basin. Surrounding vegetation: Cultivated fields.<br><a href=http://apps.neotomadb.org/explorer/?siteids=14470>Explorer Link<\/a>","<b>Jančík<\/b><br><b>Description:<\/b> Smal slope-spring mire. Physiography: Beskydy mountain. Surrounding vegetation: Moist spruce forest.<br><a href=http://apps.neotomadb.org/explorer/?siteids=14476>Explorer Link<\/a>","<b>Velký Máj<\/b><br><b>Description:<\/b> Ombrotrophic bog. Physiography: Saddle in summit ridge of Jeseniky mountains. Surrounding vegetation: Subalpine grasslands.<br><a href=http://apps.neotomadb.org/explorer/?siteids=14503>Explorer Link<\/a>","<b>Vladař<\/b><br><b>Description:<\/b> Reservoir. Physiography: Plateau in valley slightly hilly. Surrounding vegetation: Cultivated fields and forest.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15692>Explorer Link<\/a>","<b>Horní Lomná<\/b><br><b>Description:<\/b> Small spring fen. Physiography: Valley. Surrounding vegetation: Forests.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15706>Explorer Link<\/a>","<b>Velký Děd<\/b><br><b>Description:<\/b> Ombrotrophic bog. Physiography: Flat plateau of the mountain ridge. Surrounding vegetation: Calamagrosti villosae Piceetum.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15710>Explorer Link<\/a>","<b>Na bahně<\/b><br><b>Description:<\/b> Floodplain mire. Physiography: Terrace. Surrounding vegetation: Cultivated fields and forest.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15712>Explorer Link<\/a>","<b>Kunštátská kaple<\/b><br><b>Description:<\/b> Humus podsols with small peat bogs. Physiography: SW edge ofBohemian Ridge in Orlické hory. Surrounding vegetation: Spruce forest.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15713>Explorer Link<\/a>","<b>Vlčí rokle<\/b><br><b>Description:<\/b> Peat bog. Physiography: Gorge in a sandstone valley. Surrounding vegetation: Forests.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15714>Explorer Link<\/a>","<b>Kancelářský příkop<\/b><br><b>Description:<\/b> Small peat bog. Physiography: Rocky depression (Broumovsko). Surrounding vegetation: Forest.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15717>Explorer Link<\/a>","<b>Kraví hora<\/b><br><b>Description:<\/b> Small peat bog. Physiography: Rocky depression. Surrounding vegetation: Forest.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15718>Explorer Link<\/a>","<b>Rokliny<\/b><br><b>Description:<\/b> Little bog. Physiography: Little mountain. Surrounding vegetation: Forest.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15719>Explorer Link<\/a>","<b>Vernéřovice 2<\/b><br><b>Description:<\/b> Flat valley. Physiography: Valley fen, slightly sloping. Surrounding vegetation: Cultivated fields, meadow, spruce.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15720>Explorer Link<\/a>","<b>Teplice nad Metují<\/b><br><b>Description:<\/b> Bottom of former fish pond. Physiography: Valley. Surrounding vegetation: Cultivated fields and forest.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15721>Explorer Link<\/a>","<b>Březová<\/b><br><b>Description:<\/b> Physiography: Valley. Surrounding vegetation: Cultivated fields.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15722>Explorer Link<\/a>","<b>Křinice<\/b><br><b>Description:<\/b> Bog. Physiography: Valley in Broumovsko. Surrounding vegetation: Cultivated fields and forest.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15725>Explorer Link<\/a>","<b>Martínkovice<\/b><br><b>Description:<\/b> Bog. Physiography: Valley. Surrounding vegetation: Cultivated fields.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15726>Explorer Link<\/a>","<b>Broumovské stěny<\/b><br><b>Description:<\/b> Alluvial fen at old oxbow lake. Physiography: Flat alluvium.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15727>Explorer Link<\/a>","<b>Broumovské stěny 2<\/b><br><b>Description:<\/b> Alluvial fen at old oxbow lake. Physiography: Flat alluvium.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15728>Explorer Link<\/a>","<b>Rýchory<\/b><br><b>Description:<\/b> Bog. Surrounding vegetation: Fagus,Sorbus,Acer,Betula. Vegetation formation: Under the forest limit.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15730>Explorer Link<\/a>","<b>Stříbrná bystřina<\/b><br><b>Description:<\/b> Peat bog. Physiography: Palsa-bog. Surrounding vegetation: Meadow. Vegetation formation: Arctic alpine tundra.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15731>Explorer Link<\/a>","<b>Úpské rašeliniště<\/b><br><b>Description:<\/b> Raised bog. Physiography: Plateau of mountain.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15732>Explorer Link<\/a>","<b>Labský důl<\/b><br><b>Description:<\/b> Infilled cirque lake, peat bog. Physiography: Cirque basin. Surrounding vegetation: Open forest. Vegetation formation: Below the alpine timberline.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15745>Explorer Link<\/a>","<b>Pančavská louka<\/b><br><b>Description:<\/b> Mountain raised bog.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15763>Explorer Link<\/a>","<b>Hrabanovská černava<\/b><br><b>Description:<\/b> Mire. Physiography: Plateau. Surrounding vegetation: Cultivated fields.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15764>Explorer Link<\/a>","<b>Mělnický úval - Přívory<\/b><br><b>Description:<\/b> Lacustrine. Physiography: Plateau. Surrounding vegetation: Cultivated fields.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15765>Explorer Link<\/a>","<b>Chrást<\/b><br><b>Description:<\/b> Filled-in oxbow lake. Surrounding vegetation: Cultivated fields.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15770>Explorer Link<\/a>","<b>Stará Boleslav<\/b><br><b>Description:<\/b> Filled-in oxbow lake. Physiography: Flat plain. Surrounding vegetation: Cultivated fields.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15771>Explorer Link<\/a>","<b>Červená louka<\/b><br><b>Description:<\/b> Excavated mire. Surrounding vegetation: Cultivated fields and forest.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15772>Explorer Link<\/a>","<b>Klíčava<\/b><br><b>Description:<\/b> Surrounding vegetation: Forest.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15773>Explorer Link<\/a>","<b>Břve<\/b><br><b>Description:<\/b> Small spring mire. Physiography: Lowland. Surrounding vegetation: Fields and settlements.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15774>Explorer Link<\/a>","<b>Praha-Podbaba<\/b><br><b>Description:<\/b> Full glacial peat. Physiography: Deeply-cut valley of Vltava river. Surrounding vegetation: Forest, cultivated field & dweling place.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15775>Explorer Link<\/a>","<b>Jablůnka<\/b><br><b>Description:<\/b> Riverine. Physiography: Valley of the Vsetínská Becva river. Surrounding vegetation: Cultivated fields and forest.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15776>Explorer Link<\/a>","<b>Praha-Valdštejnská<\/b><br><b>Description:<\/b> Infilled old river channel. Physiography: Palaeochannel. Surrounding vegetation: Urban.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15777>Explorer Link<\/a>","<b>Kožlí<\/b><br><b>Description:<\/b> Small topogenous spring mire. Surrounding vegetation: Cultural landscape, meadows, fields.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15778>Explorer Link<\/a>","<b>Pohansko<\/b><br><b>Description:<\/b> Oxbow lakes near old Slvavonic settlement. Physiography: Flat flood plain. Surrounding vegetation: Meadows and floodplain forests.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15779>Explorer Link<\/a>","<b>Uherské Hradiště<\/b><br><b>Description:<\/b> Archaeological locality. Physiography: River in flat valley. Surrounding vegetation: Urban and cultivated fields.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15781>Explorer Link<\/a>","<b>Halámky<\/b><br><b>Description:<\/b> Swamp. Physiography: Lužnice river, valley. Surrounding vegetation: Forest and cultivated fields.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15782>Explorer Link<\/a>","<b>Hojkov<\/b><br><b>Description:<\/b> Bog. Physiography: Highlands. Surrounding vegetation: Cultivated fields and forests.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15784>Explorer Link<\/a>","<b>Doupě<\/b><br><b>Description:<\/b> Bog. Physiography: Plain. Surrounding vegetation: Cultivated fields.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15786>Explorer Link<\/a>","<b>Horní Pole<\/b><br><b>Description:<\/b> Bog. Physiography: Open valley in hilly area. Surrounding vegetation: Cultivated fields and forest.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15787>Explorer Link<\/a>","<b>Suchdol<\/b><br><b>Description:<\/b> Bog. Physiography: Plain in Bohemian-Moravian Highlands. Surrounding vegetation: Cultivated fields and forests.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15788>Explorer Link<\/a>","<b>Stálkov<\/b><br><b>Description:<\/b> Bog. Physiography: Hilly area, Bohemaian-Moravian Highland. Surrounding vegetation: Forests and cultivated fields.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15789>Explorer Link<\/a>","<b>Mladotice<\/b><br><b>Description:<\/b> Bog. Physiography: Plateau/valley. Surrounding vegetation: Cultivated fields and forests.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15790>Explorer Link<\/a>","<b>Němčice<\/b><br><b>Description:<\/b> Bog. Physiography: Hilly area (Sumava foothills). Surrounding vegetation: Cultivated fields and littles forests.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15791>Explorer Link<\/a>","<b>Vacovice<\/b><br><b>Description:<\/b> Peat. Physiography: Hilly area (Sumava hoothils). Surrounding vegetation: Cultivated fields and forests.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15792>Explorer Link<\/a>","<b>Nahořany<\/b><br><b>Description:<\/b> Bog. Physiography: Hilly area (Sumava foothills). Surrounding vegetation: Cultivated fields and forests.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15793>Explorer Link<\/a>","<b>Brušperk<\/b><br><b>Description:<\/b> Road section through a terrain. Burried peat on glacial river terraces. Physiography: Valley in the Ostrava basin. Surrounding vegetation: Cultivated fields and little forests.<br><a href=http://apps.neotomadb.org/explorer/?siteids=15795>Explorer Link<\/a>","<b>Bílé Karpaty 35<\/b><br><b>Description:<\/b> NA<br><a href=http://apps.neotomadb.org/explorer/?siteids=25992>Explorer Link<\/a>","<b>Bílé Karpaty 36<\/b><br><b>Description:<\/b> NA<br><a href=http://apps.neotomadb.org/explorer/?siteids=25993>Explorer Link<\/a>","<b>Dářko<\/b><br><b>Description:<\/b> Part of a larger wetland complex. The part investigated is called Padrtiny. The peat is up to 8.6 m deep.<br><a href=http://apps.neotomadb.org/explorer/?siteids=27171>Explorer Link<\/a>"],null,null,{"interactive":false,"permanent":false,"direction":"auto","opacity":1,"offset":[0,0],"textsize":"10px","textOnly":false,"className":"","sticky":true},null]},{"method":"addPolygons","args":[[[[{"lng":[12.4,14.1,16.95,18.91,15.24,12.4],"lat":[50.14,48.64,48.66,49.61,50.99,50.14]}]]],null,null,{"interactive":true,"className":"","stroke":true,"color":"green","weight":5,"opacity":0.5,"fill":true,"fillColor":"green","fillOpacity":0.2,"smoothFactor":1,"noClip":false},null,null,null,{"interactive":false,"permanent":false,"direction":"auto","opacity":1,"offset":[0,0],"textsize":"10px","textOnly":false,"className":"","sticky":true},null]}],"limits":{"lat":[48.64,50.99],"lng":[12.4,18.91]}},"evals":[],"jsHooks":[]}</script>
If we look at the UML diagram for the objects in the neotoma2 R package we can see that there are a set of functions that can operate on sites. As we add to sites objects, using get_datasets() or get_downloads(), we are able to use more of these helper functions. As it is, we can take advantage of sunctions like summary() to get a more complete sense of the types of data we have as part of this set of sites. The following code gives the summary table. We do some R magic here to change the way the data is displayed (turning it into a datatable() object), but the main piece is the summary() call.
neotoma2::summary(cz_sites)<div id="htmlwidget-3c152c8dae5e4b9f3a59" style="width:100%;height:auto;" class="datatables html-widget"></div>
<script type="application/json" data-for="htmlwidget-3c152c8dae5e4b9f3a59">{"x":{"filter":"none","vertical":false,"data":[[1399,3021,3021,3052,3052,3090,3152,3168,3169,3170,3170,3170,3171,3171,3171,3172,3173,3174,3174,3174,3175,3254,3269,3289,3290,3327,3341,3341,3371,3377,3452,3492,3497,3502,3502,3502,3518,3519,3519,13450,13450,13450,13451,13451,13451,13451,13452,13452,13468,13468,14264,14264,14266,14266,14272,14275,14277,14278,14282,14282,14470,14476,14476,14503,15692,15706,15710,15712,15713,15713,15714,15717,15718,15719,15720,15721,15722,15725,15726,15727,15728,15730,15731,15732,15732,15732,15732,15732,15732,15732,15745,15763,15764,15765,15770,15771,15771,15772,15773,15774,15775,15776,15777,15778,15779,15781,15782,15784,15786,15787,15788,15789,15790,15791,15792,15793,15795,25992,25993,27171,27171,27171],["Kameničky","Bláto","Bláto","Chraňbož","Chraňbož","Dvůr Anšov","Hroznotín","Spolí","Velanská cesta","Červené blato","Červené blato","Červené blato","Borkovická blata","Borkovická blata","Borkovická blata","Branná","Barbora","Švarcenberk","Švarcenberk","Švarcenberk","Jestřebské blato","Loučky","Malčín","Mokré louky (South)","Mokré louky (North)","Olbramovice","Palašiny","Palašiny","Řásná","Řežabinec","Svatobořice-Mistřín","Vernéřovice","Velké Němčice","Vracov","Vracov","Vracov","Závidkovice","Zbudovská blata","Zbudovská blata","Vrbka","Vrbka","Vrbka","Zahájí","Zahájí","Zahájí","Zahájí","Tišice","Tišice","Rynholec","Rynholec","Anenské údolí","Anenské údolí","Teplické údolí","Teplické údolí","Malá niva","Mrtvý luh","Soumarské rašeliniště","Velká niva","Černohorské rašeliniště","Černohorské rašeliniště","Čejčské jezero","Jančík","Jančík","Velký Máj","Vladař","Horní Lomná","Velký Děd","Na bahně","Kunštátská kaple","Kunštátská kaple","Vlčí rokle","Kancelářský příkop","Kraví hora","Rokliny","Vernéřovice 2","Teplice nad Metují","Březová","Křinice","Martínkovice","Broumovské stěny","Broumovské stěny 2","Rýchory","Stříbrná bystřina","Úpské rašeliniště","Úpské rašeliniště","Úpské rašeliniště","Úpské rašeliniště","Úpské rašeliniště","Úpské rašeliniště","Úpské rašeliniště","Labský důl","Pančavská louka","Hrabanovská černava","Mělnický úval - Přívory","Chrást","Stará Boleslav","Stará Boleslav","Červená louka","Klíčava","Břve","Praha-Podbaba","Jablůnka","Praha-Valdštejnská","Kožlí","Pohansko","Uherské Hradiště","Halámky","Hojkov","Doupě","Horní Pole","Suchdol","Stálkov","Mladotice","Němčice","Vacovice","Nahořany","Brušperk","Bílé Karpaty 35","Bílé Karpaty 36","Dářko","Dářko","Dářko"],["KAMEN","BLATO1","BLATO2","CHB1","CHB2","DVURANSO","HROZNOTI","JC-13-A","JC-2-A","JC-3-A","JC-3-AA","JC-3-B","JC-5-A","JC-5-C","JC-5-D","JC-6-A","JC-6-B","JC-7-B","SVARCEN3","SVARCENB","JESTREB","LOUCKY","MALCIN","MLOUKY","MLOUKY-B","OLBRAM","PALAS_A","PALASINY","RASNA","REZABIN","SVATOBOR","VERNER","VNEMCICE","VRACOV","VRACOV","VRACOV1","ZAVIDKOV","ZBUDOV1","ZBUDOV2","VRBKA","VRBKA","VRBKA","ZAHAJI","ZAHAJI","ZAHAJI","ZAHAJI","TISICE","TISICE","RYNHOLEC","RYNHOLEC","UDOLI","UDOLI","TEPLUDOL","TEPLUDOL","SA21A","SA16C","SA8A","SA5A","CRH","KR1A","CEJCKE27","MB2A","MB3A","MAJ","VLADAR","MB5A","DED","NABAHNE","OH1A","OH2A","VLCIROKL","KANCELAR","KRAVIHOR","ROCKLIN2","VERNERO2","TEPLICE","BREZOVA","KRINICE","MARTINKO","BROUMOVS","BROUMOV2","RYCHORY","STRIBRNA","KR2A","KR2B","KR2C","KR5A","KR5C","UPSKELBU","UPSKELBU","LABSKYDU","PANCALOU","HRABANOS","MELNICKY","CHRAST","STARABCI","STARABOL","CERVENAL","KLICAVA","BRVE","PRAHAPOD","JABLUNKA","PRAHA","KOZLI","POHANSKO","UHERSKEH","HALAMKY","CV3A","CV23A","CV4A","CV8A","CV6A","PS6A","PS7A","PS4A","PS3A","BRUSPERK","BK35","BK36","DARKO","DARKO","DARKO"],[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],[1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1],["pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","plant macrofossil","pollen","pollen","pollen","pollen","plant macrofossil","charcoal","pollen","plant macrofossil","charcoal","testate amoebae","pollen","charcoal","pollen","charcoal","pollen","geochemistry","pollen","geochemistry","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","plant macrofossil","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen surface sample","pollen surface sample","pollen","plant macrofossil","X-ray fluorescence (XRF)"]],"container":"<table class=\"display\">\n <thead>\n <tr>\n <th>siteid<\/th>\n <th>sitename<\/th>\n <th>collectionunit<\/th>\n <th>chronolgies<\/th>\n <th>datasets<\/th>\n <th>types<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"scrollX":"100%","dom":"t","columnDefs":[{"className":"dt-right","targets":[0,3,4]}],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script>
We can see that there are no chronologies associated with the site objects. This is because, at present, we have not pulled in the dataset information we need. All we know from get_sites() are the kinds of datasets we have.
We know that collection units and datasets are contained within sites. Similarly, a sites object contains collectionunits which contain datasets. From the table above we can see that some of the sites we've looked at contain pollen records. That said, we only have the sites, it's just that (for convenience) the sites API returns some information about datasets so to make it easier to navigate the records.
