Advanced Neotoma for Fun and Profit
Simon Goring
October 6, 2016
1 What we’ll learn
This document is intended to act as a more complete vignette of the neotoma package’s functionality. I’ll show some functions & behaviour that’s not neccessarily shown in the examples or the Open Quaternary paper. Some of these examples are pretty straightforward, some are a bit more complicated. I’ve made an effort to clearly comment code, but welcome any suggestions. If you do have bug fixes, comments, or requests for additional examples, please let me know at goring@wisc.edu or through the issues for my website’s GitHub repository.
2 Data Exploration Made Easy
It’s a bit of a pain to download lots of records and then visualize them in R, or at least, it had been. In building the package I wanted to try to limit the need to install lots of other packages, so the basic plot() method isn’t all that helpful:
library(neotoma)
# I'll try as much as I can to use the PACKAGE::FUNCTION() convention, although
# you don't need to use it. Since this is a learning document I think it help
# make it a bit more explicit where these calls are coming from.
all_wi <- neotoma::get_dataset(gpid = "Wisconsin")## The API call was successful, you have returned 501 records.plot(all_wi)
All Neotoma data points in Wisconsin, with symbols identifying dataset type.
So, we can see the different dataset types. You can pretty much make out Wisconsin, but it doesn’t look that great, and it’s certainly not publication quality. We can make a better map, an interactive map, using leaflet. That’s pretty fun, and the RStudio help page for leaflet is really great to get you started. Make sure the leaflet package is installed using install.packages('leaflet'), and then let’s check out what we get:
library(leaflet)
# We're going to use this multiple times I think, so let's make it a function:
leaflet_map <- function(dataset_in) {
dataset_summary <- do.call(rbind, lapply(dataset_in,
function(x){
# here we pull out the site information from the `dataset` objects:
data.frame(name = x$site.data$site.name,
lat = x$site.data$lat + runif(1, -0.005, 0.005),
long = x$site.data$long + runif(1, -0.005, 0.005),
type = x$dataset.meta$dataset.type)
}))
# The leaflet package documentation uses piping. For the sake of this tutorial, I won't.
# First, define a color palette for the dataset type symbol plotting.
pal <- colorFactor("Dark2", domain = levels(dataset_summary$type))
# Now make the leaflet map, add base raster tiles and then add the markers for the records:
map <- leaflet(data = dataset_summary)
map <- leaflet::addTiles(map)
map <- leaflet::addCircleMarkers(map, ~long, ~lat,
popup = ~paste0("Site: ", as.character(name), "<br>",
"Type: ",
as.character(dataset_summary$type)),
color = ~pal(type),
stroke = FALSE, fillOpacity = 0.5)
# You need to explicitly call the `map` object to make it appear!
map
}
# Since that's all wrapped in a function, we can all it with any `dataset_list`:
leaflet_map(all_wi)This is much nicer (I think), but it is still missing all the additional information that goes along with a Neotoma record. We can go directly to the Neotoma Explorer using the browse function. Unfortunately, because of the limitations of URL string length, this doesn’t always work:
# Does not work:
neotoma::browse(all_wi)
# Does work:
some_wi <- neotoma::get_dataset(gpid = "Wisconsin", datasettype = "pollen")
neotoma::browse(some_wi)
Yay! (A browser window should have opened with your datasets in it).
2.1 Plotting stratigraphic diagrams
Let’s say we’re looking for all records from Wisconsin with Larix pollen, that must have some samples within the middle Holocene:
some_wi <- neotoma::get_dataset(gpid = "Wisconsin", datasettype = "pollen", taxonname = "Larix%", ageyoung = 4000, ageold = 6000)## The API call was successful, you have returned 18 records.wi_pollen <- neotoma::get_download(some_wi, verbose = FALSE)## Warning:
## There were multiple entries for Eucalyptus tablets
## get_download has mapped aliases for the taxa in the taxon.list.
## Warning:
## There were multiple entries for Eucalyptus tablets
## get_download has mapped aliases for the taxa in the taxon.list.leaflet_map(some_wi) # This is the function we made above.What do these records look like?
wi_pollen## A download_list containing 18 objects:
## Accessed from 2016-10-13 17:27h to 2016-10-13 17:27h.
## Datasets:
## dataset.id site.name long lat age.younger age.older
## 3473 Lake Mary -89.90000 46.25000 200 10345
## 684 Devils Lake -89.73205 43.41780 0 13614
## 700 Disterhaft Farm Bog -89.16694 43.91694 699 13840
## 860 Gass Lake -87.73333 44.05000 0 15612
## 1447 Kellys Hollow -90.35000 45.30000 -29 10000
## 3452 Kellys Hollow -90.35000 45.30000 -29 10730
## 1448 Kellners Lake -87.84806 44.23806 -23 14094
## 3781 Stewart's Dark Lake -91.45000 45.30000 482 10649
## 2011 Radtke Lake -88.10000 43.40000 0 11483
## 3620 Seidel -87.51556 44.45000 32 11227
## 2624 Tamarack Creek -91.45000 44.15000 0 4500
## 3035 Wood Lake -90.08333 45.33333 0 13101
## 15302 Emrick Lake -89.59428 43.80016 -57 11878
## 15740 Hemlock Lake -91.19829 46.30730 -42 10877
## 15925 Lake O' Pines -89.25530 46.14043 -47 12854
## 16129 Lima Bog -88.84320 42.78895 -31 18406
## 17304 Capitola Lake -89.55507 45.51958 -40 13288
## 17387 Beaver Lake -88.15694 44.91960 -30 5103
## type
## pollen
## pollen
## pollen
## pollen
## pollen
## pollen
## pollen
## pollen
## pollen
## pollen
## pollen
## pollen
## pollen
## pollen
## pollen
## pollen
## pollen
## pollenI like Devil’s Lake, so let’s take a look at the pollen. To get this to work you need the analogue package:
library(analogue, quietly = TRUE)
Stratiplot(wi_pollen[[2]])
You have all the advantages of the Stratiplot() function now, and the wrapper for the neotoma package makes it more useful directly with download objects.
2.2 Re-building Age-Models
So, I’m interested in the smoothed surface of Larix pollen at 4kyr in the region. I’m going to do a lazy job of it, but that’s my perogative. I just want you to see what we might do.
First, we know there are different age types in the records. Let’s see what we’ve got here:
table(sapply(wi_pollen, function(x)x$sample.meta$age.type[1]))##
## Calibrated radiocarbon years BP Radiocarbon years BP
## 5 13So, that’s a lot of records to re-do. To do it properly, we need all the chron-controls. When you run this you will get messages letting you know the record has downloaded successfully. I’m suppressing that message here:
wi_chrons <- neotoma::get_chroncontrol(wi_pollen)Now, lets rebuild the model using Bchrononlogy() from the Bchron package. It helps to know the structure of some of these data objects, so take a bit of time to look at them using the str() funciton (for “structure”). Can you understand what I’m passing into the Bchronology() function?
focal <- wi_chrons[[1]]
new_chron <- Bchron::Bchronology(ages = focal$chron.control$age,
ageSds = focal$chron.control$age - focal$chron.control$age.young,
positions = focal$chron.control$depth,
calCurves = ifelse(focal$chron.control$control.type %in% 'Radiocarbon',
'intcal13', 'normal'),
predictPositions = wi_pollen[[1]]$sample.meta$depth)
plot(new_chron)
So, you can see that modelling can take a long time, but, we can basically wrap all that logic into a swell little function & run all the models overnight. That was part of my motivation for using the variable focal in this code example. Try turning this into a funciton that can work on all of the download objects in wi_pollen. Does it work?
