File:Puyuk lake pollen 2.svg
Original file (SVG file, nominally 720 × 900 pixels, file size: 351 KB)
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Summary
editDescriptionPuyuk lake pollen 2.svg |
English: Pollen diagram of Puyuk Lake, Alaska, Beringia |
Date | |
Source | Own work |
Author | Merikanto |
This image is based on Neotoma pollen data.
Puyuk Lake
Site ID 1920
Longitude -162,2
Latitude 63,5
Description Maar crater on volcanic island. Physiography: subdued rounded hills and volcanic cones. Surrounding vegetation: mesic low-shrub tundra.
PIs: Ager, Thomas A.
Ager, T.A. 1980. A 16,000 year pollen record from St. Michael Island, Norton Sound, western Alaska. Page 3 in American Quaternary Association, Sixth Biennial Meeting, Abstracts and Program, 18-20 August 1980. Institute for Quaternary Studies, University of Maine, Orono, Maine, USA.
Ager, T.A. 1982. Vegetational history of western Alaska during the WIsconsin glacial interval and the Holocene. Pages 75-93 in D.M. Hopkins, J.V. Matthews, Jr., C.E. Schweger, and S.B. Young, editors. Paleoecology of Beringia. Academic Press, New York, New York, USA.
Ager, T.A., and J.P. Bradbury. 1982. Quaternary history of vegetation and climate of the Yukon Delta-Norton Sound Area. In W.L. Conrad, editor. The United States Geological Survey in Alaska: Accomplishments during 1981. U.S. Geological Survey Circular 868:103-105.
Ager, T.A., and L.B. Brubaker. 1985. Quaternary palynology and vegetational history of Alaska. Pages 353-384 in V.M. Bryant, Jr. and R.G. Holloway, editors. Pollen records of late Quaternary North American sediments. American Association of Stragigraphic Palynologists Foundation, Dallas, Texas, USA.
PIs: Ager, Thomas A.
Ager, T.A. 1980. A 16,000 year pollen record from St. Michael Island, Norton Sound, western Alaska. Page 3 in American Quaternary Association, Sixth Biennial Meeting, Abstracts and Program, 18-20 August 1980. Institute for Quaternary Studies, University of Maine, Orono, Maine, USA.
Ager, T.A. 1982. Vegetational history of western Alaska during the WIsconsin glacial interval and the Holocene. Pages 75-93 in D.M. Hopkins, J.V. Matthews, Jr., C.E. Schweger, and S.B. Young, editors. Paleoecology of Beringia. Academic Press, New York, New York, USA.
Ager, T.A., and J.P. Bradbury. 1982. Quaternary history of vegetation and climate of the Yukon Delta-Norton Sound Area. In W.L. Conrad, editor. The United States Geological Survey in Alaska: Accomplishments during 1981. U.S. Geological Survey Circular 868:103-105.
Ager, T.A., and L.B. Brubaker. 1985. Quaternary palynology and vegetational history of Alaska. Pages 353-384 in V.M. Bryant, Jr. and R.G. Holloway, editors. Pollen records of late Quaternary North American sediments. American Association of Stragigraphic Palynologists Foundation, Dallas, Texas, USA.
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- Pollen diagram, arranged by pollen %
-
- "R" script, uses neotoma, ggplot2 ...
-
- 22.10.2021 0000.0000
-
- load packages
library("tidyverse")
library("neotoma")
library("rioja")
- devtools::install_github("richardjtelford/ggpalaeo") #NEW VERSION
library("ggpalaeo") #Need new version
- download data
get_dataset(1987)#check correct site
- A dataset_list containing 1 objects:
- Accessed from 2021-10-22 16:37h to 2021-10-22 16:37h.