With a sites object we can directly call get_datasets(), to pull in more metadata about the datasets. At any time we can use datasets() to get more information about any datasets that a sites object may contain. Compare the output of datasets(cz_sites) to the output of a similar call using the following:
cz_datasets <- neotoma2::get_datasets(cz_sites, all_data = TRUE)
datasets(cz_datasets)<div id="htmlwidget-77e0af58cfbafeac45d2" style="width:100%;height:auto;" class="datatables html-widget"></div>
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Pollen Database","European Pollen Database","European Pollen Database","European Pollen Database","European Pollen Database","European Pollen Database","European Pollen Database","European Pollen Database","European Pollen Database","European Pollen Database","European Pollen Database","European Pollen Database","European Pollen Database","European Pollen Database","European Pollen Database","European Pollen Database","European Pollen Database","European Pollen Database","European Pollen Database","European Pollen Database","European Pollen Database","European Pollen Database","European Pollen Database","European Pollen Database","European Pollen Database","European Pollen Database","European Pollen Database","European Pollen Database","European Pollen Database","European Pollen Database","European Pollen Database","European Pollen Database","European Pollen Database","European Pollen Database","European Pollen Database","European Pollen Database","European Pollen Database","European 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amoebae","charcoal","charcoal","pollen","charcoal","pollen","geochemistry","pollen","geochemistry","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen surface sample","pollen surface sample","pollen","plant macrofossil","X-ray fluorescence (XRF)","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","plant macrofossil","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","plant macrofossil","pollen","pollen","pollen"],[13680,11954,null,null,null,7091,9019,null,14178,null,11192,null,4407,11537,12323,9191,13656,null,null,4087,4087,null,5632,null,4888,5632,5814,5814,12387,12387,7905,9078,8558,8558,5798,6354,12817,null,10801,2501,2450,6088,5971,2130,16566,null,null,null,null,null,null,null,null,null,null,null,null,20440,4498,16943,17017,12125,null,null,2541,null,null,null,12403,null,null,null,null,null,null,null,null,null,null,null,null,null,-63,-63,14515,13923,16068.7,13835,null,null,null,17284,null,null,null,16014,13503,null,15319,13791,null,11712,17361,null,14740,15104,11129,2229,2409,null,null,null,null,3543,2764,5178,3038,1568,1568,3018,1925,null],[-107,718,null,null,null,0,0,null,-524,null,155,null,460,-36,-68,-46,-49,null,null,3183,3183,null,-43,null,3775,-43,1459,1459,399,399,651,-49,-52,-52,-25,-50,-50,null,221,-95,-54,-50,-35,-44,-40,null,null,null,null,null,null,null,null,null,null,null,null,805,-16,291,6215,246,null,null,49,null,null,null,175,null,null,null,null,null,null,null,null,null,null,null,null,null,-63,-63,-79,5854,-79,-56,null,null,null,-348,null,null,null,9400,-22,null,5203,1364,null,-486,66,null,85,-2639,-496,314,-45,null,null,null,null,105,-50,-50,-50,-8,-8,-50,385,null],["Data contributed by Rybnícková Eliska.","Data contributed by Svobodová Helena.","Data contributed by Jankovská Vlasta.","Data contributed by Jankovská Vlasta.","Data contributed by Jankovská Vlasta.","Data contributed by Jankovská Vlasta.","Data contributed by Jankovská Vlasta.","Data contributed by Jankovská Vlasta.","Data contributed by Rybníčková Eliška.","Data contributed by Svobodová Helena.","Data contributed by Svobodová Helena.","Data contributed by Jankovská Vlasta.","Data contributed by Svobodová Helena.","Data contributed by Rybníčková Eliška.","Data contributed by Rybnícková Eliska.","Data contributed by Svobodová Helena.","Data contributed by Rybnícková Eliska.","Data contributed by Svobodová Helena.","Data contributed by Jankovská Vlasta.",null,"Data contributed by Pokorny, P.",null,"Data contributed by PALYCZ via Kunes Petr.",null,"Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.",null,"Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Dried sample was grinded and mineralized (4 ml conc. HNO3 p.p. + 1 ml H2O2 + 0,1 ml HClO4). After vacuum filtration, element content was measured by AAS spectrometer: Ca (emission), Mg (absorption).","Data contributed by PALYCZ via Kunes Petr.",null,"Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by Rybnícková Eliska.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by Rybnícková Eliska.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by Publication.","Data contributed by Publication.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by Pokorn∞, P.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Vegetation relevés are stored in the Czech National Phytosociological Database (https://www.sci.muni.cz/botany/vegsci/dbase.php?lang=en)","Vegetation relevés are stored in the Czech National Phytosociological Database (https://www.sci.muni.cz/botany/vegsci/dbase.php?lang=en)",null,null,null,"Data contributed by Rybníčková Eliška.","Data contributed by Rybnícková Eliska.","Data contributed by Jankovská Vlasta.","Data contributed by Jankovská Vlasta.","Data contributed by Jankovská Vlasta.","Data contributed by Jankovská Vlasta.","Data contributed by Jankovská Vlasta.","Data contributed by Jankovská Vlasta.","Data contributed by Jankovská Vlasta.","Data contributed by Jankovská Vlasta.","Data contributed by Jankovská Vlasta.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by Svobodová Helena.","Data contributed by Jankovská Vlasta.","Data contributed by Svobodová Helena.",null,"Data contributed by Rybnícková Eliska.","Data contributed by Rybníčková Eliška.","Data contributed by Rybníčková Eliška.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.",null,"Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr.","Data contributed by PALYCZ via Kunes Petr."]],"container":"<table class=\"display\">\n <thead>\n <tr>\n <th> <\/th>\n <th>datasetid<\/th>\n <th>database<\/th>\n <th>datasettype<\/th>\n <th>age_range_old<\/th>\n <th>age_range_young<\/th>\n <th>notes<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"scrollX":"100%","dom":"t","columnDefs":[{"className":"dt-right","targets":[1,4,5]},{"orderable":false,"targets":0}],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script>
If we choose to pull in information about only a single dataset type, or if there is additional filtering we want to do before we download the data, we can use the filter() function. For example, if we only want pollen records, and want records with known chronologies, we can filter:
cz_pollen <- cz_datasets %>%
neotoma2::filter(datasettype == "pollen" & !is.na(age_range_young))
neotoma2::summary(cz_pollen)<div id="htmlwidget-aa4f8562c301fb0f4c1e" style="width:100%;height:auto;" class="datatables html-widget"></div>
<script type="application/json" data-for="htmlwidget-aa4f8562c301fb0f4c1e">{"x":{"filter":"none","vertical":false,"data":[["1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16","17","18","19","20","21","22","23","24","25","26","27","28","29","30","31","32","33","34","35","36","37","38","39","40","41","42","43","44","45","46","47","48","49","50","51","52","53","54","55"],[1399,3090,3172,3173,3254,3289,3327,3371,3377,3452,3492,13450,13451,13452,13468,14264,14266,14272,14275,14277,14470,14503,15692,15706,15710,15712,15714,15745,15763,15764,15765,15770,15774,15778,27171,3021,3170,3171,3171,3174,3174,3341,3502,3502,3519,3519,14282,14282,15732,15732,15732,15732,15732,15732,15771],["Kameničky","Dvůr Anšov","Branná","Barbora","Loučky","Mokré louky (South)","Olbramovice","Řásná","Řežabinec","Svatobořice-Mistřín","Vernéřovice","Vrbka","Zahájí","Tišice","Rynholec","Anenské údolí","Teplické údolí","Malá niva","Mrtvý luh","Soumarské rašeliniště","Čejčské jezero","Velký Máj","Vladař","Horní Lomná","Velký Děd","Na bahně","Vlčí rokle","Labský důl","Pančavská louka","Hrabanovská černava","Mělnický úval - Přívory","Chrást","Břve","Kožlí","Dářko","Bláto","Červené blato","Borkovická blata","Borkovická blata","Švarcenberk","Švarcenberk","Palašiny","Vracov","Vracov","Zbudovská blata","Zbudovská blata","Černohorské rašeliniště","Černohorské rašeliniště","Úpské rašeliniště","Úpské rašeliniště","Úpské rašeliniště","Úpské rašeliniště","Úpské rašeliniště","Úpské rašeliniště","Stará Boleslav"],["KAMEN","DVURANSO","JC-6-A","JC-6-B","LOUCKY","MLOUKY","OLBRAM","RASNA","REZABIN","SVATOBOR","VERNER","VRBKA","ZAHAJI","TISICE","RYNHOLEC","UDOLI","TEPLUDOL","SA21A","SA16C","SA8A","CEJCKE27","MAJ","VLADAR","MB5A","DED","NABAHNE","VLCIROKL","LABSKYDU","PANCALOU","HRABANOS","MELNICKY","CHRAST","BRVE","KOZLI","DARKO","BLATO1","JC-3-A","JC-5-D","JC-5-A","SVARCENB","SVARCEN3","PALASINY","VRACOV","VRACOV1","ZBUDOV1","ZBUDOV2","KR1A","CRH","KR2A","KR2B","KR2C","KR5A","UPSKELBU","KR5C","STARABCI"],[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],[1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1],["pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen","pollen"]],"container":"<table class=\"display\">\n <thead>\n <tr>\n <th> <\/th>\n <th>siteid<\/th>\n <th>sitename<\/th>\n <th>collectionunit<\/th>\n <th>chronolgies<\/th>\n <th>datasets<\/th>\n <th>types<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"scrollX":"100%","dom":"t","columnDefs":[{"className":"dt-right","targets":[1,4,5]},{"orderable":false,"targets":0}],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script>
We can see now that the data table looks different, and there are fewer total sites.
Because sample data adds a lot of overhead (for the Czech pollen data, the object that includes the dataset with samples is 20 times larger than the dataset alone), we try to call get_downloads() after we've done our preliminary filtering. After get_datasets() you have enough information to filter based on location, time bounds and dataset type. When we move to get_download() we can do more fine-tuned filtering at the analysis unit or taxon level.
The following call can take some time, but we've frozen the object as an RDS data file. You can run this command on your own, and let it run for a bit, or you can just load the object in.
## This line is commented out because we've already run it for you.
## cz_dl <- cz_pollen %>% get_downloads(all_data = TRUE)
cz_dl <- readRDS('data/czDownload.RDS')Once we've downloaded, we now have information for each site about all the associated collection units, the datasets, and, for each dataset, all the samples associated with the datasets. To extract all the samples we can call:
allSamp <- samples(cz_dl)When we've done this, we get a data.frame that is 130889 rows long and 37 columns wide. The reason the table is so wide is that we are returning data in a long format. Each row contains all the information you should need to properly interpret it:
## [1] "age" "agetype" "ageolder" "ageyounger"
## [5] "chronologyid" "chronologyname" "units" "value"
## [9] "context" "element" "taxonid" "symmetry"
## [13] "taxongroup" "elementtype" "variablename" "ecologicalgroup"
## [17] "analysisunitid" "sampleanalyst" "sampleid" "depth"
## [21] "thickness" "samplename" "datasetid" "siteid"
## [25] "sitename" "lat" "long" "area"
## [29] "sitenotes" "description" "elev" "collunitid"
## [33] "database" "datasettype" "age_range_old" "age_range_young"
## [37] "datasetnotes"
For some dataset types, or analyses some of these columns may not be needed, however, for other dataset types they may be critically important. To allow the neotoma2 package to be as useful as possible for the community we've included as many as we can.
If you want to know what taxa we have in the record you can use the helper function taxa() on the sites object. The taxa() function gives us, not only the unique taxa, but two additional columns, sites and samples that tell us how many sites the taxa appear in, and how many samples the taxa appear in, to help us better understand how common individual taxa are.
neotomatx <- neotoma2::taxa(cz_dl)<div id="htmlwidget-29c0a9a7239a67b06142" style="width:100%;height:auto;" class="datatables html-widget"></div>
<script type="application/json" data-for="htmlwidget-29c0a9a7239a67b06142">{"x":{"filter":"none","vertical":false,"data":[["grains/tablet","grains/tablet","ml","NISP","NISP","NISP","NISP","NISP","NISP","NISP","NISP","NISP","NISP","NISP","NISP","NISP","NISP","NISP","NISP","NISP"],[null,null,null,"anachronic","anachronic","anachronic",null,null,null,null,null,null,null,null,null,null,null,null,null,null],["concentration","concentration","volume","pollen/spore","spore","spore","ascospore","ascospore","ascospore","ascospore","ascospore","ascospore","ascospore","ascospore","ascospore","ascospore","ascospore","ascospore","ascospore","ascospore"],[930,932,276,2644,544,2644,1489,2193,3698,5128,5129,5407,5413,5414,5415,5584,9988,10006,27614,29431],[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],["Laboratory analyses","Laboratory analyses","Laboratory analyses","Unidentified palynomorphs","Unidentified palynomorphs","Unidentified palynomorphs","Fungi","Fungi","Fungi","Fungi","Fungi","Fungi","Fungi","Fungi","Fungi","Fungi","Fungi","Fungi","Fungi","Fungi"],["concentration","concentration","volume","pollen/spore","spore","spore","ascospore","ascospore","ascospore","ascospore","ascospore","ascospore","ascospore","ascospore","ascospore","ascospore","ascospore","ascospore","ascospore","ascospore"],["Lycopodium tablets","Lycopodium spike","Sample quantity","Unknown (Tertiary)","Unknown (Cretaceous)","Unknown (Tertiary)","Sporormiella","Gelasinospora","Microthyrium","Gelasinospora undiff.","Gelasinospora reticulispora","Helicoma","Anthostomella fuegiana","Gaeumannomyces cf. 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38542, 38559, 38563, 38575, 38580, 38584, 38620, 38621, 38626, 41780, 41792, 41793, 9995, 210, 385, 559, 561, 570, 571, 572, 608, 619, 626, 1189, 1191, 1194, 1195, 1223, 2187, 2190, 5389, 5405, 5567, 28043, 30985, 31199, 31200, 31208, 32184, 33663, 673, 18282, 5397, 27180, 1488, 1704, 30518, 41702, 1062, 1062, 1062, 1062, 930, 932, 1062, 930, 932, 1062) c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA) c("Laboratory analyses", "Laboratory analyses", "Laboratory analyses", "Unidentified palynomorphs", "Unidentified palynomorphs", "Unidentified palynomorphs", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Fungi", "Algae", "Algae", "Algae", "Algae", "Algae", "Algae", "Fungi", "Fungi", "Fungi", "Fungi", "Arthropods undiff.", "Flatworms", "Flatworms", "Algae", "Algae", "Algae", "Algae", "Algae", "Algae", "Algae", "Algae", "Algae", 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"spore", "spore", "spore", "spore", "spore", "spore", "spore", "spore", "spore", "sporocarp", "stomate", "stomate", "test", "test", "test", "test", "test", "test", "test", "test", "test", "test", "test", "test", "test", "test", "test", "test", "test", "test", "test", "test", "test", "test", "test", "test", "test", "trichoblast", "unspecified", "valve", "valve", "zygospore", "zygospore", "zygospore", "zygospore/aplanospore", "<20 µm", ">100 µm", ">50 µm", "20-50 µm", "batch number", "counted", "fragment", "quantity added", "quantity added", "fragment") c("Lycopodium tablets", "Lycopodium spike", "Sample quantity", "Unknown (Tertiary)", "Unknown (Cretaceous)", "Unknown (Tertiary)", "Sporormiella", "Gelasinospora", "Microthyrium", "Gelasinospora undiff.", "Gelasinospora reticulispora", "Helicoma", "Anthostomella fuegiana", "Gaeumannomyces cf. G. caricis", "Diporotheca", "Helicoön pluriseptatum", "Gaeumannomyces", "Ascomycota", "Ustulina deusta", "Geoglossum sphagnophilum", "Ascospora", "Lasiosphaeria-type", "Coniochaeta xylariispora", "Gelasinospora (type 1, HdV)", "Actinopeltis undiff.", "Geoglossum sphagnophilum/Trichoglossum hirsutum (type 77A/77B, HdV)", "Chaetomium undiff.", "Coniochaeta cf. C. ligniaria", "Gaeumannomyces undiff.", "Lasiosphaeria cf. L. caudata", "Lasiosphaeria sp.", "Microthyrium microscopicum", "Microthyrium undiff.", "Pleospora undiff.", "Fungi (type 19, HdV)", "Fungi (type 47, HdV)", "cf. Trichoglossum hirsutum (type 77B, HdV)", "Cercophora sp. (type 112, HdV)", "Podospora-type (type 368, HdV)", "Chaetomium sp. (type 7A, HdV)", "Tetraploa scheueri", "Caryospora sp. (type 1001, HdV)", "Gelasinospora (type 1A, HdV)", "Gelasinospora (type 1B, HdV)", "Staurastrum", "Arthrodesmus", "Penium", "Closterium", "Closterium undiff.", "Desmidiales", "Fungi (type 200, HdV)", "Fungi (type 24, HdV)", "Asterosporium", "Fungi (type 11, HdV)", "Araneae", "Platyhelminthes (type 353B, HdV)", "Platyhelminthes (type 353A, HdV)", "Pediastrum", "Botryococcus", "Pediastrum angulosum", "Pediastrum braunii", "Pediastrum duplex", "Pediastrum undiff.", "Botryococcus braunii", "Botryococcus pila", "Pediastrum duplex var. rugulosum", "Pediastrum angulosum var. asperum", "Pediastrum muticum var. scutum", "Pediastrum angulosum var. angulosum", "Pediastrum duplex var. duplex", "Coelastrum reticulatum", "Hydrodictyon", "Botryococcus sp.", "Botryococcus neglectus", "Pediastrum orientale", "Pseudopediastrum boryanum", "Pseudopediastrum kawraiskyi", "Parapediastrum biradiatum", "Pseudopediastrum boryanum var. longicorne", "Pseudopediastrum boryanum var. boryanum", "Pseudopediastrum boryanum var. boryanum sensu lato", "Pseudopediastrum brevicorne", "Pseudopediastrum integrum", "Pseudopediastrum boryanum var. cornutum", "Monactinus simplex", "Stauridium tetras", "Monactinus simplex var. echinulatum", "Monactinus simplex var. simplex", "Fungi (type 96B, HdV)", "Trichocladium opacum (type 10, HdV)", "Xylomyces chlamydosporis/X. aquaticus (type 201, HdV)", "cf. Trichocladium opacum (type 10, HdV)", "Dinoflagellata undiff.", "Dinoflagellata", "Macrobiotus", "Macrobiotus cf. M. echinogenitus", "Acrotritia ardua (type 106, HdV)", "Mougeotia cf. M. gracillima (type 61, HdV)", "Charcoal", "Fungi (type 8A, HdV)", "?Microthyrium (type 8, HdV)", "Fungi (type 8E, HdV)", "Fungi (type 8A, HdV)", "Fungi (type 8D, HdV)", "Glyptotendipes pallens group (type 509, HdV)", "Fungi (type 408, HdV)", "Fungi (type 54B, HdV)", "Tardigrada (type 902, HdV)", "Oribatida (type 396, HdV)", "Chironomidae", "Ceratophyllum", "Habrotrocha angusticollis", "Habrotrocha", "Habrotrocha angusticollis (type 37, HdV)", "Filinia longiseta", "Rotifera undiff.", "Cladocera", "Archerella flavum (type 31A, HdV)", "Gyratrix hermaphroditus", "Microdalyellia armigera", "Tardigrada", "Rotifera/Tardigrada", "Habrotrocha angusticollis", "Bryophyta (type 354, HdV)", "Spirogyra", "Zygnemataceae", "Zygnemataceae undiff.", "Algae", "Zygnema", "Mougeotia", "Mougeotia undiff.", "Coelastrum reticulatum", "Scenedesmus", "Scenedesmus undiff.", "Tetraëdron minimum", "Tetraëdron", "Trochiscia undiff.", "Desmidiaceae", "Spirogyra-type", "Zygnema-type", "cf. Penium", "Rhabdocoela", "Staurastrum undiff.", "Mougeotia-type", "Rivularia", "Ascaris", "Transeauina", "Transeauina undiff.", "Algae? (type 225, HdV)", "Ascaris lumbricoides", "Unknown (type 41, HdV)", "Chlamydomonadaceae", "Fungi-type", "Chrysophyceae", "Tardigrada undiff.", "Trichuris trichiura", "Vermes", "Unknown (type 224, HdV)", "Unknown (type 366, HdV)", "Unknown (type 33, HdV)", "Fungi (type 73, HdV)", "Unknown (type 91, HdV)", "Platyhelminthes (type 353B, HdV)", "Unknown (type 38, HdV)", "Anthostomella