Wrapping Bchronology() around neotoma’s download objects is something that’s on the TODO list, but there’s a lot of art required to build age models & I’m not sure I want to do that quite yet.
But, let’s just pretend that we’ve done a good job and added all these date into the models. Let’s make a model of the records. I’m using a gam() function from the mgcv package.
# Running these in sequence gives us a nice narrow dataset, but you should always be aware what
# taxa have been pushed into the Other class for the taxonomies. The taxonomies in Neotoma itself
# are expanding as datasets get uploaded, but the translation table in this package is only updated
# occasionally.
wi_p25 <- neotoma::compile_taxa(wi_pollen, "P25")## Warning in FUN(X[[i]], ...):
## The following taxa could not be found in the existing conversion table:
## Angiospermae undiff. (herbs)
## The following taxa could not be found in the existing conversion table:
## Amaranthaceae## Warning in FUN(X[[i]], ...):
## The following taxa could not be found in the existing conversion table:
## Amaranthaceae undiff.
## The following taxa could not be found in the existing conversion table:
## Apiaceae
## The following taxa could not be found in the existing conversion table:
## Cannabaceae sensu stricto
## The following taxa could not be found in the existing conversion table:
## Celtis
## The following taxa could not be found in the existing conversion table:
## Indeterminable
## The following taxa could not be found in the existing conversion table:
## Isoëtes
## The following taxa could not be found in the existing conversion table:
## Pediastrum
## The following taxa could not be found in the existing conversion table:
## Plantago
## The following taxa could not be found in the existing conversion table:
## Potamogetonaceae
## The following taxa could not be found in the existing conversion table:
## Rhamnaceae/Vitaceae
## The following taxa could not be found in the existing conversion table:
## Rosaceae
## The following taxa could not be found in the existing conversion table:
## Rumex
## The following taxa could not be found in the existing conversion table:
## Unknown (monolete)
## The following taxa could not be found in the existing conversion table:
## Unknown (trilete)
## The following taxa could not be found in the existing conversion table:
## Urticaceae
## The following taxa could not be found in the existing conversion table:
## Caprifoliaceae sensu lato
## The following taxa could not be found in the existing conversion table:
## Fabaceae undiff.
## The following taxa could not be found in the existing conversion table:
## Morus
## The following taxa could not be found in the existing conversion table:
## Myriophyllum
## The following taxa could not be found in the existing conversion table:
## Thalictrum
## The following taxa could not be found in the existing conversion table:
## Typha latifolia
## The following taxa could not be found in the existing conversion table:
## Angiospermae undiff. (herbs)
## The following taxa could not be found in the existing conversion table:
## Rhus
## The following taxa could not be found in the existing conversion table:
## Sarcobatus vermiculatus
## The following taxa could not be found in the existing conversion table:
## Castanea
## The following taxa could not be found in the existing conversion table:
## Ilex
## The following taxa could not be found in the existing conversion table:
## Sparganium-type
## The following taxa could not be found in the existing conversion table:
## Amorpha-type
## The following taxa could not be found in the existing conversion table:
## Ephedra
## The following taxa could not be found in the existing conversion table:
## Sagittaria
## The following taxa could not be found in the existing conversion table:
## Ericaceae
## The following taxa could not be found in the existing conversion table:
## Nuphar
## The following taxa could not be found in the existing conversion table:
## Cornus## Warning in FUN(X[[i]], ...):
## The following taxa could not be found in the existing conversion table:
## Amaranthaceae
## The following taxa could not be found in the existing conversion table:
## Celtis
## The following taxa could not be found in the existing conversion table:
## Ericaceae
## The following taxa could not be found in the existing conversion table:
## Osmunda
## The following taxa could not be found in the existing conversion table:
## Polypodiophyta undiff.
## The following taxa could not be found in the existing conversion table:
## Pteridium
## The following taxa could not be found in the existing conversion table:
## Sphagnum
## The following taxa could not be found in the existing conversion table:
## Caryophyllaceae
## The following taxa could not be found in the existing conversion table:
## Nymphaea
## The following taxa could not be found in the existing conversion table:
## Sagittaria
## The following taxa could not be found in the existing conversion table:
## Thalictrum
## The following taxa could not be found in the existing conversion table:
## Lycopodiaceae
## The following taxa could not be found in the existing conversion table:
## Apiaceae
## The following taxa could not be found in the existing conversion table:
## Rubiaceae
## The following taxa could not be found in the existing conversion table:
## Typha latifolia
## The following taxa could not be found in the existing conversion table:
## Brasenia schreberi
## The following taxa could not be found in the existing conversion table:
## Drosera
## The following taxa could not be found in the existing conversion table:
## Filipendula
## The following taxa could not be found in the existing conversion table:
## Nuphar
## The following taxa could not be found in the existing conversion table:
## Sparganium-type
## The following taxa could not be found in the existing conversion table:
## Potentilla
## The following taxa could not be found in the existing conversion table:
## Ephedra
## The following taxa could not be found in the existing conversion table:
## Plantago
## The following taxa could not be found in the existing conversion table:
## Ranunculaceae undiff.
## The following taxa could not be found in the existing conversion table:
## Polygonum sensu lato
## The following taxa could not be found in the existing conversion table:
## Brassicaceae
## The following taxa could not be found in the existing conversion table:
## Botrychium
## The following taxa could not be found in the existing conversion table:
## Equisetum
## The following taxa could not be found in the existing conversion table:
## Lamiaceae
## The following taxa could not be found in the existing conversion table:
## Rumex
## The following taxa could not be found in the existing conversion table:
## Shepherdia
## The following taxa could not be found in the existing conversion table:
## Elaeagnus## Warning in FUN(X[[i]], ...):
## The following taxa could not be found in the existing conversion table:
## Amaranthaceae undiff.
## The following taxa could not be found in the existing conversion table:
## Celtis
## The following taxa could not be found in the existing conversion table:
## Indeterminable
## The following taxa could not be found in the existing conversion table:
## Nymphaea
## The following taxa could not be found in the existing conversion table:
## Pinaceae undiff.
## The following taxa could not be found in the existing conversion table:
## Unknown
## The following taxa could not be found in the existing conversion table:
## Cephalanthus
## The following taxa could not be found in the existing conversion table:
## Myricaceae
## The following taxa could not be found in the existing conversion table:
## Polypodiophyta undiff.