- Datasets:
- dataset.id site.name long lat type
- 1987 Puyuk Lake -162.2 63.5 pollen
bambili_raw <- get_download(1987)
- API call was successful. Returned record for Bambili 1
eco_types <- get_table("EcolGroupTypes")
- extract components
cnts = counts(bambili_raw$`1987`) #table of counts
meta = bambili_raw$`1987`$sample.meta #sample depths/ages
taxa = bambili_raw$`1987`$taxon.list %>% #taxon info
mutate_all(as.character) #convert everything from a facto
bambili <- meta %>% select(age, depth) %>%
bind_cols(cnts) %>%
pivot_longer(cols = -c("age", "depth"), names_to = "species", values_to = "count") %>%
left_join(taxa, by = c("species" = "taxon.name"))
bambili %>% count(variable.element)
str(bambili)
- stop(-1)
eco_types %>%
semi_join(bambili, by = c("EcolGroupID" = "ecological.group")) %>%
select(EcolGroupID, EcolGroup)
bambili %>% filter(ecological.group == c("SEED"), count > 0) %>%
select(species, count) %>%
group_by(species) %>%
summarise(n = n(), max = max(count))
- remove unwanted variable.element/ecological.group
- bambili = bambili %>%
- filter(!ecological.group %in% c("AQVP","AQBR", "UNID", "SEED"))
- use `%in%` not `==`
- check count sums
bambili %>%
group_by(depth) %>%
summarise(s = sum(count)) %>%
arrange(s) %>%
slice(1:5)
- calculate percent
bambili = bambili %>%
group_by(depth) %>%
mutate(percent = count/sum(count) * 100)
- remove rare taxa
bambili1 = bambili %>%
group_by(species) %>%
filter(
sum(percent > 0) >= 3, #must be in at least three samples
max(percent) > 3) #must have a max percent > 3
bambili2 <- bambili1 %>%
select(age, depth, species, percent) %>%
pivot_wider(names_from = "species", values_from = "percent")
bambili_spp <- bambili2 %>% select(-age, -depth) %>%
as.data.frame()#needed as strat.plot does not li
- strat.plot
strat.plot(bambili_spp, yvar = bambili2$depth)
p.col <- c(rep("forestgreen", times=7), rep("gold2", times=20))
bambili2 <- bambili1 %>%
mutate(
- make ecological.group a factor with TRSH first
ecological.group = factor(ecological.group, levels = c("TRSH", "UPHE", "VACR", "AQBR", "AQVP", "TARD")),
- ecological.group = factor(ecological.group, levels = c("TRSH","UPHE","AQVP","VACR","AQBR","FUNGI","ALGA","FUNG","AMOE","TARD")),
mean_percent = mean(percent)) %>%
- arrange by ecological.group and mean_percent (largest first)
arrange(ecological.group, desc(mean_percent)) %>%
ungroup() %>%
- make species into a factor so we can perserve the order
mutate(species = factor(species, levels = unique(species)))
bambili2_spp <- bambili2 %>% select(-age, -depth) %>%
as.data.frame()#needed as strat.plot does not li
- reshape using tidyr::spread as pivot_wider (currently?) ignores factor order
bambili3 <- bambili2 %>%
select(age, depth, species, percent) %>%
spread(key = "species", value = "percent")
bambili_spp <- bambili3 %>%
select(-age, -depth) %>%
as.data.frame(bambili_spp)
- set up for ecological group colours
ecological_groups <- bambili2 %>%
distinct(species, ecological.group) %>%
pull(ecological.group)
ecological_colours <- c("green", "yellow", "orange","red")
- mgp <- c(2, 0.25, 0)
svg(filename="./puyuk_lake_pollen_2.svg", width=8, height=10, pointsize=16)
y.scale <- seq(0,18000,2000)
pol.plot <- strat.plot(bambili_spp, yvar=bambili3$age, y.tks=y.scale,
title="Puyuk Lake", ylabel="Age BP", xlabel="Pollen %",
y.rev=TRUE, plot.line=FALSE,
plot.poly=TRUE, plot.bar=TRUE, col.bar="black",
col.poly=ecological_colours[ecological_groups], col.poly.line="black",
xLeft = 0.2, xRight = 0.99, yBottom = 0.07, yTop = 0.7,
scale.percent=TRUE, xSpace=0.01, x.pc.lab=TRUE, x.pc.omit0=TRUE, las=2)
bambili_dist <- dist(sqrt(bambili_spp/100))#chord distance
clust <- chclust(bambili_dist, method = "coniss")
- bstick(clust)#five groups
dev.off()
print(".")
- plot ...
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Date/Time | Thumbnail | Dimensions | User | Comment | |
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current | 14:36, 22 October 2021 | 720 × 900 (351 KB) | Merikanto (talk | contribs) | Uploaded own work with UploadWizard |
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