cf. A. fuegiana (type 4, HdV)", "cf. Persiciospora (type 124, HdV)", "Fungi (type 64, HdV)", "Unknown (type 74, HdV)", "Unknown (type 86, HdV)", "Sigmopollis", "Unknown (type 160, HdV)", "Rhabdocoela (type 353, HdV)", "Dinoflagellata", "Abies", "Aesculus", "Allium", "Alnus viridis-type", "Alnus undiff.", "Ambrosia-type", "Armeria", "Artemisia", "Betula", "Bidens-type", "Boraginaceae", "Callitriche", "Caltha", "Carya", "Caryophyllaceae", "Castanea", "Corylus", "Crataegus-type", "Brassicaceae undiff.", "Cupressaceae", "Cuscuta", "Cyperaceae", "Drosera", "Dryas-type", "Empetrum", "Epilobium", "Ericaceae", "Euonymus", "Euphorbia", "Fagopyrum", "Fagus", "Galium", "Gentianaceae", "Geranium", "Geum-type", "Hippuris vulgaris", "Hypericum", "Ilex", "Impatiens", "Larix", "Rhododendron subsect. Ledum", "Fabaceae undiff.", "Lemnoideae", "Cichorioideae", "Liquidambar", "Lonicera", "Lycopus-type", "Malvaceae", "Menyanthes trifoliata", "Myriophyllum", "Nuphar", "Nymphaea", "Nyssa", "Parnassia", "Picea", "Pinus subg. Pinus", "Plantago major", "Plantago lanceolata", "Plantago media", "Platanus", "Polygonaceae undiff.", "Persicaria amphibia", "Polygonum aviculare-type", "Potentilla-type", "Primulaceae", "Prunus-type", "Quercus", "Ranunculaceae undiff.", "Rhamnaceae", "Rhododendron", "Ribes", "Rubus", "Rumex", "Sagittaria", "Salix", "Sambucus", "Saxifragaceae", "Scheuchzeria palustris", "Scrophulariaceae", "Sedum", "Sparganium-type", "Symplocos", "Taxus", "Thalictrum", "Tilia", "Tsuga", "Asteroideae undiff.", "Typha latifolia", "Ulmus", "Apiaceae", "Utricularia", "Vaccinium", "Valeriana", "Viburnum undiff.", "Vitis", "Xanthium", "Zea mays", "Alnus", "Viola", "Lythrum", "Acer", "Liliaceae", "Ambrosia", "Fabaceae", "Bidens", "Ranunculaceae", "Campanulaceae", "Alnus viridis", "Rosaceae undiff.", "Cornus", "Juniperus-type", "Ephedra", "Fraxinus", "Juglans", "Larix/Pseudotsuga", "Myrica-type", "Ostrya-type", "Pinus", "Populus", "Amaranthaceae", "Viburnum", "Asteraceae", "Avena-type", "Poaceae (Cerealia)", "Poaceae", "Asteroideae", "Brassica", "Brassicaceae", "Humulus", "Cannabis sativa", "Poaceae (Cerealia) undiff.", "Onagraceae", "Gentiana", "Lamiaceae", "Lysimachia thyrsiflora", "Oenothera", "Orchidaceae", "Pedicularis", "Plantago", "Rosaceae", "Primula", "Saxifraga", "Secale-type", "Stachys-type", "Trifolium pratense", "Trifolium repens-type", "Triticum-type", "Urtica", "Alisma", "Hydrocotyle", "Lemna", "Potamogeton", "Engelhardia-type", "Lysimachia", "Polygonum", "Solanaceae", "Stellaria", "Ranunculus", "Allium-type", "Andromeda", "Andromeda polifolia", "Arctostaphylos uva-ursi", "Butomus umbellatus", "Caltha-type", "Campanula-type", "Centaurea", "Drosera rotundifolia-type", "Elymus-type", "Linum", "Lycopus", "Lythrum salicaria", "Mentha-type", "Myriophyllum alterniflorum", "Papaveraceae", "Euphorbiaceae", "Plantaginaceae", "Plantago lanceolata-type", "Polygonaceae", "Bistorta officinalis-type", "Prunella-type", "Prunus", "Pyrola", "Rubiaceae", "Rubus chamaemorus", "Rumex-type", "Rumex acetosa-type", "Salix herbacea-type", "Saxifraga oppositifolia-type", "Micranthes stellaris-type", "Typha", "Typha angustifolia", "Trifolium-type", "Vaccinium oxycoccos", "Rhamnus", "Viburnum opulus", "Viburnum opulus-type", "Xanthium-type", "Polemonium", "Humulus/Cannabis", "Vicia-type", "Potamogeton-type", "Campanula", "Ranunculus-type", "Achillea-type", "Circaea", "Potentilla", "Plantago major-type", "Stellaria-type", "Ononis-type", "Rosa", "Melampyrum-type", "Ericales", "Ericales undiff.", "Ligustrum", "Hydrocotyle-type", "Persicaria maculosa-type", "Senecio", "Persicaria amphibia-type", "Ceratophyllum", "Rumex undiff.", "Sparganium", "Ericaceae undiff.", "Saxifragaceae undiff.", "Oxalis", "Polygonum aviculare", "Secale", "Triglochin", "Triticum", "Juniperus", "Persicaria maculosa", "cf. Pedicularis", "Arenaria", "Ranunculus acris-type", "Melampyrum", "Cerastium-type", "Bupleurum", "Caryophyllaceae undiff.", "Gentianella", "Empetrum-type", "Pinguicula", "Papaver", "Polygala", "Jasione", "Trifolium", "Plantaginaceae undiff.", "Cardamine-type", "Rumex obtusifolius-type", "Convolvulus-type", "Typha angustifolia-type", "Anemone", "Aconitum", "Anemone-type", "Astragalus-type", "Hedysarum-type", "Apiaceae undiff.", "Vaccinium-type", "Geraniaceae", "Bistorta officinalis", "Myriophyllum undiff.", "Saxifraga undiff.", "Cirsium", "Helianthemum", "Solanum", "Euphorbia-type", "Bupleurum-type", "Typha latifolia-type", "Pinus sylvestris", "Picea abies", "Carex", "Alnus glutinosa", "Sanguisorba officinalis", "Hippophaë rhamnoides", "Echinops", "Myriophyllum spicatum", "Myriophyllum verticillatum", "Sorbus aucuparia", "Corylus avellana", "Carpinus betulus", "Fagus sylvatica", "Vitis vinifera", "Fagopyrum esculentum", "Scabiosa", "Knautia arvensis", "Viscum", "Humulus lupulus", "Centaurea cyanus", "Salvia", "Dipsacoideae", "Dipsacus", "Centaurea undiff.", "Hystrix", "Galium-type", "Filipendula", "Carpinus", "Crataegus", "Tofieldia", "Sorbus", "Convolvulus", "Carpinus-type", "Persicaria cf. P. lapathifolia", "Calystegia", "Cerastium", "Rumex acetosella-type", "Impatiens noli-tangere", "Acacia", "Juglandaceae", "Thalictrum-type", "Apium", "Eryngium-type", "Vicia/Lathyrus", "Senecio-type", "Liliaceae-type", "Iris", "Poaceae (Cerealia-type)", "Lathyrus-type", "Lotus-type", "Monocotyledoneae", "Geum", "Epilobium-type", "Viburnum cf. V. opulus", "Myriophyllum verticillatum-type", "Trientalis", "Cardamine", "Cedrus", "Mentha", "Silene", "Valeriana officinalis", "Saxifraga oppositifolia", "Frangula alnus", "Myriophyllum spicatum-type", "Olea", "Oleaceae", "Carduus", "Lobelia", "Anagallis-type", "Alchemilla", "Clematis", "Gentiana undiff.", "Gentiana pneumonanthe-type", "Heracleum", "Dianthus-type", "Gentiana-type", "Montia", "Typha angustifolia/Sparganium", "Myosotis", "Castanea sativa", "Pterocarya", "Hippophaë", "Daphne", "Hedera", "Knautia", "Trapa", "Euphrasia", "Veronica", "Sequoia", "Echium", "Stachys", "Valerianella", "Calluna vulgaris", "Drosera rotundifolia", "Drosera intermedia", "Lotus", "Plantago major/P. media", "Scleranthus perennis", "Scleranthus", "Scleranthus-type", "Stellaria holostea", "Succisa", "Symphytum", "Symphytum-type", "Astragalus alpinus-type", "Cirsium-type", "Elatine", "Frangula", "Mercurialis", "Rhinanthus", "Rhinanthus-type", "Spergula", "Spergula-type", "Spergularia-type", "Vicia", "Brassicaceae-type", "Eryngium", "Ranunculus aquatilis-type", "Persicaria lapathifolia", "Rumex acetosella", "Erodium", "Betula nana", "Teucrium", "Ulex-type", "Glaucium", "Plantago media-type", "Ephedra distachya", "Ephedra fragilis", "Gypsophila-type", "Pinus cembra", "Sagina-type", "Veronica-type", "Fallopia convolvulus", "Nymphaea alba", "Alisma plantago-aquatica", "Anthemis-type", "Aster-type", "Centaurea jacea", "Centaurea scabiosa", "Epipactis", "Rumex subg. Rumex", "Galeopsis", "Galeopsis-type", "Genista-type", "Lamium-type", "Sorbus-type", "Betula pubescens", "Echium vulgare", "Tilia cordata", "Tilia platyphyllos", "Aconitum-type", "Centaurea cyanus-type", "Centaurea scabiosa-type", "Cornus sanguinea", "Ephedra distachya-type", "Ephedra fragilis-type", "Fraxinus excelsior", "Fraxinus ornus", "Helleborus", "Hypericum perforatum-type", "Loranthus", "Matricaria-type", "Plantago maritima-type", "Sambucus nigra-type", "Solanum dulcamara", "Gentianaceae undiff.", "Platycarya", "Betula nana-type", "Abies alba", "Barbarea-type", "Cardamine pratensis-type", "Chrysosplenium", "Ephedra foeminea-type", "Larix decidua", "Lysimachia vulgaris-type", "Lysimachia vulgaris", "Parnassia palustris", "Petasites-type", "Pleurospermum", "Ranunculus arvensis-type", "Silene-type", "Trifolium pratense-type", "Hordeum-type", "Achillea", "Agrimonia", "Alchemilla-type", "Alnus glutinosa-type", "Alnus glutinosa/A. incana", "Anagallis arvensis-type", "Anagallis tenella-type", "Anagallis arvensis", "Anagallis", "Anthericum", "Anthericum-type", "Anchusa/Pulmonaria", "Pulmonaria", "Pulmonaria-type", "Anthriscus caucalis", "Anthriscus sylvestris-type", "Anthriscus-type", "Anthriscus sylvestris", "Anthyllis", "Silene dioica-type", "Silene vulgaris-type", "Apium-type", "Apium inundatum-type", "Arctium", "Cirsium/Carduus", "Arctous alpina", "Arctostaphylos uva-ursi-type", "Armeria maritima-type", "Armeria maritima (type B)", "Armeria maritima (type A)", "Aruncus", "Astragalus danicus-type", "Vicia cracca-type", "Avena/Triticum-type", "Hordeum", "Secale cereale", "Fallopia convolvulus-type", "Fallopia convolvulus/F. dumetorum", "Bupleurum falcatum-type", "Butomus-type", "Butomus", "Caltha palustris-type", "Campanula rapunculoides", "Scilla-type", "Castanea-type", "Centaurea jacea-type", "Centaurea montana-type", "Centaurea nigra-type", "Cerastium fontanum-type", "Dryas octopetala", "Rumex acetosa", "Rumex aquaticus-type", "Rumex obtusifolius", "Rumex maritimus-type", "cf. Papaver", "Papaver rhoeas-type", "Pedicularis palustris-type", "Rhinanthus/Veronica", "Veronica beccabunga-type", "Veronica beccabunga", "Saussurea-type", "Sedum-type", "Digitalis purpurea-type", "cf. Lobelia", "Scrophularia-type", "Scrophularia", "Chrysosplenium-type", "Cicuta virosa", "Convolvulus arvensis", "Helianthemum nummularium-type", "Helianthemum oelandicum subsp. alpestris-type", "Cladium mariscus", "Convallaria", "Cornus suecica", "Cornus mas", "Cuscuta europaea-type", "Daucus-type", "Daucus carota", "Daucus", "Dianthus", "Echium-type", "Erica ciliaris-type", "Ephedra foeminea", "Ephedra cf. E. foeminea", "Ephedra cf. E. fragilis", "Ephedra cf. E. distachya", "Eriophorum", "Euonymus europaeus", "Euphrasia-type", "Fagopyrum-type", "Genista", "Gentiana cruciata-type", "Gentianella campestris-type", "Geranium-type", "Gnaphalium-type", "Gypsophila", "Gypsophila repens-type", "Gypsophila repens", "Hedera helix", "Heracleum-type", "Heracleum sphondylium", "Herniaria", "Herniaria-type", "Hottonia palustris", "Samolus valerandi", "Hydrocotyle vulgaris", "Iris pseudacorus-type", "Iris-type", "Iris pseudacorus", "Jasione montana", "Jasione-type", "Juniperus communis", "Succisa pratensis", "Succisa-type", "Larix-type", "Rhododendron tomentosum", "Linum catharticum", "Linum catharticum-type", "Linum usitatissimum-type", "Linum flavum", "Linum austriacum-type", "Listera-type", "Lithospermum officinale", "Lonicera periclymenum", "Lonicera xylosteum", "Loranthus europaeus", "Lotus cf. L. corniculatus", "Lysimachia nemorum", "Lysimachia-type", "Lysimachia cf. L. vulgaris", "Lysimachia nemorum-type", "Lythrum portula-type", "Lythrum-type", "Maianthemum bifolium", "Malus", "Malus-type", "Malva-type", "Marrubium", "Menyanthes trifoliata-type", "Mercurialis perennis-type", "Muscari", "Myosotis arvensis-type", "Myricaria germanica", "Myriophyllum cf. M. spicatum", "Myriophyllum cf. M. verticillatum", "Nymphaea cf. N. candida", "Nymphaea alba-type", "Odontites", "Odontites-type", "Onobrychis", "Ononis", "Ornithogalum-type", "Phragmites", "Phragmites-type", "Phragmites australis", "Pimpinella major-type", "Pimpinella anisum", "Pinus subg. Strobus-type", "Pinus sylvestris-type", "Pinus cembra-type", "Pisum sativum", "Plantago coronopus", "Plantago alpina-type", "Plantago atrata-type", "Plantago alpina", "Pleurospermum austriacum", "Pleurospermum austriacum-type", "Polemonium caeruleum", "Primula farinosa-type", "Primula veris-type", "Pterocarya fraxinifolia", "Quercus coccifera", "Ranunculus flammula-type", "Ranunculus arvensis", "Reseda", "Reseda lutea-type", "Ribes alpinum", "Rosa-type", "Sagina", "Sambucus ebulus", "Sambucus nigra", "Sambucus racemosa", "Sambucus cf. S. nigra", "Sambucus cf. S. ebulus", "Sambucus cf. S. racemosa", "Sanguisorba minor-type", "Saxifraga granulata-type", "Saxifraga hirculus-type", "Micranthes stellaris", "Saxifraga granulata", "Saxifraga aizoides-type", "Scabiosa columbaria-type", "Sciadopitys", "Scleranthus annuus", "Serratula-type", "Serratula", "Sinapis-type", "Solanum cf. S. nigrum", "Solanum nigrum", "Solanum nigrum-type", "Stratiotes aloides", "Taxus baccata", "Thesium", "Tilia undiff.", "Sparganium erectum", "Trapa natans", "Trientalis europaea", "Trollius", "Trollius europaeus", "Trollius-type", "Ulmus/Zelkova", "Valeriana dioica", "Valeriana officinalis-type", "Valeriana cf. V. dioica", "Valeriana dioica-type", "Verbascum", "Viburnum lantana", "Viola palustris-type", "Viola tricolor", "Viola palustris", "cf. Lamiaceae", "Scutellaria", "Glyceria-type", "Sanicula europaea", "Sanicula-type", "Anemone nemorosa-type", "Veratrum-type", "Veratrum", "Veratrum album", "Oenanthe-type", "Oenanthe", "Chelidonium", "Chelidonium majus", "Polygonatum", "Peucedanum palustre-type", "Peucedanum-type", "Peucedanum", "Hyoscyamus", "Cerinthe", "Cerinthe minor", "Androsace-type", "Crupina", "Phyteuma-type", "Astrantia-type", "Swertia perennis", "Agrostemma githago", "Petasites", "Chaerophyllum", "Succisella", "Lamiaceae (tricolpate)", "Laserpitium", "Betula pubescens-type", "Chaerophyllum hirsutum-type", "Falcaria vulgaris", "Heliotropium europaeum", "Ludwigia palustris", "Phyteuma", "Ailanthus", "Plantago major/P. media-type", "Rumex acetosa/R. acetosella", "Cannabis-type", "Vaccinioideae", "Menyanthes", "Persicaria", "Bistorta", "Scheuchzeria", "Faboideae", "Calla", "Calluna", "Typhaceae", "Chamaenerion angustifolium", "Centaurea stoebe", "Prunus sp.", "Potamogeton natans-type", "Potentilla/Comarum", "Cryptomeria", "Pinus sp.", "Parnassia-type", "Polygonum sp.", "Anemone sect. Pulsatilla", "Anemone sect. Hepatica-type", "Oxyria-type", "Ranunculus sect. Batrachium", "Arnica montana", "Silenoideae-type", "Cerastium arvense-type", "Cerastium cerastoides-type", "Medicago falcata-type", "Minuartia-type", "Seseli-type", "Soldanella", "Rhus-type", "Chamaenerion angustifolium-type", "Sium latifolium-type", "Humulus/Cannabis-type", "Bruckenthalia-type", "Consolida-type", "Cuscuta epithymum", "Comarum", "Comarum palustre", "Comarum-type", "Chamaenerion", "Sagittaria-type", "Orlaya grandiflora", "Plantago sp.", "Actaea spicata", "Adonis annua-type", "Adonis aestivalis-type", "Adonis aestivalis/A. flammea", "Aethusa cynapium", "Androsace elongata-type", "Anemone nemorosa group", "Aphanes", "Arenaria serpyllifolia-type", "Astragalus exscapus", "Astrantia major", "Bambusa-type", "Ranunculus sect. Batrachium-type", "Bryonia alba/Helianthemum", "Campanula/Phyteuma", "Carum carvi", "Sileneae", "Cedrus-type", "Centaurea alpina-type", "Centaurea stoebe-type", "Centaurea jacea/C. stoebe", "Centaurea sp.", "Poaceae (Cerealia) excluding Secale", "Chaerophyllum hirsutum", "cf. Helianthemum", "Illecebrum verticillatum", "Falcaria-type", "Laserpitium latifolium-type", "Silene flos-cuculi", "Silene viscaria-type", "Silene vulgaris", "Microrrhinum minus", "Onopordum", "Potentilla/Comarum-type", "Coniferae-type", "Consolida regalis", "Coronilla undiff.", "Descurainia sophia", "Empetrum nigrum-type", "Eranthis hyemalis-type", "Filipendula ulmaria/F. vulgaris", "Fumaria-type", "Galeopsis/Ballota-type", "Glaucium corniculatum", "Gratiola officinalis", "Anemone hepatica", "Hypericum perforatum/H. androsaemum-type", "Impatiens parviflora", "Juglandaceae-type", "Knautia arvensis-type", "Lamium album-type", "Vicia/Lathyrus-type", "Listera ovata", "Magnolia-type", "Malus undiff.", "Myriophyllum heterophyllum", "Nymphaea undiff.", "Normapolles", "Nymphoides peltata-type", "Ornithogalum umbellatum-type", "Papaver somniferum", "Pimpinella major", "Pimpinella major/P. saxifraga", "Poaceae (Cerealia-type excluding Secale)", "Podocarpus-type", "Koenigia alpina", "Potentilla/Fragaria", "Primula clusiana-type", "Quercus pubescens", "Ribes uva-crispa", "Poterium sanguisorba", "Poterium sanguisorba subsp. sanguisorba", "Rumex cf. R. alpinus", "Rumex/Oxyria-type", "Sagina procumbens-type", "Sambucus nigra/S. racemosa", "Scabiosa columbaria subsp. pratensis-type", "Scandix pecten-veneris/Caucalis platycarpos", "Sciadopitys-type", "Scleranthus annuus-type", "Scleranthus cf. S. annuus", "Scleranthus cf. S. perennis", "Scleranthus perennis-type", "Securigera varia", "Silene latifolia", "Sorbus aria-type", "Sorbus torminalis", "Sorbus group", "Typha angustifolia/Sparganium-type", "Symphytum cf. S. officinale", "Pinus (Tertiary)", "Thesium-type", "Tsuga diversifolia-type", "Tsuga-type", "Turgenia latifolia", "Umbilicus rupestris-type", "Valeriana cf. V. officinalis", "Viola canina-type", "Anthemis arvensis-type", "Silene-type undiff.", "Lotus pedunculatus", "cf. Androsace", "Adenostyles alliariae", "Petasites hybridus-type", "Ranunculus acris/R. flammula/R. sceleratus group", "Senecio/Aster", "Juncus sp. (type 2.2, MI)", "Indeterminable", "Unknown", "Indeterminable undiff.", "Varia", "Alona rustica (type 72, HdV)", "Copepoda", "Porifera", "Athyrium", "Botrychium", "Dryopteris-type", "Equisetum", "Fungi undiff.", "Isoëtes", "Lycopodiaceae undiff.", "Diphasiastrum alpinum", "Lycopodium annotinum", "Lycopodium clavatum", "Lycopodiella inundata", "Huperzia selago", "Unknown (monolete) undiff.", "Polypodiaceae", "Selaginella", "Sphagnum", "Unknown (trilete) undiff.", "Unknown", "Unknown (trilete)", "Unknown (monolete)", "Ophioglossum", "Fungi", "Athyrium filix-femina", "Cystopteris", "Dryopteris", "Diphasiastrum complanatum", "Diphasiastrum alpinum-type", "Lycopodium annotinum-type", "Pteridophyta", "Pteridium aquilinum", "Selaginella selaginoides", "Pteridium", "Dryopteris carthusiana-type", "Polypodium", "Tilletia sphagni", "Lycopodium clavatum-type", "Bryales", "Marchantiophyta", "Bryophyta", "Lycopodiaceae", "Ophioglossum vulgatum", "Riccia", "Anthoceros", "Dryopteris filix-mas-type", "Asplenium", "Thelypteris palustris", "Sporormiella", "Thecaphora", "Hymenophyllum", "Anthoceros laevis", "Pteridophyta (monolete, verrucate)", "Asplenium-type", "cf. Entophlyctis lobata", "Lycopodiaceae cf. Diphasiastrum complanatum", "Polypodium vulgare", "Unknown (monolete, psilate)", "Isoëtes lacustris", "Athyrium-type", "Blechnum", "Thelypteris", "Microthyrium", "Gymnocarpium dryopteris", "Lycopodium", "Lycopodium undiff.", "Pilularia", "Pteridophyta (monolete) undiff.", "Phegopteris connectilis", "cf. Riccia", "Anthoceros laevis-type", "Entophlyctis lobata", "Diporotheca", "Glomus", "Microthyrium-type", "Sordariaceae", "Dryopteris dilatata-type", "Helicoön pluriseptatum", "Polypodiophyta (monolete, psilate)", "Phegopteris", "Equisetaceae", "Unknown (pre-Quaternary)", "Meliola", "Neurospora", "Xylariaceae", "Ustulina deusta", "Polypodiophyta (monolete, verrucate)", "Geoglossum sphagnophilum", "Sordaria-type (type 55A, HdV)", "Fungi (type 200, HdV)", "Adiantum capillus-veneris", "Anthoceros punctatus-type", "Byssothecium circinans", "cf. Diphasiastrum-type", "Cicatricosporites australiensis", "Coniochaeta cf. C. ligniaria", "Encalypta-type", "Glomus cf. G. fasciculatum", "Selaginellaceae", "Unknown (type 181, HdV)", "Fungi (type 18, HdV)", "Byssothecium circinans (type 16C, HdV)", "Fungi (type 17, HdV)", "Fungi (type 3A, HdV)", "Fungi (type 8E, HdV)", "Fungi (type 83, HdV)", "Fungi (type 90, HdV)", "Fungi (type 571, HdV)", "cf. Endophragmia (type 572, HdV)", "Fungi (type 23, HdV)", "Aspiromitus punctatus", "Fungi (type 73, HdV)", "Byssothecium circinans (type 16B, HdV)", "Fungi (type 53, HdV)", "Sordariaceae/Sordaria (type 55B, HdV)", "Geoglossum sphagnophilum (type 77A, HdV)", "cf. Spadicoides bina (type 98, HdV)", "Delitschia", "Fungi (type 65, HdV)", "Brachysporium obovatum/B. bloxami/Bactrodesmium betulicola (type 359, HdV)", "Helicosporium/Helicoön