## The following taxa could not be found in the existing conversion table:
## Pteridium-type
## The following taxa could not be found in the existing conversion table:
## Typha latifolia
## The following taxa could not be found in the existing conversion table:
## Lycopodium annotinum
## The following taxa could not be found in the existing conversion table:
## Nuphar
## The following taxa could not be found in the existing conversion table:
## Sphagnum
## The following taxa could not be found in the existing conversion table:
## Vitis
## The following taxa could not be found in the existing conversion table:
## Fabaceae
## The following taxa could not be found in the existing conversion table:
## Galium
## The following taxa could not be found in the existing conversion table:
## Rumex
## The following taxa could not be found in the existing conversion table:
## Sparganium-type
## The following taxa could not be found in the existing conversion table:
## Urtica-type
## The following taxa could not be found in the existing conversion table:
## Thalictrum
## The following taxa could not be found in the existing conversion table:
## Cornus
## The following taxa could not be found in the existing conversion table:
## Huperzia lucidula
## The following taxa could not be found in the existing conversion table:
## Potamogetonaceae
## The following taxa could not be found in the existing conversion table:
## Menyanthes trifoliata
## The following taxa could not be found in the existing conversion table:
## Myriophyllum
## The following taxa could not be found in the existing conversion table:
## Sarcobatus vermiculatus
## The following taxa could not be found in the existing conversion table:
## Unknown (trilete)
## The following taxa could not be found in the existing conversion table:
## Botrychium
## The following taxa could not be found in the existing conversion table:
## Polypodiaceae
## The following taxa could not be found in the existing conversion table:
## Caltha
## The following taxa could not be found in the existing conversion table:
## Rosaceae
## The following taxa could not be found in the existing conversion table:
## Shepherdia## Warning in FUN(X[[i]], ...):
## The following taxa could not be found in the existing conversion table:
## Indeterminable
## The following taxa could not be found in the existing conversion table:
## Osmunda
## The following taxa could not be found in the existing conversion table:
## Plantago major
## The following taxa could not be found in the existing conversion table:
## Rubus chamaemorus
## The following taxa could not be found in the existing conversion table:
## Sphagnum
## The following taxa could not be found in the existing conversion table:
## Unknown
## The following taxa could not be found in the existing conversion table:
## Cornus canadensis
## The following taxa could not be found in the existing conversion table:
## Cyclachaena xanthiifolia-type
## The following taxa could not be found in the existing conversion table:
## Polypodiophyta undiff.
## The following taxa could not be found in the existing conversion table:
## Typha latifolia
## The following taxa could not be found in the existing conversion table:
## cf. Rhamnus alnifolia
## The following taxa could not be found in the existing conversion table:
## Ericaceae undiff.
## The following taxa could not be found in the existing conversion table:
## Huperzia selago-type
## The following taxa could not be found in the existing conversion table:
## Lycopodium annotinum
## The following taxa could not be found in the existing conversion table:
## Equisetum
## The following taxa could not be found in the existing conversion table:
## Sarracenia
## The following taxa could not be found in the existing conversion table:
## Sarcobatus vermiculatus
## The following taxa could not be found in the existing conversion table:
## Caryophyllaceae
## The following taxa could not be found in the existing conversion table:
## Pteridium aquilinum
## The following taxa could not be found in the existing conversion table:
## Prunus americana-type
## The following taxa could not be found in the existing conversion table:
## Rhododendron subsect. Ledum/Chamaedaphne calyculata
## The following taxa could not be found in the existing conversion table:
## Dryopteris
## The following taxa could not be found in the existing conversion table:
## Galium
## The following taxa could not be found in the existing conversion table:
## Gaultheria procumbens
## The following taxa could not be found in the existing conversion table:
## Potentilla-type
## The following taxa could not be found in the existing conversion table:
## Rosaceae undiff.
## The following taxa could not be found in the existing conversion table:
## Urtica
## The following taxa could not be found in the existing conversion table:
## Humulus/Cannabis sativa
## The following taxa could not be found in the existing conversion table:
## Myrica
## The following taxa could not be found in the existing conversion table:
## Nuphar## Warning in FUN(X[[i]], ...):
## The following taxa could not be found in the existing conversion table:
## cf. Rhamnus alnifolia
## The following taxa could not be found in the existing conversion table:
## Cyclachaena xanthiifolia-type
## The following taxa could not be found in the existing conversion table:
## Dryopteris
## The following taxa could not be found in the existing conversion table:
## Fabaceae cf. Melilotus
## The following taxa could not be found in the existing conversion table:
## Humulus/Cannabis sativa
## The following taxa could not be found in the existing conversion table:
## Indeterminable
## The following taxa could not be found in the existing conversion table:
## Myrica
## The following taxa could not be found in the existing conversion table:
## Osmunda cinnamomea
## The following taxa could not be found in the existing conversion table:
## Plantago major
## The following taxa could not be found in the existing conversion table:
## Sphagnum
## The following taxa could not be found in the existing conversion table:
## Thalictrum
## The following taxa could not be found in the existing conversion table:
## Typha latifolia
## The following taxa could not be found in the existing conversion table:
## Unknown
## The following taxa could not be found in the existing conversion table:
## Geum
## The following taxa could not be found in the existing conversion table:
## Ilex
## The following taxa could not be found in the existing conversion table:
## Pteridium aquilinum
## The following taxa could not be found in the existing conversion table:
## Sarracenia
## The following taxa could not be found in the existing conversion table:
## Polypodiophyta undiff.
## The following taxa could not be found in the existing conversion table:
## Huperzia selago-type
## The following taxa could not be found in the existing conversion table:
## Ericaceae undiff.
## The following taxa could not be found in the existing conversion table:
## Ephedra
## The following taxa could not be found in the existing conversion table:
## Rhododendron subsect. Ledum/Chamaedaphne calyculata
## The following taxa could not be found in the existing conversion table:
## Caryophyllaceae
## The following taxa could not be found in the existing conversion table:
## Lycopodium annotinum
## The following taxa could not be found in the existing conversion table:
## Rosaceae undiff.
## The following taxa could not be found in the existing conversion table:
## Athyrium filix-femina
## The following taxa could not be found in the existing conversion table:
## Ranunculus flabellaris-type
## The following taxa could not be found in the existing conversion table:
## Rubus chamaemorus
## The following taxa could not be found in the existing conversion table:
## cf. Viburnum lentago
## The following taxa could not be found in the existing conversion table:
## Prunus americana-type
## The following taxa could not be found in the existing conversion table:
## Gaultheria procumbens
## The following taxa could not be found in the existing conversion table:
## Dalea
## The following taxa could not be found in the existing conversion table:
## Equisetum
## The following taxa could not be found in the existing conversion table:
## Caltha-type
## The following taxa could not be found in the existing conversion table:
## Toxicodendron radicans-type
## The following taxa could not be found in the existing conversion table:
## Cornus canadensis
## The following taxa could not be found in the existing conversion table:
## Apiaceae
## The following taxa could not be found in the existing conversion table:
## Nymphaea
## The following taxa could not be found in the existing conversion table:
## Isoëtes
## The following taxa could not be found in the existing conversion table:
## Castanea
## The following taxa could not be found in the existing conversion table:
## cf. Amorpha
## The following taxa could not be found in the existing conversion table:
## Nuphar
## The following taxa could not be found in the existing conversion table:
## Potentilla-type
## The following taxa could not be found in the existing conversion table:
## Laportea
## The following taxa could not be found in the existing conversion table:
## Lycopodiella inundata
## The following taxa could not be found in the existing conversion table:
## Diphasiastrum complanatum-type
## The following taxa could not be found in the existing conversion table:
## Potamogetonaceae
## The following taxa could not be found in the existing conversion table:
## Sagittaria## Warning in FUN(X[[i]], ...):
## The following taxa could not be found in the existing conversion table:
## Angiospermae undiff. (herbs)
## The following taxa could not be found in the existing conversion table:
## Brasenia schreberi
## The following taxa could not be found in the existing conversion table:
## Celtis
## The following taxa could not be found in the existing conversion table:
## Cornus
## The following taxa could not be found in the existing conversion table:
## Pediastrum
## The following taxa could not be found in the existing conversion table:
## Potamogetonaceae
## The following taxa could not be found in the existing conversion table:
## Unknown
## The following taxa could not be found in the existing conversion table:
## Unknown (monolete)
## The following taxa could not be found in the existing conversion table:
## Unknown (trilete)
## The following taxa could not be found in the existing conversion table:
## Amaranthaceae undiff.
## The following taxa could not be found in the existing conversion table:
## Brassicaceae
## The following taxa could not be found in the existing conversion table:
## Thalictrum
## The following taxa could not be found in the existing conversion table:
## Urtica
## The following taxa could not be found in the existing conversion table:
## Ericaceae
## The following taxa could not be found in the existing conversion table:
## Nymphaea
## The following taxa could not be found in the existing conversion table:
## Typha
## The following taxa could not be found in the existing conversion table:
## Spermatophyta undiff. (trees)
## The following taxa could not be found in the existing conversion table:
## Sarcobatus vermiculatus
## The following taxa could not be found in the existing conversion table:
## Nuphar
## The following taxa could not be found in the existing conversion table:
## Ranunculaceae undiff.
## The following taxa could not be found in the existing conversion table:
## Myriophyllum
## The following taxa could not be found in the existing conversion table:
## Nyssa
## The following taxa could not be found in the existing conversion table:
## Rubus
## The following taxa could not be found in the existing conversion table:
## Ephedra
## The following taxa could not be found in the existing conversion table:
## Humulus## Warning in FUN(X[[i]], ...):
## The following taxa could not be found in the existing conversion table:
## Aquifoliaceae
## The following taxa could not be found in the existing conversion table:
## Brasenia schreberi
## The following taxa could not be found in the existing conversion table:
## Indeterminable
## The following taxa could not be found in the existing conversion table:
## Menyanthes trifoliata
## The following taxa could not be found in the existing conversion table:
## Myrica
## The following taxa could not be found in the existing conversion table:
## Nymphaea
## The following taxa could not be found in the existing conversion table:
## Osmunda
## The following taxa could not be found in the existing conversion table:
## Polypodiophyta undiff.
## The following taxa could not be found in the existing conversion table:
## Pteridium-type
## The following taxa could not be found in the existing conversion table:
## Rumex
## The following taxa could not be found in the existing conversion table:
## Sagittaria
## The following taxa could not be found in the existing conversion table:
## Spermatophyta undiff. (trees)
## The following taxa could not be found in the existing conversion table:
## Sphagnum
## The following taxa could not be found in the existing conversion table:
## Thalictrum
## The following taxa could not be found in the existing conversion table:
## Rhamnaceae/Vitaceae undiff.
## The following taxa could not be found in the existing conversion table:
## Spermatophyta undiff. (aquatics)
## The following taxa could not be found in the existing conversion table:
## Typha/Sparganium
## The following taxa could not be found in the existing conversion table:
## Unknown
## The following taxa could not be found in the existing conversion table:
## Unknown (monolete)
## The following taxa could not be found in the existing conversion table:
## Amaranthaceae undiff.
## The following taxa could not be found in the existing conversion table:
## Amorpha-type
## The following taxa could not be found in the existing conversion table:
## Dalea
## The following taxa could not be found in the existing conversion table:
## Ericaceae
## The following taxa could not be found in the existing conversion table:
## Lycopodium-type
## The following taxa could not be found in the existing conversion table:
## Polygonum sensu lato
## The following taxa could not be found in the existing conversion table:
## Brassicaceae
## The following taxa could not be found in the existing conversion table:
## Ceanothus
## The following taxa could not be found in the existing conversion table:
## Nuphar
## The following taxa could not be found in the existing conversion table:
## Salsola
## The following taxa could not be found in the existing conversion table:
## Athyrium
## The following taxa could not be found in the existing conversion table:
## Ephedra
## The following taxa could not be found in the existing conversion table:
## Pediastrum
## The following taxa could not be found in the existing conversion table:
## Sarcobatus vermiculatus
## The following taxa could not be found in the existing conversion table:
## Woodsia
## The following taxa could not be found in the existing conversion table:
## Equisetum
## The following taxa could not be found in the existing conversion table:
## Celtis
## The following taxa could not be found in the existing conversion table:
## Cyclachaena xanthiifolia-type
## The following taxa could not be found in the existing conversion table:
## Myriophyllum
## The following taxa could not be found in the existing conversion table:
## Isoëtes
## The following taxa could not be found in the existing conversion table:
## Morus
## The following taxa could not be found in the existing conversion table:
## Prunus/Sorbus
## The following taxa could not be found in the existing conversion table:
## Crataegus-type
## The following taxa could not be found in the existing conversion table:
## Moraceae undiff.
## The following taxa could not be found in the existing conversion table:
## Saxifragaceae
## The following taxa could not be found in the existing conversion table:
## Lamiaceae
## The following taxa could not be found in the existing conversion table:
## Oxyria digyna
## The following taxa could not be found in the existing conversion table:
## Angiospermae undiff. (herbs)
## The following taxa could not be found in the existing conversion table:
## Cornus
## The following taxa could not be found in the existing conversion table:
## Galium
## The following taxa could not be found in the existing conversion table:
## Ranunculaceae undiff.
## The following taxa could not be found in the existing conversion table:
## Fabaceae undiff.
## The following taxa could not be found in the existing conversion table:
## Dryopteris-type
## The following taxa could not be found in the existing conversion table:
## Potentilla-type
## The following taxa could not be found in the existing conversion table:
## Anacardiaceae
## The following taxa could not be found in the existing conversion table:
## Apiaceae
## The following taxa could not be found in the existing conversion table:
## Gleditsia
## The following taxa could not be found in the existing conversion table:
## Shepherdia
## The following taxa could not be found in the existing conversion table:
## Vitis
## The following taxa could not be found in the existing conversion table:
## Spermatophyta undiff. (shrubs)
## The following taxa could not be found in the existing conversion table:
## Araceae subf. Lemnoideae
## The following taxa could not be found in the existing conversion table:
## Rosaceae undiff.
## The following taxa could not be found in the existing conversion table:
## Pyrus-type## Warning in FUN(X[[i]], ...):
## The following taxa could not be found in the existing conversion table:
## Amaranthaceae undiff.
## The following taxa could not be found in the existing conversion table:
## Indeterminable
## The following taxa could not be found in the existing conversion table:
## Plantago
## The following taxa could not be found in the existing conversion table:
## Polypodiophyta undiff.
## The following taxa could not be found in the existing conversion table:
## Potamogetonaceae
## The following taxa could not be found in the existing conversion table:
## Sparganium-type
## The following taxa could not be found in the existing conversion table:
## Typha latifolia
## The following taxa could not be found in the existing conversion table:
## Unknown
## The following taxa could not be found in the existing conversion table:
## Nuphar
## The following taxa could not be found in the existing conversion table:
## Pteridium-type
## The following taxa could not be found in the existing conversion table:
## Rosaceae undiff.