pluriseptatum (type 30, HdV)", "Fungi (type 173, HdV)", "Fungi (type 20, HdV)", "Fungi (type 729, HdV)", "Podospora sp./Zopfiella sp. (type 466, HdV)", "Fungi (type 778. HdV)", "Brachysporium pendulisporum (type 360, HdV)", "Byssothecium circinans (type 16A, HdV)", "Sporormiella (type 113, HdV)", "cf. Actinopeltis (type 8C, HdV)", "Algae (type 209, HdV)", "Ustulina deusta (type 44, HdV)", "Tilletia sphagni (type 27, HdV)", "Pleospora sp. (type 3B, HdV)", "Lasiosphaeria sp. (type 63C, HdV)", "Entorrhiza sp. (type HdV-527)", "Fungi (type 123, HdV)", "Unknown (type 708, HdV)", "Clasterosporium caricinum (type 126, HdV)", "Coniochaeta ligniaria (type 172, HdV)", "cf. Richonia variospora (type 140, HdV)", "Fungi (type 404, HdV)", "Gelasinospora (type 1A, HdV)", "Gelasinospora (type 1B, HdV)", "Microthyriaceae", "Picea", "Pinus", "Amphitrema", "Amphitrema wrightianum", "Assulina", "Assulina muscorum", "Assulina seminulum", "Difflugia", "Euglypha", "Hyalosphenia papilio", "Arcella", "Centropyxis", "Hyalosphenia subflava", "Nebela", "Amphitrema undiff.", "Centropyxis aculeata", "Arcella discoides", "Rhizopoda undiff.", "Nebela undiff.", "Nebela parvula", "Archerella flavum", "Amphitrema sp.", "Arcella cf. A. megastoma", "Arcella sp.", "Assulina sp.", "Rhizopoda", "Pyxidicula", "Nymphaeaceae", "Lepidoptera", "Pinnularia", "Eunotia sp.", "Spirogyra", "Zygnemataceae", "Spirogyra cf. S. scrobiculata", "Transeauina (type 214, HdV)", "Charcoal", "Charcoal", "Charcoal", "Charcoal", "Lycopodium tablets", "Lycopodium spike", "Charcoal", "Lycopodium tablets", "Lycopodium spike", "Charcoal") c("LABO", "LABO", "LABO", "ANAC", "ANAC", "ANAC", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "ALGA", "ALGA", "ALGA", "ALGA", "ALGA", "ALGA", "FUNG", "FUNG", "FUNG", "FUNG", "ARTH", "FLWO", "FLWO", "ALGA", "ALGA", "ALGA", "ALGA", "ALGA", "ALGA", "ALGA", "ALGA", "ALGA", "ALGA", "ALGA", "ALGA", "ALGA", "ALGA", "ALGA", "ALGA", "ALGA", "ALGA", "ALGA", "ALGA", "ALGA", "ALGA", "ALGA", "ALGA", "ALGA", "ALGA", "ALGA", "ALGA", "ALGA", "ALGA", "ALGA", "FUNG", "FUNG", "FUNG", "FUNG", "DINO", "DINO", "ANIM", "ANIM", "ACAR", "ALGA", "CHAR", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "DIPT", "FUNG", "FUNG", "ANIM", "ACAR", "DIPT", "AQVP", "ROTI", "ROTI", "ROTI", "ROTI", "ROTI", "CLAD", "TEAM", "FLWO", "FLWO", "ANIM", "ANIM", "ROTI", "UPBR", "ALGA", "ALGA", "ALGA", "ALGA", "ALGA", "ALGA", "ALGA", "ALGA", "ALGA", "ALGA", "ALGA", "ALGA", "ALGA", "ALGA", "ALGA", "ALGA", "ALGA", "FLWO", "ALGA", "ALGA", "ALGA", "NEMA", "ALGA", "ALGA", "ALGA", "NEMA", "UNID", "ALGA", "UNID", "ALGA", "ANIM", "NEMA", "ANIM", "UNID", "UNID", "UNID", "FUNG", "UNID", "FLWO", "UNID", "FUNG", "FUNG", "FUNG", "UNID", "UNID", "ALGA", "UNID", "FLWO", "DINO", "TRSH", "TRSH", "UPHE", "TRSH", "TRSH", "UPHE", "UPHE", "UPHE", "TRSH", "UPHE", "UPHE", "AQVP", "AQVP", "TRSH", "UPHE", "TRSH", "TRSH", "TRSH", "UPHE", "TRSH", "UPHE", "UPHE", "AQVP", "UPHE", "TRSH", "UPHE", "TRSH", "TRSH", "UPHE", "UPHE", "TRSH", "UPHE", "UPHE", "UPHE", "UPHE", "AQVP", "UPHE", "TRSH", "UPHE", "TRSH", "TRSH", "UPHE", "AQVP", "UPHE", "TRSH", "TRSH", "UPHE", "UPHE", "AQVP", "AQVP", "AQVP", "AQVP", "TRSH", "UPHE", "TRSH", "TRSH", "UPHE", "UPHE", "UPHE", "TRSH", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "TRSH", "TRSH", "UPHE", "TRSH", "TRSH", "TRSH", "TRSH", "UPHE", "AQVP", "TRSH", "TRSH", "UPHE", "AQVP", "UPHE", "UPHE", "AQVP", "TRSH", "TRSH", "UPHE", "TRSH", "TRSH", "UPHE", "AQVP", "TRSH", "UPHE", "AQVP", "TRSH", "UPHE", "TRSH", "TRSH", "UPHE", "UPHE", "TRSH", "UPHE", "UPHE", "TRSH", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "TRSH", "UPHE", "TRSH", "TRSH", "TRSH", "TRSH", "TRSH", "TRSH", "TRSH", "TRSH", "TRSH", "TRSH", "UPHE", "TRSH", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "AQVP", "AQVP", "AQVP", "AQVP", "TRSH", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "TRSH", "TRSH", "TRSH", "AQVP", "UPHE", "UPHE", "UPHE", "AQVP", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "AQVP", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "TRSH", "UPHE", "TRSH", "TRSH", "UPHE", "UPHE", "TRSH", "UPHE", "UPHE", "AQVP", "AQVP", "UPHE", "TRSH", "TRSH", "TRSH", "TRSH", "UPHE", "UPHE", "UPHE", "UPHE", "AQVP", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "TRSH", "UPHE", "TRSH", "TRSH", "TRSH", "AQVP", "UPHE", "UPHE", "UPHE", "AQVP", "UPHE", "AQVP", "TRSH", "UPHE", "UPHE", "UPHE", "UPHE", "AQVP", "UPHE", "TRSH", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "TRSH", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "AQVP", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "TRSH", "UPHE", "UPHE", "AQVP", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "AQVP", "TRSH", "TRSH", "UPHE", "TRSH", "UPHE", "TRSH", "UPHE", "AQVP", "AQVP", "TRSH", "TRSH", "TRSH", "TRSH", "TRSH", "UPHE", "UPHE", "UPHE", "TRSH", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "TRSH", "TRSH", "UPHE", "TRSH", "UPHE", "TRSH", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "TRSH", "TRSH", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "SEED", "UPHE", "UPHE", "TRSH", "AQVP", "UPHE", "UPHE", "TRSH", "UPHE", "UPHE", "UPHE", "UPHE", "TRSH", "AQVP", "TRSH", "TRSH", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "AQVP", "UPHE", "TRSH", "TRSH", "TRSH", "TRSH", "TRSH", "UPHE", "AQVP", "UPHE", "UPHE", "TRSH", "UPHE", "UPHE", "UPHE", "TRSH", "AQVP", "AQVP", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "AQVP", "TRSH", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "AQVP", "UPHE", "UPHE", "UPHE", "TRSH", "UPHE", "TRSH", "UPHE", "UPHE", "TRSH", "TRSH", "UPHE", "TRSH", "UPHE", "UPHE", "UPHE", "AQVP", "AQVP", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "TRSH", "UPHE", "TRSH", "TRSH", "UPHE", "TRSH", "TRSH", "UPHE", "UPHE", "UPHE", "TRSH", "TRSH", "TRSH", "TRSH", "TRSH", "UPHE", "UPHE", "TRSH", "UPHE", "UPHE", "TRSH", "UPHE", "UPHE", "TRSH", "TRSH", "TRSH", "UPHE", "UPHE", "UPHE", "TRSH", "TRSH", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "TRSH", "TRSH", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "TRSH", "TRSH", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "AQVP", "AQVP", "AQVP", "UPHE", "UPHE", "TRSH", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "AQVP", "AQVP", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "AQVP", "UPHE", "TRSH", "TRSH", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "TRSH", "TRSH", "TRSH", "TRSH", "TRSH", "AQVP", "TRSH", "UPHE", "UPHE", "TRSH", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "TRSH", "UPHE", "UPHE", "UPHE", "UPHE", "AQVP", "AQVP", "AQVP", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "TRSH", "UPHE", "UPHE", "TRSH", "TRSH", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "TRSH", "TRSH", "TRSH", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "TRSH", "TRSH", "UPHE", "UPHE", "AQVP", "UPHE", "UPHE", "UPHE", "TRSH", "AQVP", "AQVP", "AQVP", "AQVP", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "AQVP", "AQVP", "AQVP", "UPHE", "UPHE", "TRSH", "TRSH", "TRSH", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "TRSH", "TRSH", "UPHE", "UPHE", "UPHE", "UPHE", "TRSH", "UPHE", "UPHE", "TRSH", "TRSH", "TRSH", "TRSH", "TRSH", "TRSH", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "TRSH", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "AQVP", "TRSH", "UPHE", "TRSH", "AQVP", "AQVP", "UPHE", "UPHE", "UPHE", "UPHE", "TRSH", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "TRSH", "AQVP", "UPHE", "AQVP", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "AQVP", "AQVP", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "TRSH", "UPHE", "UPHE", "UPHE", "AQVP", "UPHE", "TRSH", "UPHE", "UPHE", "UPHE", "TRSH", "AQVP", "UPHE", "UPHE", "AQVP", "UPHE", "AQVP", "TRSH", "AQVP", "UPHE", "UPHE", "TRSH", "AQVP", "UPHE", "TRSH", "TRSH", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "AQVP", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "TRSH", "UPHE", "UPHE", "UPHE", "TRSH", "UPHE", "UPHE", "AQVP", "AQVP", "UPHE", "UPHE", "AQVP", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "TRSH", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "TRSH", "UPHE", "UPHE", "UPHE", "TRSH", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "TRSH", "UPHE", "UPHE", "UPHE", "UPHE", "TRSH", "TRSH", "AQVP", "AQVP", "TRSH", "AQVP", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "TRSH", "UPHE", "UPHE", "UPHE", "TRSH", "TRSH", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "TRSH", "UPHE", "UPHE", "TRSH", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "TRSH", "TRSH", "TRSH", "AQVP", "UPHE", "TRSH", "UPHE", "TRSH", "TRSH", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "UPHE", "AQVP", "UNID", "UNID", "UNID", "UNID", "CLAD", "COPE", "SPNG", "VACR", "VACR", "VACR", "VACR", "FUNG", "AQVP", "VACR", "VACR", "VACR", "VACR", "VACR", "VACR", "UNID", "VACR", "VACR", "AQBR", "UNID", "UNID", "UNID", "UNID", "VACR", "FUNG", "VACR", "VACR", "VACR", "VACR", "VACR", "VACR", "VACR", "VACR", "VACR", "VACR", "VACR", "VACR", "FUNG", "VACR", "UPBR", "UPBR", "UPBR", "VACR", "VACR", "AQBR", "UPBR", "VACR", "VACR", "VACR", "FUNG", "FUNG", "VACR", "UPBR", "VACR", "VACR", "FUNG", "VACR", "VACR", "UNID", "AQVP", "VACR", "VACR", "VACR", "FUNG", "VACR", "VACR", "VACR", "VACR", "VACR", "VACR", "AQBR", "UPBR", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "VACR", "FUNG", "VACR", "VACR", "VACR", "ANAC", "FUNG", "FUNG", "FUNG", "FUNG", "VACR", "FUNG", "FUNG", "FUNG", "VACR", "UPBR", "FUNG", "VACR", "PTER", "FUNG", "UPBR", "FUNG", "VACR", "UNID", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "UPBR", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "ALGA", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "UNID", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "FUNG", "TRSH", "TRSH", "TEAM", "TEAM", "TEAM", "TEAM", "TEAM", "TEAM", "TEAM", "TEAM", "TEAM", "TEAM", "TEAM", "TEAM", "TEAM", "TEAM", "TEAM", "TEAM", "TEAM", "TEAM", "TEAM", "TEAM", "TEAM", "TEAM", "TEAM", "TEAM", "TEAM", "AQVP", "LEPI", "DIAT", "DIAT", "ALGA", "ALGA", "ALGA", "ALGA", "CHAR", "CHAR", "CHAR", "CHAR", "LABO", "LABO", "CHAR", "LABO", "LABO", "CHAR") c(3, 1, 6, 4, 1, 2, 1, 6, 30, 1, 1, 3, 1, 6, 6, 5, 4, 4, 4, 1, 1, 1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 22, 5, 1, 10, 3, 11, 3, 8, 2, 2, 3, 1, 1, 1, 3, 3, 1, 13, 6, 1, 9, 5, 5, 3, 11, 8, 4, 2, 2, 2, 1, 2, 3, 1, 1, 3, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 11, 1, 1, 1, 1, 1, 1, 6, 6, 2, 1, 3, 2, 6, 2, 1, 7, 3, 12, 2, 4, 11, 2, 9, 7, 1, 3, 3, 5, 1, 3, 1, 1, 1, 3, 1, 3, 1, 1, 2, 1, 1, 1, 1, 2, 1, 1, 1, 2, 1, 2, 1, 2, 1, 1, 1, 1, 2, 1, 1, 1, 1, 72, 2, 3, 1, 1, 5, 4, 87, 83, 3, 12, 2, 4, 4, 28, 4, 68, 2, 1, 2, 8, 84, 15, 1, 3, 42, 21, 12, 13, 23, 75, 14, 6, 32, 10, 2, 27, 2, 10, 30, 3, 1, 1, 81, 1, 13, 11, 6, 33, 2, 15, 14, 2, 4, 74, 3, 20, 68, 17, 1, 1, 8, 8, 27, 2, 13, 85, 4, 1, 1, 16, 12, 36, 4, 86, 13, 13, 6, 14, 13, 8, 1, 1, 75, 79, 4, 2, 41, 85, 70, 17, 22, 30, 1, 9, 3, 5, 79, 13, 19, 78, 25, 5, 51, 12, 57, 5, 8, 3, 8, 1, 6, 68, 57, 1, 1, 1, 77, 44, 85, 10, 13, 23, 14, 86, 65, 1, 65, 7, 7, 20, 1, 10, 40, 1, 1, 2, 19, 3, 65, 4, 3, 16, 4, 6, 11, 27, 71, 13, 1, 4, 36, 2, 30, 1, 1, 2, 1, 4, 1, 1, 1, 1, 45, 7, 11, 1, 1, 3, 9, 9, 24, 17, 10, 1, 3, 18, 3, 25, 1, 6, 1, 56, 1, 2, 41, 2, 4, 5, 1, 8, 22, 5, 11, 5, 1, 1, 9, 32, 24, 12, 45, 31, 15, 9, 9, 13, 2, 1, 6, 1, 3, 1, 5, 1, 27, 1, 2, 1, 4, 12, 7, 1, 9, 56, 35, 3, 27, 56, 13, 2, 6, 20, 54, 5, 5, 1, 2, 6, 3, 6, 6, 5, 6, 1, 19, 4, 1, 1, 1, 11, 19, 6, 1, 15, 37, 1, 23, 2, 2, 12, 42, 1, 1, 5, 13, 3, 23, 1, 1, 50, 10, 1, 24, 16, 2, 26, 26, 11, 2, 1, 9, 2, 47, 5, 62, 1, 3, 3, 7, 2, 31, 81, 65, 1, 1, 24, 7, 1, 1, 7, 3, 9, 1, 1, 2, 3, 1, 1, 1, 12, 2, 2, 16, 11, 32, 8, 11, 3, 1, 6, 1, 2, 1, 7, 3, 20, 1, 38, 1, 2, 1, 12, 2, 1, 5, 1, 1, 5, 6, 4, 3, 4, 33, 3, 1, 3, 7, 3, 24, 21, 1, 2, 9, 1, 18, 5, 2, 57, 6, 1, 1, 48, 1, 4, 5, 3, 15, 21, 2, 1, 41, 7, 27, 8, 9, 2, 2, 1, 1, 1, 6, 2, 1, 1, 20, 4, 8, 3, 1, 2, 3, 10, 4, 4, 6, 2, 4, 3, 2, 1, 13, 9, 11, 22, 1, 2, 1, 2, 7, 21, 8, 1, 2, 9, 10, 1, 7, 7, 17, 9, 10, 14, 1, 1, 3, 8, 1, 3, 10, 9, 1, 1, 1, 23, 17, 13, 20, 3, 2, 19, 7, 16, 13, 2, 1, 23, 22, 7, 1, 1, 4, 5, 1, 2, 1, 1, 2, 3, 1, 1, 1, 6, 1, 4, 1, 1, 2, 8, 8, 1, 1, 1, 4, 1, 1, 1, 2, 2, 1, 3, 1, 1, 1, 32, 3, 1, 1, 1, 6, 1, 1, 1, 3, 31, 1, 2, 1, 3, 10, 1, 3, 1, 1, 2, 1, 1, 2, 1, 1, 2, 1, 1, 3, 3, 4, 2, 9, 1, 1, 2, 1, 1, 10, 2, 11, 1, 1, 3, 2, 1, 1, 3, 1, 1, 1, 1, 2, 4, 1, 1, 4, 1, 11, 5, 4, 1, 26, 6, 2, 1, 2, 1, 1, 1, 2, 3, 1, 8, 1, 1, 8, 1, 1, 4, 12, 1, 3, 1, 2, 2, 1, 2, 3, 2, 1, 1, 9, 1, 1, 3, 1, 1, 2, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 3, 4, 1, 1, 2, 5, 2, 12, 1, 1, 2, 3, 4, 2, 3, 1, 6, 13, 1, 5, 1, 4, 1, 2, 1, 4, 1, 1, 1, 1, 3, 5, 18, 12, 6, 1, 4, 1, 3, 1, 2, 1, 2, 1, 2, 3, 1, 1, 1, 1, 1, 6, 3, 2, 4, 4, 2, 3, 2, 5, 11, 1, 1, 1, 8, 1, 8, 9, 2, 5, 1, 5, 1, 1, 5, 1, 1, 15, 2, 5, 1, 1, 4, 3, 1, 2, 1, 12, 1, 1, 2, 1, 1, 1, 1, 4, 2, 10, 3, 1, 1, 1, 1, 2, 6, 1, 1, 1, 6, 2, 8, 1, 11, 11, 7, 1, 3, 6, 3, 1, 27, 1, 12, 1, 1, 1, 9, 1, 1, 1, 3, 5, 1, 2, 13, 1, 12, 6, 6, 1, 4, 1, 1, 1, 1, 1, 6, 1, 6, 1, 18, 2, 4, 6, 1, 1, 2, 2, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 4, 1, 1, 1, 28, 1, 1, 2, 1, 1, 1, 2, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 12, 2, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 2, 1, 10, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 4, 1, 1, 1, 1, 1, 1, 1, 23, 1, 57, 1, 8, 1, 2, 44, 20, 74, 3, 1, 2, 1, 56, 44, 4, 7, 5, 42, 3, 77, 7, 4, 1, 14, 13, 6, 6, 1, 2, 1, 1, 5, 3, 46, 19, 22, 1, 15, 12, 3, 40, 3, 10, 12, 2, 3, 5, 4, 1, 7, 1, 4, 1, 5, 2, 1, 3, 1, 30, 2, 1, 1, 2, 1, 2, 8, 4, 1, 1, 5, 1, 1, 1, 8, 2, 2, 1, 1, 2, 3, 1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 1, 2, 1, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 2, 4, 2, 3, 4, 2, 2, 2, 13, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 7, 4, 2, 5, 5, 6, 7, 3, 1, 8, 1, 14, 1, 5, 5, 1, 1, 2, 5, 1, 1, 20, 1, 1, 2, 2, 4, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 2, 5, 1, 5) c(130, 80, 368, 137, 6, 16, 27, 19, 223, 1, 5, 17, 1, 131, 50, 155, 55, 53, 83, 1, 7, 8, 56, 13, 7, 3, 1, 90, 12, 63, 2, 18, 32, 42, 4, 1, 98, 12, 1, 7, 2, 1, 5, 1, 38, 4, 2, 3, 2, 1, 21, 52, 1, 3, 1, 60, 23, 58, 475, 36, 4, 165, 41, 148, 18, 211, 2, 4, 69, 1, 1, 1, 21, 7, 37, 208, 36, 1, 253, 58, 211, 6, 297, 150, 29, 14, 32, 47, 30, 14, 17, 49, 9, 34, 2, 2, 1, 4, 140, 32, 15, 4, 14, 21, 2, 4, 5, 1, 2, 4, 128, 200, 8, 34, 22, 6, 5, 26, 66, 140, 13, 1, 51, 4, 72, 21, 40, 18, 20, 188, 2, 49, 225, 7, 138, 137, 5, 48, 5, 25, 2, 71, 1, 1, 7, 13, 1, 8, 1, 2, 17, 2, 8, 1, 3, 6, 1, 4, 6, 19, 1, 9, 33, 2, 5, 1, 52, 2, 2, 2, 5, 10, 54, 1822, 3, 46, 5, 130, 26, 11, 3419, 3727, 3, 37, 11, 25, 37, 288, 18, 2273, 7, 22, 11, 64, 3751, 20, 1, 5, 150, 202, 28, 18, 46, 2328, 218, 15, 79, 31, 3, 143, 15, 17, 99, 12, 5, 12, 1869, 3, 29, 66, 14, 264, 2, 110, 135, 15, 11, 2576, 210, 203, 1352, 330, 1, 2, 11, 57, 496, 3, 52, 3128, 129, 1, 1, 57, 37, 610, 5, 2878, 31, 42, 30, 40, 43, 181, 1, 2, 1446, 2445, 21, 43, 378, 2862, 1767, 65, 304, 170, 2, 13, 10, 7, 3219, 27, 87, 1157, 85, 6, 350, 83, 1409, 10, 190, 45, 9, 12, 21, 1293, 194, 1, 6, 1, 3518, 473, 1977, 27, 134, 325, 129, 3892, 1119, 30, 1163, 16, 95, 239, 1, 39, 422, 1, 1, 2, 30, 7, 787, 11, 6, 136, 10, 20, 29, 225, 1140, 51, 1, 17, 460, 19, 152, 1, 2, 10, 24, 6, 1, 3, 5, 1, 365, 19, 35, 4, 2, 6, 27, 48, 253, 87, 26, 3, 12, 203, 5, 139, 1, 19, 1, 1248, 7, 3, 874, 20, 11, 14, 2, 42, 178, 37, 39, 29, 4, 26, 15, 497, 115, 163, 239, 417, 216, 13, 132, 119, 4, 1, 24, 2, 207, 118, 27, 1, 69, 1, 5, 2, 35, 111, 44, 3, 13, 402, 467, 12, 291, 862, 38, 10, 8, 445, 445, 29, 11, 30, 2, 50, 4, 14, 7, 8, 13, 27, 151, 12, 1, 2, 2, 76, 89, 15, 2, 331, 362, 2, 121, 2, 2, 52, 308, 1, 5, 8, 254, 99, 1005, 7, 20, 183, 43, 2, 225, 126, 7, 1107, 620, 438, 3, 3, 12, 5, 164, 80, 432, 1, 4, 5, 13, 9, 572, 2359, 1148, 1, 1, 81, 22, 130, 1, 14, 12, 172, 5, 1, 13, 4, 1, 1, 11, 38, 4, 3, 148, 14, 162, 41, 23, 9, 1, 112, 1, 46, 2, 39, 7, 96, 2, 327, 1, 5, 1, 44, 2, 1, 23, 3, 9, 8, 40, 25, 3, 6, 358, 3, 1, 12, 20, 8, 49, 33, 3, 2, 42, 4, 40, 12, 6, 895, 16, 5, 6, 452, 2, 10, 11, 6, 40, 43, 4, 1, 416, 13, 188, 14, 51, 5, 8, 1, 1, 10, 153, 31, 3, 1, 252, 5, 177, 16, 1, 7, 6, 35, 25, 40, 85, 2, 23, 3, 62, 8, 331, 152, 57, 74, 1, 2, 2, 2, 19, 85, 80, 29, 3, 144, 106, 3, 35, 14, 50, 30, 37, 484, 1, 1, 50, 18, 20, 12, 63, 57, 1, 1, 42, 836, 186, 163, 88, 6, 3, 142, 21, 37, 185, 2, 16, 126, 85, 74, 1, 1, 56, 172, 94, 7, 1, 2, 3, 6, 4, 1, 1, 9, 1, 24, 1, 8, 4, 18, 19, 30, 1, 1, 49, 1, 1, 1, 3, 3, 1, 8, 1, 2, 3, 408, 3, 9, 2, 2, 37, 1, 3, 1, 15, 136, 1, 2, 7, 15, 86, 3, 6, 1, 10, 3, 1, 6, 4, 8, 1, 2, 1, 1, 7, 8, 24, 11, 46, 3, 1, 7, 1, 1, 72, 31, 320, 1, 1, 3, 2, 2, 1, 7, 1, 7, 1, 5, 3, 12, 2, 1, 10, 9, 82, 16, 26, 1, 128, 25, 6, 1, 2, 5, 1, 5, 3, 11, 1, 11, 2, 4, 9, 2, 10, 30, 22, 2, 6, 2, 2, 12, 2, 2, 3, 2, 1, 3, 62, 1, 1, 5, 20, 4, 2, 3, 2, 1, 3, 3, 1, 2, 1, 19, 2, 61, 5, 4, 66, 25, 1, 5, 22, 219, 11, 136, 1, 27, 80, 9, 21, 2, 22, 1, 26, 22, 2, 10, 2, 12, 2, 24, 9, 4, 2, 1, 2, 3, 4, 10, 121, 30, 40, 1, 10, 5, 7, 3, 15, 5, 2, 1, 18, 6, 1, 4, 2, 1, 3, 14, 3, 10, 11, 50, 19, 28, 3, 16, 27, 1, 3, 2, 28, 2, 24, 18, 4, 10, 1, 10, 19, 3, 21, 1, 1, 108, 18, 9, 1, 1, 16, 6, 2, 2, 25, 207, 16, 6, 3, 1, 1, 1, 4, 8, 2, 29, 52, 1, 1, 17, 2, 80, 45, 1, 9, 3, 11, 10, 50, 29, 180, 95, 32, 2, 10, 32, 5, 3, 356, 1, 28, 3, 1, 3, 105, 3, 15, 1, 26, 13, 1, 15, 155, 2, 82, 18, 27, 3, 7, 1, 1, 3, 2, 2, 40, 5, 32, 10, 337, 20, 36, 42, 1, 1, 3, 3, 5, 3, 5, 1, 11, 1, 1, 1, 2, 1, 2, 17, 27, 3, 1, 275, 1, 3, 7, 14, 2, 26, 5, 1, 1, 3, 1, 65, 1, 1, 1, 3, 85, 8, 2, 1, 1, 89, 1, 18, 2, 4, 1, 1, 1, 23, 12, 6, 6, 2, 3, 1, 3, 1, 44, 3, 1, 1, 1, 4, 11, 4, 77, 3, 2, 6, 1, 14, 1, 14, 5, 1, 1, 1, 4, 2, 1, 3, 3, 2, 2, 1, 1, 1, 2, 2, 2, 50, 7, 1, 1, 1, 7, 1, 3, 16, 1, 16, 1, 18, 2, 1, 2, 16, 10, 1, 26, 667, 51, 2165, 1, 64, 1, 36, 231, 744, 1686, 60, 1, 3, 30, 370, 178, 6, 19, 150, 1022, 5, 2145, 60, 74, 5, 628, 28, 116, 20, 2, 67, 2, 7, 23, 81, 517, 73, 85, 2, 430, 92, 11, 614, 8, 203, 95, 3, 3, 17, 8, 1, 60, 8, 18, 3, 12, 8, 1, 47, 2, 151, 178, 2, 1, 2, 3, 23, 47, 8, 1, 2, 255, 1, 2, 1, 59, 18, 13, 7, 26, 2, 41, 35, 2, 1, 25, 2, 1, 4, 11, 2, 15, 8, 9, 2, 1, 20, 1, 1, 13, 1, 19, 1, 4, 47, 38, 11, 80, 47, 79, 141, 2, 18, 5, 38, 10, 1, 34, 2, 21, 1, 1, 1, 2, 20, 1, 4, 7, 6, 1, 1, 3, 10, 12, 1, 23, 28, 2, 2, 3, 2, 8, 37, 9, 15, 1, 5, 1, 78, 34, 30, 119, 18, 30, 189, 51, 2, 66, 2, 79, 2, 12, 8, 1, 1, 6, 31, 1, 1, 190, 2, 2, 5, 31, 26, 2, 86, 1, 2, 1, 9, 1, 3, 1, 80, 80, 80, 80, 80, 546, 96, 315, 53, 311)\">\n <thead>\n <tr>\n <th>units<\/th>\n <th>context<\/th>\n <th>element<\/th>\n <th>taxonid<\/th>\n <th>symmetry<\/th>\n <th>taxongroup<\/th>\n <th>elementtype<\/th>\n <th>variablename<\/th>\n <th>ecologicalgroup<\/th>\n <th>sites<\/th>\n <th>samples<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"scrollX":"100%","dom":"t","columnDefs":[{"className":"dt-right","targets":[3,9,10]}],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script>
The taxonid values can be linked to the taxonid column in the samples(). This allows us to build taxon harmonization tables if we choose to. You may also note that the taxonname is in the field variablename. Individual sample counts are reported in Neotoma as variables. A "variable" may be either a species, something like laboratory measurements, or a non-organic proxy, like charcoal or XRF measurements, and includes the units of measurement and the value.