## The following taxa could not be found in the existing conversion table:
## Vitis
## The following taxa could not be found in the existing conversion table:
## Myricaceae
## The following taxa could not be found in the existing conversion table:
## Sambucus
## The following taxa could not be found in the existing conversion table:
## Sphagnum
## The following taxa could not be found in the existing conversion table:
## Brasenia schreberi
## The following taxa could not be found in the existing conversion table:
## Nymphaea
## The following taxa could not be found in the existing conversion table:
## Rubus
## The following taxa could not be found in the existing conversion table:
## Cornus
## The following taxa could not be found in the existing conversion table:
## Ericaceae
## The following taxa could not be found in the existing conversion table:
## Lamiaceae
## The following taxa could not be found in the existing conversion table:
## Thalictrum
## The following taxa could not be found in the existing conversion table:
## Viburnum
## The following taxa could not be found in the existing conversion table:
## Dalea
## The following taxa could not be found in the existing conversion table:
## Apiaceae
## The following taxa could not be found in the existing conversion table:
## Celtis
## The following taxa could not be found in the existing conversion table:
## Lycopodium obscurum
## The following taxa could not be found in the existing conversion table:
## Myriophyllum
## The following taxa could not be found in the existing conversion table:
## Botrychium
## The following taxa could not be found in the existing conversion table:
## Pinaceae undiff.
## The following taxa could not be found in the existing conversion table:
## Urtica-type
## The following taxa could not be found in the existing conversion table:
## Polygonum sensu lato
## The following taxa could not be found in the existing conversion table:
## Araceae subf. Lemnoideae
## The following taxa could not be found in the existing conversion table:
## Lycopodium annotinum
## The following taxa could not be found in the existing conversion table:
## Osmunda
## The following taxa could not be found in the existing conversion table:
## Sarcobatus vermiculatus## Warning in FUN(X[[i]], ...):
## The following taxa could not be found in the existing conversion table:
## Amaranthaceae
## The following taxa could not be found in the existing conversion table:
## Ericaceae
## The following taxa could not be found in the existing conversion table:
## Ilex
## The following taxa could not be found in the existing conversion table:
## Polypodiophyta undiff.
## The following taxa could not be found in the existing conversion table:
## Pteridium
## The following taxa could not be found in the existing conversion table:
## Sparganium-type
## The following taxa could not be found in the existing conversion table:
## Sphagnum
## The following taxa could not be found in the existing conversion table:
## Typha latifolia
## The following taxa could not be found in the existing conversion table:
## Nuphar
## The following taxa could not be found in the existing conversion table:
## Potentilla
## The following taxa could not be found in the existing conversion table:
## Rubiaceae
## The following taxa could not be found in the existing conversion table:
## Menyanthes trifoliata
## The following taxa could not be found in the existing conversion table:
## Brasenia schreberi
## The following taxa could not be found in the existing conversion table:
## Ranunculaceae undiff.
## The following taxa could not be found in the existing conversion table:
## Lycopodiaceae
## The following taxa could not be found in the existing conversion table:
## Brassicaceae
## The following taxa could not be found in the existing conversion table:
## Nymphaeaceae undiff.
## The following taxa could not be found in the existing conversion table:
## Apiaceae
## The following taxa could not be found in the existing conversion table:
## Thalictrum
## The following taxa could not be found in the existing conversion table:
## Sagittaria
## The following taxa could not be found in the existing conversion table:
## Plantago
## The following taxa could not be found in the existing conversion table:
## Botrychium
## The following taxa could not be found in the existing conversion table:
## Shepherdia
## The following taxa could not be found in the existing conversion table:
## Selaginella
## The following taxa could not be found in the existing conversion table:
## Osmunda
## The following taxa could not be found in the existing conversion table:
## Myriophyllum
## The following taxa could not be found in the existing conversion table:
## Equisetum
## The following taxa could not be found in the existing conversion table:
## Filipendula
## The following taxa could not be found in the existing conversion table:
## Polypodiaceae
## The following taxa could not be found in the existing conversion table:
## Polygonum sensu lato## Warning in FUN(X[[i]], ...):
## The following taxa could not be found in the existing conversion table:
## Amaranthaceae
## The following taxa could not be found in the existing conversion table:
## Dryopteris-type
## The following taxa could not be found in the existing conversion table:
## Sparganium-type
## The following taxa could not be found in the existing conversion table:
## Typha latifolia## Warning in FUN(X[[i]], ...):
## The following taxa could not be found in the existing conversion table:
## Celtis
## The following taxa could not be found in the existing conversion table:
## Cyclachaena xanthiifolia-type
## The following taxa could not be found in the existing conversion table:
## Equisetum
## The following taxa could not be found in the existing conversion table:
## Ilex
## The following taxa could not be found in the existing conversion table:
## Indeterminable
## The following taxa could not be found in the existing conversion table:
## Isoëtes
## The following taxa could not be found in the existing conversion table:
## Nuphar
## The following taxa could not be found in the existing conversion table:
## Nyssa
## The following taxa could not be found in the existing conversion table:
## Polygonum sensu lato
## The following taxa could not be found in the existing conversion table:
## Potamogetonaceae
## The following taxa could not be found in the existing conversion table:
## Pteridium-type
## The following taxa could not be found in the existing conversion table:
## Pteridophyta undiff.
## The following taxa could not be found in the existing conversion table:
## Typha latifolia
## The following taxa could not be found in the existing conversion table:
## Unknown
## The following taxa could not be found in the existing conversion table:
## Vaccinium
## The following taxa could not be found in the existing conversion table:
## Vitis
## The following taxa could not be found in the existing conversion table:
## Amaranthaceae undiff.
## The following taxa could not be found in the existing conversion table:
## Athyrium
## The following taxa could not be found in the existing conversion table:
## Comptonia peregrina
## The following taxa could not be found in the existing conversion table:
## Fabaceae undiff.
## The following taxa could not be found in the existing conversion table:
## Lycopodium clavatum
## The following taxa could not be found in the existing conversion table:
## Morus
## The following taxa could not be found in the existing conversion table:
## Myrica
## The following taxa could not be found in the existing conversion table:
## Nymphaea
## The following taxa could not be found in the existing conversion table:
## Thalictrum
## The following taxa could not be found in the existing conversion table:
## Urtica-type
## The following taxa could not be found in the existing conversion table:
## Amorpha-type
## The following taxa could not be found in the existing conversion table:
## Caltha
## The following taxa could not be found in the existing conversion table:
## Huperzia selago
## The following taxa could not be found in the existing conversion table:
## Lycopodium annotinum
## The following taxa could not be found in the existing conversion table:
## Myriophyllum
## The following taxa could not be found in the existing conversion table:
## Osmunda
## The following taxa could not be found in the existing conversion table:
## Plantago major
## The following taxa could not be found in the existing conversion table:
## Shepherdia
## The following taxa could not be found in the existing conversion table:
## Sparganium-type
## The following taxa could not be found in the existing conversion table:
## Cornus
## The following taxa could not be found in the existing conversion table:
## Potentilla-type
## The following taxa could not be found in the existing conversion table:
## Castanea
## The following taxa could not be found in the existing conversion table:
## Dalea
## The following taxa could not be found in the existing conversion table:
## Dryopteris-type
## The following taxa could not be found in the existing conversion table:
## Hydrophyllum
## The following taxa could not be found in the existing conversion table:
## Ranunculus
## The following taxa could not be found in the existing conversion table:
## Sambucus
## The following taxa could not be found in the existing conversion table:
## Liliaceae
## The following taxa could not be found in the existing conversion table:
## Rhododendron subsect. Ledum/Chamaedaphne calyculata
## The following taxa could not be found in the existing conversion table:
## Sphagnum
## The following taxa could not be found in the existing conversion table:
## Lamiaceae
## The following taxa could not be found in the existing conversion table:
## Cannabaceae sensu stricto
## The following taxa could not be found in the existing conversion table:
## Galium
## The following taxa could not be found in the existing conversion table:
## Ephedra
## The following taxa could not be found in the existing conversion table:
## Rhamnaceae
## The following taxa could not be found in the existing conversion table:
## Rubus
## The following taxa could not be found in the existing conversion table:
## Hypericum
## The following taxa could not be found in the existing conversion table:
## Sarcobatus vermiculatus
## The following taxa could not be found in the existing conversion table:
## Sarracenia
## The following taxa could not be found in the existing conversion table:
## Utricularia
## The following taxa could not be found in the existing conversion table:
## Apiaceae
## The following taxa could not be found in the existing conversion table:
## Laportea-type
## The following taxa could not be found in the existing conversion table:
## Brasenia schreberi
## The following taxa could not be found in the existing conversion table:
## Saxifragaceae
## The following taxa could not be found in the existing conversion table:
## Valeriana
## The following taxa could not be found in the existing conversion table:
## Rosaceae undiff.
## The following taxa could not be found in the existing conversion table:
## Caryophyllaceae## Warning in FUN(X[[i]], ...):
## The following taxa could not be found in the existing conversion table:
## Castanea
## The following taxa could not be found in the existing conversion table:
## Equisetum
## The following taxa could not be found in the existing conversion table:
## Nuphar
## The following taxa could not be found in the existing conversion table:
## Nymphaea
## The following taxa could not be found in the existing conversion table:
## Unknown
## The following taxa could not be found in the existing conversion table:
## Menispermaceae
## The following taxa could not be found in the existing conversion table:
## Polygonum
## The following taxa could not be found in the existing conversion table:
## Rubus
## The following taxa could not be found in the existing conversion table:
## Celtis
## The following taxa could not be found in the existing conversion table:
## Myriophyllum
## The following taxa could not be found in the existing conversion table:
## Urtica
## The following taxa could not be found in the existing conversion table:
## Indeterminable
## The following taxa could not be found in the existing conversion table:
## Stellaria
## The following taxa could not be found in the existing conversion table:
## Planera aquatica
## The following taxa could not be found in the existing conversion table:
## Mitella
## The following taxa could not be found in the existing conversion table:
## Tilletia
## The following taxa could not be found in the existing conversion table:
## Myrica
## The following taxa could not be found in the existing conversion table:
## Brassicaceae
## The following taxa could not be found in the existing conversion table:
## Plantago
## The following taxa could not be found in the existing conversion table:
## Rhamnus
## The following taxa could not be found in the existing conversion table:
## Nyssa
## The following taxa could not be found in the existing conversion table:
## Aquifoliaceae
## The following taxa could not be found in the existing conversion table:
## Potamogeton
## The following taxa could not be found in the existing conversion table:
## Typha
## The following taxa could not be found in the existing conversion table:
## Geranium
## The following taxa could not be found in the existing conversion table:
## Thalictrum
## The following taxa could not be found in the existing conversion table:
## Epilobium
## The following taxa could not be found in the existing conversion table:
## Cornus
## The following taxa could not be found in the existing conversion table:
## Oxalis
## The following taxa could not be found in the existing conversion table:
## Ruppia## Warning in FUN(X[[i]], ...):
## The following taxa could not be found in the existing conversion table:
## Amaranthaceae
## The following taxa could not be found in the existing conversion table:
## Fabaceae undiff.
## The following taxa could not be found in the existing conversion table:
## Ilex
## The following taxa could not be found in the existing conversion table:
## Isoëtes
## The following taxa could not be found in the existing conversion table:
## Myrica
## The following taxa could not be found in the existing conversion table:
## Osmunda cinnamomea
## The following taxa could not be found in the existing conversion table:
## Pteridium aquilinum
## The following taxa could not be found in the existing conversion table:
## Rumex
## The following taxa could not be found in the existing conversion table:
## Sarcobatus vermiculatus
## The following taxa could not be found in the existing conversion table:
## Ulmus americana
## The following taxa could not be found in the existing conversion table:
## Unknown
## The following taxa could not be found in the existing conversion table:
## Unknown (monolete)
## The following taxa could not be found in the existing conversion table:
## Cyclachaena xanthiifolia
## The following taxa could not be found in the existing conversion table:
## Lycopodium undiff.
## The following taxa could not be found in the existing conversion table:
## Nuphar
## The following taxa could not be found in the existing conversion table:
## Rosaceae undiff.
## The following taxa could not be found in the existing conversion table:
## Unknown (trilete)
## The following taxa could not be found in the existing conversion table:
## Typha latifolia
## The following taxa could not be found in the existing conversion table:
## Thalictrum
## The following taxa could not be found in the existing conversion table:
## Diphasiastrum complanatum
## The following taxa could not be found in the existing conversion table:
## Sagittaria
## The following taxa could not be found in the existing conversion table:
## Vitis
## The following taxa could not be found in the existing conversion table:
## Lycopodium annotinum
## The following taxa could not be found in the existing conversion table:
## Apiaceae
## The following taxa could not be found in the existing conversion table:
## Huperzia lucidula
## The following taxa could not be found in the existing conversion table:
## Impatiens
## The following taxa could not be found in the existing conversion table:
## Lycopodium clavatum
## The following taxa could not be found in the existing conversion table:
## Sparganium
## The following taxa could not be found in the existing conversion table:
## Eriocaulon
## The following taxa could not be found in the existing conversion table:
## Sphagnum
## The following taxa could not be found in the existing conversion table:
## Myriophyllum
## The following taxa could not be found in the existing conversion table:
## Urtica
## The following taxa could not be found in the existing conversion table:
## Brasenia schreberi
## The following taxa could not be found in the existing conversion table:
## Pediastrum
## The following taxa could not be found in the existing conversion table:
## Liliaceae
## The following taxa could not be found in the existing conversion table:
## Violaceae
## The following taxa could not be found in the existing conversion table:
## Persicaria lapathifolia
## The following taxa could not be found in the existing conversion table:
## Potamogeton
## The following taxa could not be found in the existing conversion table:
## Ephedra
## The following taxa could not be found in the existing conversion table:
## Osmunda regalis/O. claytoniana
## The following taxa could not be found in the existing conversion table:
## Ceanothus
## The following taxa could not be found in the existing conversion table:
## Brassicaceae
## The following taxa could not be found in the existing conversion table:
## Amorpha
## The following taxa could not be found in the existing conversion table:
## Nymphaea
## The following taxa could not be found in the existing conversion table:
## Celtis
## The following taxa could not be found in the existing conversion table:
## Potentilla
## The following taxa could not be found in the existing conversion table:
## Botrychium
## The following taxa could not be found in the existing conversion table:
## Campanula
## The following taxa could not be found in the existing conversion table:
## Persicaria amphibia
## The following taxa could not be found in the existing conversion table:
## Caryophyllaceae
## The following taxa could not be found in the existing conversion table:
## Adiantum pedatum
## The following taxa could not be found in the existing conversion table:
## Pteridophyta undiff.