Lets say we want all samples from which Plantago taxa have been reported to be grouped together into one pseudo-taxon called Plantago. There are several ways of doing this, either directly by exporting the file and editing each individual cell, or by creating an external "harmonization" table (which we did in the prior neotoma package).
Programmatically, we can harmonize taxon by taxon using matching and transformation. We're using dplyr type coding here to mutate() the column variablename so that any time we detect (str_detect()) a variablename that starts with Plantago (the .* represents a wildcard for any character [.], zero or more times [*]) we replace() it with the character string "Plantago". Note that this changes Plantago in the allSamp object, but if we were to call samples() again, the taxonomy would return to its original form.
We're going to filter the ecological groups to include only UPHE (upleand/heath) and TRSH (trees and shrubs). More information about ecological groups is available from the Neotoma Online Manual.
allSamp <- allSamp %>%
dplyr::filter(ecologicalgroup %in% c("UPHE", "TRSH")) %>%
mutate(variablename = replace(variablename,
stringr::str_detect(variablename, "Plantago.*"),
"Plantago"))There were originally 15 different taxa identified as being within the genus Plantago (including Plantago, Plantago major, and Plantago alpina-type). The above code reduces them all to a single taxonomic group Plantago.
If we want to have an artifact of our choices, we can use an external table. For example, a table of pairs (what we want changed, and the name we want it replaced with) can be generated, and it can include regular expressions (if we choose):
| original | replacement |
|---|---|
| Abies.* | Abies |
| Vaccinium.* | Ericaceae |
| Typha.* | Aquatic |
| Nymphaea | Aquatic |
| ... | ... |
We can get the list of original names directly from the taxa() call, applied to a sites object, and then export it using write.csv().
taxaplots <- taxa(cz_dl)
# Save the taxon list to file so we can edit it subsequently.
readr::write_csv(taxaplots, "data/mytaxontable.csv")
The plot is mostly for illustration, but we can see, as a sanity check, that the relationship is as we'd expect.
You can then export either one of these tables and add a column with the counts, you could also add extra contextual information, such as the ecologicalgroup or taxongroup to help you out. Once you've cleaned up the translation table you can load it in, and then apply the transformation:
translation <- readr::read_csv("data/taxontable.csv")<div id="htmlwidget-4256f998197292bd58ce" style="width:100%;height:auto;" class="datatables html-widget"></div>
<script type="application/json" data-for="htmlwidget-4256f998197292bd58ce">{"x":{"filter":"none","vertical":false,"data":[["?Microthyrium (type 8, HdV)","Abies","Abies alba","Acacia","Acer","Achillea","Achillea-type","Aconitum","Aconitum-type","Acrotritia ardua (type 106, HdV)","Actaea spicata","Actinopeltis undiff.","Adenostyles alliariae","Adiantum capillus-veneris","Adonis aestivalis-type","Adonis aestivalis/A. flammea","Adonis annua-type","Aesculus","Aethusa cynapium","Agrimonia","Agrostemma githago","Ailanthus","Alchemilla","Alchemilla-type","Algae","Algae (type 209, HdV)","Algae? (type 225, HdV)","Alisma","Alisma plantago-aquatica","Allium","Allium-type","Alnus","Alnus glutinosa","Alnus glutinosa-type","Alnus glutinosa/A. incana","Alnus undiff.","Alnus viridis","Alnus viridis-type","Alona rustica (type 72, HdV)","Amaranthaceae","Ambrosia","Ambrosia-type","Amphitrema","Amphitrema sp.","Amphitrema undiff.","Amphitrema wrightianum","Anagallis","Anagallis arvensis","Anagallis arvensis-type","Anagallis tenella-type","Anagallis-type","Anchusa/Pulmonaria","Andromeda","Andromeda polifolia","Androsace elongata-type","Androsace-type","Anemone","Anemone hepatica","Anemone nemorosa group","Anemone nemorosa-type","Anemone sect. Hepatica-type","Anemone sect. Pulsatilla","Anemone-type","Anthemis arvensis-type","Anthemis-type","Anthericum","Anthericum-type","Anthoceros","Anthoceros laevis","Anthoceros laevis-type","Anthoceros punctatus-type","Anthostomella cf. A. fuegiana (type 4, HdV)","Anthostomella fuegiana","Anthriscus caucalis","Anthriscus sylvestris","Anthriscus sylvestris-type","Anthriscus-type","Anthyllis","Aphanes","Apiaceae","Apiaceae undiff.","Apium","Apium inundatum-type","Apium-type","Araneae","Arcella","Arcella cf. A. megastoma","Arcella discoides","Arcella sp.","Archerella flavum","Archerella flavum (type 31A, HdV)","Arctium","Arctostaphylos uva-ursi","Arctostaphylos uva-ursi-type","Arctous alpina","Arenaria","Arenaria serpyllifolia-type","Armeria","Armeria maritima (type A)","Armeria maritima (type B)","Armeria maritima-type","Arnica montana","Artemisia","Arthrodesmus","Aruncus","Ascaris","Ascaris lumbricoides","Ascomycota","Ascospora","Aspiromitus punctatus","Asplenium","Asplenium-type","Assulina","Assulina muscorum","Assulina seminulum","Assulina sp.","Aster-type","Asteraceae","Asteroideae","Asteroideae undiff.","Asterosporium","Astragalus alpinus-type","Astragalus danicus-type","Astragalus exscapus","Astragalus-type","Astrantia major","Astrantia-type","Athyrium","Athyrium filix-femina","Athyrium-type","Avena-type","Avena/Triticum-type","Bambusa-type","Barbarea-type","Betula","Betula nana","Betula nana-type","Betula pubescens","Betula pubescens-type","Bidens","Bidens-type","Bistorta","Bistorta officinalis","Bistorta officinalis-type","Blechnum","Boraginaceae","Botrychium","Botryococcus","Botryococcus braunii","Botryococcus neglectus","Botryococcus pila","Botryococcus sp.","Brachysporium obovatum/B. bloxami/Bactrodesmium betulicola (type 359, HdV)","Brachysporium pendulisporum (type 360, HdV)","Brassica","Brassicaceae","Brassicaceae undiff.","Brassicaceae-type","Bruckenthalia-type","Bryales","Bryonia alba/Helianthemum","Bryophyta","Bryophyta (type 354, HdV)","Bupleurum","Bupleurum falcatum-type","Bupleurum-type","Butomus","Butomus umbellatus","Butomus-type","Byssothecium circinans","Byssothecium circinans (type 16A, HdV)","Byssothecium circinans (type 16B, HdV)","Byssothecium circinans (type 16C, HdV)","Calla","Callitriche","Calluna","Calluna vulgaris","Caltha","Caltha palustris-type","Caltha-type","Calystegia","Campanula","Campanula rapunculoides","Campanula-type","Campanula/Phyteuma","Campanulaceae","Cannabis sativa","Cannabis-type","Cardamine","Cardamine pratensis-type","Cardamine-type","Carduus","Carex","Carpinus","Carpinus betulus","Carpinus-type","Carum carvi","Carya","Caryophyllaceae","Caryophyllaceae undiff.","Caryospora sp. (type 1001, HdV)","Castanea","Castanea sativa","Castanea-type","Cedrus","Cedrus-type","Centaurea","Centaurea alpina-type","Centaurea cyanus","Centaurea cyanus-type","Centaurea jacea","Centaurea jacea-type","Centaurea jacea/C. stoebe","Centaurea montana-type","Centaurea nigra-type","Centaurea scabiosa","Centaurea scabiosa-type","Centaurea sp.","Centaurea stoebe","Centaurea stoebe-type","Centaurea undiff.","Centropyxis","Centropyxis aculeata","Cerastium","Cerastium arvense-type","Cerastium cerastoides-type","Cerastium fontanum-type","Cerastium-type","Ceratophyllum","Cercophora sp. (type 112, HdV)","Cerinthe","Cerinthe minor","cf. Actinopeltis (type 8C, HdV)","cf. Androsace","cf. Diphasiastrum-type","cf. Endophragmia (type 572, HdV)","cf. Entophlyctis lobata","cf. Helianthemum","cf. Lamiaceae","cf. Lobelia","cf. Papaver","cf. Pedicularis","cf. Penium","cf. Persiciospora (type 124, HdV)","cf. Riccia","cf. Richonia variospora (type 140, HdV)","cf. Spadicoides bina (type 98, HdV)","cf. Trichocladium opacum (type 10, HdV)","cf. Trichoglossum hirsutum (type 77B, HdV)","Chaerophyllum","Chaerophyllum hirsutum","Chaerophyllum hirsutum-type","Chaetomium sp. (type 7A, HdV)","Chaetomium undiff.","Chamaenerion","Chamaenerion angustifolium","Chamaenerion angustifolium-type","Charcoal","Chelidonium","Chelidonium majus","Chironomidae","Chlamydomonadaceae","Chrysophyceae","Chrysosplenium","Chrysosplenium-type","Cicatricosporites australiensis","Cichorioideae","Cicuta virosa","Circaea","Cirsium","Cirsium-type","Cirsium/Carduus","Cladium mariscus","Cladocera","Clasterosporium caricinum (type 126, HdV)","Clematis","Closterium","Closterium undiff.","Coelastrum reticulatum","Comarum","Comarum palustre","Comarum-type","Coniferae-type","Coniochaeta cf. C. ligniaria","Coniochaeta ligniaria (type 172, HdV)","Coniochaeta xylariispora","Consolida regalis","Consolida-type","Convallaria","Convolvulus","Convolvulus arvensis","Convolvulus-type","Copepoda","Cornus","Cornus mas","Cornus sanguinea","Cornus suecica","Coronilla undiff.","Corylus","Corylus avellana","Crataegus","Crataegus-type","Crupina","Cryptomeria","Cupressaceae","Cuscuta","Cuscuta epithymum","Cuscuta europaea-type","Cyperaceae","Cystopteris","Daphne","Daucus","Daucus carota","Daucus-type","Delitschia","Descurainia sophia","Desmidiaceae","Desmidiales","Dianthus","Dianthus-type","Difflugia","Digitalis purpurea-type","Dinoflagellata","Dinoflagellata undiff.","Diphasiastrum alpinum","Diphasiastrum alpinum-type","Diphasiastrum complanatum","Diporotheca","Dipsacoideae","Dipsacus","Drosera","Drosera intermedia","Drosera rotundifolia","Drosera rotundifolia-type","Dryas octopetala","Dryas-type","Dryopteris","Dryopteris carthusiana-type","Dryopteris dilatata-type","Dryopteris filix-mas-type","Dryopteris-type","Echinops","Echium","Echium vulgare","Echium-type","Elatine","Elymus-type","Empetrum","Empetrum nigrum-type","Empetrum-type","Encalypta-type","Engelhardia-type","Entophlyctis lobata","Entorrhiza sp. (type HdV-527)","Ephedra","Ephedra cf. E. distachya","Ephedra cf. E. foeminea","Ephedra cf. E. fragilis","Ephedra distachya","Ephedra distachya-type","Ephedra foeminea","Ephedra foeminea-type","Ephedra fragilis","Ephedra fragilis-type","Epilobium","Epilobium-type","Epipactis","Equisetaceae","Equisetum","Eranthis hyemalis-type","Erica ciliaris-type","Ericaceae","Ericaceae undiff.","Ericales","Ericales undiff.","Eriophorum","Erodium","Eryngium","Eryngium-type","Euglypha","Eunotia sp.","Euonymus","Euonymus europaeus","Euphorbia","Euphorbia-type","Euphorbiaceae","Euphrasia","Euphrasia-type","Fabaceae","Fabaceae undiff.","Faboideae","Fagopyrum","Fagopyrum esculentum","Fagopyrum-type","Fagus","Fagus sylvatica","Falcaria vulgaris","Falcaria-type","Fallopia convolvulus","Fallopia convolvulus-type","Fallopia convolvulus/F. dumetorum","Filinia longiseta","Filipendula","Filipendula ulmaria/F. vulgaris","Frangula","Frangula alnus","Fraxinus","Fraxinus excelsior","Fraxinus ornus","Fumaria-type","Fungi","Fungi (type 11, HdV)","Fungi (type 123, HdV)","Fungi (type 17, HdV)","Fungi (type 173, HdV)","Fungi (type 18, HdV)","Fungi (type 19, HdV)","Fungi (type 20, HdV)","Fungi (type 200, HdV)","Fungi (type 23, HdV)","Fungi (type 24, HdV)","Fungi (type 3A, HdV)","Fungi (type 404, HdV)","Fungi (type 408, HdV)","Fungi (type 47, HdV)","Fungi (type 53, HdV)","Fungi (type 54B, HdV)","Fungi (type 571, HdV)","Fungi (type 64, HdV)","Fungi (type 65, HdV)","Fungi (type 729, HdV)","Fungi (type 73, HdV)","Fungi (type 778. HdV)","Fungi (type 83, HdV)","Fungi (type 8A, HdV)","Fungi (type 8D, HdV)","Fungi (type 8E, HdV)","Fungi (type 90, HdV)","Fungi (type 96B, HdV)","Fungi undiff.","Fungi-type","Gaeumannomyces","Gaeumannomyces cf. G. caricis","Gaeumannomyces undiff.","Galeopsis","Galeopsis-type","Galeopsis/Ballota-type","Galium","Galium-type","Gelasinospora","Gelasinospora (type 1, HdV)","Gelasinospora (type 1A, HdV)","Gelasinospora (type 1B, HdV)","Gelasinospora reticulispora","Gelasinospora undiff.","Genista","Genista-type","Gentiana","Gentiana cruciata-type","Gentiana pneumonanthe-type","Gentiana undiff.","Gentiana-type","Gentianaceae","Gentianaceae undiff.","Gentianella","Gentianella campestris-type","Geoglossum sphagnophilum","Geoglossum sphagnophilum (type 77A, HdV)","Geoglossum sphagnophilum/Trichoglossum hirsutum (type 77A/77B, HdV)","Geraniaceae","Geranium","Geranium-type","Geum","Geum-type","Glaucium","Glaucium corniculatum","Glomus","Glomus cf. G. fasciculatum","Glyceria-type","Glyptotendipes pallens group (type 509, HdV)","Gnaphalium-type","Gratiola officinalis","Gymnocarpium dryopteris","Gypsophila","Gypsophila repens","Gypsophila repens-type","Gypsophila-type","Gyratrix hermaphroditus","Habrotrocha","Habrotrocha angusticollis","Habrotrocha angusticollis (type 37, HdV)","Hedera","Hedera helix","Hedysarum-type","Helianthemum","Helianthemum nummularium-type","Helianthemum oelandicum subsp. alpestris-type","Helicoma","Helicoön pluriseptatum","Helicosporium/Helicoön pluriseptatum (type 30, HdV)","Heliotropium europaeum","Helleborus","Heracleum","Heracleum sphondylium","Heracleum-type","Herniaria","Herniaria-type","Hippophaë","Hippophaë rhamnoides","Hippuris vulgaris","Hordeum","Hordeum-type","Hottonia palustris","Humulus","Humulus lupulus","Humulus/Cannabis","Humulus/Cannabis-type","Huperzia selago","Hyalosphenia papilio","Hyalosphenia subflava","Hydrocotyle","Hydrocotyle vulgaris","Hydrocotyle-type","Hydrodictyon","Hymenophyllum","Hyoscyamus","Hypericum","Hypericum perforatum-type","Hypericum perforatum/H. androsaemum-type","Hystrix","Ilex","Illecebrum verticillatum","Impatiens","Impatiens noli-tangere","Impatiens parviflora","Indeterminable","Indeterminable undiff.","Iris","Iris pseudacorus","Iris pseudacorus-type","Iris-type","Isoëtes","Isoëtes lacustris","Jasione","Jasione montana","Jasione-type","Juglandaceae","Juglandaceae-type","Juglans","Juncus sp. (type 2.2, MI)","Juniperus","Juniperus communis","Juniperus-type","Knautia","Knautia arvensis","Knautia arvensis-type","Koenigia alpina","Lamiaceae","Lamiaceae (tricolpate)","Lamium album-type","Lamium-type","Larix","Larix decidua","Larix-type","Larix/Pseudotsuga","Laserpitium","Laserpitium latifolium-type","Lasiosphaeria cf. L. caudata","Lasiosphaeria sp.","Lasiosphaeria sp. (type 63C, HdV)","Lasiosphaeria-type","Lathyrus-type","Lemna","Lemnoideae","Lepidoptera","Ligustrum","Liliaceae","Liliaceae-type","Linum","Linum austriacum-type","Linum catharticum","Linum catharticum-type","Linum flavum","Linum usitatissimum-type","Liquidambar","Listera ovata","Listera-type","Lithospermum officinale","Lobelia","Lonicera","Lonicera periclymenum","Lonicera xylosteum","Loranthus","Loranthus europaeus","Lotus","Lotus cf. L. corniculatus","Lotus pedunculatus","Lotus-type","Ludwigia palustris","Lycopodiaceae","Lycopodiaceae cf. Diphasiastrum complanatum","Lycopodiaceae undiff.","Lycopodiella inundata","Lycopodium","Lycopodium annotinum","Lycopodium annotinum-type","Lycopodium clavatum","Lycopodium clavatum-type","Lycopodium spike","Lycopodium tablets","Lycopodium undiff.","Lycopus","Lycopus-type","Lysimachia","Lysimachia cf. L. vulgaris","Lysimachia nemorum","Lysimachia nemorum-type","Lysimachia thyrsiflora","Lysimachia vulgaris","Lysimachia vulgaris-type","Lysimachia-type","Lythrum","Lythrum portula-type","Lythrum salicaria","Lythrum-type","Macrobiotus","Macrobiotus cf. M. echinogenitus","Magnolia-type","Maianthemum bifolium","Malus","Malus undiff.","Malus-type","Malva-type","Malvaceae","Marchantiophyta","Marrubium","Matricaria-type","Medicago falcata-type","Melampyrum","Melampyrum-type","Meliola","Mentha","Mentha-type","Menyanthes","Menyanthes trifoliata","Menyanthes trifoliata-type","Mercurialis","Mercurialis perennis-type","Micranthes stellaris","Micranthes stellaris-type","Microdalyellia armigera","Microrrhinum minus","Microthyriaceae","Microthyrium","Microthyrium microscopicum","Microthyrium undiff.","Microthyrium-type","Minuartia-type","Monactinus simplex","Monactinus simplex var. echinulatum","Monactinus simplex var. simplex","Monocotyledoneae","Montia","Mougeotia","Mougeotia cf. M. gracillima (type 61, HdV)","Mougeotia undiff.","Mougeotia-type","Muscari","Myosotis","Myosotis arvensis-type","Myrica-type","Myricaria germanica","Myriophyllum","Myriophyllum alterniflorum","Myriophyllum cf. M. spicatum","Myriophyllum cf. M. verticillatum","Myriophyllum heterophyllum","Myriophyllum spicatum","Myriophyllum spicatum-type","Myriophyllum undiff.","Myriophyllum verticillatum","Myriophyllum verticillatum-type","Nebela","Nebela parvula","Nebela undiff.","Neurospora","Normapolles","Nuphar","Nymphaea","Nymphaea alba","Nymphaea alba-type","Nymphaea cf. N. candida","Nymphaea undiff.","Nymphaeaceae","Nymphoides peltata-type","Nyssa","Odontites","Odontites-type","Oenanthe","Oenanthe-type","Oenothera","Olea","Oleaceae","Onagraceae","Onobrychis","Ononis","Ononis-type","Onopordum","Ophioglossum","Ophioglossum