## The following taxa could not be found in the existing conversion table:
## Ericaceae## Warning in FUN(X[[i]], ...):
## The following taxa could not be found in the existing conversion table:
## Amaranthaceae
## The following taxa could not be found in the existing conversion table:
## Arceuthobium pusillum
## The following taxa could not be found in the existing conversion table:
## Betulaceae undiff.
## The following taxa could not be found in the existing conversion table:
## Cyclachaena xanthiifolia
## The following taxa could not be found in the existing conversion table:
## Humulus
## The following taxa could not be found in the existing conversion table:
## Indeterminable
## The following taxa could not be found in the existing conversion table:
## Lycopodiaceae undiff.
## The following taxa could not be found in the existing conversion table:
## Myrica-type
## The following taxa could not be found in the existing conversion table:
## Plantago undiff.
## The following taxa could not be found in the existing conversion table:
## Pteridium
## The following taxa could not be found in the existing conversion table:
## Sambucus
## The following taxa could not be found in the existing conversion table:
## Unknown
## The following taxa could not be found in the existing conversion table:
## Dryopteris-type
## The following taxa could not be found in the existing conversion table:
## Ericaceae-type
## The following taxa could not be found in the existing conversion table:
## Celtis
## The following taxa could not be found in the existing conversion table:
## cf. Osmunda
## The following taxa could not be found in the existing conversion table:
## Chamaesyce
## The following taxa could not be found in the existing conversion table:
## Ilex
## The following taxa could not be found in the existing conversion table:
## Potamogeton
## The following taxa could not be found in the existing conversion table:
## Rumex
## The following taxa could not be found in the existing conversion table:
## Isoëtes
## The following taxa could not be found in the existing conversion table:
## Unknown (monolete)
## The following taxa could not be found in the existing conversion table:
## Huperzia lucidula
## The following taxa could not be found in the existing conversion table:
## Pinaceae undiff.
## The following taxa could not be found in the existing conversion table:
## Shepherdia argentea
## The following taxa could not be found in the existing conversion table:
## Unknown (trilete)
## The following taxa could not be found in the existing conversion table:
## Diphasiastrum complanatum
## The following taxa could not be found in the existing conversion table:
## Unknown (trilete, psilate)
## The following taxa could not be found in the existing conversion table:
## Rosaceae undiff.
## The following taxa could not be found in the existing conversion table:
## Nuphar
## The following taxa could not be found in the existing conversion table:
## Sarcobatus vermiculatus
## The following taxa could not be found in the existing conversion table:
## Lycopodium annotinum
## The following taxa could not be found in the existing conversion table:
## Sphagnum
## The following taxa could not be found in the existing conversion table:
## cf. Taxus
## The following taxa could not be found in the existing conversion table:
## Lycopodium obscurum
## The following taxa could not be found in the existing conversion table:
## Osmunda cinnamomea
## The following taxa could not be found in the existing conversion table:
## Osmunda regalis-type
## The following taxa could not be found in the existing conversion table:
## Polygonum undiff.
## The following taxa could not be found in the existing conversion table:
## Adiantum-type
## The following taxa could not be found in the existing conversion table:
## Ranunculaceae undiff.
## The following taxa could not be found in the existing conversion table:
## Ephedra
## The following taxa could not be found in the existing conversion table:
## Brasenia schreberi
## The following taxa could not be found in the existing conversion table:
## Prunus
## The following taxa could not be found in the existing conversion table:
## Rhamnaceae
## The following taxa could not be found in the existing conversion table:
## Apiaceae
## The following taxa could not be found in the existing conversion table:
## Nymphaea
## The following taxa could not be found in the existing conversion table:
## Botrychium undiff.
## The following taxa could not be found in the existing conversion table:
## Typha latifolia
## The following taxa could not be found in the existing conversion table:
## Epilobium
## The following taxa could not be found in the existing conversion table:
## Hudsonia
## The following taxa could not be found in the existing conversion table:
## Urtica
## The following taxa could not be found in the existing conversion table:
## Campanulaceae
## The following taxa could not be found in the existing conversion table:
## cf. Morus
## The following taxa could not be found in the existing conversion table:
## Humulus-type
## The following taxa could not be found in the existing conversion table:
## Caryophyllaceae
## The following taxa could not be found in the existing conversion table:
## Plantago major-type
## The following taxa could not be found in the existing conversion table:
## cf. Cupressaceae
## The following taxa could not be found in the existing conversion table:
## Lycopus-type
## The following taxa could not be found in the existing conversion table:
## Shepherdia## Warning in FUN(X[[i]], ...):
## The following taxa could not be found in the existing conversion table:
## Angiospermae undiff. (herbs)
## The following taxa could not be found in the existing conversion table:
## Brasenia schreberi
## The following taxa could not be found in the existing conversion table:
## Brassicaceae
## The following taxa could not be found in the existing conversion table:
## cf. Utricularia
## The following taxa could not be found in the existing conversion table:
## Fabaceae
## The following taxa could not be found in the existing conversion table:
## Myriophyllum
## The following taxa could not be found in the existing conversion table:
## Nuphar
## The following taxa could not be found in the existing conversion table:
## Pediastrum
## The following taxa could not be found in the existing conversion table:
## Potamogeton
## The following taxa could not be found in the existing conversion table:
## Ranunculaceae undiff.
## The following taxa could not be found in the existing conversion table:
## Rhus
## The following taxa could not be found in the existing conversion table:
## Rosaceae
## The following taxa could not be found in the existing conversion table:
## Rumex
## The following taxa could not be found in the existing conversion table:
## Sparganium
## The following taxa could not be found in the existing conversion table:
## Spermatophyta undiff. (aquatics)
## The following taxa could not be found in the existing conversion table:
## Spermatophyta undiff. (trees/shrubs)
## The following taxa could not be found in the existing conversion table:
## Unknown
## The following taxa could not be found in the existing conversion table:
## Unknown (monolete)
## The following taxa could not be found in the existing conversion table:
## Unknown (trilete)
## The following taxa could not be found in the existing conversion table:
## Amaranthaceae
## The following taxa could not be found in the existing conversion table:
## Sagittaria
## The following taxa could not be found in the existing conversion table:
## Cannabis sativa
## The following taxa could not be found in the existing conversion table:
## Polygonaceae undiff.