vulgatum","Orchidaceae","Oribatida (type 396, HdV)","Orlaya grandiflora","Ornithogalum umbellatum-type","Ornithogalum-type","Ostrya-type","Oxalis","Oxyria-type","Papaver","Papaver rhoeas-type","Papaver somniferum","Papaveraceae","Parapediastrum biradiatum","Parnassia","Parnassia palustris","Parnassia-type","Pediastrum","Pediastrum angulosum","Pediastrum angulosum var. angulosum","Pediastrum angulosum var. asperum","Pediastrum braunii","Pediastrum duplex","Pediastrum duplex var. duplex","Pediastrum duplex var. rugulosum","Pediastrum muticum var. scutum","Pediastrum orientale","Pediastrum undiff.","Pedicularis","Pedicularis palustris-type","Penium","Persicaria","Persicaria amphibia","Persicaria amphibia-type","Persicaria cf. P. lapathifolia","Persicaria lapathifolia","Persicaria maculosa","Persicaria maculosa-type","Petasites","Petasites hybridus-type","Petasites-type","Peucedanum","Peucedanum palustre-type","Peucedanum-type","Phegopteris","Phegopteris connectilis","Phragmites","Phragmites australis","Phragmites-type","Phyteuma","Phyteuma-type","Picea","Picea abies","Pilularia","Pimpinella anisum","Pimpinella major","Pimpinella major-type","Pimpinella major/P. saxifraga","Pinguicula","Pinnularia","Pinus","Pinus (Tertiary)","Pinus cembra","Pinus cembra-type","Pinus sp.","Pinus subg. Pinus","Pinus subg. Strobus-type","Pinus sylvestris","Pinus sylvestris-type","Pisum sativum","Plantaginaceae","Plantaginaceae undiff.","Plantago","Plantago alpina","Plantago alpina-type","Plantago atrata-type","Plantago coronopus","Plantago lanceolata","Plantago lanceolata-type","Plantago major","Plantago major-type","Plantago major/P. media","Plantago major/P. media-type","Plantago maritima-type","Plantago media","Plantago media-type","Plantago sp.","Platanus","Platycarya","Platyhelminthes (type 353A, HdV)","Platyhelminthes (type 353B, HdV)","Pleospora sp. (type 3B, HdV)","Pleospora undiff.","Pleurospermum","Pleurospermum austriacum","Pleurospermum austriacum-type","Poaceae","Poaceae (Cerealia-type excluding Secale)","Poaceae (Cerealia-type)","Poaceae (Cerealia)","Poaceae (Cerealia) excluding Secale","Poaceae (Cerealia) undiff.","Podocarpus-type","Podospora sp./Zopfiella sp. (type 466, HdV)","Podospora-type (type 368, HdV)","Polemonium","Polemonium caeruleum","Polygala","Polygonaceae","Polygonaceae undiff.","Polygonatum","Polygonum","Polygonum aviculare","Polygonum aviculare-type","Polygonum sp.","Polypodiaceae","Polypodiophyta (monolete, psilate)","Polypodiophyta (monolete, verrucate)","Polypodium","Polypodium vulgare","Populus","Porifera","Potamogeton","Potamogeton natans-type","Potamogeton-type","Potentilla","Potentilla-type","Potentilla/Comarum","Potentilla/Comarum-type","Potentilla/Fragaria","Poterium sanguisorba","Poterium sanguisorba subsp. sanguisorba","Primula","Primula clusiana-type","Primula farinosa-type","Primula veris-type","Primulaceae","Prunella-type","Prunus","Prunus sp.","Prunus-type","Pseudopediastrum boryanum","Pseudopediastrum boryanum var. boryanum","Pseudopediastrum boryanum var. boryanum sensu lato","Pseudopediastrum boryanum var. cornutum","Pseudopediastrum boryanum var. longicorne","Pseudopediastrum brevicorne","Pseudopediastrum integrum","Pseudopediastrum kawraiskyi","Pteridium","Pteridium aquilinum","Pteridophyta","Pteridophyta (monolete, verrucate)","Pteridophyta (monolete) undiff.","Pterocarya","Pterocarya fraxinifolia","Pulmonaria","Pulmonaria-type","Pyrola","Pyxidicula","Quercus","Quercus coccifera","Quercus pubescens","Ranunculaceae","Ranunculaceae undiff.","Ranunculus","Ranunculus acris-type","Ranunculus acris/R. flammula/R. sceleratus group","Ranunculus aquatilis-type","Ranunculus arvensis","Ranunculus arvensis-type","Ranunculus flammula-type","Ranunculus sect. Batrachium","Ranunculus sect. Batrachium-type","Ranunculus-type","Reseda","Reseda lutea-type","Rhabdocoela","Rhabdocoela (type 353, HdV)","Rhamnaceae","Rhamnus","Rhinanthus","Rhinanthus-type","Rhinanthus/Veronica","Rhizopoda","Rhizopoda undiff.","Rhododendron","Rhododendron subsect. Ledum","Rhododendron tomentosum","Rhus-type","Ribes","Ribes alpinum","Ribes uva-crispa","Riccia","Rivularia","Rosa","Rosa-type","Rosaceae","Rosaceae undiff.","Rotifera undiff.","Rotifera/Tardigrada","Rubiaceae","Rubus","Rubus chamaemorus","Rumex","Rumex acetosa","Rumex acetosa-type","Rumex acetosa/R. acetosella","Rumex acetosella","Rumex acetosella-type","Rumex aquaticus-type","Rumex cf. R. alpinus","Rumex maritimus-type","Rumex obtusifolius","Rumex obtusifolius-type","Rumex subg. Rumex","Rumex undiff.","Rumex-type","Rumex/Oxyria-type","Sagina","Sagina procumbens-type","Sagina-type","Sagittaria","Sagittaria-type","Salix","Salix herbacea-type","Salvia","Sambucus","Sambucus cf. S. ebulus","Sambucus cf. S. nigra","Sambucus cf. S. racemosa","Sambucus ebulus","Sambucus nigra","Sambucus nigra-type","Sambucus nigra/S. racemosa","Sambucus racemosa","Samolus valerandi","Sample quantity","Sanguisorba minor-type","Sanguisorba officinalis","Sanicula europaea","Sanicula-type","Saussurea-type","Saxifraga","Saxifraga aizoides-type","Saxifraga granulata","Saxifraga granulata-type","Saxifraga hirculus-type","Saxifraga oppositifolia","Saxifraga oppositifolia-type","Saxifraga undiff.","Saxifragaceae","Saxifragaceae undiff.","Scabiosa","Scabiosa columbaria subsp. pratensis-type","Scabiosa columbaria-type","Scandix pecten-veneris/Caucalis platycarpos","Scenedesmus","Scenedesmus undiff.","Scheuchzeria","Scheuchzeria palustris","Sciadopitys","Sciadopitys-type","Scilla-type","Scleranthus","Scleranthus annuus","Scleranthus annuus-type","Scleranthus cf. S. annuus","Scleranthus cf. S. perennis","Scleranthus perennis","Scleranthus perennis-type","Scleranthus-type","Scrophularia","Scrophularia-type","Scrophulariaceae","Scutellaria","Secale","Secale cereale","Secale-type","Securigera varia","Sedum","Sedum-type","Selaginella","Selaginella selaginoides","Selaginellaceae","Senecio","Senecio-type","Senecio/Aster","Sequoia","Serratula","Serratula-type","Seseli-type","Sigmopollis","Silene","Silene dioica-type","Silene flos-cuculi","Silene latifolia","Silene viscaria-type","Silene vulgaris","Silene vulgaris-type","Silene-type","Silene-type undiff.","Sileneae","Silenoideae-type","Sinapis-type","Sium latifolium-type","Solanaceae","Solanum","Solanum cf. S. nigrum","Solanum dulcamara","Solanum nigrum","Solanum nigrum-type","Soldanella","Sorbus","Sorbus aria-type","Sorbus aucuparia","Sorbus group","Sorbus torminalis","Sorbus-type","Sordaria-type (type 55A, HdV)","Sordariaceae","Sordariaceae/Sordaria (type 55B, HdV)","Sparganium","Sparganium erectum","Sparganium-type","Spergula","Spergula-type","Spergularia-type","Sphagnum","Spirogyra","Spirogyra cf. S. scrobiculata","Spirogyra-type","Sporormiella","Sporormiella (type 113, HdV)","Stachys","Stachys-type","Staurastrum","Staurastrum undiff.","Stauridium tetras","Stellaria","Stellaria holostea","Stellaria-type","Stratiotes aloides","Succisa","Succisa pratensis","Succisa-type","Succisella","Swertia perennis","Symphytum","Symphytum cf. S. officinale","Symphytum-type","Symplocos","Tardigrada","Tardigrada (type 902, HdV)","Tardigrada undiff.","Taxus","Taxus baccata","Tetraëdron","Tetraëdron minimum","Tetraploa scheueri","Teucrium","Thalictrum","Thalictrum-type","Thecaphora","Thelypteris","Thelypteris palustris","Thesium","Thesium-type","Tilia","Tilia cordata","Tilia platyphyllos","Tilia undiff.","Tilletia sphagni","Tilletia sphagni (type 27, HdV)","Tofieldia","Transeauina","Transeauina (type 214, HdV)","Transeauina undiff.","Trapa","Trapa natans","Trichocladium opacum (type 10, HdV)","Trichuris trichiura","Trientalis","Trientalis europaea","Trifolium","Trifolium pratense","Trifolium pratense-type","Trifolium repens-type","Trifolium-type","Triglochin","Triticum","Triticum-type","Trochiscia undiff.","Trollius","Trollius europaeus","Trollius-type","Tsuga","Tsuga diversifolia-type","Tsuga-type","Turgenia latifolia","Typha","Typha angustifolia","Typha angustifolia-type","Typha angustifolia/Sparganium","Typha angustifolia/Sparganium-type","Typha latifolia","Typha latifolia-type","Typhaceae","Ulex-type","Ulmus","Ulmus/Zelkova","Umbilicus rupestris-type","Unknown","Unknown (Cretaceous)","Unknown (monolete, psilate)","Unknown (monolete)","Unknown (monolete) undiff.","Unknown (pre-Quaternary)","Unknown (Tertiary)","Unknown (trilete)","Unknown (trilete) undiff.","Unknown (type 160, HdV)","Unknown (type 181, HdV)","Unknown (type 224, HdV)","Unknown (type 33, HdV)","Unknown (type 366, HdV)","Unknown (type 38, HdV)","Unknown (type 41, HdV)","Unknown (type 708, HdV)","Unknown (type 74, HdV)","Unknown (type 86, HdV)","Unknown (type 91, HdV)","Urtica","Ustulina deusta","Ustulina deusta (type 44, HdV)","Utricularia","Vaccinioideae","Vaccinium","Vaccinium oxycoccos","Vaccinium-type","Valeriana","Valeriana cf. V. dioica","Valeriana cf. V. officinalis","Valeriana dioica","Valeriana dioica-type","Valeriana officinalis","Valeriana officinalis-type","Valerianella","Varia","Veratrum","Veratrum album","Veratrum-type","Verbascum","Vermes","Veronica","Veronica beccabunga","Veronica beccabunga-type","Veronica-type","Viburnum","Viburnum cf. V. opulus","Viburnum lantana","Viburnum opulus","Viburnum opulus-type","Viburnum undiff.","Vicia","Vicia cracca-type","Vicia-type","Vicia/Lathyrus","Vicia/Lathyrus-type","Viola","Viola canina-type","Viola palustris","Viola palustris-type","Viola tricolor","Viscum","Vitis","Vitis vinifera","Xanthium","Xanthium-type","Xylariaceae","Xylomyces chlamydosporis/X. aquaticus (type 201, HdV)","Zea mays","Zygnema","Zygnema-type","Zygnemataceae","Zygnemataceae undiff."],[1,72,23,1,78,1,15,11,1,1,2,2,1,2,1,1,1,2,1,1,10,2,5,4,7,1,1,13,1,3,4,79,1,5,1,1,8,1,1,85,5,5,5,1,1,5,2,1,2,1,1,1,1,1,2,1,1,1,1,15,1,5,19,1,13,3,1,5,5,1,1,1,1,1,1,4,1,2,1,70,15,1,1,1,1,14,1,2,2,20,1,1,1,1,1,6,1,4,2,2,1,1,87,1,1,3,1,4,1,13,1,1,6,7,3,2,9,13,65,2,1,1,3,1,6,1,4,2,6,1,23,1,1,17,83,8,1,1,2,12,3,3,23,25,2,12,44,22,11,3,3,3,1,1,1,65,1,6,1,40,1,10,2,5,1,5,6,1,1,3,1,1,3,1,2,27,57,4,1,45,7,45,1,7,1,5,7,11,2,13,19,12,1,65,26,1,1,4,28,1,1,4,1,3,1,1,11,1,62,7,11,31,1,1,2,22,7,1,1,2,7,1,1,3,6,6,1,5,6,1,2,1,1,1,1,2,3,1,1,1,1,2,1,1,1,2,1,1,1,1,2,6,1,1,6,12,1,9,3,1,2,1,1,20,4,1,81,2,9,12,41,4,2,1,1,1,2,1,5,18,2,4,1,2,1,2,1,6,1,7,9,1,8,8,10,17,1,1,68,26,1,2,1,1,2,8,1,2,84,1,3,1,1,11,1,1,3,1,3,4,1,1,4,1,1,1,1,8,3,3,15,1,6,1,3,1,2,1,2,4,20,1,18,2,2,7,1,3,1,6,1,2,8,1,6,1,3,1,10,9,1,3,4,10,42,3,1,1,74,1,1,21,7,3,1,1,4,2,1,8,1,12,1,13,1,1,2,2,51,1,3,23,1,4,75,11,1,1,3,3,1,1,81,1,27,38,68,14,1,1,6,1,1,2,1,3,2,2,2,2,1,4,1,1,1,1,1,2,1,1,1,2,1,3,3,1,3,4,1,3,1,4,6,1,1,2,1,14,31,6,1,1,1,1,1,1,7,10,1,5,1,3,6,1,2,4,2,2,1,1,32,1,11,10,2,1,2,1,5,1,11,1,8,5,1,4,4,6,1,14,1,24,26,1,42,1,1,3,8,1,1,1,6,2,6,1,2,7,10,2,1,7,1,7,5,32,6,7,1,5,1,1,1,1,1,1,27,3,1,2,2,1,10,1,1,1,1,2,1,2,3,1,1,5,8,1,2,1,57,1,56,1,1,21,2,3,1,40,1,1,21,30,2,1,1,1,1,1,1,1,1,11,4,1,1,5,25,2,3,2,12,1,1,3,1,1,2,1,2,13,2,3,8,2,1,1,4,32,1,12,1,2,4,4,56,5,44,3,8,5,1,9,11,30,1,1,1,1,7,19,9,19,3,9,1,1,1,1,1,2,1,1,1,6,3,1,1,1,54,1,1,7,24,7,33,2,8,2,2,5,6,1,7,32,4,2,1,4,4,2,2,8,4,12,1,2,1,1,3,1,1,1,2,17,1,1,3,24,1,2,16,6,5,1,1,1,1,15,14,2,1,1,1,5,1,2,2,3,4,1,1,2,1,1,4,1,1,1,13,2,2,1,1,1,1,1,9,2,6,2,1,10,1,4,16,1,9,5,3,2,1,10,1,8,2,1,3,19,1,1,1,8,2,1,1,13,27,3,1,13,1,1,12,2,1,2,2,5,6,1,74,23,1,1,1,12,1,3,1,77,1,6,3,1,3,1,3,2,4,3,1,3,6,3,1,2,68,18,20,13,48,8,3,17,3,2,1,1,1,2,1,1,2,13,1,86,2,16,14,1,20,1,1,1,9,5,6,3,1,2,1,56,8,3,42,1,1,15,30,44,1,36,1,12,9,27,9,11,1,12,2,4,1,1,4,2,1,6,1,13,13,5,5,8,9,3,11,6,22,46,3,2,5,3,1,1,6,1,1,85,2,1,57,4,1,20,1,1,4,1,1,13,4,31,1,1,3,1,1,11,9,2,1,4,5,1,3,4,1,16,1,1,3,1,6,1,65,3,1,1,56,12,1,36,10,41,1,20,9,1,1,1,3,4,2,4,2,1,3,1,2,4,1,86,2,1,13,1,6,4,5,18,10,1,12,1,6,1,50,1,1,1,3,2,1,3,1,1,4,2,13,1,9,1,1,1,11,2,6,6,2,1,1,4,3,2,1,1,1,1,5,3,3,14,1,35,32,16,1,13,2,3,19,1,1,12,1,1,1,1,1,1,3,8,8,1,1,1,8,23,1,28,12,1,1,1,1,1,9,1,6,1,24,1,2,1,2,8,3,1,1,12,2,8,2,1,1,77,7,1,3,2,1,5,4,6,1,2,2,3,2,3,15,8,1,1,2,21,1,2,1,2,1,1,1,2,7,9,1,3,75,3,4,1,7,4,1,79,9,10,4,12,1,1,1,1,3,1,3,2,2,1,2,6,6,22,11,22,3,27,27,1,5,11,1,4,1,1,1,1,8,1,33,10,41,13,1,1,85,1,1,24,1,2,14,5,2,5,1,7,1,1,1,2,1,2,2,1,1,2,2,71,5,1,17,11,22,5,37,30,1,3,1,8,20,8,2,57,5,1,2,9,1,9,1,2,4,10,1,2,5,1,1,1,1,24,1,1,13,1,5,5,1,47,9,2,3,1,1,3,5,3,5,3,1],[15,1822,836,1,1157,1,216,76,3,1,3,7,1,2,3,5,5,3,1,1,29,10,23,56,18,1,1,51,8,46,6,3219,20,172,94,130,190,5,1,1977,6,26,119,2,1,18,3,2,7,1,1,1,1,3,11,1,2,1,1,108,1,13,89,16,331,6,4,17,12,1,1,5,1,1,8,24,1,4,1,1767,331,1,1,30,1,79,2,6,5,190,26,1,5,1,1,8,1,11,3,3,1,2,3419,4,1,13,2,53,7,38,1,1,30,189,51,31,152,134,1119,43,1,1,8,2,15,1,8,36,20,1,325,2,2,186,3727,177,42,29,80,83,3,10,121,139,2,37,231,475,148,7,18,21,2,1,30,1163,22,153,5,614,27,203,4,11,2,8,37,1,2,20,3,1,38,3,11,356,895,25,1,365,14,239,3,19,3,10,95,180,46,163,151,44,7,1148,620,130,1,37,288,30,1,18,1,15,2,1,35,3,432,35,57,136,14,1,2,74,14,2,3,7,13,2,1,12,18,27,7,29,130,12,3,1,12,2,1,18,47,1,19,1,10,10,2,1,2,15,1,49,98,1,5,45,7,1,42,28,2,867,6,2,4,2,1,88,24,1,1869,11,13,52,416,49,7,5,37,3,3,2,50,337,20,36,8,103,9,56,2,32,1,22,46,1,64,9,72,50,1,1,2273,1107,1,7,1,3,11,64,10,31,3751,2,8,1,1,320,1,1,48,1,3,25,2,1,88,9,30,7,2,68,4,5,20,5,16,4,15,1,67,2,2,8,744,2,40,3,2,13,2,5,89,50,1,19,59,3,21,7,7,1,35,30,1,6,25,37,150,9,1,1,1686,1,2,202,44,207,118,1,5,31,1,66,1,28,5,18,5,3,2,3,350,5,5,46,3,12,2328,438,1,3,3,3,9,22,2359,18,188,327,1293,484,1,2,116,3,2,11,1,47,4,4,30,5,52,80,1,4,1,34,5,2,52,1,7,11,1,79,46,21,51,141,30,60,8,55,131,12,2,2,4,218,572,19,13,10,2,5,1,2,19,39,1,8,9,3,15,1,2,10,16,21,3,2,79,9,23,31,7,1,13,19,21,2,82,1,47,16,1,26,40,66,8,251,34,49,128,2,308,3,1,17,196,20,9,1,40,6,25,1,2,20,43,3,3,74,5,16,80,497,40,19,2,12,1,5,1,1,3,6,143,50,23,9,15,1,17,5,12,26,51,3,1,3,11,1,2,8,11,2,13,6,194,1,862,4,12,33,5,6,2,422,17,2,85,99,3,10,1,2,1,63,2,2,8,14,17,12,1,27,85,4,6,2,22,2,2,6,3,1,12,2,2,29,2,3,18,2,6,1,18,162,3,95,2,3,6,8,370,23,178,11,679,525,1,27,66,152,1,3,1,1,21,142,62,87,5,48,20,2,2,3,4,2,1,3,2,14,8,1,20,3,445,2,2,39,253,32,264,3,14,3,15,14,140,1,78,246,18,32,7,7,29,32,47,41,6,188,4,2,1,1,3,2,6,1,2,87,19,2,44,225,1,2,126,112,8,1,1,1,1,110,135,62,5,61,3,86,1,15,4,66,16,1,1,5,1,1,25,1,1,3,28,3,2,2,1,1,5,1,13,15,14,3,4,26,1,11,37,1,58,36,69,2,4,165,1,211,4,37,41,30,1,2,2,11,5,1,1,38,69,52,2,185,16,25,207,2,1,22,11,219,11,4,2610,1005,2,1,11,136,4,4,2,3548,1,85,9,15,210,27,99,80,21,12,27,7,26,22,1,2,1352,203,203,119,452,50,12,330,6,3,1,1,23,93,2,42,2,22,2,3892,77,148,129,26,239,3,6,1,15,10,7,5,2,2,1,402,57,26,1022,35,2,430,151,473,1,460,3,163,132,496,105,85,6,14,5,11,1,2,12,3,1,19,1,52,208,58,211,150,253,6,297,36,85,517,81,8,255,12,2,1,9,1,2,3128,24,14,1409,129,24,445,16,3,4,16,9,155,17,417,2,1,71,10,1,39,51,5,6,26,31,1,12,30,3,57,2,1,3,7,24,3,787,45,6,1,1248,37,7,610,86,874,29,252,172,3,1,1,6,12,2,35,3,1,4,1,2,5,1,2878,20,1,31,1,40,10,10,121,63,4,30,1,368,5,183,1,1,1,6,2,5,7,3,2,11,2,42,3,12,2,1,1,225,7,32,30,18,3,1,10,6,3,2,2,2,1,11,8,7,40,3,467,408,136,1,43,2,5,73,1,1,38,10,4,4,1,1,2,7,18,65,1,1,1,19,126,1,275,82,2,2,2,1,1,57,3,14,1,81,2,7,2,2,80,8,26,2,111,19,181,8,1,1,2145,81,3,5,35,10,12,10,38,1,14,10,6,4,3,40,9,2,1,2,43,7,4,1,13,1,3,2,10,137,138,2,16,1446,4,18,3,60,11,1,2445,144,106,50,92,28,1,1,1,8,3,28,14,6,1,3,13,20,85,29,178,12,291,225,5,16,27,1,21,1,7,1,2,42,2,358,50,378,254,1,1,2862,3,3,741,6,178,628,150,25,153,5,60,5,4,4,19,6,2,17,8,2,2,9,1140,94,23,65,95,304,37,362,170,2,16,2,24,96,28,6,2165,9,1,18,18,1,42,8,4,23,27,1,4,29,4,2,10,1,115,11,3,27,1,10,10,1,164,13,3,10,26,4,17,7,20,25,22,40],["Other","Abies","Abies","Acacia","Acer","Achillea","Achillea","Aconitum","Aconitum","Other","Actaea","Other","Other","Other","Adonis","Adonis","Adonis","Aesculus","Other","Agrimonia","Agrostemma githago","Ailanthus","Alchemilla","Alchemilla","Algae","Algae","Algae","Alisma","Alisma","Allium","Allium","Alnus","Alnus","Alnus","Alnus","Alnus","Alnus","Alnus","Other","Amaranthaceae","Ambrosia","Ambrosia","Amphitrema","Amphitrema","Amphitrema","Amphitrema","Anagallis","Anagallis","Anagallis","Anagallis","Anagallis","Other","Other","Other","Other","Other","Anemone","Anemone","Anemone","Anemone","Anemone","Anemone","Anemone","Anthemis","Anthemis","Anthericum","Anthericum","Anthoceros","Anthoceros","Anthoceros","Anthoceros","Fungi","Fungi","Anthriscus caucalis","Anthriscus sylvestris","Anthriscus sylvestris-type","Anthriscus-type","Anthyllis","Aphanes","Apiaceae","Apiaceae undiff.","Apium","Apium inundatum-type","Apium-type","Araneae","Arcella","Arcella cf. A. megastoma","Arcella discoides","Arcella sp.","Fungi","Fungi","Arctium","Arctostaphylos uva-ursi","Arctostaphylos uva-ursi-type","Arctous alpina","Arenaria","Arenaria serpyllifolia-type","Armeria","Armeria","Armeria","Armeria","Arnica montana","Artemisia","Arthrodesmus","Aruncus","Ascaris","Ascaris lumbricoides","Ascomycota","Ascospora","Aspiromitus punctatus","Asplenium","Asplenium-type","Assulina","Assulina muscorum","Assulina seminulum","Assulina sp.","Aster-type","Asteraceae","Asteroideae","Asteroideae undiff.","Asterosporium","Astragalus alpinus-type","Astragalus danicus-type","Astragalus exscapus","Astragalus-type","Astrantia major","Astrantia-type","Athyrium","Athyrium filix-femina","Athyrium-type","Avena-type","Avena/Triticum-type","Bambusa-type","Barbarea-type","Betula","Betula","Betula","Betula","Betula","Bidens","Bidens-type","Bistorta","Bistorta officinalis","Bistorta officinalis-type","Blechnum","Boraginaceae","Botrychium","Botryococcus","Botryococcus braunii","Botryococcus neglectus","Botryococcus pila","Botryococcus sp.","Brachysporium obovatum/B. bloxami/Bactrodesmium betulicola (type 359, HdV)","Brachysporium pendulisporum (type 360, HdV)","Brassica","Brassicaceae","Brassicaceae undiff.","Brassicaceae-type","Bruckenthalia-type","Bryales","Bryonia alba/Helianthemum","Bryophyta","Bryophyta (type 354, HdV)","Bupleurum","Bupleurum falcatum-type","Bupleurum-type","Butomus","Butomus umbellatus","Butomus-type","Byssothecium circinans","Byssothecium circinans (type 16A, HdV)","Byssothecium circinans (type 16B, HdV)","Byssothecium circinans (type 16C, HdV)","Calla","Callitriche","Calluna","Calluna vulgaris","Caltha","Caltha palustris-type","Caltha-type","Calystegia","Campanula","Campanula rapunculoides","Campanula-type","Campanula/Phyteuma","Campanulaceae","Cannabis sativa","Cannabis-type","Cardamine","Cardamine pratensis-type","Cardamine-type","Carduus","Carex","Carpinus","Carpinus","Carpinus","Carum carvi","Carya","Caryophyllaceae","Caryophyllaceae undiff.","Caryospora sp. (type 1001, HdV)","Castanea","Castanea sativa","Castanea-type","Cedrus","Cedrus-type","Centaurea","Centaurea","Centaurea","Centaurea","Centaurea","Centaurea","Centaurea","Centaurea","Centaurea","Centaurea","Centaurea","Centaurea","Centaurea","Centaurea","Centaurea","Centropyxis","Centropyxis aculeata","Cerastium","Cerastium arvense-type","Cerastium cerastoides-type","Cerastium fontanum-type","Cerastium-type","Ceratophyllum","Cercophora sp. (type 112, HdV)","Cerinthe","Cerinthe minor","cf. Actinopeltis (type 8C, HdV)","cf. Androsace","cf. Diphasiastrum-type","cf. Endophragmia (type 572, HdV)","cf. Entophlyctis lobata","cf. Helianthemum","cf. Lamiaceae","cf. Lobelia","cf. Papaver","cf. Pedicularis","cf. Penium","cf. Persiciospora (type 124, HdV)","cf. Riccia","cf. Richonia variospora (type 140, HdV)","cf. Spadicoides bina (type 98, HdV)","cf. Trichocladium opacum (type 10, HdV)","cf. Trichoglossum hirsutum (type 77B, HdV)","Chaerophyllum","Chaerophyllum hirsutum","Chaerophyllum hirsutum-type","Chaetomium sp. (type 7A, HdV)","Chaetomium undiff.","Chamaenerion","Chamaenerion angustifolium","Chamaenerion angustifolium-type","Charcoal","Chelidonium","Chelidonium majus","Chironomidae","Chlamydomonadaceae","Chrysophyceae","Chrysosplenium","Chrysosplenium-type","Cicatricosporites australiensis","Cichorioideae","Cicuta virosa","Circaea","Cirsium","Cirsium-type","Cirsium/Carduus","Cladium mariscus","Cladocera","Clasterosporium caricinum (type 126, HdV)","Clematis","Closterium","Closterium undiff.","Coelastrum reticulatum","Comarum","Comarum palustre","Comarum-type","Coniferae-type","Coniochaeta cf. C. ligniaria","Coniochaeta ligniaria (type 172, HdV)","Coniochaeta xylariispora","Consolida regalis","Consolida-type","Convallaria","Convolvulus","Convolvulus arvensis","Convolvulus-type","Copepoda","Cornus","Cornus","Cornus","Cornus","Coronilla undiff.","Corylus","Corylus avellana","Crataegus","Crataegus-type","Crupina","Cryptomeria","Cupressaceae","Cuscuta","Cuscuta epithymum","Cuscuta europaea-type","Cyperaceae","Cystopteris","Daphne","Daucus","Daucus carota","Daucus-type","Delitschia","Descurainia sophia","Desmidiaceae","Desmidiales","Dianthus","Dianthus-type","Difflugia","Digitalis purpurea-type","Dinoflagellata","Dinoflagellata undiff.","Diphasiastrum alpinum","Diphasiastrum alpinum-type","Diphasiastrum complanatum","Diporotheca","Dipsacoideae","Dipsacus","Drosera","Drosera intermedia","Drosera rotundifolia","Drosera rotundifolia-type","Dryas octopetala","Dryas-type","Dryopteris","Dryopteris carthusiana-type","Dryopteris dilatata-type","Dryopteris filix-mas-type","Dryopteris-type","Echinops","Echium","Echium vulgare","Echium-type","Elatine","Elymus-type","Empetrum","Empetrum nigrum-type","Empetrum-type","Encalypta-type","Engelhardia-type","Entophlyctis lobata","Entorrhiza sp. (type HdV-527)","Ephedra","Ephedra cf. E. distachya","Ephedra cf. E. foeminea","Ephedra cf. E. fragilis","Ephedra distachya","Ephedra distachya-type","Ephedra foeminea","Ephedra foeminea-type","Ephedra fragilis","Ephedra fragilis-type","Epilobium","Epilobium-type","Epipactis","Equisetaceae","Equisetum","Eranthis hyemalis-type","Erica ciliaris-type","Ericaceae","Ericaceae undiff.","Ericales","Ericales undiff.","Eriophorum","Erodium","Eryngium","Eryngium-type","Euglypha","Eunotia sp.","Euonymus","Euonymus europaeus","Euphorbia","Euphorbia-type","Euphorbiaceae","Euphrasia","Euphrasia-type","Fabaceae","Fabaceae undiff.","Faboideae","Fagopyrum","Fagopyrum esculentum","Fagopyrum-type","Fagus","Fagus sylvatica","Falcaria vulgaris","Falcaria-type","Fallopia convolvulus","Fallopia convolvulus-type","Fallopia convolvulus/F. dumetorum","Filinia longiseta","Filipendula","Filipendula ulmaria/F. vulgaris","Frangula","Frangula alnus","Fraxinus","Fraxinus excelsior","Fraxinus ornus","Fumaria-type","Fungi","Fungi (type 11, HdV)","Fungi (type 123, HdV)","Fungi (type 17, HdV)","Fungi","Fungi (type 18, HdV)","Fungi (type 19, HdV)","Fungi (type 20, HdV)","Fungi (type 200, HdV)","Fungi (type 23, HdV)","Fungi (type 24, HdV)","Fungi (type 3A, HdV)","Fungi","Fungi (type 408, HdV)","Fungi","Fungi (type 53, HdV)","Fungi (type 54B, HdV)","Fungi (type 571, HdV)","Fungi (type 64, HdV)","Fungi","Fungi (type 729, HdV)","Fungi (type 73, HdV)","Fungi","Fungi (type 83, HdV)","Fungi (type 8A, HdV)","Fungi (type 8D, HdV)","Fungi (type 8E, HdV)","Fungi (type 90, HdV)","Fungi (type 96B, HdV)","Fungi undiff.","Fungi-type","Gaeumannomyces","Gaeumannomyces cf. G. caricis","Gaeumannomyces undiff.","Galeopsis","Galeopsis-type","Galeopsis/Ballota-type","Galium","Galium-type","Gelasinospora","Gelasinospora (type 1, HdV)","Gelasinospora (type 1A, HdV)","Gelasinospora (type 1B, HdV)","Gelasinospora reticulispora","Gelasinospora undiff.","Genista","Genista-type","Gentiana","Gentiana cruciata-type","Gentiana pneumonanthe-type","Gentiana undiff.","Gentiana-type","Gentianaceae","Gentianaceae undiff.","Gentianella","Gentianella campestris-type","Geoglossum sphagnophilum","Geoglossum sphagnophilum (type 77A, HdV)","Geoglossum sphagnophilum/Trichoglossum hirsutum (type 77A/77B, HdV)","Geraniaceae","Geranium","Geranium-type","Geum","Geum-type","Glaucium","Glaucium corniculatum","Glomus","Glomus cf. G. fasciculatum","Glyceria-type","Glyptotendipes pallens group (type 509, HdV)","Gnaphalium-type","Gratiola officinalis","Gymnocarpium dryopteris","Gypsophila","Gypsophila repens","Gypsophila repens-type","Gypsophila-type","Gyratrix hermaphroditus","Habrotrocha","Habrotrocha angusticollis","Habrotrocha angusticollis (type 37, HdV)","Hedera","Hedera helix","Hedysarum-type","Helianthemum","Helianthemum nummularium-type","Helianthemum oelandicum subsp. alpestris-type","Helicoma","Helicoön pluriseptatum","Helicosporium/Helicoön pluriseptatum (type 30, HdV)","Heliotropium europaeum","Helleborus","Heracleum","Heracleum sphondylium","Heracleum-type","Herniaria","Herniaria-type","Hippophaë","Hippophaë rhamnoides","Hippuris vulgaris","Hordeum","Hordeum-type","Hottonia palustris","Humulus","Humulus lupulus","Humulus/Cannabis","Humulus/Cannabis-type","Huperzia selago","Hyalosphenia papilio","Hyalosphenia subflava","Hydrocotyle","Hydrocotyle vulgaris","Hydrocotyle-type","Hydrodictyon","Hymenophyllum","Hyoscyamus","Hypericum","Hypericum perforatum-type","Hypericum perforatum/H. androsaemum-type","Hystrix","Ilex","Illecebrum verticillatum","Impatiens","Impatiens noli-tangere","Impatiens parviflora","Indeterminable","Indeterminable undiff.","Iris","Iris pseudacorus","Iris pseudacorus-type","Iris-type","Isoëtes","Isoëtes lacustris","Jasione","Jasione montana","Jasione-type","Juglandaceae","Juglandaceae-type","Juglans","Juncus sp. (type 2.2, MI)","Juniperus","Juniperus communis","Juniperus-type","Knautia","Knautia arvensis","Knautia arvensis-type","Koenigia alpina","Lamiaceae","Lamiaceae (tricolpate)","Lamium album-type","Lamium-type","Larix","Larix decidua","Larix-type","Larix/Pseudotsuga","Laserpitium","Laserpitium latifolium-type","Lasiosphaeria cf. L. caudata","Lasiosphaeria sp.","Lasiosphaeria sp. (type 63C, HdV)","Lasiosphaeria-type","Lathyrus-type","Lemna","Lemnoideae","Lepidoptera","Ligustrum","Liliaceae","Liliaceae-type","Linum","Linum austriacum-type","Linum catharticum","Linum catharticum-type","Linum flavum","Linum usitatissimum-type","Liquidambar","Listera ovata","Listera-type","Lithospermum officinale","Lobelia","Lonicera","Lonicera periclymenum","Lonicera xylosteum","Loranthus","Loranthus europaeus","Lotus","Lotus cf. L. corniculatus","Lotus pedunculatus","Lotus-type","Ludwigia palustris","Lycopodiaceae","Lycopodiaceae cf. Diphasiastrum complanatum","Lycopodiaceae undiff.","Lycopodiella inundata","Lycopodium","Lycopodium annotinum","Lycopodium annotinum-type","Lycopodium clavatum","Lycopodium clavatum-type","Lycopodium spike","Lycopodium tablets","Lycopodium undiff.","Lycopus","Lycopus-type","Lysimachia","Lysimachia cf. L. vulgaris","Lysimachia nemorum","Lysimachia nemorum-type","Lysimachia thyrsiflora","Lysimachia vulgaris","Lysimachia vulgaris-type","Lysimachia-type","Lythrum","Lythrum portula-type","Lythrum salicaria","Lythrum-type","Macrobiotus","Macrobiotus cf. M. echinogenitus","Magnolia-type","Maianthemum bifolium","Malus","Malus undiff.","Malus-type","Malva-type","Malvaceae","Marchantiophyta","Marrubium","Matricaria-type","Medicago falcata-type","Melampyrum","Melampyrum-type","Meliola","Mentha","Mentha-type","Menyanthes","Menyanthes trifoliata","Menyanthes trifoliata-type","Mercurialis","Mercurialis perennis-type","Micranthes stellaris","Micranthes stellaris-type","Microdalyellia armigera","Microrrhinum minus","Microthyriaceae","Microthyrium","Microthyrium microscopicum","Microthyrium undiff.","Microthyrium-type","Minuartia-type","Monactinus simplex","Monactinus simplex var. echinulatum","Monactinus simplex var. simplex","Monocotyledoneae","Montia","Mougeotia","Mougeotia cf. M. gracillima (type 61, HdV)","Mougeotia undiff.","Mougeotia-type","Muscari","Myosotis","Myosotis arvensis-type","Myrica-type","Myricaria germanica","Myriophyllum","Myriophyllum alterniflorum","Myriophyllum cf. M. spicatum","Myriophyllum cf. M. verticillatum","Myriophyllum heterophyllum","Myriophyllum spicatum","Myriophyllum spicatum-type","Myriophyllum undiff.","Myriophyllum verticillatum","Myriophyllum verticillatum-type","Nebela","Nebela parvula","Nebela undiff.","Neurospora","Normapolles","Nuphar","Nymphaea","Nymphaea alba","Nymphaea alba-type","Nymphaea cf. N. candida","Nymphaea undiff.","Nymphaeaceae","Nymphoides peltata-type","Nyssa","Odontites","Odontites-type","Oenanthe","Oenanthe-type","Oenothera","Olea","Oleaceae","Onagraceae","Onobrychis","Ononis","Ononis-type","Onopordum","Ophioglossum","Ophioglossum vulgatum","Orchidaceae","Oribatida (type 396, HdV)","Orlaya grandiflora","Ornithogalum umbellatum-type","Ornithogalum-type","Ostrya-type","Oxalis","Oxyria-type","Papaver","Papaver rhoeas-type","Papaver somniferum","Papaveraceae","Parapediastrum biradiatum","Parnassia","Parnassia palustris","Parnassia-type","Pediastrum","Pediastrum angulosum","Pediastrum angulosum var. angulosum","Pediastrum angulosum var. asperum","Pediastrum braunii","Pediastrum duplex","Pediastrum duplex var. duplex","Pediastrum duplex var. rugulosum","Pediastrum muticum var. scutum","Pediastrum orientale","Pediastrum undiff.","Pedicularis","Pedicularis palustris-type","Penium","Persicaria","Persicaria amphibia","Persicaria amphibia-type","Persicaria cf. P. lapathifolia","Persicaria lapathifolia","Persicaria maculosa","Persicaria maculosa-type","Petasites","Petasites hybridus-type","Petasites-type","Peucedanum","Peucedanum palustre-type","Peucedanum-type","Phegopteris","Phegopteris connectilis","Phragmites","Phragmites australis","Phragmites-type","Phyteuma","Phyteuma-type","Picea","Picea abies","Pilularia","Pimpinella anisum","Pimpinella major","Pimpinella major-type","Pimpinella major/P. saxifraga","Pinguicula","Pinnularia","Pinus","Pinus (Tertiary)","Pinus cembra","Pinus cembra-type","Pinus sp.","Pinus subg. Pinus","Pinus subg. Strobus-type","Pinus sylvestris","Pinus sylvestris-type","Pisum sativum","Plantaginaceae","Plantaginaceae undiff.","Plantago","Plantago alpina","Plantago alpina-type","Plantago atrata-type","Plantago coronopus","Plantago lanceolata","Plantago lanceolata-type","Plantago major","Plantago major-type","Plantago major/P. media","Plantago major/P. media-type","Plantago maritima-type","Plantago media","Plantago media-type","Plantago sp.","Platanus","Platycarya","Platyhelminthes (type 353A, HdV)","Platyhelminthes (type 353B, HdV)","Pleospora sp. (type 3B, HdV)","Pleospora undiff.","Pleurospermum","Pleurospermum austriacum","Pleurospermum austriacum-type","Poaceae","Poaceae (Cerealia-type excluding Secale)","Poaceae (Cerealia-type)","Poaceae (Cerealia)","Poaceae (Cerealia) excluding Secale","Poaceae (Cerealia) undiff.","Podocarpus-type","Podospora sp./Zopfiella sp. (type 466, HdV)","Podospora-type (type 368, HdV)","Polemonium","Polemonium caeruleum","Polygala","Polygonaceae","Polygonaceae undiff.","Polygonatum","Polygonum","Polygonum aviculare","Polygonum aviculare-type","Polygonum sp.","Polypodiaceae","Polypodiophyta (monolete, psilate)","Polypodiophyta (monolete, verrucate)","Polypodium","Polypodium vulgare","Populus","Porifera","Potamogeton","Potamogeton natans-type","Potamogeton-type","Potentilla","Potentilla-type","Potentilla/Comarum","Potentilla/Comarum-type","Potentilla/Fragaria","Poterium sanguisorba","Poterium sanguisorba subsp. sanguisorba","Primula","Primula clusiana-type","Primula farinosa-type","Primula veris-type","Primulaceae","Prunella-type","Prunus","Prunus sp.","Prunus-type","Pseudopediastrum boryanum","Pseudopediastrum boryanum var. boryanum","Pseudopediastrum boryanum var. boryanum sensu lato","Pseudopediastrum boryanum var. cornutum","Pseudopediastrum boryanum var. longicorne","Pseudopediastrum brevicorne","Pseudopediastrum integrum","Pseudopediastrum kawraiskyi","Pteridium","Pteridium aquilinum","Pteridophyta","Pteridophyta (monolete, verrucate)","Pteridophyta (monolete) undiff.","Pterocarya","Pterocarya fraxinifolia","Pulmonaria","Pulmonaria-type","Pyrola","Pyxidicula","Quercus","Quercus coccifera","Quercus pubescens","Ranunculaceae","Ranunculaceae","Ranunculaceae","Ranunculaceae","Ranunculaceae","Ranunculaceae","Ranunculaceae","Ranunculaceae","Ranunculaceae","Ranunculaceae","Ranunculaceae","Ranunculaceae","Reseda","Reseda lutea-type","Rhabdocoela","Rhabdocoela (type 353, HdV)","Rhamnaceae","Rhamnus","Rhinanthus","Rhinanthus-type","Rhinanthus/Veronica","Rhizopoda","Rhizopoda undiff.","Rhododendron","Rhododendron subsect. Ledum","Rhododendron tomentosum","Rhus-type","Ribes","Ribes","Ribes","Riccia","Rivularia","Rosa","Rosa-type","Rosaceae","Rosaceae undiff.","Rotifera undiff.","Rotifera/Tardigrada","Rubiaceae","Rubus","Rubus","Rumex","Rumex","Rumex","Rumex","Rumex","Rumex","Rumex","Rumex","Rumex","Rumex","Rumex","Rumex","Rumex","Rumex","Rumex","Sagina","Sagina procumbens-type","Sagina-type","Sagittaria","Sagittaria-type","Salix","Salix herbacea-type","Salvia","Sambucus","Sambucus","Sambucus","Sambucus","Sambucus","Sambucus","Sambucus","Sambucus","Sambucus","Samolus valerandi","Sample quantity","Sanguisorba minor-type","Sanguisorba officinalis","Sanicula europaea","Sanicula-type","Saussurea-type","Saxifraga","Saxifraga aizoides-type","Saxifraga