## The following taxa could not be found in the existing conversion table:
## Typha latifolia
## The following taxa could not be found in the existing conversion table:
## Caryophyllaceae
## The following taxa could not be found in the existing conversion table:
## Apiaceae
## The following taxa could not be found in the existing conversion table:
## Thalictrum
## The following taxa could not be found in the existing conversion table:
## Vitis
## The following taxa could not be found in the existing conversion table:
## Liliaceae
## The following taxa could not be found in the existing conversion table:
## Ephedra
## The following taxa could not be found in the existing conversion table:
## Polemoniaceae
## The following taxa could not be found in the existing conversion table:
## Sarcobatus vermiculatus
## The following taxa could not be found in the existing conversion table:
## Humulus
## The following taxa could not be found in the existing conversion table:
## Urtica
## The following taxa could not be found in the existing conversion table:
## Plantago
## The following taxa could not be found in the existing conversion table:
## Isoëtes## Warning in FUN(X[[i]], ...):
## The following taxa could not be found in the existing conversion table:
## Amaranthaceae
## The following taxa could not be found in the existing conversion table:
## Huperzia lucidula
## The following taxa could not be found in the existing conversion table:
## Ilex
## The following taxa could not be found in the existing conversion table:
## Myrica
## The following taxa could not be found in the existing conversion table:
## Plantago
## The following taxa could not be found in the existing conversion table:
## Pteridium
## The following taxa could not be found in the existing conversion table:
## Ericaceae
## The following taxa could not be found in the existing conversion table:
## Sphagnum
## The following taxa could not be found in the existing conversion table:
## Unknown (monolete, psilate)
## The following taxa could not be found in the existing conversion table:
## Nymphaeaceae undiff.
## The following taxa could not be found in the existing conversion table:
## Indeterminable
## The following taxa could not be found in the existing conversion table:
## Osmunda cinnamomea
## The following taxa could not be found in the existing conversion table:
## Unknown
## The following taxa could not be found in the existing conversion table:
## Unknown (trilete)
## The following taxa could not be found in the existing conversion table:
## Vitis
## The following taxa could not be found in the existing conversion table:
## Rosaceae
## The following taxa could not be found in the existing conversion table:
## Thalictrum
## The following taxa could not be found in the existing conversion table:
## Ranunculaceae undiff.
## The following taxa could not be found in the existing conversion table:
## Lycopodium obscurum
## The following taxa could not be found in the existing conversion table:
## Typha latifolia
## The following taxa could not be found in the existing conversion table:
## Unknown (monolete, verrucate)
## The following taxa could not be found in the existing conversion table:
## Lycopodium clavatum
## The following taxa could not be found in the existing conversion table:
## Lycopodium undiff.
## The following taxa could not be found in the existing conversion table:
## Nuphar
## The following taxa could not be found in the existing conversion table:
## Caryophyllaceae
## The following taxa could not be found in the existing conversion table:
## Celtis
## The following taxa could not be found in the existing conversion table:
## Apiaceae
## The following taxa could not be found in the existing conversion table:
## Typha angustifolia
## The following taxa could not be found in the existing conversion table:
## Rumex
## The following taxa could not be found in the existing conversion table:
## Lamiaceae
## The following taxa could not be found in the existing conversion table:
## Botrychium
## The following taxa could not be found in the existing conversion table:
## Epilobium
## The following taxa could not be found in the existing conversion table:
## Adiantum
## The following taxa could not be found in the existing conversion table:
## Ephedra
## The following taxa could not be found in the existing conversion table:
## Cyclachaena xanthiifolia
## The following taxa could not be found in the existing conversion table:
## Polypodiaceae
## The following taxa could not be found in the existing conversion table:
## Diphasiastrum complanatum
## The following taxa could not be found in the existing conversion table:
## Persicaria lapathifolia-type## Warning in FUN(X[[i]], ...):
## The following taxa could not be found in the existing conversion table:
## Amaranthaceae
## The following taxa could not be found in the existing conversion table:
## Caprifoliaceae
## The following taxa could not be found in the existing conversion table:
## Celtis
## The following taxa could not be found in the existing conversion table:
## Fabaceae
## The following taxa could not be found in the existing conversion table:
## Nymphaeaceae
## The following taxa could not be found in the existing conversion table:
## Osmunda
## The following taxa could not be found in the existing conversion table:
## Potamogeton
## The following taxa could not be found in the existing conversion table:
## Pteridium
## The following taxa could not be found in the existing conversion table:
## Rumex
## The following taxa could not be found in the existing conversion table:
## Typha
## The following taxa could not be found in the existing conversion table:
## Urticaceae
## The following taxa could not be found in the existing conversion table:
## Sphagnum
## The following taxa could not be found in the existing conversion table:
## Vitaceae
## The following taxa could not be found in the existing conversion table:
## Rosaceae
## The following taxa could not be found in the existing conversion table:
## Lycopodiaceae
## The following taxa could not be found in the existing conversion table:
## Myrica/Comptonia
## The following taxa could not be found in the existing conversion table:
## Ranunculaceae
## The following taxa could not be found in the existing conversion table:
## Rhus
## The following taxa could not be found in the existing conversion table:
## Ericaceae
## The following taxa could not be found in the existing conversion table:
## Apiaceae
## The following taxa could not be found in the existing conversion table:
## Ilex/Nemopanthusall_output <- suppressWarnings(neotoma::compile_downloads(wi_p25))
# Convert taxon counts to proportions:
all_output[,11:ncol(all_output)] <- all_output[,11:ncol(all_output)] /
rowSums(all_output[,11:ncol(all_output)], na.rm = TRUE)
# Combine the
larix_df <- data.frame(lat = all_output$lat,
long = all_output$long,
age = all_output$age,
larix = all_output[,grep("Larix", colnames(all_output))])
lar_model <- mgcv::gam(larix ~ s(lat, long, age), data = larix_df, family = binomial)## Warning: non-integer #successes in a binomial glm!## Warning: non-integer #successes in a binomial glm!
## Warning: non-integer #successes in a binomial glm!
## Warning: non-integer #successes in a binomial glm!
## Warning: non-integer #successes in a binomial glm!
## Warning: non-integer #successes in a binomial glm!
## Warning: non-integer #successes in a binomial glm!lar_predict <- expand.grid(lat = seq(min(larix_df$lat),
max(larix_df$lat), by = 0.5),
long = seq(min(larix_df$long),
max(larix_df$long), by = 0.5),
age = 4000)
lar_predict$pred <- predict(lar_model, newdata = lar_predict)
image(y = seq(min(larix_df$lat), max(larix_df$lat), by = 0.5),
x = seq(min(larix_df$long), max(larix_df$long), by = 0.5),
z = matrix(lar_predict$pred, ncol = length(unique(lar_predict$long))))
points(larix_df[!duplicated(larix_df[,1:2]), 1:2])
2.2.1 Finding records by Handle
Someties people only publish their records using handles:
data_ca <- get_dataset(datasettype = "pollen", gpid = "Canada")## The API call was successful, you have returned 453 records.data_us <- get_dataset(datasettype = "pollen", gpid = "United States")## The API call was successful, you have returned 1014 records.datasets <- neotoma::bind(data_ca, data_us)
handles <- sapply(datasets, function(x)x$dataset.meta$collection.handle)
codes <- c("JACKSON","ARRINGTO","BINNEWTR","WOLFCRK","CAMEL","ROCKYHOC","TULANEG","ANDERSON","CLEARPND","QUICKSND","SANDYRUN","WHITEPND","ALEXISLK")
test_datasets <- sapply(codes, function(x)grep(paste0("^", x, "$"), handles))
output <- datasets[test_datasets]
class(output) <- c("dataset_list", "list")
leaflet_map(output)