granulata","Saxifraga granulata-type","Saxifraga hirculus-type","Saxifraga oppositifolia","Saxifraga oppositifolia-type","Saxifraga undiff.","Saxifragaceae","Saxifragaceae undiff.","Scabiosa","Scabiosa columbaria subsp. pratensis-type","Scabiosa columbaria-type","Scandix pecten-veneris/Caucalis platycarpos","Scenedesmus","Scenedesmus undiff.","Scheuchzeria","Scheuchzeria palustris","Sciadopitys","Sciadopitys-type","Scilla-type","Scleranthus","Scleranthus annuus","Scleranthus annuus-type","Scleranthus cf. S. annuus","Scleranthus cf. S. perennis","Scleranthus perennis","Scleranthus perennis-type","Scleranthus-type","Scrophularia","Scrophularia-type","Scrophulariaceae","Scutellaria","Secale","Secale cereale","Secale-type","Securigera varia","Sedum","Sedum-type","Selaginella","Selaginella selaginoides","Selaginellaceae","Senecio","Senecio-type","Senecio/Aster","Sequoia","Serratula","Serratula-type","Seseli-type","Sigmopollis","Silene","Silene dioica-type","Silene flos-cuculi","Silene latifolia","Silene viscaria-type","Silene vulgaris","Silene vulgaris-type","Silene-type","Silene-type undiff.","Sileneae","Silenoideae-type","Sinapis-type","Sium latifolium-type","Solanaceae","Solanum","Solanum cf. S. nigrum","Solanum dulcamara","Solanum nigrum","Solanum nigrum-type","Soldanella","Sorbus","Sorbus aria-type","Sorbus aucuparia","Sorbus group","Sorbus torminalis","Sorbus-type","Sordaria-type (type 55A, HdV)","Sordariaceae","Sordariaceae/Sordaria (type 55B, HdV)","Sparganium","Sparganium erectum","Sparganium-type","Spergula","Spergula-type","Spergularia-type","Sphagnum","Spirogyra","Spirogyra cf. S. scrobiculata","Spirogyra-type","Sporormiella","Sporormiella (type 113, HdV)","Stachys","Stachys-type","Staurastrum","Staurastrum undiff.","Stauridium tetras","Stellaria","Stellaria holostea","Stellaria-type","Stratiotes aloides","Succisa","Succisa pratensis","Succisa-type","Succisella","Swertia perennis","Symphytum","Symphytum cf. S. officinale","Symphytum-type","Symplocos","Tardigrada","Tardigrada (type 902, HdV)","Tardigrada undiff.","Taxus","Taxus baccata","Tetraëdron","Tetraëdron minimum","Tetraploa scheueri","Teucrium","Thalictrum","Thalictrum-type","Thecaphora","Thelypteris","Thelypteris palustris","Thesium","Thesium-type","Tilia","Tilia cordata","Tilia platyphyllos","Tilia undiff.","Tilletia sphagni","Tilletia sphagni (type 27, HdV)","Tofieldia","Transeauina","Transeauina (type 214, HdV)","Transeauina undiff.","Trapa","Trapa natans","Trichocladium opacum (type 10, HdV)","Trichuris trichiura","Trientalis","Trientalis europaea","Trifolium","Trifolium pratense","Trifolium pratense-type","Trifolium repens-type","Trifolium-type","Triglochin","Triticum","Triticum-type","Trochiscia undiff.","Trollius","Trollius europaeus","Trollius-type","Tsuga","Tsuga diversifolia-type","Tsuga-type","Turgenia latifolia","Typha","Typha angustifolia","Typha angustifolia-type","Typha angustifolia/Sparganium","Typha angustifolia/Sparganium-type","Typha latifolia","Typha latifolia-type","Typhaceae","Ulex-type","Ulmus","Ulmus/Zelkova","Umbilicus rupestris-type","Unknown","Unknown (Cretaceous)","Unknown (monolete, psilate)","Unknown (monolete)","Unknown (monolete) undiff.","Unknown (pre-Quaternary)","Unknown (Tertiary)","Unknown (trilete)","Unknown (trilete) undiff.","Unknown (type 160, HdV)","Unknown (type 181, HdV)","Unknown (type 224, HdV)","Unknown (type 33, HdV)","Unknown (type 366, HdV)","Unknown (type 38, HdV)","Unknown (type 41, HdV)","Unknown (type 708, HdV)","Unknown (type 74, HdV)","Unknown (type 86, HdV)","Unknown (type 91, HdV)","Urtica","Ustulina deusta","Ustulina deusta (type 44, HdV)","Utricularia","Vaccinioideae","Vaccinium","Vaccinium oxycoccos","Vaccinium-type","Valeriana","Valeriana cf. V. dioica","Valeriana cf. V. officinalis","Valeriana dioica","Valeriana dioica-type","Valeriana officinalis","Valeriana officinalis-type","Valerianella","Varia","Veratrum","Veratrum album","Veratrum-type","Verbascum","Vermes","Veronica","Veronica beccabunga","Veronica beccabunga-type","Veronica-type","Viburnum","Viburnum cf. V. opulus","Viburnum lantana","Viburnum opulus","Viburnum opulus-type","Viburnum undiff.","Vicia","Vicia cracca-type","Vicia-type","Vicia/Lathyrus","Vicia/Lathyrus-type","Viola","Viola canina-type","Viola palustris","Viola palustris-type","Viola tricolor","Viscum","Vitis","Vitis vinifera","Xanthium","Xanthium-type","Xylariaceae","Xylomyces chlamydosporis/X. aquaticus (type 201, HdV)","Zea mays","Zygnema","Zygnema-type","Zygnemataceae","Zygnemataceae undiff."]],"container":"<table class=\"display\">\n <thead>\n <tr>\n <th>variablename<\/th>\n <th>sites<\/th>\n <th>samples<\/th>\n <th>replacement<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"scrollX":"100%","dom":"t","columnDefs":[{"className":"dt-right","targets":[1,2]}],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script>
You can see we've changed some of the taxon names in the taxon table (don't look too far, I just did this as an example). To replace the names in the samples() output, we'll join the two tables using an inner_join() (meaning the variablename must appear in both tables for the result to be included), and then we're going to select only those elements of the sample tables that are relevant to our later analysis:
allSamp <- samples(cz_dl)
allSamp <- allSamp %>%
inner_join(translation, by = c("variablename" = "variablename")) %>%
dplyr::select(!c("variablename", "sites", "samples")) %>%
group_by(siteid, sitename, replacement,
sampleid, units, age,
agetype, depth, datasetid,
long, lat) %>%
summarise(value = sum(value), .groups='keep')<div id="htmlwidget-e4b979760c2805780d58" style="width:100%;height:auto;" class="datatables html-widget"></div>
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Physiography: Valley. Surrounding vegetation: Spruce forest.","Peat bog in a sandstone valley. Physiography: Valley. Surrounding vegetation: Spruce forest.","Peat bog in a sandstone valley. Physiography: Valley. Surrounding vegetation: Spruce forest.","Peat bog in a sandstone valley. Physiography: Valley. Surrounding vegetation: Spruce forest.","Peat bog in a sandstone valley. Physiography: Valley. Surrounding vegetation: Spruce forest.","Peat bog in a sandstone valley. Physiography: Valley. Surrounding vegetation: Spruce forest.","Peat bog in a sandstone valley. Physiography: Valley. Surrounding vegetation: Spruce forest.","Peat bog in a sandstone valley. Physiography: Valley. Surrounding vegetation: Spruce forest.","Peat bog in a sandstone valley. Physiography: Valley. Surrounding vegetation: Spruce forest.","Peat bog in a sandstone valley. Physiography: Valley. Surrounding vegetation: Spruce forest.","Peat bog in a sandstone valley. Physiography: Valley. Surrounding vegetation: Spruce forest.","Peat bog in a sandstone valley. Physiography: Valley. Surrounding vegetation: Spruce forest.","Peat bog in a sandstone valley. Physiography: Valley. Surrounding vegetation: Spruce forest.","Peat bog in a sandstone valley. Physiography: Valley. Surrounding vegetation: Spruce forest.","Peat bog in a sandstone valley. Physiography: Valley. Surrounding vegetation: Spruce forest.","Peat bog in a sandstone valley. Physiography: Valley. Surrounding vegetation: Spruce forest.","Peat bog in a sandstone valley. Physiography: Valley. Surrounding vegetation: Spruce forest.","Peat bog in a sandstone valley. Physiography: Valley. Surrounding vegetation: Spruce forest.","Peat bog in a sandstone valley. Physiography: Valley. Surrounding vegetation: Spruce forest.","Peat bog in a sandstone valley. Physiography: Valley. Surrounding vegetation: Spruce forest.","Peat bog in a sandstone valley. Physiography: Valley. Surrounding vegetation: Spruce forest.","Peat bog in a sandstone valley. Physiography: Valley. Surrounding vegetation: Spruce forest.","Peat bog in a sandstone valley. Physiography: Valley. Surrounding vegetation: Spruce forest.","Peat bog in a sandstone valley. Physiography: Valley. Surrounding vegetation: Spruce forest.","Peat bog in a sandstone valley. Physiography: Valley. Surrounding vegetation: Spruce forest.","Peat bog in a sandstone valley. Physiography: Valley. Surrounding vegetation: Spruce forest.","Peat bog in a sandstone valley. Physiography: Valley. Surrounding vegetation: Spruce forest.","Peat bog in a sandstone valley. Physiography: Valley. Surrounding vegetation: Spruce forest.","Peat bog in a sandstone valley. Physiography: Valley. Surrounding vegetation: Spruce forest.","Peat bog in a sandstone valley. Physiography: Valley. Surrounding vegetation: Spruce forest.","Peat bog in a sandstone valley. Physiography: Valley. 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<th>age_range_old<\/th>\n <th>age_range_young<\/th>\n <th>datasetnotes<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"scrollX":"100%","dom":"t","columnDefs":[{"className":"dt-right","targets":[0,2,3,4,7,10,16,18,19,20,22,23,25,26,27,30,31,34,35]}],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script>
We can use packages like rioja to do stratigraphic plotting for a single record, but first we need to do some different data management. Although we could do harmonization again we're going to simply take the top ten most common taxa at a single site and plot them in a stratigraphic diagram.
We're using the arrange() call to sort by the number of times that the taxon appears within the core. This way we can take out samples and select the taxa that appear in the first ten rows of the plottingTaxa data.frame.
# Get a particular site, select only taxa identified from pollen (and only trees/shrubs)
plottingSite <- cz_dl[[1]]
plottingTaxa <- taxa(plottingSite) %>%
filter(ecologicalgroup %in% c("TRSH")) %>%
filter(elementtype == "pollen") %>%
arrange(desc(samples)) %>%
head(n = 10)
# Clean up. Select only pollen measured using NISP.
# We repeat the filters for pollen & ecological group on the samples
shortSamples <- samples(plottingSite) %>%
filter(variablename %in% plottingTaxa$variablename) %>%
filter(ecologicalgroup %in% c("TRSH")) %>%
filter(elementtype == "pollen") %>%
filter(units == "NISP")
# Transform to proportion values.
onesite <- shortSamples %>%
group_by(age) %>%
mutate(pollencount = sum(value, na.rm = TRUE)) %>%
group_by(variablename) %>%
mutate(prop = value / pollencount) %>%
arrange(desc(age))
# Spread the data to a "wide" table, with taxa as column headings.
widetable <- onesite %>%
dplyr::select(age, variablename, prop) %>%
mutate(prop = as.numeric(prop))
counts <- tidyr::pivot_wider(widetable,
id_cols = age,
names_from = variablename,
values_from = prop,
values_fill = 0)This appears to be a fairly long set of commands, but the code is pretty straightforward, and it provides you with significant control over the taxa, units and other elements of your data before you get them into the wide matrix (depth by taxon) that most statistical tools such as the vegan package or rioja use.
To plot we can use rioja's strat.plot(), sorting the taxa using weighted averaging scores (wa.order). I've also added a CONISS plot to the edge of the the plot, to show how the new wide data frame works with distance metric funcitons.
clust <- rioja::chclust(dist(sqrt(counts)),
method = "coniss")
plot <- rioja::strat.plot(counts[,-1] * 100, yvar = counts$age,
title = cz_dl[[1]]$sitename,
ylabel = "Calibrated Years BP",
xlabel = "Pollen (%)",
y.rev = TRUE,
clust = clust,
wa.order = "topleft", scale.percent = TRUE)
rioja::addClustZone(plot, clust, 4, col = "red")
We now have site information across the Czech Republic, with samples, and with taxon names. I'm interested in looking at the distributions of taxa across time, their presence/absence. I'm going to pick the top 20 taxa (based on the number of times they appear in the records) and look at their distributions in time:
plottingTaxa <- taxa(plottingSite) %>%
filter(ecologicalgroup %in% c("TRSH")) %>%
filter(elementtype == "pollen") %>%
arrange(desc(sites)) %>%
head(n = 20)
taxabyage <- samples(cz_dl) %>%
filter(variablename %in% plottingTaxa$variablename) %>%
group_by(variablename, "age" = round(age * 2, -3) / 2) %>%
summarise(n = length(unique(siteid)), .groups = 'keep')
samplesbyage <- samples(cz_dl) %>%
filter(variablename %in% plottingTaxa$variablename) %>%
group_by("age" = round(age * 2, -3) / 2) %>%
summarise(samples = length(unique(siteid)), .groups = 'keep')
groupbyage <- taxabyage %>%
inner_join(samplesbyage, by = "age") %>%
mutate(proportion = n / samples)
ggplot(groupbyage, aes(x = age, y = proportion)) +
geom_point() +
geom_smooth(method = 'gam',
method.args = list(family = 'binomial')) +
facet_wrap(~variablename) +
coord_cartesian(xlim = c(20000, 0), ylim = c(0, 1)) +
scale_x_reverse(breaks = c(10000, 20000)) +
xlab("Proportion of Sites with Taxon") +
theme_bw()
We can see clear patterns of change, and the smooths are modeled using Generalized Additive Models (GAMs) in R, so we can have more or less control over the actual modeling using the gam or mgcv packages. Depending on how we divide the data we can also look at shifts in altitude, latitude or longitude to better understand how species distributions and abundances changed over time in this region.
We are often interested in the interaction between taxa and climate, assuming that time is a proxy for changing environments. The development of large-scale global datasets for climate has made it relatively straightforward to access data from the cloud in raster format. R provides a number of tools (in the sf and raster packages) for managing spatial data, and providing support for spatial analysis of data.
The first step is taking our sample data and turning it into a spatial object using the sf package in R:
modern <- samples(cz_dl) %>%
filter(age < 50) %>%
filter(ecologicalgroup == "TRSH" & elementtype == "pollen" & units == "NISP")
spatial <- sf::st_as_sf(modern,
coords = c("long", "lat"),
crs = "+proj=longlat +datum=WGS84")The data is effectively the same, sf makes an object called spatial that is a data.frame with all the information from samples(), and a column (geometry) that contains the spatial data.
We can use the getData() function in the raster package to get climate data from WorldClim. The operations that follow here can be applied to any sort of raster data, provided it is loaded into R as a raster object.
Here we pull in the raster data, at a 10 minute resolution for the extract() function we just get information for the seventh month, July.
worldTmax <- raster::getData('worldclim', var = 'tmax', res = 10)
spatial$tmax7 <- raster::extract(worldTmax, spatial)[,7]This adds a column to the data.frame spatial, that contains the maximum July temperature for each taxon at each site (all taxa at a site will share the same value). We've already filtered to all UPHE taxa, but that still leaves us with 1 distinct names for the taxa. We're going to use dplyr's mutate() function to extract just the genus:
spatial <- spatial %>%
mutate(variablename = stringr::str_replace(variablename, "[[:punct:]]", " ")) %>%
mutate(variablename = stringr::word(variablename, 1)) %>%
group_by(variablename, siteid) %>%
summarise(tmax7 = max(tmax7), .groups = "keep") %>%
group_by(variablename) %>%
filter(n() > 3)We want to get the background distribution of July temperatures in the Czech Republic, to plot our taxon distributions against by taking the maximum value of the temperature, however, since all values at the site are the same (because we used a spatial overlay) the maximum is the same as the actual July temperature at the site.
maxsamp <- spatial %>%
dplyr::group_by(siteid) %>%
dplyr::summarise(tmax7 = max(tmax7), .groups = 'keep')Now we're going to plot it out, using facet_wrap() to plot each taxon in its own panel:
ggplot() +
geom_density(data = spatial,
aes(x = round(tmax7 / 10, 0)), col = 2) +
facet_wrap(~variablename) +
geom_density(data = maxsamp, aes(x = tmax7 / 10)) +
xlab("Maximum July Temperature") +
ylab("Kernel Density")
So, we've done a lot in this example. We've (1) searched for sites using site names and geographic parameters, (2) filtered results using temporal and spatial parameters, (3) obtained sample information for the selected datasets and (4) performed basic analysis including the use of climate data from rasters. Hopefully you can use these examples as templates for your own future work, or as a building block for something new and cool!